This is the list of related activities, ordered by the start time. To
show detailed information about an activity (description, input,
output, responsibilities), click on the small triangle ▾ on the left
side. Click the triangle again to hide the details.
▾
|
1 |
OBJECT exposure at 2014-10-29T00:29:23 |
|
2014-10-29 00:29:23 - 2014-10-29 00:29:53 |
|
▾
|
2 |
OBJECT exposure at 2014-10-29T00:50:43 |
|
2014-10-29 00:50:43 - 2014-10-29 00:51:13 |
|
▾
|
3 |
OBJECT exposure at 2014-10-29T01:12:40 |
|
2014-10-29 01:12:40 - 2014-10-29 01:13:10 |
|
▾
|
4 |
scibasic_object |
1.2 |
2015-10-07 18:54:28 - 2015-10-07 18:57:47 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
13 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_13_e2248a5d.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_13_ab2d148e.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_13_5f9dadfe.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_13_4144e6cc.fits | Master bias |
illum
|
ILLUM_20141029T002738_13_3450f566.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T002923_13_5ffb3885.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_13_543e779b.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_13_a7f442f6.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_5872d584.log | Log file |
|
▾
|
5 |
scibasic_object |
1.2 |
2015-10-07 18:54:28 - 2015-10-07 19:00:24 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
6 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_06_718a8eda.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_06_12324817.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_06_c5986c2b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_06_8c18e69c.fits | Master bias |
illum
|
ILLUM_20141029T002738_06_5b5b48a9.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T002923_06_2ac17640.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_06_bd33f7fc.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_06_a60a715d.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_e2168233.log | Log file |
|
▾
|
6 |
scibasic_object |
1.2 |
2015-10-07 18:54:28 - 2015-10-07 18:59:12 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
9 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T093504_09_caf41e47.fits | Master flat |
trace_table
|
TRACETABLE_20141028T093504_09_be42cbb7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141028T094945_09_26f11b56.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141028T092026_09_1ee2c475.fits | Master bias |
illum
|
ILLUM_20141029T002738_09_6954c541.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu09_0.92.0_59e8d0c2.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_09_09af29d1.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_09_45a9472e.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_09_0f4e1082.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_87f68724.log | Log file |
|
▾
|
7 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:01:16 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
2 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_02_b1d30960.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_02_68086d4a.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_02_b1e7c060.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_02_602ed524.fits | Master bias |
illum
|
ILLUM_20141029T002738_02_a9bf33e5.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T002923_02_d0752f64.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_02_9f3e8869.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_02_ee66b864.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_d6de0871.log | Log file |
|
▾
|
8 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:34 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
5 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_05_beeea1ee.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_05_3799eb4f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_05_33eb21ab.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_05_f5f13716.fits | Master bias |
illum
|
ILLUM_20141029T002738_05_523f906c.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu05_0.92.0_f16e5979.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_05_765e0454.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_05_185b90c1.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_05_51166265.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_d1b6d042.log | Log file |
|
▾
|
9 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:03:54 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
17 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_17_03959c80.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_17_7d3af99b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_17_5fa4b9dc.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_17_c3383da7.fits | Master bias |
illum
|
ILLUM_20141029T002738_17_49e05c54.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu17_0.92.0_d50734cd.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_17_b31ef85f.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_17_c74cb22a.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_17_8b832f5a.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185332_scibasic_object_82183a8d.log | Log file |
|
▾
|
10 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:01:43 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
10 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_10_1a97c580.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_10_ef4b829f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_10_b544012b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_10_ca42cbcb.fits | Master bias |
illum
|
ILLUM_20141029T002738_10_eb52cdac.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu10_0.92.0_d7241430.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_10_748fbbb9.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_10_f0a2906c.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_10_67e6d67b.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185331_scibasic_object_d9a19079.log | Log file |
|
▾
|
11 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:01:42 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
14 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_14_4b63e100.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_14_43272ad0.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_14_c8276035.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_14_005e7a53.fits | Master bias |
illum
|
ILLUM_20141029T002738_14_0082e275.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu14_0.92.0_f75ecc95.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_14_e183ef4c.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_14_3557be62.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_14_db015607.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_9e94457c.log | Log file |
|
▾
|
12 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:02:32 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
23 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_23_8db3a920.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_23_b62d3e51.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_23_5c905e20.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_23_5c62ec96.fits | Master bias |
illum
|
ILLUM_20141029T002738_23_718e9b30.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu23_0.92.0_d9738915.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_23_677c32c7.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_23_58d3ebc2.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_23_7c542472.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185332_scibasic_object_34add1a1.log | Log file |
|
▾
|
13 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:34 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
22 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_22_51d4a082.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_22_c8d26f9d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_22_69605756.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_22_b9214661.fits | Master bias |
illum
|
ILLUM_20141029T002738_22_0651ab89.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu22_0.92.0_ed8e0030.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_22_6c8c6d40.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_22_d144352a.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_22_664becc2.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_7a04b3e9.log | Log file |
|
▾
|
14 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:33 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
19 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_19_16cef25a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_19_7c3a0076.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_19_c558b1c5.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_19_f6b46a79.fits | Master bias |
illum
|
ILLUM_20141029T002738_19_c99bf318.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu19_0.92.0_d1646d1d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_19_6d2f8573.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_19_2d658f9f.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_19_818ab318.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_a3055f26.log | Log file |
|
▾
|
15 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:02:32 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
7 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_07_96f01c52.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_07_af7875be.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_07_bc5f5491.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_07_3c6c5959.fits | Master bias |
illum
|
ILLUM_20141029T002738_07_cd8fd54f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu07_0.92.0_796de9d4.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_07_3433ab92.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_07_4d0cbacd.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_07_7299cf7b.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_ca4d39a3.log | Log file |
|
▾
|
16 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:01:42 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
24 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_24_bff4e1f1.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_24_1aad0628.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_24_90f3a17f.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_24_f375c0f8.fits | Master bias |
illum
|
ILLUM_20141029T002738_24_fe9c0606.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu24_0.92.0_ccd34602.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_24_6fc5d3b3.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_24_f4d08ed8.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_24_57d14f39.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_e85733ff.log | Log file |
|
▾
|
17 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:00:46 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
8 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_08_132bf852.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_08_6752f8a1.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_08_f84b6f19.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_08_adb18979.fits | Master bias |
illum
|
ILLUM_20141029T002738_08_ef300be5.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu08_0.92.0_21ee214b.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_08_68edae5b.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_08_2c2200ac.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_08_f263c2da.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_ab5a4749.log | Log file |
|
▾
|
18 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:34 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
4 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_04_80a6e7e4.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_04_bef4ac0d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_04_218795e9.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_04_672ed91e.fits | Master bias |
illum
|
ILLUM_20141029T002738_04_3112847f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu04_0.92.0_94fa71c9.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_04_c6e8ace8.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_04_f516a8bb.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_04_3ddef47f.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_e1bf452d.log | Log file |
|
▾
|
19 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:34 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
12 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_12_1c1de1d6.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_12_5898de91.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_12_bfcf222b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_12_2df90763.fits | Master bias |
illum
|
ILLUM_20141029T002738_12_4453c7f7.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu12_0.92.0_6b231479.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_12_3f27f341.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_12_fda5b8a8.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_12_5104e8d5.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_8307cc78.log | Log file |
|
▾
|
20 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:33 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
11 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_11_6e709aa8.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_11_e065b91c.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_11_958631a2.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_11_2da72ed2.fits | Master bias |
illum
|
ILLUM_20141029T002738_11_b592cd32.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu11_0.92.0_582e2944.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_11_c12ae259.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_11_5bd43638.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_11_d20b17b3.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_733683d0.log | Log file |
|
▾
|
21 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:00:45 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
15 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_15_efdb5344.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_15_30d04448.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_15_f15d14ff.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_15_fca5348a.fits | Master bias |
illum
|
ILLUM_20141029T002738_15_23f1a904.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu15_0.92.0_0f854bdf.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_15_bebd7727.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_15_224f9991.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_15_e5a4c49f.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_0a8c9566.log | Log file |
|
▾
|
22 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:02:32 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
20 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_20_8522799f.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_20_fb1a8fa7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_20_62e74d66.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_20_c5fa97a0.fits | Master bias |
illum
|
ILLUM_20141029T002738_20_9c0334cb.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu20_0.92.0_0e74eb04.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_20_01d1ecee.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_20_3bd5e813.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_20_4a4bf0f0.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_640ffc8f.log | Log file |
|
▾
|
23 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:01:17 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
21 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_21_e34adfb0.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_21_8d8fea05.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_21_c0152f87.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_21_8fa88311.fits | Master bias |
illum
|
ILLUM_20141029T002738_21_9800352a.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu21_0.92.0_ef5c70a6.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_21_23792f82.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_21_fb8d1084.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_21_75525e93.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_2415b975.log | Log file |
|
▾
|
24 |
scibasic_object |
1.2 |
2015-10-07 18:54:30 - 2015-10-07 19:04:34 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
16 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_16_5741f34b.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_16_9ea938f7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_16_87a171d7.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_16_7c1ff1a8.fits | Master bias |
illum
|
ILLUM_20141029T002738_16_0ae425cb.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu16_0.92.0_f4c9ba85.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_16_334ca2d4.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_16_14b12421.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_16_310770c8.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_5e8e14e8.log | Log file |
|
▾
|
25 |
scibasic_object |
1.2 |
2015-10-07 18:54:31 - 2015-10-07 19:02:33 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
3 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_03_852ed967.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_03_1aab1ecf.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_03_042307dd.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_03_239dfce6.fits | Master bias |
illum
|
ILLUM_20141029T002738_03_809d3efd.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu03_0.92.0_e27ac68d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_03_3aa1465e.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_03_5e1542b1.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_03_14d986b9.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185332_scibasic_object_f08ef59c.log | Log file |
|
▾
|
26 |
scibasic_object |
1.2 |
2015-10-07 18:54:31 - 2015-10-07 19:00:46 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
1 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_01_794c3a65.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_01_2401a41b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_01_58fea775.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_01_369b6a1a.fits | Master bias |
illum
|
ILLUM_20141029T002738_01_1ee46f9f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu01_0.92.0_c2b69ac3.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_01_73feeef8.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_01_4f0086eb.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_01_1bbbcfae.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_df825b56.log | Log file |
|
▾
|
27 |
scibasic_object |
1.2 |
2015-10-07 18:54:31 - 2015-10-07 19:03:52 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
18 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_18_3282518a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_18_a4b6c988.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_18_0ee74063.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_18_6a0bc1b9.fits | Master bias |
illum
|
ILLUM_20141029T002738_18_5fe3826a.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu18_0.92.0_4bbecb6f.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T002923_18_5e45e53e.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T002923_18_1536e90c.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T002923_18_8203deae.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_185333_scibasic_object_08c9d3c6.log | Log file |
|
▾
|
28 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:43:54 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
2 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_02_b1d30960.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_02_68086d4a.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_02_b1e7c060.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_02_602ed524.fits | Master bias |
illum
|
ILLUM_20141029T002738_02_a9bf33e5.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T005043_02_f49ba036.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_02_5ef9ca2a.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_02_42c74e38.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_830120d4.log | Log file |
|
▾
|
29 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:10 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
6 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_06_718a8eda.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_06_12324817.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_06_c5986c2b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_06_8c18e69c.fits | Master bias |
illum
|
ILLUM_20141029T002738_06_5b5b48a9.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T005043_06_d27e6510.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_06_14bd9a78.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_06_2d9b206a.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_5754436a.log | Log file |
|
▾
|
30 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:48:26 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
13 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_13_e2248a5d.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_13_ab2d148e.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_13_5f9dadfe.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_13_4144e6cc.fits | Master bias |
illum
|
ILLUM_20141029T002738_13_3450f566.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T005043_13_ef646725.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_13_210e6af4.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_13_af714d2c.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_c07c9528.log | Log file |
|
▾
|
31 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:45:14 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
23 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_23_8db3a920.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_23_b62d3e51.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_23_5c905e20.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_23_5c62ec96.fits | Master bias |
illum
|
ILLUM_20141029T002738_23_718e9b30.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu23_0.92.0_d9738915.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_23_62ac823b.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_23_0da821aa.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_23_91d69f24.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_ed43de1e.log | Log file |
|
▾
|
32 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:44:37 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
17 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_17_03959c80.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_17_7d3af99b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_17_5fa4b9dc.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_17_c3383da7.fits | Master bias |
illum
|
ILLUM_20141029T002738_17_49e05c54.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu17_0.92.0_d50734cd.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_17_046c9c07.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_17_03f3ede3.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_17_4850ffe6.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193411_scibasic_object_5a658a9a.log | Log file |
|
▾
|
33 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:44:38 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
19 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_19_16cef25a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_19_7c3a0076.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_19_c558b1c5.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_19_f6b46a79.fits | Master bias |
illum
|
ILLUM_20141029T002738_19_c99bf318.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu19_0.92.0_d1646d1d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_19_6bdf261f.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_19_cecdc08a.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_19_3c5a1aa9.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_3d950fc1.log | Log file |
|
▾
|
34 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:10 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
3 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_03_852ed967.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_03_1aab1ecf.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_03_042307dd.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_03_239dfce6.fits | Master bias |
illum
|
ILLUM_20141029T002738_03_809d3efd.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu03_0.92.0_e27ac68d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_03_3b2cf944.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_03_d315e3fe.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_03_182bda1c.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_3e329048.log | Log file |
|
▾
|
35 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
16 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_16_5741f34b.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_16_9ea938f7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_16_87a171d7.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_16_7c1ff1a8.fits | Master bias |
illum
|
ILLUM_20141029T002738_16_0ae425cb.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu16_0.92.0_f4c9ba85.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_16_1ffa350d.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_16_ebfb5bbf.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_16_4b3476aa.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_c509d899.log | Log file |
|
▾
|
36 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:10 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
7 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_07_96f01c52.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_07_af7875be.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_07_bc5f5491.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_07_3c6c5959.fits | Master bias |
illum
|
ILLUM_20141029T002738_07_cd8fd54f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu07_0.92.0_796de9d4.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_07_5a196531.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_07_6145da61.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_07_654e9f70.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_38c704be.log | Log file |
|
▾
|
37 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:43:37 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
9 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T093504_09_caf41e47.fits | Master flat |
trace_table
|
TRACETABLE_20141028T093504_09_be42cbb7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141028T094945_09_26f11b56.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141028T092026_09_1ee2c475.fits | Master bias |
illum
|
ILLUM_20141029T002738_09_6954c541.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu09_0.92.0_59e8d0c2.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_09_59fc7e90.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_09_6a855006.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_09_445e96b7.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_a8ee42de.log | Log file |
|
▾
|
38 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:43:19 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
5 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_05_beeea1ee.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_05_3799eb4f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_05_33eb21ab.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_05_f5f13716.fits | Master bias |
illum
|
ILLUM_20141029T002738_05_523f906c.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu05_0.92.0_f16e5979.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_05_35f821bb.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_05_4cca3037.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_05_4dfa040c.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_264baeb6.log | Log file |
|
▾
|
39 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
11 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_11_6e709aa8.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_11_e065b91c.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_11_958631a2.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_11_2da72ed2.fits | Master bias |
illum
|
ILLUM_20141029T002738_11_b592cd32.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu11_0.92.0_582e2944.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_11_c417d52f.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_11_2ad1a4dd.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_11_92a7f898.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_00eb0c95.log | Log file |
|
▾
|
40 |
scibasic_object |
1.2 |
2015-10-07 19:34:25 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
10 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_10_1a97c580.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_10_ef4b829f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_10_b544012b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_10_ca42cbcb.fits | Master bias |
illum
|
ILLUM_20141029T002738_10_eb52cdac.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu10_0.92.0_d7241430.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_10_8ded7f4a.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_10_0967e7c4.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_10_9865d1d4.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_b5374d5b.log | Log file |
|
▾
|
41 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:44:38 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
1 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_01_794c3a65.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_01_2401a41b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_01_58fea775.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_01_369b6a1a.fits | Master bias |
illum
|
ILLUM_20141029T002738_01_1ee46f9f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu01_0.92.0_c2b69ac3.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_01_38ef54e2.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_01_5d2a5491.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_01_505fa06b.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_efd29552.log | Log file |
|
▾
|
42 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
14 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_14_4b63e100.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_14_43272ad0.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_14_c8276035.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_14_005e7a53.fits | Master bias |
illum
|
ILLUM_20141029T002738_14_0082e275.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu14_0.92.0_f75ecc95.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_14_ef0fdc35.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_14_637bad40.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_14_122fddab.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_3d0c8b33.log | Log file |
|
▾
|
43 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:45:14 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
24 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_24_bff4e1f1.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_24_1aad0628.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_24_90f3a17f.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_24_f375c0f8.fits | Master bias |
illum
|
ILLUM_20141029T002738_24_fe9c0606.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu24_0.92.0_ccd34602.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_24_f9548606.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_24_300a8a4d.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_24_a046197e.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_269ee730.log | Log file |
|
▾
|
44 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:48:24 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
18 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_18_3282518a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_18_a4b6c988.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_18_0ee74063.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_18_6a0bc1b9.fits | Master bias |
illum
|
ILLUM_20141029T002738_18_5fe3826a.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu18_0.92.0_4bbecb6f.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_18_1a23afea.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_18_6a2e22b6.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_18_1e5f1ba5.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193413_scibasic_object_1d6fa9ab.log | Log file |
|
▾
|
45 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
22 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_22_51d4a082.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_22_c8d26f9d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_22_69605756.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_22_b9214661.fits | Master bias |
illum
|
ILLUM_20141029T002738_22_0651ab89.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu22_0.92.0_ed8e0030.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_22_67e72d61.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_22_0108a9bb.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_22_ef0ed795.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_1cc81936.log | Log file |
|
▾
|
46 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:43:53 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
20 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_20_8522799f.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_20_fb1a8fa7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_20_62e74d66.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_20_c5fa97a0.fits | Master bias |
illum
|
ILLUM_20141029T002738_20_9c0334cb.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu20_0.92.0_0e74eb04.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_20_e1053437.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_20_27052acc.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_20_ccfb37e8.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_a0efda47.log | Log file |
|
▾
|
47 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:46:11 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
15 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_15_efdb5344.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_15_30d04448.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_15_f15d14ff.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_15_fca5348a.fits | Master bias |
illum
|
ILLUM_20141029T002738_15_23f1a904.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu15_0.92.0_0f854bdf.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_15_3fa61f2b.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_15_655c6f63.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_15_313349c3.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_710e0a2d.log | Log file |
|
▾
|
48 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:45:15 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
8 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_08_132bf852.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_08_6752f8a1.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_08_f84b6f19.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_08_adb18979.fits | Master bias |
illum
|
ILLUM_20141029T002738_08_ef300be5.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu08_0.92.0_21ee214b.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_08_d8a21f07.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_08_4feae9c9.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_08_3fbf74db.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_23fe377b.log | Log file |
|
▾
|
49 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:45:14 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
4 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_04_80a6e7e4.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_04_bef4ac0d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_04_218795e9.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_04_672ed91e.fits | Master bias |
illum
|
ILLUM_20141029T002738_04_3112847f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu04_0.92.0_94fa71c9.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_04_493715d4.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_04_80368a1d.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_04_b38a6dcd.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_7093dd63.log | Log file |
|
▾
|
50 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:44:37 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
12 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_12_1c1de1d6.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_12_5898de91.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_12_bfcf222b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_12_2df90763.fits | Master bias |
illum
|
ILLUM_20141029T002738_12_4453c7f7.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu12_0.92.0_6b231479.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_12_0751f665.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_12_e19d5e33.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_12_c901b9d2.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193411_scibasic_object_76bb01e0.log | Log file |
|
▾
|
51 |
scibasic_object |
1.2 |
2015-10-07 19:34:26 - 2015-10-07 19:48:27 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
21 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_21_e34adfb0.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_21_8d8fea05.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_21_c0152f87.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_21_8fa88311.fits | Master bias |
illum
|
ILLUM_20141029T002738_21_9800352a.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu21_0.92.0_ef5c70a6.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T005043_21_0d279bd7.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T005043_21_2cc852d6.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T005043_21_9b12b8c9.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_193410_scibasic_object_964f8fa2.log | Log file |
|
▾
|
52 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:38:39 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
12 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_12_1c1de1d6.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_12_5898de91.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_12_bfcf222b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_12_2df90763.fits | Master bias |
illum
|
ILLUM_20141029T013910_12_fb2fdaa4.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu12_0.92.0_6b231479.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_12_e0779df9.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_12_bf6a856b.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_12_0502c0d2.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_ea8bcece.log | Log file |
|
▾
|
53 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:04 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
9 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T093504_09_caf41e47.fits | Master flat |
trace_table
|
TRACETABLE_20141028T093504_09_be42cbb7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141028T094945_09_26f11b56.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141028T092026_09_1ee2c475.fits | Master bias |
illum
|
ILLUM_20141029T013910_09_d419a1a2.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu09_0.92.0_59e8d0c2.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_09_a9ded681.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_09_3cec21d9.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_09_7229e958.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_b5bb5a5f.log | Log file |
|
▾
|
54 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
1 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_01_794c3a65.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_01_2401a41b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_01_58fea775.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_01_369b6a1a.fits | Master bias |
illum
|
ILLUM_20141029T013910_01_967eb721.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu01_0.92.0_c2b69ac3.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_01_cf8d84ae.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_01_3fa6743f.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_01_a77b1e19.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_32f3744d.log | Log file |
|
▾
|
55 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:38:30 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
6 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_06_718a8eda.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_06_12324817.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_06_c5986c2b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_06_8c18e69c.fits | Master bias |
illum
|
ILLUM_20141029T013910_06_6fbe9533.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T011240_06_1eb9911b.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_06_01da8250.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_06_dc5811e7.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_555252e9.log | Log file |
|
▾
|
56 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:01 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
24 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_24_bff4e1f1.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_24_1aad0628.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_24_90f3a17f.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_24_f375c0f8.fits | Master bias |
illum
|
ILLUM_20141029T013910_24_3948d766.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu24_0.92.0_ccd34602.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_24_177cb226.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_24_8ba149b9.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_24_2401449c.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_9dd03af2.log | Log file |
|
▾
|
57 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
13 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_13_e2248a5d.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_13_ab2d148e.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_13_5f9dadfe.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_13_4144e6cc.fits | Master bias |
illum
|
ILLUM_20141029T013910_13_7edb8878.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T011240_13_9de70c00.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_13_393c6e2f.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_13_1941e774.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_a4c598db.log | Log file |
|
▾
|
58 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
17 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_17_03959c80.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_17_7d3af99b.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_17_5fa4b9dc.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_17_c3383da7.fits | Master bias |
illum
|
ILLUM_20141029T013910_17_6f80ee5f.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu17_0.92.0_d50734cd.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_17_5805e149.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_17_467b1440.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_17_acea2bea.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_8ca68731.log | Log file |
|
▾
|
59 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
19 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_19_16cef25a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_19_7c3a0076.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_19_c558b1c5.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_19_f6b46a79.fits | Master bias |
illum
|
ILLUM_20141029T013910_19_bcac55e4.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu19_0.92.0_d1646d1d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_19_d1f0f3ac.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_19_b1a02600.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_19_6cf1e080.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_02819eeb.log | Log file |
|
▾
|
60 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
2 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_02_b1d30960.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_02_68086d4a.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_02_b1e7c060.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_02_602ed524.fits | Master bias |
illum
|
ILLUM_20141029T013910_02_b9c6c153.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
Main |
object
|
OBJECT_20141029T011240_02_8b54df15.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_02_b53b7fc4.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_02_ded3cc5f.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_d0482a36.log | Log file |
|
▾
|
61 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:59 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
15 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_15_efdb5344.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_15_30d04448.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_15_f15d14ff.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_15_fca5348a.fits | Master bias |
illum
|
ILLUM_20141029T013910_15_5b18ff59.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu15_0.92.0_0f854bdf.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_15_a884173f.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_15_e9b855f7.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_15_ac754c6a.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_576bbfb5.log | Log file |
|
▾
|
62 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:59 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
14 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_14_4b63e100.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_14_43272ad0.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_14_c8276035.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_14_005e7a53.fits | Master bias |
illum
|
ILLUM_20141029T013910_14_c50422f2.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu14_0.92.0_f75ecc95.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_14_04b25363.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_14_b5b8eba3.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_14_efd03fb3.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_48d5e7bb.log | Log file |
|
▾
|
63 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:59 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
22 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_22_51d4a082.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_22_c8d26f9d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_22_69605756.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_22_b9214661.fits | Master bias |
illum
|
ILLUM_20141029T013910_22_9fe1cb16.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu22_0.92.0_ed8e0030.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_22_4f132290.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_22_0ee20de2.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_22_c5170cdb.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_7d8dc371.log | Log file |
|
▾
|
64 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
4 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_04_80a6e7e4.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_04_bef4ac0d.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_04_218795e9.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_04_672ed91e.fits | Master bias |
illum
|
ILLUM_20141029T013910_04_4673dc2b.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu04_0.92.0_94fa71c9.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_04_cd618c42.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_04_075d4fe7.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_04_88ede962.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_0b04fc07.log | Log file |
|
▾
|
65 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
23 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_23_8db3a920.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_23_b62d3e51.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_23_5c905e20.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_23_5c62ec96.fits | Master bias |
illum
|
ILLUM_20141029T013910_23_11bbee49.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu23_0.92.0_d9738915.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_23_9d6180b8.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_23_52bca990.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_23_b720be72.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_35d1f664.log | Log file |
|
▾
|
66 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:59 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
8 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_08_132bf852.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_08_6752f8a1.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_08_f84b6f19.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_08_adb18979.fits | Master bias |
illum
|
ILLUM_20141029T013910_08_343d9559.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu08_0.92.0_21ee214b.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_08_984706a3.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_08_83c80114.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_08_e91b6730.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_9b923fc7.log | Log file |
|
▾
|
67 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:04 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
3 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_03_852ed967.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_03_1aab1ecf.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_03_042307dd.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_03_239dfce6.fits | Master bias |
illum
|
ILLUM_20141029T013910_03_04e4c428.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu03_0.92.0_e27ac68d.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_03_b370d81d.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_03_0fc9c159.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_03_c616e00a.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_6f568108.log | Log file |
|
▾
|
68 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:57 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
10 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_10_1a97c580.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_10_ef4b829f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_10_b544012b.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_10_ca42cbcb.fits | Master bias |
illum
|
ILLUM_20141029T013910_10_ba8abba5.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu10_0.92.0_d7241430.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_10_d456c14f.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_10_4c02d94a.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_10_d93ea25c.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_1b47fb10.log | Log file |
|
▾
|
69 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
11 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_11_6e709aa8.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_11_e065b91c.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_11_958631a2.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_11_2da72ed2.fits | Master bias |
illum
|
ILLUM_20141029T013910_11_8f77f662.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu11_0.92.0_582e2944.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_11_665797e7.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_11_6b7991ec.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_11_4c3c94d6.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_65710f0b.log | Log file |
|
▾
|
70 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:03 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
21 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_21_e34adfb0.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_21_8d8fea05.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_21_c0152f87.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_21_8fa88311.fits | Master bias |
illum
|
ILLUM_20141029T013910_21_207c814c.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu21_0.92.0_ef5c70a6.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_21_879bb4b8.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_21_6715553d.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_21_bcdf5fab.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_28f3c818.log | Log file |
|
▾
|
71 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:03 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
7 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_07_96f01c52.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_07_af7875be.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_07_bc5f5491.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_07_3c6c5959.fits | Master bias |
illum
|
ILLUM_20141029T013910_07_c0cb7ad8.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu07_0.92.0_796de9d4.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_07_f42c8e29.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_07_235b74d3.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_07_3065d787.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_1f005864.log | Log file |
|
▾
|
72 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
16 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_16_5741f34b.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_16_9ea938f7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_16_87a171d7.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_16_7c1ff1a8.fits | Master bias |
illum
|
ILLUM_20141029T013910_16_309cc436.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu16_0.92.0_f4c9ba85.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_16_e45858f8.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_16_7a73bc66.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_16_b2bc74da.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203219_scibasic_object_00ff466e.log | Log file |
|
▾
|
73 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:41:00 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
20 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_20_8522799f.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_20_fb1a8fa7.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_20_62e74d66.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_20_c5fa97a0.fits | Master bias |
illum
|
ILLUM_20141029T013910_20_3d5e4171.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu20_0.92.0_0e74eb04.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_20_20b223b1.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_20_21ef533e.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_20_0e544427.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203217_scibasic_object_36c83d7f.log | Log file |
|
▾
|
74 |
scibasic_object |
1.2 |
2015-10-07 20:32:28 - 2015-10-07 20:39:02 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
18 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_18_3282518a.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_18_a4b6c988.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_18_0ee74063.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_18_6a0bc1b9.fits | Master bias |
illum
|
ILLUM_20141029T013910_18_77a68a7b.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu18_0.92.0_4bbecb6f.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_18_18f9bb9d.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_18_337d6416.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_18_7c083aca.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203218_scibasic_object_bf90da77.log | Log file |
|
▾
|
75 |
scibasic_object |
1.2 |
2015-10-07 20:32:30 - 2015-10-07 20:40:58 |
Description |
Version | 1.2 | Type | recipe | Description | Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.
▾
Processing handles each raw input image separately: it trims the raw
data and records the overscan statistics, subtracts the bias (taking
account of the overscan, if --overscan is not "none"), optionally
detects cosmic rays (note that by default cosmic ray rejection is
handled in the post processing recipes while the data is reformatted
into a datacube, so that the default setting is cr="none" here),
converts the images from adu to count, subtracts the dark, divides by
the flat-field, and (optionally) propagates the integrated flux value
from the twilight-sky cube.
[For special cases, users can choose to combine all input files at the
image level, so that the pixel table is only created once, for the
combined data. This is not recommended for science data, where the
combination should take place after correcting for atmospheric effects,
before the creation of the final cube.]
The reduced image is then saved (if --saveimage=true).
The input calibrations geometry table, trace table, and wavelength
calibration table are used to assign 3D coordinates to each CCD-based
pixel, thereby creating a pixel table for each exposure.
If --skylines contains one or more wavelengths for (bright and isolated)
sky emission lines, these lines are used to correct the wavelength
calibration using an offset.
The data is then cut to a useful wavelength range (if --crop=true).
If an ILLUM exposure was given as input, it is then used to correct the
relative illumination between all slices of one IFU. For this, the data
of each slice is multiplied by the normalized median flux of that slice
in the ILLUM exposure.
As last step, the data is divided by the normalized twilight cube (if
given), using the 3D coordinate of each pixel in the pixel table to
interpolate the twilight correction onto the data.
This pre-reduced pixel table for each exposure is then saved to disk.
| Input |
Configuration |
scale
|
True | Scale the individual images to a common exposure time before combining them. |
ybox
|
40 pixel | Search box size in y.
▾
Only used if cr=dcr.
|
lsigma
|
3.0 count | Low sigma for pixel rejection with sigclip |
cr
|
none | Type of cosmic ray cleaning to use (for quick-look data processing). |
thres
|
5.8 | Threshold for detection gap in factors of standard deviation.
▾
Only used if cr=dcr.
|
crop
|
True | Automatically crop the output pixel tables in wavelength.
▾
This depends on the expected useful wavelength range of the observation mode used (4750-9350 Angstrom for nominal mode, 4600-9350 Angstrom for extended mode).
|
ovscsigma
|
30.0 pixel | If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing.
▾
If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset".
|
skyhalfwidth
|
5.0 Angstrom | Half-width of the extraction box (in Angstrom) around each sky emission line. |
skybinsize
|
0.1 Angstrom | Size of the bins (in Angstrom per pixel) for the intermediate spectrum to do the Gaussian fit to each sky emission line. |
combine
|
none | Type of combination to use.
▾
Note that in most cases, science exposures cannot easily be combined on the CCD level, so this should usually be kept as "none"! This does not pay attention about the type of input data, and will combine all raw inputs!
|
merge
|
False | Merge output products from different IFUs into a common file. |
nlow
|
1 pixel | Number of minimum pixels to reject with minmax |
passes
|
2 | Maximum number of cleaning passes.
▾
Only used if cr=dcr.
|
resample
|
0 | Resample the input science data into 2D spectral images using tracing and wavelength calibration solutions for a visual check.
▾
Note that the image produced will show small wiggles even when the input calibrations are good and were applied successfully!
|
nifu
|
5 | IFU to handle.
▾
If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel.
|
nkeep
|
1 pixel | Number of pixels to keep with minmax |
ovscignore
|
3 pixel | The number of pixels of the overscan adjacent to the data region of the CCD that are ignored when computing statistics or fits. |
overscan
|
vpoly | Overscan handling.
▾
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant.
|
dlambda
|
1.25 Angstrom | Wavelength step (in Angstrom per pixel) to use for resampling. |
ovscreject
|
dcr | This influences how values are rejected when computing overscan statistics.
▾
Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit").
|
hsigma
|
3.0 count | High sigma for pixel rejection with sigclip |
xbox
|
15 pixel | Search box size in x.
▾
Only used if cr=dcr.
|
nhigh
|
1 pixel | Number of maximum pixels to reject with minmax |
Calibration |
master_flat
|
MASTERFLAT_20141028T175622_05_beeea1ee.fits | Master flat |
trace_table
|
TRACETABLE_20141028T175622_05_3799eb4f.fits | Trace table |
wavecal_table
|
WAVECALTABLE_20141029T094935_05_33eb21ab.fits | Wavelength calibration table |
twilight_cube
|
TWILIGHTCUBE_20141028T225657_edf9b1b2.fits | Smoothed cube of twilight sky |
geometry_table
|
geometry_table_wfm_gto02_0.92.0_498dbc95.fits | Relative positions of the slices in the field of view |
master_bias
|
MASTERBIAS_20141029T092016_05_f5f13716.fits | Master bias |
illum
|
ILLUM_20141029T013910_05_ded6dc24.fits | Single optional raw (attached/illumination) flat-field exposure |
Reference |
skylines
|
5577.339,6300.304 Angstrom | List of wavelengths of sky emission lines (in Angstrom) to use as reference for wavelength offset correction using a Gaussian fit.
▾
It can contain multiple (isolated) lines, as comma-separated list, individual shifts are then combined into one weighted average offset. Set to "none" to deactivate.
|
badpix_table
|
badpix_table_ifu05_0.92.0_f16e5979.fits | Known bad pixels |
Main |
object
|
OBJECT_20141029T011240_05_0423ecf2.fits | Raw exposure of a science target |
Debug |
saveimage
|
True | Save the pre-processed CCD-based image of each input exposure before it is transformed into a pixel table. |
Output |
Main |
PIXTABLE_OBJECT
|
PIXTABLEOBJECTscibasic_20141029T011240_05_3d79917c.fits | Output pixel table for OBJECT input |
Debug |
OBJECT_RED
|
OBJECTRED_20141029T011240_05_3c3c6914.fits | Pre-processed CCD-based images for OBJECT input (if --saveimage=true) |
LOGFILE
|
20151007_203221_scibasic_object_6ff7377d.log | Log file |
|
▾
|
76 |
scipost |
1.2 |
2015-11-18 12:52:53 - 2015-11-18 13:28:35 |
Description |
Version | 1.2 | Type | recipe | Description | Prepare reduced and combined science products.
▾
Sort input pixel tables into lists of files per exposure, merge pixel
tables from all IFUs of each exposure.
Correct each exposure for differential atmopheric refraction (unless
--lambdaraf is far outside the MUSE wavelength range).
Then the flux calibration is carried out, if a respnse curve was given
in the input; it includes a correction of telluric absorption, if a
telluric absorptin correction file was given.
Then the sky subtraction is carried out (unless --skymethod="none"),
either directly subtracting an input sky continuum and an input sky
emission lines (for --skymethod="subtract-model"), or
(--skymethod="model") create a sky spectrum from the darkest fraction
(--skymodel_fraction, after ignoring the lowest --skymodel_ignore as
artifacts) of the field of view, then fitting and subtracting
sky emission lines using an initial estimate of the input sky lines;
then the continuum (residuals after subtracting the sky lines from the
sky spectrum) is subtracted as well. If --save contains "skymodel", all
sky-related products are saved for each exposure.
Afterwards the data is corrected for the radial velocity of the
observer (--rvcorr), before the input (or a default) astrometric
solution is applied.
Now each individual exposure is fully reduced; the pixel tables at this
stage can be saved by setting "individual" in --save.
If multiple exposures were given, they are then combined. If --save
contains "combined", this final merged pixel table is saved.
Finally (if --save contains "cube"), the data is resampled into a
datacube, using all parameters given to the recipe. The extent and
orientation of the cube is normally computed from the data itself, but
this can be overridden by passing a file with the output world
coordinate system (OUTPUT_WCS), for example a MUSE cube. This can also
be used to sample the wavelength axis logorithmically (in that file set
"CTYPE3='AWAV-LOG'").
As a last step, the computed cube is integrated over all filter
functions given (--filter) that are also present in the input filter
list table.
| Input |
Configuration |
sky_crsigma
|
15.,0. | Sigma level clipping for cube-based and spectrum-based CR rejection when creating the sky spectrum.
▾
This has to be a string of two comma-separated floating-point numbers. The first value gives the sigma-level rejection for cube-based CR rejection (using "median", see muse_scipost), the second value the sigma-level for spectrum-based CR cleaning. Both can be switched off, by passing zero or a negative value; by default, the spectrum-based rejection is switched off.
|
astrometry
|
True | If false, skip any astrometric calibration, even if one was passed in the input set of files.
▾
This causes creation of an output cube with a linear WCS and may result in errors. If you want to use a sensible default, leave this true but do not pass an ASTROMETRY_WCS.
|
skymethod
|
none | The method used to subtract the sky background.
▾
"model" should work in all cases, it uses a global sky spectrum model with a local LSF. If "model" is selected, calibration frames for SKY_LINES and LSF_PROFILE must be set; SKY_CONTINUUM and SKY_MASK are optional. If "subtract-model" is selected, precalculated sky lines and continuum are subtracted if specified by SKY_LINES and SKY_CONTINUUM. An LSF_PROFILE is necessary for the two model-based methods. "simple" directly subtracts a sky spectrum created from the data, without regard to LSF variations; it also works on data taht was not flux calibrated.
|
skymodel_csampling
|
0.3125 Angstrom | Spectral sampling of the continuum spectrum [Angstrom]. |
astrometry_wcs
|
astrometry_wcs_wfm_gto02_0.92.0_2f6df8d2.fits | Astrometric solution derived from astrometric science frame |
rc
|
1.25 pixel | Critical radius for the "renka" resampling method. |
dy
|
0.0 arcsec | Vertical step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
dx
|
0.0 arcsec | Horizontal step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
crsigma
|
15.0 | Sigma rejection factor to use for cosmic ray rejection during final resampling.
▾
A zero or negative value switches cosmic ray rejection off.
|
skymodel_sampling
|
0.3125 Angstrom | Spectral sampling of the sky spectrum [Angstrom]. |
crtype
|
median | Type of statistics used for detection of cosmic rays during final resampling.
▾
"iraf" uses the variance information, "mean" uses standard (mean/stdev) statistics, "median" uses median and the median median of the absolute median deviation.
|
lambdamax
|
10000.0 Angstrom | Cut off the data above this wavelength after loading the pixel table(s). |
resample
|
drizzle | The resampling technique to use for the final output cube. |
lambdamin
|
4000.0 Angstrom | Cut off the data below this wavelength after loading the pixel table(s). |
save
|
individual,cube | Select output product(s) to save.
▾
Can contain one or more of "cube", "skymodel", "individual", "positioned", "combined", and "stacked". If several options are given, they have to be comma-separated.
("cube": output cube and associated images, if this is not given, no final resampling is done at all --
"skymodel": up to four additional output products about the effectively used sky that was subtracted with the "model" method --
"individual": fully reduced pixel table for each individual exposure --
"positioned": fully reduced and positioned pixel table for each individual exposure, the difference to "individual" is that here, the output pixel tables have coordinates in RA and DEC; this is only useful, if both the relative exposure weighting and the final resampling are to be done externally --
"combined": fully reduced and combined pixel table for the full set of exposures, the difference to "positioned" is that all pixel tables are combined into one, with an added weight column; this is useful, if only the final resampling step is to be done separately --
"stacked": an additional output file in form of a 2D column-stacked image, i.e. x direction is pseudo-spatial, y direction is wavelength.)
|
skymodel_ignore
|
0.05 | Fraction of the image to be ignored.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 0.
|
darcheck
|
none | Carry out a check of the theoretical DAR correction using source centroiding.
▾
If "correct" it will also apply an empirical correction.
|
ld
|
1 | Number of adjacent pixels to take into account during resampling in all three directions (loop distance).
▾
This affects all resampling methods except "nearest".
|
rvcorr
|
bary | Radial velocity correction.
▾
Correct the radial velocity of the telescope with reference to either the barycenter of the Solar System (bary), the center of the Sun (helio), or to the center of the Earth (geo).
|
format
|
Cube | Type of output file format.
▾
"Cube" is a standard FITS cube with NAXIS=3 and multiple extensions (for data and variance). The extended "x" formats include the reconstructed image(s) in FITS image extensions within the same file.
|
skymodel_fraction
|
0.1 | Fraction of the image (without the ignored part) to be considered as sky.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 1.
|
weight
|
exptime | Type of weighting scheme to use when combining multiple exposures.
▾
"exptime" just uses the exposure time to weight the exposures, "fwhm" uses the best available seeing information from the headers as well, "none" preserves an existing weight column in the input pixel tables without changes.
|
pixfrac
|
0.8 pixel | Pixel down-scaling factor for the "drizzle" resampling method. |
dlambda
|
0.0 Angstrom | Wavelength step size (in Angstrom).
▾
Natural instrument sampling is used, if this is 0.0
|
filter
|
white | The filter name(s) to be used for the output field-of-view image.
▾
Each name has to correspond to an EXTNAME in an extension of the FILTER_LIST file. If an unsupported filter name is given, creation of the respective image is omitted. If multiple filter names are given, they have to be comma separated.
|
Calibration |
lambdaref
|
7000.0 Angstrom | Reference wavelength used for correction of differential atmospheric refraction.
▾
The R-band (peak wavelength ~7000 Angstrom) that is usually used for guiding, is close to the central wavelength of MUSE, so a value of 7000.0 Angstrom should be used if nothing else is known. A value less than zero switches DAR correction off.
|
std_response
|
STDRESPONSE_20141029T085501_763d145b.fits | Response curve as derived from standard star(s) |
Reference |
extinct_table
|
extinct_table_0.92.0_00cfbcd2.fits | Atmospheric extinction table |
filter_list
|
filter_list_1.0_7e45ce1c.fits | File to be used to create field-of-view images. |
Main |
pixtable_object
|
PIXTABLEOBJECTscibasic_20141029T002923_01_4f0086eb.fits PIXTABLEOBJECTscibasic_20141029T002923_02_9f3e8869.fits PIXTABLEOBJECTscibasic_20141029T002923_03_5e1542b1.fits PIXTABLEOBJECTscibasic_20141029T002923_04_f516a8bb.fits PIXTABLEOBJECTscibasic_20141029T002923_05_185b90c1.fits PIXTABLEOBJECTscibasic_20141029T002923_06_bd33f7fc.fits PIXTABLEOBJECTscibasic_20141029T002923_07_4d0cbacd.fits PIXTABLEOBJECTscibasic_20141029T002923_08_2c2200ac.fits PIXTABLEOBJECTscibasic_20141029T002923_09_45a9472e.fits PIXTABLEOBJECTscibasic_20141029T002923_10_f0a2906c.fits PIXTABLEOBJECTscibasic_20141029T002923_11_5bd43638.fits PIXTABLEOBJECTscibasic_20141029T002923_12_fda5b8a8.fits PIXTABLEOBJECTscibasic_20141029T002923_13_543e779b.fits PIXTABLEOBJECTscibasic_20141029T002923_14_3557be62.fits PIXTABLEOBJECTscibasic_20141029T002923_15_224f9991.fits PIXTABLEOBJECTscibasic_20141029T002923_16_14b12421.fits PIXTABLEOBJECTscibasic_20141029T002923_17_c74cb22a.fits PIXTABLEOBJECTscibasic_20141029T002923_18_1536e90c.fits PIXTABLEOBJECTscibasic_20141029T002923_19_2d658f9f.fits PIXTABLEOBJECTscibasic_20141029T002923_20_3bd5e813.fits PIXTABLEOBJECTscibasic_20141029T002923_21_fb8d1084.fits PIXTABLEOBJECTscibasic_20141029T002923_22_d144352a.fits PIXTABLEOBJECTscibasic_20141029T002923_23_58d3ebc2.fits PIXTABLEOBJECTscibasic_20141029T002923_24_f4d08ed8.fits | Pixel table of a science object |
Output |
Main |
DATACUBE_FINAL
|
DATACUBEFINALscipost_20141029T002923_a063d440.fits | Output datacube |
PIXTABLE_REDUCED
|
PIXTABLEREDUCEDscipost_20141029T002923_5e7df35a.fits | Output pixel table |
Debug |
LOGFILE
|
20151118_125235_scipost_0e4485ec.log | Log file |
|
▾
|
77 |
scipost |
1.2 |
2015-11-18 15:53:19 - 2015-11-18 16:26:49 |
Description |
Version | 1.2 | Type | recipe | Description | Prepare reduced and combined science products.
▾
Sort input pixel tables into lists of files per exposure, merge pixel
tables from all IFUs of each exposure.
Correct each exposure for differential atmopheric refraction (unless
--lambdaraf is far outside the MUSE wavelength range).
Then the flux calibration is carried out, if a respnse curve was given
in the input; it includes a correction of telluric absorption, if a
telluric absorptin correction file was given.
Then the sky subtraction is carried out (unless --skymethod="none"),
either directly subtracting an input sky continuum and an input sky
emission lines (for --skymethod="subtract-model"), or
(--skymethod="model") create a sky spectrum from the darkest fraction
(--skymodel_fraction, after ignoring the lowest --skymodel_ignore as
artifacts) of the field of view, then fitting and subtracting
sky emission lines using an initial estimate of the input sky lines;
then the continuum (residuals after subtracting the sky lines from the
sky spectrum) is subtracted as well. If --save contains "skymodel", all
sky-related products are saved for each exposure.
Afterwards the data is corrected for the radial velocity of the
observer (--rvcorr), before the input (or a default) astrometric
solution is applied.
Now each individual exposure is fully reduced; the pixel tables at this
stage can be saved by setting "individual" in --save.
If multiple exposures were given, they are then combined. If --save
contains "combined", this final merged pixel table is saved.
Finally (if --save contains "cube"), the data is resampled into a
datacube, using all parameters given to the recipe. The extent and
orientation of the cube is normally computed from the data itself, but
this can be overridden by passing a file with the output world
coordinate system (OUTPUT_WCS), for example a MUSE cube. This can also
be used to sample the wavelength axis logorithmically (in that file set
"CTYPE3='AWAV-LOG'").
As a last step, the computed cube is integrated over all filter
functions given (--filter) that are also present in the input filter
list table.
| Input |
Configuration |
sky_crsigma
|
15.,0. | Sigma level clipping for cube-based and spectrum-based CR rejection when creating the sky spectrum.
▾
This has to be a string of two comma-separated floating-point numbers. The first value gives the sigma-level rejection for cube-based CR rejection (using "median", see muse_scipost), the second value the sigma-level for spectrum-based CR cleaning. Both can be switched off, by passing zero or a negative value; by default, the spectrum-based rejection is switched off.
|
astrometry
|
True | If false, skip any astrometric calibration, even if one was passed in the input set of files.
▾
This causes creation of an output cube with a linear WCS and may result in errors. If you want to use a sensible default, leave this true but do not pass an ASTROMETRY_WCS.
|
skymethod
|
none | The method used to subtract the sky background.
▾
"model" should work in all cases, it uses a global sky spectrum model with a local LSF. If "model" is selected, calibration frames for SKY_LINES and LSF_PROFILE must be set; SKY_CONTINUUM and SKY_MASK are optional. If "subtract-model" is selected, precalculated sky lines and continuum are subtracted if specified by SKY_LINES and SKY_CONTINUUM. An LSF_PROFILE is necessary for the two model-based methods. "simple" directly subtracts a sky spectrum created from the data, without regard to LSF variations; it also works on data taht was not flux calibrated.
|
skymodel_csampling
|
0.3125 Angstrom | Spectral sampling of the continuum spectrum [Angstrom]. |
astrometry_wcs
|
astrometry_wcs_wfm_gto02_0.92.0_2f6df8d2.fits | Astrometric solution derived from astrometric science frame |
rc
|
1.25 pixel | Critical radius for the "renka" resampling method. |
dy
|
0.0 arcsec | Vertical step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
dx
|
0.0 arcsec | Horizontal step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
crsigma
|
15.0 | Sigma rejection factor to use for cosmic ray rejection during final resampling.
▾
A zero or negative value switches cosmic ray rejection off.
|
skymodel_sampling
|
0.3125 Angstrom | Spectral sampling of the sky spectrum [Angstrom]. |
crtype
|
median | Type of statistics used for detection of cosmic rays during final resampling.
▾
"iraf" uses the variance information, "mean" uses standard (mean/stdev) statistics, "median" uses median and the median median of the absolute median deviation.
|
lambdamax
|
10000.0 Angstrom | Cut off the data above this wavelength after loading the pixel table(s). |
resample
|
drizzle | The resampling technique to use for the final output cube. |
lambdamin
|
4000.0 Angstrom | Cut off the data below this wavelength after loading the pixel table(s). |
save
|
individual,cube | Select output product(s) to save.
▾
Can contain one or more of "cube", "skymodel", "individual", "positioned", "combined", and "stacked". If several options are given, they have to be comma-separated.
("cube": output cube and associated images, if this is not given, no final resampling is done at all --
"skymodel": up to four additional output products about the effectively used sky that was subtracted with the "model" method --
"individual": fully reduced pixel table for each individual exposure --
"positioned": fully reduced and positioned pixel table for each individual exposure, the difference to "individual" is that here, the output pixel tables have coordinates in RA and DEC; this is only useful, if both the relative exposure weighting and the final resampling are to be done externally --
"combined": fully reduced and combined pixel table for the full set of exposures, the difference to "positioned" is that all pixel tables are combined into one, with an added weight column; this is useful, if only the final resampling step is to be done separately --
"stacked": an additional output file in form of a 2D column-stacked image, i.e. x direction is pseudo-spatial, y direction is wavelength.)
|
skymodel_ignore
|
0.05 | Fraction of the image to be ignored.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 0.
|
darcheck
|
none | Carry out a check of the theoretical DAR correction using source centroiding.
▾
If "correct" it will also apply an empirical correction.
|
ld
|
1 | Number of adjacent pixels to take into account during resampling in all three directions (loop distance).
▾
This affects all resampling methods except "nearest".
|
rvcorr
|
bary | Radial velocity correction.
▾
Correct the radial velocity of the telescope with reference to either the barycenter of the Solar System (bary), the center of the Sun (helio), or to the center of the Earth (geo).
|
format
|
Cube | Type of output file format.
▾
"Cube" is a standard FITS cube with NAXIS=3 and multiple extensions (for data and variance). The extended "x" formats include the reconstructed image(s) in FITS image extensions within the same file.
|
skymodel_fraction
|
0.1 | Fraction of the image (without the ignored part) to be considered as sky.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 1.
|
weight
|
exptime | Type of weighting scheme to use when combining multiple exposures.
▾
"exptime" just uses the exposure time to weight the exposures, "fwhm" uses the best available seeing information from the headers as well, "none" preserves an existing weight column in the input pixel tables without changes.
|
pixfrac
|
0.8 pixel | Pixel down-scaling factor for the "drizzle" resampling method. |
dlambda
|
0.0 Angstrom | Wavelength step size (in Angstrom).
▾
Natural instrument sampling is used, if this is 0.0
|
filter
|
white | The filter name(s) to be used for the output field-of-view image.
▾
Each name has to correspond to an EXTNAME in an extension of the FILTER_LIST file. If an unsupported filter name is given, creation of the respective image is omitted. If multiple filter names are given, they have to be comma separated.
|
Calibration |
lambdaref
|
7000.0 Angstrom | Reference wavelength used for correction of differential atmospheric refraction.
▾
The R-band (peak wavelength ~7000 Angstrom) that is usually used for guiding, is close to the central wavelength of MUSE, so a value of 7000.0 Angstrom should be used if nothing else is known. A value less than zero switches DAR correction off.
|
std_response
|
STDRESPONSE_20141029T085501_763d145b.fits | Response curve as derived from standard star(s) |
Reference |
extinct_table
|
extinct_table_0.92.0_00cfbcd2.fits | Atmospheric extinction table |
filter_list
|
filter_list_1.0_7e45ce1c.fits | File to be used to create field-of-view images. |
Main |
pixtable_object
|
PIXTABLEOBJECTscibasic_20141029T005043_01_5d2a5491.fits PIXTABLEOBJECTscibasic_20141029T005043_02_5ef9ca2a.fits PIXTABLEOBJECTscibasic_20141029T005043_03_d315e3fe.fits PIXTABLEOBJECTscibasic_20141029T005043_04_80368a1d.fits PIXTABLEOBJECTscibasic_20141029T005043_05_4cca3037.fits PIXTABLEOBJECTscibasic_20141029T005043_06_14bd9a78.fits PIXTABLEOBJECTscibasic_20141029T005043_07_6145da61.fits PIXTABLEOBJECTscibasic_20141029T005043_08_4feae9c9.fits PIXTABLEOBJECTscibasic_20141029T005043_09_6a855006.fits PIXTABLEOBJECTscibasic_20141029T005043_10_0967e7c4.fits PIXTABLEOBJECTscibasic_20141029T005043_11_2ad1a4dd.fits PIXTABLEOBJECTscibasic_20141029T005043_12_e19d5e33.fits PIXTABLEOBJECTscibasic_20141029T005043_13_210e6af4.fits PIXTABLEOBJECTscibasic_20141029T005043_14_637bad40.fits PIXTABLEOBJECTscibasic_20141029T005043_15_655c6f63.fits PIXTABLEOBJECTscibasic_20141029T005043_16_ebfb5bbf.fits PIXTABLEOBJECTscibasic_20141029T005043_17_03f3ede3.fits PIXTABLEOBJECTscibasic_20141029T005043_18_6a2e22b6.fits PIXTABLEOBJECTscibasic_20141029T005043_19_cecdc08a.fits PIXTABLEOBJECTscibasic_20141029T005043_20_27052acc.fits PIXTABLEOBJECTscibasic_20141029T005043_21_2cc852d6.fits PIXTABLEOBJECTscibasic_20141029T005043_22_0108a9bb.fits PIXTABLEOBJECTscibasic_20141029T005043_23_0da821aa.fits PIXTABLEOBJECTscibasic_20141029T005043_24_300a8a4d.fits | Pixel table of a science object |
Output |
Main |
DATACUBE_FINAL
|
DATACUBEFINALscipost_20141029T005043_220af1b8.fits | Output datacube |
PIXTABLE_REDUCED
|
PIXTABLEREDUCEDscipost_20141029T005043_31c0f6b8.fits | Output pixel table |
Debug |
LOGFILE
|
20151118_155305_scipost_7c6207f8.log | Log file |
|
▾
|
78 |
scipost |
1.2 |
2015-11-18 18:42:42 - 2015-11-18 19:19:04 |
Description |
Version | 1.2 | Type | recipe | Description | Prepare reduced and combined science products.
▾
Sort input pixel tables into lists of files per exposure, merge pixel
tables from all IFUs of each exposure.
Correct each exposure for differential atmopheric refraction (unless
--lambdaraf is far outside the MUSE wavelength range).
Then the flux calibration is carried out, if a respnse curve was given
in the input; it includes a correction of telluric absorption, if a
telluric absorptin correction file was given.
Then the sky subtraction is carried out (unless --skymethod="none"),
either directly subtracting an input sky continuum and an input sky
emission lines (for --skymethod="subtract-model"), or
(--skymethod="model") create a sky spectrum from the darkest fraction
(--skymodel_fraction, after ignoring the lowest --skymodel_ignore as
artifacts) of the field of view, then fitting and subtracting
sky emission lines using an initial estimate of the input sky lines;
then the continuum (residuals after subtracting the sky lines from the
sky spectrum) is subtracted as well. If --save contains "skymodel", all
sky-related products are saved for each exposure.
Afterwards the data is corrected for the radial velocity of the
observer (--rvcorr), before the input (or a default) astrometric
solution is applied.
Now each individual exposure is fully reduced; the pixel tables at this
stage can be saved by setting "individual" in --save.
If multiple exposures were given, they are then combined. If --save
contains "combined", this final merged pixel table is saved.
Finally (if --save contains "cube"), the data is resampled into a
datacube, using all parameters given to the recipe. The extent and
orientation of the cube is normally computed from the data itself, but
this can be overridden by passing a file with the output world
coordinate system (OUTPUT_WCS), for example a MUSE cube. This can also
be used to sample the wavelength axis logorithmically (in that file set
"CTYPE3='AWAV-LOG'").
As a last step, the computed cube is integrated over all filter
functions given (--filter) that are also present in the input filter
list table.
| Input |
Configuration |
sky_crsigma
|
15.,0. | Sigma level clipping for cube-based and spectrum-based CR rejection when creating the sky spectrum.
▾
This has to be a string of two comma-separated floating-point numbers. The first value gives the sigma-level rejection for cube-based CR rejection (using "median", see muse_scipost), the second value the sigma-level for spectrum-based CR cleaning. Both can be switched off, by passing zero or a negative value; by default, the spectrum-based rejection is switched off.
|
astrometry
|
True | If false, skip any astrometric calibration, even if one was passed in the input set of files.
▾
This causes creation of an output cube with a linear WCS and may result in errors. If you want to use a sensible default, leave this true but do not pass an ASTROMETRY_WCS.
|
skymethod
|
none | The method used to subtract the sky background.
▾
"model" should work in all cases, it uses a global sky spectrum model with a local LSF. If "model" is selected, calibration frames for SKY_LINES and LSF_PROFILE must be set; SKY_CONTINUUM and SKY_MASK are optional. If "subtract-model" is selected, precalculated sky lines and continuum are subtracted if specified by SKY_LINES and SKY_CONTINUUM. An LSF_PROFILE is necessary for the two model-based methods. "simple" directly subtracts a sky spectrum created from the data, without regard to LSF variations; it also works on data taht was not flux calibrated.
|
skymodel_csampling
|
0.3125 Angstrom | Spectral sampling of the continuum spectrum [Angstrom]. |
astrometry_wcs
|
astrometry_wcs_wfm_gto02_0.92.0_2f6df8d2.fits | Astrometric solution derived from astrometric science frame |
rc
|
1.25 pixel | Critical radius for the "renka" resampling method. |
dy
|
0.0 arcsec | Vertical step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
dx
|
0.0 arcsec | Horizontal step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
crsigma
|
15.0 | Sigma rejection factor to use for cosmic ray rejection during final resampling.
▾
A zero or negative value switches cosmic ray rejection off.
|
skymodel_sampling
|
0.3125 Angstrom | Spectral sampling of the sky spectrum [Angstrom]. |
crtype
|
median | Type of statistics used for detection of cosmic rays during final resampling.
▾
"iraf" uses the variance information, "mean" uses standard (mean/stdev) statistics, "median" uses median and the median median of the absolute median deviation.
|
lambdamax
|
10000.0 Angstrom | Cut off the data above this wavelength after loading the pixel table(s). |
resample
|
drizzle | The resampling technique to use for the final output cube. |
lambdamin
|
4000.0 Angstrom | Cut off the data below this wavelength after loading the pixel table(s). |
save
|
individual,cube | Select output product(s) to save.
▾
Can contain one or more of "cube", "skymodel", "individual", "positioned", "combined", and "stacked". If several options are given, they have to be comma-separated.
("cube": output cube and associated images, if this is not given, no final resampling is done at all --
"skymodel": up to four additional output products about the effectively used sky that was subtracted with the "model" method --
"individual": fully reduced pixel table for each individual exposure --
"positioned": fully reduced and positioned pixel table for each individual exposure, the difference to "individual" is that here, the output pixel tables have coordinates in RA and DEC; this is only useful, if both the relative exposure weighting and the final resampling are to be done externally --
"combined": fully reduced and combined pixel table for the full set of exposures, the difference to "positioned" is that all pixel tables are combined into one, with an added weight column; this is useful, if only the final resampling step is to be done separately --
"stacked": an additional output file in form of a 2D column-stacked image, i.e. x direction is pseudo-spatial, y direction is wavelength.)
|
skymodel_ignore
|
0.05 | Fraction of the image to be ignored.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 0.
|
darcheck
|
none | Carry out a check of the theoretical DAR correction using source centroiding.
▾
If "correct" it will also apply an empirical correction.
|
ld
|
1 | Number of adjacent pixels to take into account during resampling in all three directions (loop distance).
▾
This affects all resampling methods except "nearest".
|
rvcorr
|
bary | Radial velocity correction.
▾
Correct the radial velocity of the telescope with reference to either the barycenter of the Solar System (bary), the center of the Sun (helio), or to the center of the Earth (geo).
|
format
|
Cube | Type of output file format.
▾
"Cube" is a standard FITS cube with NAXIS=3 and multiple extensions (for data and variance). The extended "x" formats include the reconstructed image(s) in FITS image extensions within the same file.
|
skymodel_fraction
|
0.1 | Fraction of the image (without the ignored part) to be considered as sky.
▾
If an input sky mask is provided, the fraction is applied to the regions within the mask. If the whole sky mask should be used, set this parameter to 1.
|
weight
|
exptime | Type of weighting scheme to use when combining multiple exposures.
▾
"exptime" just uses the exposure time to weight the exposures, "fwhm" uses the best available seeing information from the headers as well, "none" preserves an existing weight column in the input pixel tables without changes.
|
pixfrac
|
0.8 pixel | Pixel down-scaling factor for the "drizzle" resampling method. |
dlambda
|
0.0 Angstrom | Wavelength step size (in Angstrom).
▾
Natural instrument sampling is used, if this is 0.0
|
filter
|
white | The filter name(s) to be used for the output field-of-view image.
▾
Each name has to correspond to an EXTNAME in an extension of the FILTER_LIST file. If an unsupported filter name is given, creation of the respective image is omitted. If multiple filter names are given, they have to be comma separated.
|
Calibration |
lambdaref
|
7000.0 Angstrom | Reference wavelength used for correction of differential atmospheric refraction.
▾
The R-band (peak wavelength ~7000 Angstrom) that is usually used for guiding, is close to the central wavelength of MUSE, so a value of 7000.0 Angstrom should be used if nothing else is known. A value less than zero switches DAR correction off.
|
std_response
|
STDRESPONSE_20141029T085501_763d145b.fits | Response curve as derived from standard star(s) |
Reference |
extinct_table
|
extinct_table_0.92.0_00cfbcd2.fits | Atmospheric extinction table |
filter_list
|
filter_list_1.0_7e45ce1c.fits | File to be used to create field-of-view images. |
Main |
pixtable_object
|
PIXTABLEOBJECTscibasic_20141029T011240_01_3fa6743f.fits PIXTABLEOBJECTscibasic_20141029T011240_02_b53b7fc4.fits PIXTABLEOBJECTscibasic_20141029T011240_03_0fc9c159.fits PIXTABLEOBJECTscibasic_20141029T011240_04_075d4fe7.fits PIXTABLEOBJECTscibasic_20141029T011240_05_3d79917c.fits PIXTABLEOBJECTscibasic_20141029T011240_06_01da8250.fits PIXTABLEOBJECTscibasic_20141029T011240_07_235b74d3.fits PIXTABLEOBJECTscibasic_20141029T011240_08_83c80114.fits PIXTABLEOBJECTscibasic_20141029T011240_09_3cec21d9.fits PIXTABLEOBJECTscibasic_20141029T011240_10_4c02d94a.fits PIXTABLEOBJECTscibasic_20141029T011240_11_6b7991ec.fits PIXTABLEOBJECTscibasic_20141029T011240_12_bf6a856b.fits PIXTABLEOBJECTscibasic_20141029T011240_13_393c6e2f.fits PIXTABLEOBJECTscibasic_20141029T011240_14_b5b8eba3.fits PIXTABLEOBJECTscibasic_20141029T011240_15_e9b855f7.fits PIXTABLEOBJECTscibasic_20141029T011240_16_7a73bc66.fits PIXTABLEOBJECTscibasic_20141029T011240_17_467b1440.fits PIXTABLEOBJECTscibasic_20141029T011240_18_337d6416.fits PIXTABLEOBJECTscibasic_20141029T011240_19_b1a02600.fits PIXTABLEOBJECTscibasic_20141029T011240_20_21ef533e.fits PIXTABLEOBJECTscibasic_20141029T011240_21_6715553d.fits PIXTABLEOBJECTscibasic_20141029T011240_22_0ee20de2.fits PIXTABLEOBJECTscibasic_20141029T011240_23_52bca990.fits PIXTABLEOBJECTscibasic_20141029T011240_24_8ba149b9.fits | Pixel table of a science object |
Output |
Main |
DATACUBE_FINAL
|
DATACUBEFINALscipost_20141029T011240_4b5500c2.fits | Output datacube |
PIXTABLE_REDUCED
|
PIXTABLEREDUCEDscipost_20141029T011240_bb9eb552.fits | Output pixel table |
Debug |
LOGFILE
|
20151118_184227_scipost_0788351e.log | Log file |
|
▾
|
79 |
exp_combine |
1.2 |
2015-11-21 08:22:57 - 2015-11-21 09:50:36 |
Description |
Version | 1.2 | Type | recipe | Description | Combine several exposures into one datacube.
▾
Sort reduced pixel tables, one per exposure, by exposure and combine
them with applied weights into one final datacube.
| Input |
Configuration |
save
|
cube | Select output product(s) to save.
▾
Can contain one or more of "cube" (output cube and associated images; if this is not given, no resampling is done at all) or "combined" (fully reduced and combined pixel table for the full set of exposures; this is useful, if the final resampling step is to be done again separately). If several options are given, they have to be comma-separated.
|
resample
|
drizzle | The resampling technique to use for the final output cube. |
format
|
Cube | Type of output file format.
▾
"Cube" is a standard FITS cube with NAXIS=3 and multiple extensions (for data and variance). The extended "x" formats include the reconstructed image(s) in FITS image extensions within the same file.
|
pixfrac
|
0.6 pixel | Pixel down-scaling factor for the "drizzle" resampling method. |
rc
|
1.25 pixel | Critical radius for the "renka" resampling method. |
dy
|
0.0 arcsec | Vertical step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
dx
|
0.0 arcsec | Horizontal step size for resampling (in arcsec or pixel).
▾
The following defaults are taken when this value is set to 0.0: 0.2'' for WFM, 0.075'' for NFM, 1.0 if data is in pixel units.
|
dlambda
|
0.0 Angstrom | Wavelength step size (in Angstrom).
▾
Natural instrument sampling is used, if this is 0.0
|
crsigma
|
10.0 | Sigma rejection factor to use for cosmic ray rejection during final resampling.
▾
A zero or negative value switches cosmic ray rejection off.
|
crtype
|
median | Type of statistics used for detection of cosmic rays during final resampling.
▾
"iraf" uses the variance information, "mean" uses standard (mean/stdev) statistics, "median" uses median and the median median of the absolute median deviation.
|
lambdamax
|
10000.0 Angstrom | Cut off the data above this wavelength after loading the pixel table(s). |
filter
|
white | The filter name(s) to be used for the output field-of-view image.
▾
Each name has to correspond to an EXTNAME in an extension of the FILTER_LIST file. If an unsupported filter name is given, creation of the respective image is omitted. If multiple filter names are given, they have to be comma separated.
|
lambdamin
|
4000.0 Angstrom | Cut off the data below this wavelength after loading the pixel table(s). |
ld
|
1 | Number of adjacent pixels to take into account during resampling in all three directions (loop distance).
▾
This affects all resampling methods except "nearest".
|
weight
|
fwhm | Type of weighting scheme to use when combining multiple exposures.
▾
"exptime" just uses the exposure time to weight the exposures, "fwhm" uses the best available seeing information from the headers as well, "none" preserves an existing weight column in the input pixel tables without changes.
|
Calibration |
offset_list
|
OFFSET_LIST_1.2_c51421ad.fits | List of coordinate offsets (and optional flux scale factors) |
Reference |
filter_list
|
filter_list_1.0_7e45ce1c.fits | File to be used to create field-of-view images. |
Main |
pixtable_reduced
|
PIXTABLEREDUCEDscipost_20141029T005043_31c0f6b8.fits PIXTABLEREDUCEDscipost_20141029T002923_5e7df35a.fits PIXTABLEREDUCEDscipost_20141029T011240_bb9eb552.fits | Input pixel tables |
Output |
Main |
DATACUBE_FINAL
|
DATACUBEFINALexpcombine_20141029T002923_8c737a0f.fits | Output datacube (if --save contains "cube") |
Debug |
LOGFILE
|
20151121_082256_exp_combine_947ec189.log | Log file |
|