Data Files
Data Files
The COSMOS pipeline requires a number of data files as input, in addition to the CCD frames. Some are provided, but some must be generated by the user. Each is described below.
Image Files
IMACS
Each IMACS exposure produces 8 FITS image files, one for each CCD; These have names ccdmmmmcn.fits, if produced by the SITE dewar, or iftmmmcn.fits, if produced by the E2V dewar, where mmmm is the exposure sequence number and n is the chip number. Note that the chips are not numbered in the expected order; the arrangement of chips is as shown below. The red dot indicates the corner of the CCD with pixel (0,0). If binning is set to 1, each image file is 2048x4096 pixels in size, after removal of bias lines and overscan.
LDSS3
Each LDSS3 exposure produces either 1, 2 or 4 FITS images files, depending
on the current setup. These have names ccdmmmmcn.fits, where mmmm is the
exposure sequence number and n is the chip number; the arrangement of chips for
the three different setups are as shown below. The red dot indicates the corner
of the CCD with pixel (0,0). If binning is set to 1, each file in the 4-file
mode is 2032x2032 pixels in size, after removal of bias lines and overscan.
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CCD files produced by reduction programs have additional labels appended; for example
| Bias corrected: | ccdmmmm_b_cn.fits
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| Flat fielded: | ccdmmmm_f_cn.fits
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| Sky subtracted: | ccdmmmm_s_cn.fits
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| Spectroscopic flats: | ccdmmmm_flat_cn.fits
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| Mosaiced images: | ccdmmmm_mos.fits
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| Extracted spectra: | ccdmmmm_2spec.fits
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Note that some of these designations are hierarchical (i.e. flat-fielded implies bias-corrected, and sky-subtracted implies flat-fielded and bias- corrected).
Dewar Offset File
The dewar offset file defines the position offsets for a particular
instrument setup, including rotation, xy position, and scale. Default dewar
offset files exist in $COSMOS_HOME/examples/dewoff for most combinations of
camera (long or short), each dewar mounting (Normal or Nod&Shuffle;) and each
disperser. The IMACS names are constructed as shown in the following tables:
| + |
| + |
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Thus, for example, the dewar offset file for the long camera with the 300 l/mm
grating and a nod & shuffle dewar mount is called LC300l_NS.dewoff.
The LDSS dewar offset file names are
| + |
| ||||||||||||||||||||||||
Thus, the dewar offset file for the LDSS3 instrument with the VPH blue grism is
called L3VPH_B.dewoff
A more accurate dewar offset file can be generated for an observation set using
the program align-mask. They can be adjusted manually using the program adjust-offset.
Important: note that the dewar offset file type, N or NS, corresponds to the dewar mounting, not the type of spectra obtained. In particular, IMACS Nod&Shuffle; observations after April 2007 are taken with the dewar in the Normal mounting, and the _N dewoff files should be used.
Mask Definition File
The mask definition file is generated by the program maskgen which was used
to design the slitmask. Files names are of the form maskname.SMF.
Observation Definition File
The observation definition file defines a particular observational setup, including:
- Dewar (SITE, SITE2, E2V, LDSS2, or LDSS3)
- Camera (LONG or SHORT if IMACS)
- Mode (DIRECT or SPECTROSCOPIC)
- Disperser
- Disperser angle
- Disperser order
- Slit mask name
- Dewar offset file name
Existing obsdef files can be edited or new ones created from existing ones
using the program defineobs.Note that disperser order and angle are only
relevant for gratings, not for grisms or direct. Template obsdef files can be
found in the $COSMOS_HOME/examples/obsdef directory. Note that SITE2 refers to
the SITE dewar after August 1, 2005, when chip 6 was changed. If, as is always
recommended, the program defineobs is used to construct the obsdef file, the specification of SITE or SITE2 is done by the program based on the observation date.
Spectral Map File
The mapping of wavelength and slit position onto the individual CCDs is described by a spectral map file. Map files form the basis for all of the spectral reduction procedures. They are generated from the information in the mask definition and observation definition files using the program map-spectra. Using a comparison arc image, spectral maps can be improved using the program adjust-map.
Program Parameter Files
Most COSMOS programs have an accompanying IRAF-like parameter file, which modifies the program's behavior. These parameter files are edited by the program editpar. Programs search for their parameter files first in the directory defined by the environment variable COSMOS_PAR_DIR.
Bad Pixel Map
Maps of bad pixels in the dewars are contained in the files dewarname.badpix,
located in $COSMOS_HOME/sdata. These maps are needed by the reduction pipeline.
Users may also create their own bad pixel files, if desired. These files are
tables, in which each line contains information on one bad pixel group. The
format of the first and all following lines is:
Chip Xmin Xmax Ymin Ymax [Binning] Chip Xmin Xmax Ymin Ymax etc
The optional parameter Binning, on line 1 must be specified only if the bad
pixel group coordinates are NOT for 1 x 1 binning, and is either a one digit
number if the x and y binning is the same, or a two digit number if x and y
binning are different. For example, if x binning is 1 x 1 and y binning is 2 x
2, the Binning parameter will be 12. Note that bad pixel files of any binning
can be used in the reduction of data of any binning, the two need not match,
but it is clearly undesirable to use bad pixel files of higher binning than
that of the data to be reduced, i.e. do NOT use a 2 x 2 bad pixel file to
reduce 1 x 1 data. The bad pixel files provided in $COSMOS_HOME/sdata are all 1
x 1 binned.
New bad pixel maps, which include the locations of features from other spectral orders, which one might wish to mask out, can be created using the program badpixels.
Dewar Definition File
This file is not directly accessed by the user, but is described for
completeness. The dewar definition file describes the physical layout of CCDs
inside the dewar, and has a name like dewarname.dewdef. At the Magellan
Telescopes (and Santa Barbara Street, if you use the default installation described in
Installing and running COSMOS) these files are located in the directory $COSMOS_HOME/sdata. Do not
mess with these files! Because chip 6 of the IMACS SITE dewar was changed on
August 1, 2005, there are two dewdef files for the SITE dewar. The currently
existing files are:
| Instrument/configuration | Dewar Name |
|---|---|
| IMACS w/SITE dewar before 01 Aug '05 | SITE |
| IMACS w/SITE dewar after 01 Aug '05 | SITE2 |
| IMACS w/E2V dewar | E2V |
| LDSS2 | LDSS2 |
| LDSS3/ 4 chip data | LDSS3-4 |
| LDSS3/ 2 chip data | LDSS3-2 |
| LDSS3/ 1 chip data | LDSS3 |
File Location
COSMOS expects all input files to be in the following locations:
dewarname.dewdef, anddewarname.badpix, in the directory$COSMOS_HOME/sdata. The environment variable COSMOS_HOME is predefined (either by the system or by you when you installed the software), and should not be messed with.- Parameter files are looked for in the directory specified by COSMOS_PAR_DIR.
- All other data files in the working data directory, unless you specify filenames with full paths.
- CCD fits files, i.e. bias, flatfield, comparison arc, and object spectra, in the directory tree specified by the environment variable COSMOS_IMAGE_DIR. For example, if COSMOS_IMAGE_DIR is defined as
/home/joe_user/dataand your images are in/home/joe_user/data/night1, the file names should be specified asnight1/filename. If you want to keep both data files and image files in the same working directory, simply define COSMOS_IMAGE_DIR to be "." This is the default at startup. The value of COSMOS_IMAGE_DIR may be changed by using the usual system commands (i.e. setenv under csh), but a handy GUI setcosdir saves some typing.