User's Quick guide for reduction of OSIRIS/MOS spectral data using GTCMOS pipeline
Divakara Mayya (ydm@inaoep.mx)
Summary
GTCMOS is an IRAF-based script that works directly on the files in the
GTC raw data directory. Contains automatic wavelength calibration
routines that transform the original spectral image into a
wavelength-calibrated longslit-like 2D image. Even the slanted slitlets
are aligned parallel to other slitlets. Sky spectra from any
object-free slitlet (or object-free part of a slitlet) can be used to
subtract sky from objects in any other slitlet.
THERE IS NO NECESSITY TO OBSERVE SKY FOR EACH SLITLET, which can save you as
much as 50% of observing time if planned properly. In less than 2 hours you can get
wavelength-calibrated sky-subtracted 2D image, with minimum level of interaction.
This cookbook contains a log of reduction of my own data, which gives users
an idea of the sequential order of the commands. It also guides users on the
command syntax. Each task contains a detailed IRAF-format help, with practical
examples. Throughout this cookbook, it is assumed that you are already an IRAF user.
General information
- It is an IRAF-based pipeline. You can download the package at the website:
http://www.inaoep.mx/~ydm/gtcmos/gtcmos.html.
You can also find installation instructions there.
Once you are in the IRAF environment
(i.e. with the cl> prompt), load GTCMOS package by typing
gtcmos . At anytime you can type phelp gtcmos for general
guidelines on the package or phelp taskname for help on
a particular task.
All gtcmos commands start with om for the OSIRIS-MOS
spectra.
- Read IRAF reduction manuals
if you are new to spectroscopic reductions.
Summary of Reduction commands
vocl> gtcmos
+------------------- GTCMOS IRAF Package -------------------+
| Version 1.4, Aug 04, 2016 |
| Tested with IRAF v2.16 on Fedora |
| Developed by Divakara Mayya at INAOE, Puebla, Mexico |
| |
| Type help before using it for the first time |
| |
| User's guide is available at |
| file:///iraf/iraf/extern/gtcmos/html/mos_reduction.html |
| |
|Please contact ydm@inaoep.mx if you have questions/comments|
+-----------------------------------------------------------+
omcombine omflat omreidentify omslits omunlearn
omextract omidentify omskysub omstart
omfindstd omreduce omslice omstd
gtcmos> help
+---------------------------------------------------------------+
omunlearn - Reset the IRAF task parameters [up]
omstart - examine/analyse the rawdata [up]
omcombine - combine different exposures of same field [up]
omslits - locate the slitlets of mos [up]
omslice - Slice slitlets of mos [up]
omidentify - identify the arc lamp lines automatically [up]
omreidentify - improve the results from omidentify [up]
omreduce - reduce the mos spectra [up]
omskusub - 2D mos spectra after sky subtration [up]
omextract - Extract spectrum in each slitlet [up]
omflat - Prepare spectroscopic flat [up]
omfindstd - Find the directory of standard star data [up]
omstd - Reduce standard star to get sensitive curve [up]
+---------------------------------------------------------------+
Tips:
- Expected already to be an IRAF and ds9 user
- Use xgterm for running IRAF
- Keep xgterm as wide as possible
- Don't include .fits extension, while giving filenames i.e. for
identifying arclines in gtc14aob001_arc_sum.fits, omidentify gtc14aob001_arc_sum
Set up the data directory and check the data
- Create the working directory using a console window
% pwd
/Users/dmayya/gh2018_tutorials/gtcmos
% mkdir work
% cd work
- Unzip the GTC-DATA tarball
% tar zxvf ~/Downloads/GTC5-15BMEX.OB0005.tar.gz
% ls
GTC5-15BMEX
% du -h
25M ./GTC5-15BMEX/OB0005/arc
123M ./GTC5-15BMEX/OB0005/bias
41M ./GTC5-15BMEX/OB0005/flat
41M ./GTC5-15BMEX/OB0005/object
25M ./GTC5-15BMEX/OB0005/stds
255M ./GTC5-15BMEX/OB0005
255M ./GTC5-15BMEX
255M .
cl> gtcmos
gtcmos> cd /Users/dmayya/gh2018_tutorials/gtcmos/work
- MOS spectral reduction steps
1. Prepare bias using omstart and omcombine
2. Prepare object files using omstart and omcombine
3. Prepare arc files using omstart and omcombine
4. Run omidentify to get the wavelength solutions
5. Reduce standard star file using omstart and omstd (optional)
6. Run omreduce to get the wavelength (and flux) calibrated 2-D image.
7. Run omskysub to get 2-D sky-subtracted image
8. Run omextract to get 1-D spectrum of each slitlet
- LONGSLIT reduction steps
Same steps (1-6) as for the MOS. However you can skip step#4, in which case run "omreduce filarc=std"
If you want the illumination correction, prepare flatfield using
omflat gtc12bob001_flat_master flatcor=long illcor=illum
and then give the output (illimination image) in step#6 (omreduce filflat=gtc12bob001_flat_master_norm)
Steps 7 and 8 are not relevent for long-slit. Use apall interactively to subtract sky during extraction.
- Flux calibration steps
Refers to step 6 of MOS
- Image data reduction steps
Only need to use steps 1 and 2.
General information
- It is an IRAF-based pipeline. You can download the package at the website:
http://www.inaoep.mx/~ydm/gtcmos/gtcmos.html.
You can also find installation instructions there.
Once you are in the IRAF environment
(i.e. with the cl> prompt), load GTCMOS package by typing
gtcmos . At anytime you can type phelp gtcmos for general
guidelines on the package or phelp taskname for help on
a particular task.
All gtcmos commands start with om for the OSIRIS-MOS
spectra.
- The first command that you should use is omstart . This task joins
the 2 CCDs into a single mosaic image, directly from the raw data
directory and stores the resultant file in the working directory.
A unique output filename is automatically generated by the task.
This output file is the input for the subsequent tasks of GTCMOS.
All images in the raw data directory can be processed by a single command.
- The task omcombine combines multiple images of flat, bias, object or arclamp,
which is the logical second active task to execute.
- The package contains a few passive tasks, to handle the files.
They are omslits and omunlearn
( passive tasks do not create an output image, whereas an active
task always creates an output image).
-
The package carries out bias subtraction ( omstart ) and illumination correction ( omreduce ).
However, comparison of skylines of illumination corrected and uncorrected images show
better results without illumination correction.
-
The task omidentify automatically identifies the arc lamp lines for all the slitlets.
Users can improve the solution obtained by the
automatic routine by examining each solution individually using the task omreidentify .
Even when an arclamp is not available (e.g. standard star), an accurate wavelength calibration
is achieved using the standard dispersion solutions for the corresponding grism.
- The task omreduce wavelength calibrates all the slitlet spectra one by one and puts them
back onto a 2D image at their original position. Corrects for tilts of
spectral lines, if asked to do so. The resultant 2D image looks similar
to a longslit image, except that there are gaps in the spatial direction.
- The task omskysub subtracts sky from the output of omreduce .
Various sky subtraction options are available.
- The task omextract extracts one 1-D spectrum for each slitlet, even
when the continuum spectrum is weak or absent. Alternatively, you can use the
"apall" task of IRAF, using which you can extract multiple spectra in each slitlet.
- The task omstd obtains the sensitivity curve using standard star
observations, which are always carried out in the LONGSLIT mode.
- Longslit spectra can also be analyzed using this package. This applies to even
those taken before the MOS commissioning. The reduction procedure is exactly
the same as for MOS spectra. The commands omstart and omcombine can be
used even for images.
- Read IRAF reduction manuals
if you are new to spectroscopic reductions.
OSIRIS/MOS DATA reduction
gtcmos>
gtcmos> lpar omstart
datadir = "GTC4-14AMEX/OB0001a1/object" Data directory
(filein = "all") File Name
(mosaic = no) Mosaic the 2 CCDs (no==>list only)
(verify = no) Verify each file before mosaic?
(biasim = "") Bias image [empty means no Sub Bias]
(fixpix = no) Fix bad pixels?
(mask1 = "DEFAULT") Bad pixel image for CCD1
(mask2 = "DEFAULT") Bad pixel image for CCD2
(filenam = no) Print long filename?
(mode = "ql")
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/bias
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652346-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652347-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652348-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652349-20140403-OSIRIS-OsirisBias[1] 7ias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652350-20140403-OSIRIS-OsirisBias[1] 7ias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652351-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652352-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652353-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652354-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652355-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/bias mos+
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652346-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652346-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_346
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652347-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652347-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_347
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652348-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652348-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_348
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652349-20140403-OSIRIS-OsirisBias[1] 7ias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652349-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_349
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652350-20140403-OSIRIS-OsirisBias[1] 7ias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652350-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_350
../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652351-20140403-OSIRIS-OsirisBias[1] Bias 1049 2051 OPEN fOtelo911/42 OPEN 0. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/bias/0000652351-20140403-OSIRIS-OsirisBias
Output stored as gtc14aob001_bias_351
gtcmos> lpar omcomb
filein = "gtc14bob065_arc_*" Input File Name(s)
(fileout = "omcombine") File Name
(imtype = "obj") Image type [bias|obj|arc|flat]
(combine = "median") Type of combine operation
(reject = "none") Type of rejection
(normsec = "[*,*]") Image Section to Normalize flat
(logfile = "omcombine.log") Type of rejection
(mode = "ql")
gtcmos> omcomb gtc14aob001_bias_* imtype=bias
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc14aob001_bias_346.fits 4327610 6.705 33.02 -1223. 3328. 7.369
gtc14aob001_bias_347.fits 4327610 6.732 34.12 -1223. 11968. 7.984
gtc14aob001_bias_348.fits 4327610 6.86 33.41 -1229. 6447. 8.153
gtc14aob001_bias_349.fits 4327610 6.918 33.26 -1229. 3141. 8.434
gtc14aob001_bias_350.fits 4327610 6.907 32.87 -1230. 1280. 7.578
gtc14aob001_bias_351.fits 4327610 6.934 37.11 -1229. 33230. 8.468
gtc14aob001_bias_352.fits 4327610 6.909 32.96 -1229. 2703. 7.501
gtc14aob001_bias_353.fits 4327610 6.944 34.12 -1229. 9904. 8.134
gtc14aob001_bias_354.fits 4327610 6.916 33.12 -1229. 4884. 8.027
gtc14aob001_bias_355.fits 4327610 6.929 34.67 -1228. 13979. 8.286
Apr 17 18:35: IMCOMBINE
combine = median, scale = none, zero = median, weight = none
blank = 0.
Images Median Zero
gtc14aob001_bias_346.fits 8.1591 0.
gtc14aob001_bias_347.fits 8.1569 0.0022
gtc14aob001_bias_348.fits 8.293 -0.1339
gtc14aob001_bias_349.fits 8.3533 -0.1942
gtc14aob001_bias_350.fits 8.3566 -0.1975
gtc14aob001_bias_351.fits 8.3313 -0.1722
gtc14aob001_bias_352.fits 8.3415 -0.1824
gtc14aob001_bias_353.fits 8.3533 -0.1942
gtc14aob001_bias_354.fits 8.3401 -0.181
gtc14aob001_bias_355.fits 8.3295 -0.1704
Output image = omcombine, ncombine = 10
Output is stored in omcombine
gtcmos> imrename omcombine gtc14aob001_bias_master
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/object
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652265-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 OPEN OPEN Sloan_r OPEN 10. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652266-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 OPEN OPEN Sloan_r OPEN 60. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652267-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652268-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652269-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
Note that the first two files are pre-images (GRISM=OPEN and FILTER=Sloan_r),
while the other 3 are spectral images (GRISM=R1000B). Follow the following steps
to combine only the spectral images.
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/object mosaic+ biasim=gtc14aob001_bias_master verify+
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652265-20140403-OSIRIS-OsirisMOS[1] OsirisMOS 1049 2051 OPEN OPEN Sloan_r OPEN 10. "2 2"
Want to mosaic 0000652265-20140403-OSIRIS-OsirisMOS?
no
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652266-20140403-OSIRIS-OsirisMOS[1] OsirisMOS 1049 2051 OPEN OPEN Sloan_r OPEN 60. "2 2"
Want to mosaic 0000652266-20140403-OSIRIS-OsirisMOS?
no
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652267-20140403-OSIRIS-OsirisMOS[1] OsirisMOS 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2"
Want to mosaic 0000652267-20140403-OSIRIS-OsirisMOS?
yes
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652267-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/object/0000652267-20140403-OSIRIS-OsirisMOS
Bias subtracted output stored as gtc14aob001_object_267
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652268-20140403-OSIRIS-OsirisMOS[1] OsirisMOS 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2"
Want to mosaic 0000652268-20140403-OSIRIS-OsirisMOS?
yes
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652268-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/object/0000652268-20140403-OSIRIS-OsirisMOS
Bias subtracted output stored as gtc14aob001_object_268
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652269-20140403-OSIRIS-OsirisMOS[1] OsirisMOS 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2"
Want to mosaic 0000652269-20140403-OSIRIS-OsirisMOS?
yes
../m81/MOS/GTC4-14AMEX/OB0001/object/0000652269-20140403-OSIRIS-OsirisMOS[1] M81-MOS1 1049 2051 R1000B OPEN OPEN OPEN 1308. "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/object/0000652269-20140403-OSIRIS-OsirisMOS
Bias subtracted output stored as gtc14aob001_object_269
Note that the answer is "no" for the first two and "yes" for the last 3.
gtcmos>
gtcmos> omslits gtc14aob001_object_269
OBSMODE= OsirisMOS
R1000B 3700 7000 2.12 3.569E+03 1.698E+00 1.990E-04 0.02 0.0025
36 slitlets found in gtc14aob001_object_269
## ix1 ix2 x_cen y_mos y_CCD stype angle
1 312 392 352.16351348683 960.42809724925 948.39095873527 rectangular 0.4662
2 406 422 413.97124290466 674.67596244812 663.72045919895 circular 0.
3 544 623 583.80621672308 1041.9322213566 1033.9488301492 rectangular 0.325
4 650 690 670.33060135485 1129.2172741342 1122.7480596579 rectangular 0.1953
....................................................................
....................................................................
35 1874 1889 1881.7553126431 1140.20518784 1121.2656933055 rectangular 0.3024
36 1897 1974 1935.7530967888 1091.816709784 1071.6622651062 rectangular 0.3743
## ix1 ix2 x_cen y_mos y_CCD stype angle
You man open the pre-image in ds9 and load the slitlets region file gtc14aob001_object_269_slits.reg
Pre-image after joining the CCDs with slitlet numbers overlaid as a ds9 reg file
Raw spectra after joining the CCDs with slitlet numbers overlaid as a ds9 reg file
gtcmos> hselect gtc14aob001_object_*.fits "$I EXPTIME BIASSUB" expr+
gtc14aob001_object_267.fits 1308. gtc14aob001_bias_master
gtc14aob001_object_268.fits 1308. gtc14aob001_bias_master
gtc14aob001_object_269.fits 1308. gtc14aob001_bias_master
Note the image has a new keyword BIASSUB containing the name of the bias image
Make sure bias="" when you don't want to subtract bias.
gtcmos> omcombine gtc14aob001_object_*.fits imtype=obj
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc14aob001_object_267.fits 4327610 1090. 4966. -17.35 64465. 404.
gtc14aob001_object_268.fits 4327610 1082. 5003. -21.96 64463. 403.
gtc14aob001_object_269.fits 4327610 1060. 4937. -19.78 64465. 400.3
Apr 17 18:59: IMCOMBINE
combine = median, scale = median, zero = none, weight = none
blank = 0.
Images Median Scale
gtc14aob001_object_267.fits 274.5 1.000
gtc14aob001_object_268.fits 269.18 1.020
gtc14aob001_object_269.fits 268.22 1.023
Output image = omcombine, ncombine = 3
Output is stored in omcombine
gtcmos> imrename omcombine gtc14aob001_object_av
Result of combining 3 spectra with slitlet numbers overlaid as a ds9 reg file
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/arc
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652314-20140403-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 3.6 "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652315-20140403-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 2.1 "2 2" 0.
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/arc mosaic+
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652314-20140403-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 3.6 "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652314-20140403-OSIRIS-OsirisCalibrationLamp
Output stored as gtc14aob001_arc_314
../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652315-20140403-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 2.1 "2 2" 0.
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/arc/0000652315-20140403-OSIRIS-OsirisCalibrationLamp
Output stored as gtc14aob001_arc_315
gtcmos> omcomb gtc14aob001_arc_314,gtc14aob001_arc_315 imtype=arc
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc14aob001_arc_314 4327610 133.4 1323. -1208. 45346. 51.31
gtc14aob001_arc_315 4327610 427.9 2511. -1210. 61064. -45.27
Apr 17 19:06: IMCOMBINE
combine = sum, scale = none, zero = none, weight = none
blank = 0.
Images
gtc14aob001_arc_314
gtc14aob001_arc_315
Output image = omcombine, ncombine = 2
Output is stored in omcombine
gtcmos> imrename omcombine gtc14aob001_arc_sum
Arc spectra after "summing" HgAr and Ne lamps
gtcmos> lpar omidentify
filarc = "gtc14aob009_arc_sum" Comparison arc file [arcfile]
coordli = "DEFAULT" Line id coordinate list
(cursor = "gtcinputs$identify_spline3_2.cursor") Cursor file for identify
(display = no) Display graph showing each identification?
(lastlis = "gtcinputs$R2000B_HgAr_Ne_Xe.dat") Line id coordinate list
(mode = "ql")
gtcmos> omidentify gtc14aob001_arc_sum coordli=DEFAULT
Linelist is = gtcinputs$R1000B_HgAr_Ne_Xe.dat
OBSMODE= OsirisMOS
R1000B 3700 7000 2.12 3.569E+03 1.698E+00 1.990E-04 0.02 0.0025
1 948.39095873527 41 [312:392,*]
units Angstroms
features 4
219.7655 4046.563 4046.563 4.0 1 1
399.1017 4358.328 4358.328 4.0 1 1
957.6974 5460.735 5460.735 4.0 1 1 HgI
1656.272 7032.413 7032.413 4.0 1 1
identify gtc14aob001_arc_sum_1[41,*]
........................................................
........................................................
36 1071.6622651062 39 [1897:1974,*]
units Angstroms
features 5
349.291 4046.563 4046.563 4.0 1 1
527.4118 4358.328 4358.328 4.0 1 1
1084.179 5460.735 5460.735 4.0 1 1 HgI
1784.463 7032.413 7032.413 4.0 1 1
98.62508 INDEF INDEF 4.0 1 1
identify gtc14aob001_arc_sum_36[39,*]
##########################################
The solution files are stored in database
The statistics of the rms of the solution is shown below
# identify.rms_stat c1
# nrows mean stddev median min max
36 0.6473315097 0.411766 0.48177 0.390404 2.0338
Use omreidentify to check and improve individual solutions
With the default "display = no" option, the graphs showing line identifications
and fits are stored in a metacode file that can be visualized using gkiextract.
With "display=yes", these graphs are displayed on the graphic terminal. However,
the display rate is too fast to note any false identification.
Result of autoidentification of arc spectral lines of the last slitlet
gtcmos> ls *.rms
identify.rms
gtcmos> page identify.rms
Wed 23:28:25 04-Feb-2015
Features identified in image gtc14aob001_arcs_1.
Pixel Fit User Residual Fwidth Wt Label
1 219.77 4046.5704 4046.563 0.00735675 4.00 1 HgI
2 399.10 4358.2962 4358.328 -0.0317851 4.00 1 HgI
3 957.70 5461.0573 5460.735 0.32227432 4.00 1 HgI
4 1110.96 5790.7551 5790.663 0.09208835 4.00 1 HgI
5 1139.01 5852.159 5852.488 -0.3289591 4.00 1 NeI
6 1180.96 5944.5444 5944.834 -0.2895656 4.00 1 NeI
..........................................................
..........................................................
..........................................................
The file "identify.rms" contains residual of all lines identified in each of the slitlets.
To improve the fits you may run omreidentify
gtcmos> omreidentify
rms file from omidentify (identify.rms):
######### Summary of Identification errors ############
No of slits with rms > 0.5 = 12
Additional number of slits with at least 1 badly identified line = 0
######### Summary of Identification errors ############
Exit [0], Reidentify all [999], Slit# to identify from the list below :
Slit# arcfil rms
1 gtc14aob001_arc_sum_1 0.67578588
3 gtc14aob001_arc_sum_3 0.64711966
4 gtc14aob001_arc_sum_4 0.71349521
6 gtc14aob001_arc_sum_6 0.6456216
7 gtc14aob001_arc_sum_7 0.62050815
10 gtc14aob001_arc_sum_10 0.52383421
14 gtc14aob001_arc_sum_14 0.50641107
15 gtc14aob001_arc_sum_15 0.50398614
19 gtc14aob001_arc_sum_19 0.64343367
23 gtc14aob001_arc_sum_23 0.56145567
24 gtc14aob001_arc_sum_24 0.50685462
33 gtc14aob001_arc_sum_33 0.50767427
Number to Analyze [0, 999, #] :
1
identify gtc14aob001_arc_sum_1[41,*]
Exit [0], Reidentify all [999], Slit# to identify from the list below :
Slit# arcfil rms
1 gtc14aob001_arc_sum_1 0.67578588
3 gtc14aob001_arc_sum_3 0.64711966
4 gtc14aob001_arc_sum_4 0.71349521
6 gtc14aob001_arc_sum_6 0.6456216
7 gtc14aob001_arc_sum_7 0.62050815
10 gtc14aob001_arc_sum_10 0.52383421
14 gtc14aob001_arc_sum_14 0.50641107
15 gtc14aob001_arc_sum_15 0.50398614
19 gtc14aob001_arc_sum_19 0.64343367
23 gtc14aob001_arc_sum_23 0.56145567
24 gtc14aob001_arc_sum_24 0.50685462
33 gtc14aob001_arc_sum_33 0.50767427
Number to Analyze [0, 999, #] :
0
DONE
Note that "Number to Analyze = 0" exits.
gtcmos> lpar omreduce
filnam = "gtc14a_mos1abc" File Name
filarc = "std" Comparison arc file [std|arcfile]
(filflat = "") Master Flat file [gtc14a_p1_m_flat_b or empty]
(senscur = "") Sensitivity curve imagename
(dlam = INDEF) Wavelength interval in Ang/pixel
(pixref = INDEF) Pixel at which lambda=lamref [INDEF=middle]
(lamref = INDEF) Lambda in Ang at pixref
(tilt_slit = no) Correct for Slit tilt?
(fiducial = no) Retain fiducial stars?
(checksky = no) Improve lambda calibration by checking a skyline?
(lamsky = 5577.339) Lambda of a sky line in Ang[e.g. 5577.339, 6300.304 etc
(slitrej = "") Slitlet numbers to reject
(cleanlev = 2) Clean Level [2=del all intermediate fits] [0=retain all]
(mode = "ql")
gtcmos> omreduce gtc14aob001_object_av filarc=gtc14aob001_arc_sum
OBSMODE= OsirisMOS
R1000B 3700 7000 2.12 3.569E+03 1.698E+00 1.990E-04 0.02 0.0025
Reference Slitlet: i=11 x=1111 ydist=1.1778959717411
1 rectangular gtc14aob001_object_av[312:392,*] 960.42809724925 948.39095873527 352.16351348683 312 392
3 rectangular gtc14aob001_object_av[544:623,*] 1041.9322213566 1033.9488301492 583.80621672308 544 623
.........................................................................................................
.........................................................................................................
36 rectangular gtc14aob001_object_av[1897:1974,*] 1091.816709784 1071.6622651062 1935.7530967888 1897 1974
Wavelength calibrated data are stored in gtc14aob001_object_av_wl
gtcmos>
gtcmos> omreduce gtc14aob001_object_av filarc=gtc14aob001_arc_sum tilt_slit+
.........................................................................................................
36 rectangular gtc14aob001_object_av[1897:1974,*] 1091.816709784 1071.6622651062 1935.7530967888 1897 1974
Wavelength calibrated data are stored in gtc14aob001_object_av_wl_tlt
Note that the fiducial spectra are eliminated with fiducial-
Wavelength calibrated and "longslit-like" output
Skylines of different slitlets are aligned using the values of dlam, pixref and lamref.
Tilt of slanted slitlets (and all other slitlets) can be corrected with tilt_slit+ option.
This option is relatively slower (takes around 10 seconds for each slitlet)
gtcmos> omreduce gtc14aob001_object_abc filarc=gtc14aob001_arcs tilt_slit+
Wavelength calibrated and "longslit-like" output with tilt_slit+
Each individual slitlets are cut and stored (without wavelength calibration)
gtcmos> splot gtc14aob001_object_av_wl_tlt
Image line/aperture to plot (0:) (1480):
Splot cuts through various slitlets
Note the position of skylines (eg. 5577, 6300) which exactly coincide
independent of the original slitlet y-position. Thanks to this feature of the
pipeline, sky slitlets for each object slitlet is needed only in case of variable
backgound (when observing large nearby galaxies).
gtcmos> lpar omskysub
filnam = "gtc14aob4_object_sum_wl_tlt" File Name
(skytype = "same") Sky type [same, pair, skyslits, bg]
(method = "median") Method of obtaining sky spectrum [median, percent]
(percent = 20.) Percentile value for sky [1-50]
(normali = no) Normalize the sky spectrum before subtration?
(pairlis = "pair.sky") Object-Sky pair list
(skyslit = "1,10,30") Sky slitlet numbers
(skyrang = "") Sky range in pixels 240:260,300:310,1500:1520
(mode = "ql")
gtcmos> omskysub gtc14aob001_object_av_wl_tlt
OBSMODE= OsirisMOS
R1000B 3700 7000 2.12 3.569E+03 1.698E+00 1.990E-04 0.02 0.0025
Analyzing slitlet no 1 Section = [312:392,*]
Analyzing slitlet no 3 Section = [544:623,*]
.........................................................................................................
.........................................................................................................
Analyzing slitlet no 36 Section = [1897:1974,*]
Sky subtrated 2D spectrum is = gtc14aob001_object_av_wl_tlt_obj
Sky spectrum= gtc14aob001_object_av_wl_tlt_sky and SNR spectrum= gtc14aob001_object_av_wl_tlt_snr are also stored.
Sky subtracted and "longslit-like" output
gtcmos>
gtcmos> lpar omextract
filnam = "gtc14a_mos1abc" File Name
slitno = "all" Slit numbers to slice [all, #]
(nfind = 1) Number of apertures to be found automatically
(lamline = INDEF) Dispersion line
(referen = "") List of aperture reference images
(interac = no) Run task interactively?
(extras = yes) Extract sky, sigma, etc.?
(llimit = INDEF) Lower aperture limit relative to center
(ulimit = INDEF) Upper aperture limit relative to center
(ylevel = 0.1) Fraction of peak or intensity for automatic width
(t_funct = "legendre") Trace fitting function
(t_order = 5) Trace fitting function order
(backgro = "none") Background to subtract
(mode = "ql")
gtcmos> omextract gtc14aob001_object_av_wl_tlt_obj
Slit numbers to slice [all, #] (all):
OBSMODE= OsirisMOS
R1000B 3700 7000 2.12 3.569E+03 1.698E+00 1.990E-04 0.02 0.0025
Examining a cut at lambda=INDEF Ang, line = INDEF
Extracting slitlet #1 and saving in gtc14aob001_object_av_wl_tlt_obj_1.ms
............................................................................
............................................................................
Extracting slitlet #34 and saving in gtc14aob001_object_av_wl_tlt_obj_34.ms
Extracting slitlet #35 and saving in gtc14aob001_object_av_wl_tlt_obj_35.ms
Extracting slitlet #36 and saving in gtc14aob001_object_av_wl_tlt_obj_36.ms
gtcmos>
Flux Calibration using Standard star
Standard star spectra are taken using longslit. As illustrated in the cookbook for the reduction of longslit spectra, the procedure
to be followed to analyze longslit spectra is identical to that of MOS spectra.
Flux calibration involves 4 steps:
- Basic reduction to get a wavelength-calibrated 2D-spectrum (GTCMOS tasks)
- Identification of the star and extraction of its 1-D spectrum using the IRAF task "apall"
- Obtaining the sensitivity curve using the IRAF flux calibration tasks (standard, sensfunc)
- Apply the sensitivity correction to the object spectra using the IRAF task "calibrate"
The first 3 steps are combined in a single task called omstd.
gtcmos> lpar omstd
filstd = "gtc12bob003_stds_316" Stadard star file
star_nam = "Feige34" Star name in calibration list
(filflat = "DEFAULT") Master Flat file
(lamsky = "DEFAULT") Lambda of a sky line in Ang
(checksky = no) Improve lambda calibration by checking a skyline?
(interac = no) Run apall interactively?
(line = INDEF) Line number to plot to search stars
(nfind = 1) Number of stars to find
(extras = yes) Extract sky, sigma, etc.?
(llimit = INDEF) Lower aperture limit relative to center
(ulimit = INDEF) Upper aperture limit relative to center
(ylevel = 0.1) Fraction of peak or intensity for automatic width
(b_sampl = "-50:-40,40:50") Background sample regions
(t_funct = "legendre") Trace fitting function
(t_order = 5) Trace fitting function order
(backgro = "median") Background to subtract
(stdflux = "gtc_flux.std") Output flux file (used by SENSFUNC)
(extinct = "gtcinputs$tn_ext_curve.dat") Extinction curve file
(caldir = "find") Directory containing calibration data
(sensfunc = yes) Run sensfunc?
(senscur = "gtc_sense_curve") Sensitivity function imagename
(mode = "ql")
gtcmos> omstart ../GTC5-12BMEX/OB0003/stds mos+ biasim=gtc12bob003_bias_av
gtcmos> imhead gtc12bob003_stds_315
gtc12bob003_stds_315[2110,2051][real]: SpectStand_Feige34
gtcmos> omstd gtc12bob003_stds_315 Feige34
gtcmos> splot gtc_sense_curve
Sensfunc graph | Typical sensitivity Curve
You can alternatively follow the steps 1 to 3.
Step 1
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/stds mos-
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652303-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 OPEN OPEN Sloan_r OPEN 1. "2 2" 0.
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652304-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 OPEN OPEN Sloan_r OPEN 1. "2 2" 2.52
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652305-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 R1000B OPEN OPEN OPEN 10. "2 2" 2.52
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652306-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 R1000B OPEN OPEN OPEN 100. "2 2" 2.52
gtcmos> omstart ../m81/MOS/GTC4-14AMEX/OB0001/stds mos+ biasim=gtc14aob001_bias_master verify+
Analyzing the following files
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652303-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] OsirisLongSlitSpectroscopy 1049 2051 OPEN OPEN Sloan_r OPEN 1. "2 2"
Want to mosaic 0000652303-20140403-OSIRIS-OsirisLongSlitSpectroscopy?
no
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652304-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] OsirisLongSlitSpectroscopy 1049 2051 OPEN OPEN Sloan_r OPEN 1. "2 2"
Want to mosaic 0000652304-20140403-OSIRIS-OsirisLongSlitSpectroscopy?
no
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652305-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] OsirisLongSlitSpectroscopy 1049 2051 R1000B OPEN OPEN OPEN 10. "2 2"
Want to mosaic 0000652305-20140403-OSIRIS-OsirisLongSlitSpectroscopy?
yes
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652305-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 R1000B OPEN OPEN OPEN 10. "2 2" 2.52
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652305-20140403-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc14aob001_stds_305
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652306-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] OsirisLongSlitSpectroscopy 1049 2051 R1000B OPEN OPEN OPEN 100. "2 2"
Want to mosaic 0000652306-20140403-OSIRIS-OsirisLongSlitSpectroscopy?
yes
../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652306-20140403-OSIRIS-OsirisLongSlitSpectroscopy[1] Ross640 1049 2051 R1000B OPEN OPEN OPEN 100. "2 2" 2.52
Running mosaic_2x2_v2 ../m81/MOS/GTC4-14AMEX/OB0001/stds/0000652306-20140403-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc14aob001_stds_306
gtcmos>
Note that the first two spectra are pre-images (answer to the question is no), and the last two are spectra of standard star Ross640
gtcmos> omcomb gtc14aob001_stds_305,gtc14aob001_stds_306 fileout=gtc14aob001_stds_av imtype=obj
gtcmos> omreduce gtc14aob001_stds_av filarc=std checksky+
1 rectangular gtc14aob001_stds_av[160:179,*] 994.966 993.566 170. 160 179
2 rectangular gtc14aob001_stds_av[180:199,*] 994.966 993.916 190. 180 199
............................................................................
............................................................................
90 rectangular gtc14aob001_stds_av[1990:2009,*] 994.966 987.191 2000. 1990 2009
91 rectangular gtc14aob001_stds_av[2010:2030,*] 994.966 986.741 2020. 2010 2030
Wavelength calibrated data are stored in gtc14aob001_stds_av_wl
Note that there is no "arc" lamps observed for longslit spectrum in the MOS mode.
However, longslit is always placed at the same Y-direction, and hence the standard
dispersion solution is used in the above example using the option filarc=std.
The checksky = yes option corrects for any zeropoint offset in wavelength calibration.
Step 2
gtcmos> apall gtc14aob001_stds_av_wl interac+ extras+ resi- lower=-20 upper=20 b_sampl="-50:-40,40:50" t_funct=legendre t_order=5 backgro=median
Read apall help to interactively choose the critical extraction parameters.
Step 3
gtcmos> standard gtc14aob001_stds_av_wl.ms gtc14aob001_stds_flux.std extinct=gtcinputs$tn_ext_curve.dat caldir=onedstds$/redcal/ star_nam=ross640
Boxes for evaluating Sensitivity function
Note that the boxes at the position of the absorption features have been already deleted
In the above example the standard spectrum of star "Ross640" is available in the
IRAF directory "onedstds$/redcal/" with name ross640.dat.
You should delete boxes near absorption lines. If you have more than one star or
the same star observed several times, repete the command standard for each
observation, but give the same output file (e.g. gtc14aob001_stds_flux.std).
Flux and count rate values for each observation are appended to the already existing
output text file.
gtcmos> sensfunc gtc14aob001_stds_flux.std gtc14aob001_stds_flux.sens extinct=gtcinputs$tn_ext_curve.dat inter+
Sensitivity function for aperture 1:
Fitting function is spline3 of order 6 with 18 points and RMS of 0.0338.
Image Airmass Points Shift RMS Fit Dev 1 Dev 2 Dev 3
gtc14aob001_stds_av_wl.ms 1.033 18 0.0000 0.0328 -0.0027 0.0016 0.0012
Read sensfunc help to interactively change the fitting parameters. In this example the rms of the fit is 0.0328
Sensitivity function and the rms error at each wavelength
Comparsion of Sensitivity functions from 2012 and 2014 runs
Step 4
gtcmos> calibrate gtc14aob001_object_av_wl_tlt gtc14aob001_object_av_wl_tlt_cal extinct+ flux+ extinct=home$tn_ext_curve.dat sensiti=gtc12bob001_stds_flux.sens.0001
gtcmos> omskysub gtc14aob001_object_av_wl_tlt_cal
gtcmos> omextract gtc14aob001_object_av_wl_tlt_cal_obj
gtcmos> splot gtc14aob001_object_av_wl_tlt_cal_obj_8.ms
Note that you can run omskysub and omextract before or after flux calibration.
Final calibrated and extracted spectrum of one of the slitlets
Reduction of Longslit spectra using GTCMOS package
GTCMOS tasks interpret longslit as a series of contiguous slitlets (i.e zero-pixel space between
successive slitlets). Hence, the procedure to be followed to analyze longslit spectra are
identical to that of MOS spectra.
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/arc"
Analyzing the following files
../m81/GTC5-12BMEX/OB0001/arc/0000290984-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 5. "2 2" 1.23
../m81/GTC5-12BMEX/OB0001/arc/0000290985-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 3. "2 2" 1.23
../m81/GTC5-12BMEX/OB0001/arc/0000290986-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 3. "2 2" 1.23
../m81/GTC5-12BMEX/OB0001/arc/0000290987-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 1.4 "2 2" 1.23
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/arc" mos+
Analyzing the following files
../m81/GTC5-12BMEX/OB0001/arc/0000290984-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 5. "2 2" 1.23
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/arc/0000290984-20130111-OSIRIS-OsirisCalibrationLamp
Output stored as gtc12bob001_arc_984
../m81/GTC5-12BMEX/OB0001/arc/0000290985-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_HgAr 1049 2051 R1000B OPEN OPEN OPEN 3. "2 2" 1.23
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/arc/0000290985-20130111-OSIRIS-OsirisCalibrationLamp
Output stored as gtc12bob001_arc_985
../m81/GTC5-12BMEX/OB0001/arc/0000290986-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 3. "2 2" 1.23
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/arc/0000290986-20130111-OSIRIS-OsirisCalibrationLamp
Output stored as gtc12bob001_arc_986
../m81/GTC5-12BMEX/OB0001/arc/0000290987-20130111-OSIRIS-OsirisCalibrationLamp[1] ArcLamp_Ne 1049 2051 R1000B OPEN OPEN OPEN 1.4 "2 2" 1.23
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/arc/0000290987-20130111-OSIRIS-OsirisCalibrationLamp
Output stored as gtc12bob001_arc_987
gtcmos> omcombi gtc12bob001_arc_*.fits fileout=gtc12bob001_arc_sum imtype=arc
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc12bob001_arc_984.fits 4327610 203.6 1665. -1005. 51723. 81.21
gtc12bob001_arc_985.fits 4327610 111.6 1098. -1005. 36176. 41.37
gtc12bob001_arc_986.fits 4327610 877.5 4200. -1005. 64509. 69.37
gtc12bob001_arc_987.fits 4327610 415.4 2003. -1004. 38691. 107.6
Apr 22 11:30: IMCOMBINE
combine = sum, scale = none, zero = none, weight = none
blank = 0.
Images
gtc12bob001_arc_984.fits
gtc12bob001_arc_985.fits
gtc12bob001_arc_986.fits
gtc12bob001_arc_987.fits
Output image = gtc12bob001_arc_sum, ncombine = 4
Output is stored in gtc12bob001_arc_sum
gtcmos> omidentify gtc12bob001_arc_sum
.................................................
.................................................
identify gtc12bob001_arc_sum_90[10,*]
91 986.741 11 [2010:2030,*]
units Angstroms
features 4
251.0527 4046.563 4046.563 4.0 1 1
418.3986 4358.328 4358.328 4.0 1 1
984.2291 5460.735 5460.735 4.0 1 1 HgI
1691.874 7032.413 7032.413 4.0 1 1
identify gtc12bob001_arc_sum_91[11,*]
##########################################
The solution files are stored in database
The statistics of the rms of the solution is shown below
# identify.rms_stat c1
# nrows mean stddev median min max
91 0.174976417 0.272068 0.135168 3.31810E-11 2.68449
Use omreidentify to check and improve individual solutions
gtcmos> omreidentify
rms file from omidentify (identify.rms):
######### Summary of Identification errors ############
No of slits with rms > 0.5 = 1
Additional number of slits with at least 1 badly identified line = 1
######### Summary of Identification errors ############
Exit [0], Reidentify all [999], Slit# to identify from the list below :
Slit# arcfil rms
87 gtc12bob001_arc_sum_87 2.6844871
91 gtc12bob001_arc_sum_91 3.3180979000000E-11
Number to Analyze [0, 999, #] :
87
identify gtc12bob001_arc_sum_87[10,*]
Write feature data to the database (yes)?
Exit [0], Reidentify all [999], Slit# to identify from the list below :
Slit# arcfil rms
87 gtc12bob001_arc_sum_87 2.6844871
91 gtc12bob001_arc_sum_91 3.3180979000000E-11
Number to Analyze [0, 999, #] :
91
identify gtc12bob001_arc_sum_91[11,*]
Write feature data to the database (yes)?
Exit [0], Reidentify all [999], Slit# to identify from the list below :
Slit# arcfil rms
87 gtc12bob001_arc_sum_87 2.6844871
91 gtc12bob001_arc_sum_91 3.3180979000000E-11
Number to Analyze [0, 999, #] :
0
DONE
gtcmos>
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/bias" mos+
gtcmos> omcomb gtc12bob001_bias_*.fits imtype=bias
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc12bob001_bias_966.fits 4327610 2.607 26.44 -1002. 8706. 3.757
gtc12bob001_bias_967.fits 4327610 2.636 27.77 -1003. 8328. 3.703
gtc12bob001_bias_968.fits 4327610 2.578 26.09 -1003. 3621. 3.23
gtc12bob001_bias_969.fits 4327610 2.617 28.59 -1002. 10481. 3.537
gtc12bob001_bias_970.fits 4327610 2.596 26.37 -1003. 6691. 3.608
gtc12bob001_bias_971.fits 4327610 2.589 26.52 -1003. 5697. 3.545
gtc12bob001_bias_972.fits 4327610 2.569 26.04 -1002. 3853. 3.529
gtc12bob001_bias_973.fits 4327610 2.562 25.76 -1003. 2187. 2.995
gtc12bob001_bias_974.fits 4327610 2.571 26.82 -1002. 6649. 3.334
gtc12bob001_bias_975.fits 4327610 2.578 27.3 -1002. 10756. 3.48
Apr 22 12:12: IMCOMBINE
combine = median, scale = none, zero = median, weight = none
blank = 0.
Images Median Zero
gtc12bob001_bias_966.fits 3.6793 0.
gtc12bob001_bias_967.fits 3.6655 0.01387
gtc12bob001_bias_968.fits 3.6473 0.03205
gtc12bob001_bias_969.fits 3.6582 0.0211
gtc12bob001_bias_970.fits 3.6817 -0.0023
gtc12bob001_bias_971.fits 3.6342 0.04515
gtc12bob001_bias_972.fits 3.6381 0.04119
gtc12bob001_bias_973.fits 3.6538 0.02557
gtc12bob001_bias_974.fits 3.6307 0.04864
gtc12bob001_bias_975.fits 3.6283 0.05103
Output image = omcombine, ncombine = 10
gtcmos> imrename omcombine gtc12bob001_bias_av
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/object" mos+ biasim=gtc12bob001_bias_av
gtcmos> omcomb gtc12bob001_object_927,gtc12bob001_object_928,gtc12bob001_object_929
# IMAGE NPIX MEAN STDDEV MIN MAX MIDPT
gtc12bob001_object_927 4327610 516.4 645. -1011. 29537. 363.5
gtc12bob001_object_928 4327610 533.8 676.8 -1010. 27737. 370.1
gtc12bob001_object_929 4327610 542.4 693.6 -1010. 63482. 376.
Apr 22 12:17: IMCOMBINE
combine = median, scale = median, zero = none, weight = none
blank = 0.
Images Median Scale
gtc12bob001_object_927 364.7 1.000
gtc12bob001_object_928 372.89 0.978
gtc12bob001_object_929 375.67 0.971
Output image = omcombine, ncombine = 3
Output is stored in omcombine
gtcmos> imrename omcombine gtc12bob001_object_av
gtcmos>
gtcmos> omreduce gtc12bob001_object_av filarc=gtc12bob001_arc_sum checksky+ lamsky = 5577.838
Reference Slitlet: i=1 x=170 ydist=0.033999999999764
1 rectangular gtc12bob001_object_av[160:179,*] 994.966 993.566 170. 160 179
..............................................................................
91 rectangular gtc12bob001_object_av[2010:2030,*] 994.966 986.741 2020. 2010 2030
Wavelength calibrated data are stored in gtc12bob001_object_av_wl
gtcmos> omskysub gtc12bob001_object_av_wl
Analyzing slitlet no 1 Section = [160:179,*]
..............................................................................
Analyzing slitlet no 91 Section = [2010:2030,*]
Sky subtrated 2D spectrum is = gtc12bob001_object_av_wl_obj
Sky spectrum= gtc12bob001_object_av_wl_sky and SNR spectrum= gtc12bob001_object_av_wl_snr are also stored.
gtcmos>
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/stds" mos-
Analyzing the following files
../m81/GTC5-12BMEX/OB0001/stds/0000290947-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051OPEN OPEN Sloan_g OPEN 1. "2 2" 0.
../m81/GTC5-12BMEX/OB0001/stds/0000290948-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051OPEN OPEN Sloan_g OPEN 1. "2 2" 2.52
../m81/GTC5-12BMEX/OB0001/stds/0000290949-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051R1000B OPEN OPEN OPEN 20. "2 2" 2.52
../m81/GTC5-12BMEX/OB0001/stds/0000290950-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051R1000B OPEN OPEN OPEN 30. "2 2" 2.52
gtcmos> omstart "../m81/GTC5-12BMEX/OB0001/stds" mos+ biasim=gtc12bob001_bias_av
Analyzing the following files
../m81/GTC5-12BMEX/OB0001/stds/0000290947-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051OPEN OPEN Sloan_g OPEN 1. "2 2" 0.
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/stds/0000290947-20130111-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc12bob001_stds_947
../m81/GTC5-12BMEX/OB0001/stds/0000290948-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051OPEN OPEN Sloan_g OPEN 1. "2 2" 2.52
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/stds/0000290948-20130111-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc12bob001_stds_948
../m81/GTC5-12BMEX/OB0001/stds/0000290949-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051R1000B OPEN OPEN OPEN 20. "2 2" 2.52
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/stds/0000290949-20130111-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc12bob001_stds_949
../m81/GTC5-12BMEX/OB0001/stds/0000290950-20130111-OSIRIS-OsirisLongSlitSpectroscopy[1] SpectStand_GD140 1049 2051R1000B OPEN OPEN OPEN 30. "2 2" 2.52
Running mosaic_2x2_v2 ../m81/GTC5-12BMEX/OB0001/stds/0000290950-20130111-OSIRIS-OsirisLongSlitSpectroscopy
Bias subtracted output stored as gtc12bob001_stds_950
There are 4 files in the "stds" directory, two pre-images and other two spectral images. The pre-image gtc12bob001_stds_949 looks like this.
Note that the spectral images are of exposures 20 and 30 seconds, and hence if they are averaged, the EXPTIME keyword
should be set as 25 sec (using hedit). Here we will reduce the two spectra idependently.
gtcmos> omreduce gtc12bob001_stds_949
gtcmos> omreduce gtc12bob001_stds_950
2-D Spectrum of standard star before and after wavelength calibration. Note how the "curvature" of skylines gets corrected on wavelength calibration.
gtcmos> apall gtc12bob001_stds_949_wl interac+ extras+ resi- lower=-20 upper=20 b_sampl="-50:-40,40:50" t_funct=legendre t_order=5 backgro=median
Recenter apertures for gtc12bob001_stds_949_wl? (yes):
Edit apertures for gtc12bob001_stds_949_wl? (yes):
Tracing the spectrum for extraction
gtcmos> apall gtc12bob001_stds_950_wl interac+ extras+ resi- lower=-20 upper=20 b_sampl="-50:-40,40:50" t_funct=legendre t_order=5 backgro=median
Name of the standard star is GD140, which is in the onedstds$/spec50cal/ directory of IRAF.
gtcmos> standard gtc12bob001_stds_949_wl.ms gtc12bob001_stds_flux.std extinct=gtcinputs$tn_ext_curve.dat caldir=onedstds$/spec50cal/ star_nam=gd140
gtcmos> standard gtc12bob001_stds_950_wl.ms gtc12bob001_stds_flux.std extinct=gtcinputs$tn_ext_curve.dat caldir=onedstds$/spec50cal/ star_nam=gd140
Boxes for evaluating Sensitivity function Note that the boxes at the position of the absorption features have been already deleted
gtcmos> sensfunc gtc12bob001_stds_flux.std gtc12bob001_stds_flux.sens extinct=gtcinputs$tn_ext_curve.dat inter+
Sensitivity function for aperture 1:
Fitting function is spline3 of order 6 with 124 points and RMS of 0.0328.
Image Airmass Points Shift RMS Fit Dev 1 Dev 2 Dev 3
gtc12bob001_stds_949_wl.ms 1.087 60 0.0502 0.0326 -0.0024 -0.0021 0.0041
gtc12bob001_stds_950_wl.ms 1.091 64 0.0000 0.0328 -0.0001 -0.0017 0.0021
Sensitivity function and the rms error at each wavelength
Calibrate the 2-D or 1-D spectra of objects using the sensitivity function as in the floowing 2 examples.
gtcmos> calibrate gtc12bob001_object_av_wl gtc12bob001_object_av_wl_cal extinct+ flux+ extinct=home$tn_ext_curve.dat sensiti=gtc12bob001_stds_flux.sens
gtcmos> calibrate gtc12b_p1abc_ccd1tbf_wl.ms gtc12b_p1abc_ccd1tbf_wl.ms_cal extinct+ flux+ extinct=home$tn_ext_curve.dat sensiti=sens_gtc12b_p1GD140_ccd2tbf.std
Comments by the author
1. All the examples in this cookbook are from the data obtained for the projects by the Author.
2. The tasks are tested only on Ubuntu and Fedora systems for the IRAF V2.14 version.
3. If you find this pipeline/cookbook useful, please acknowledge its use in the publication.
4. Author acknowledges the GTC/OSIRIS staff, especially Antonio Cabrera for providing useful calibration tables figures in the corresponding webpage. Thanks to these data files,
it was possible to keep the interaction level to the minimum.
5. The author acknowledges the contribution of Victor Mauricio Gomez Gonzalez, a Ph.D. student at INAOE who has helped extensively in doing the tedious job of identifying the arc lamp lines in several MOS
images that formed the basis for various emperical relations that the script uses. He also contributed in testing all the tasks in this package.
6. The pipeline couldn't have been realized without the enthusiastic support from friends and colleagues at INAOE and IAC.
Last updated on 5 September 2018 ydm@inaoep.mx