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.
|
|