gmosinfo -- Generic information of GMOS data




The GMOS package contains tasks for processing GMOS imaging, long-slit, multi-object (MOS) and integral-field (IFU) spectroscopy data. The specifics of the individual tasks can be found in their help files. This document describes the common features of the generic tasks and gives a description of the GMOS data format.

The tasks are designed to provide a fairly complete and flexible reduction for the purpose of assessing data quality at the time of observation. Real-time reductions may not be optimal for a particular science application. The GMOS package scripts can be optimized for a particular application using the hidden parameters to achieve the best possible results.

The tasks produce logfiles of the performed processing steps. The name of the logfile may be set in each individual task, or at the package level by setting gmos.logfile.

The tasks add header keywords to the output images. These header keywords contain information about the performed processing steps and the values of the critical parameters that were used.

All GMOS images are written as multi-extension FITS (MEF) files. Raw data can have up to six unnamed extensions. For full frame read-outs the number of pixel extensions match the number of amplifiers used. Thus, the images have either three or six pixel extensions. Most science observations will be done using the amplifiers with the lowest noise and therefore have three pixel extensions. Most of the header information is written to the primary header unit (PHU) which is extension [0].

After being processed with GPREPARE, GMOS data extensions will be named as defined by the parameters and several additional header keywords will be added. The default is to name the pixel extensions using the keywords EXTNAME and EXTVER:

    Extension in raw image        EXTNAME   EXTVER
    [1]                           SCI       1
    [2]                           SCI       2
    [3]                           SCI       3

The named extensions can be accessed as, e.g., gmosimage[SCI,1], gmosimage[SCI,2], gmosimage[SCI,3] etc.

Additional information and ways to handle MEF files can be found in:

GMOS data can be binned in both axis. The header keyword CCDSUM in each pixel extension shows the type of binning. The region on the detector that is read can be changed to any section on the array. The region read out is contained in the keyword DETSEC in the pixel extensions. The content of DETSEC refers to unbinned pixels.

Each amplifier has its own bias level, gain value, and read out noise (RON), therefore, the count levels of each extension will not match when these are in units of ADU. To match the count levels between each CCD, the images can be bias subtracted and multiplied by the gains. This is incorporated in the reduction tasks described in GMOSINFOIMAG, GMOSINFOSPEC, and GMOSINFOIFU.

There are four display buffer sizes, imtgmos, imtgmos2, imtgmos4, and imtgmos8, available to display the GMOS images. The display task GDISPLAY requires that one of these buffer sizes is used. The buffer size to use is set by setting the IRAF parameter stdimage, e.g.

    set stdimage=imtgmos

The sizes of the buffers are as follows

    Name       Size         Notes
    imtgmos    6400x4644    Full size display of unbinned full 
                            frame images from GMOS
    imtgmos2   3200x2322    Full size display of full frame 
                            images from GMOS binned 2x2
    imtgmos4   1600x1161    Full size display of full frame 
                            images from GMOS binned 4x4
    imtgmos8    800x581     Full size display of full frame 
                            images from GMOS binned 8x8

It is recommended to use imtype="fits". This is set automatically when loading the GEMINI package.


    Abbreviation   Explanations
    GMOS           Gemini Multi-Object Spectrograph
    IFU            Integral field unit
    MDF            Mask definition file (a binary FITS table)
    MEF            Multi-extension FITS
    MOS            Multi-object spectroscopy
    PHU            Primary header unit (extension [0] of a MEF file)


GDISPLAY - Display GMOS images.
GDISPLAY displays GMOS MEF images with three extensions as a single image. The user has the option to examine the image using imexam if the flag fl_paste=yes. An approximate bias subtraction may also be performed by setting fl_bias=yes.
GPREPARE - Prepare raw data for reduction.
All data must be processed with GPREPARE before further processing. The other tasks in the GMOS package will call GPREPARE as needed if the input data has not already been GPREPAREd. GPREPARE adds certain essential header keywords to the PHU. Spectroscopic data (Longslit, MOS and IFU) should be processed with fl_addmdf=yes in order to add a mask definition file (MDF) to the MEF file .
GMOSAIC - Mosaic 3 GMOS CCDs into one image.
GMOSAIC will create a MEF file with a single pixel extension that contains the a mosaic of the 3 CCDs. Because GMOSAIC correctly accounts for the gaps between the CCDs, and with the default parameters it interpolates the data on fractional pixel scales. For full-frame raw data with three extensions, the data from the first and third extensions are interpolated, the central is not. It is possible to avoid interpolating the data by using geointer="nearest". This will lead to a small loss in the accuracy of the mosaicing and is only recommended if the data are oversampled (e.g. unbinned data) or it is essential that the data are not interpolated at this stage.
GGAIN - Update headers with ron and gain; Multiply extensions by gain (hidden task)
GGAIN can be used to update the headers with the correct read-noise and gain, and to multiply each pixel extension by their gains to remove chip-to-chip variations. This task is used by GPREPARE to update the headers. GSREDUCE and GIREDUCE call GGAIN to multiply the extensions with the gains. GIFLAT and GSFLAT multiply with the gains if flatfielding, but do not use GGAIN. GGAIN is not normally used by the user.
GBIAS - Create combined bias image
GBIAS takes a list of raw bias images and creates an average bias image. The user has the option to trim and subtract the overscan level with GIREDUCE to each individual bias image before combining them.
GBPM - Create a bad pixel mask from GMOS flat field and bias images
GBPM takes flat field and bias images and creates a bad pixel mask (BPM).


The tasks in the GMOS package have been tested with up to three extension MEF files.

The tasks in the GMOS package are designed to operate on MEF FITS images that have been processed using GPREPARE. GPREPARE will not run on data from instruments other than GMOS. The GMOS tasks will not run on simple FITS files.

Input image names should in general not contain directory paths as not all tasks have been tested in this mode.

Improvements to the (previously semi-functional) variance and data quality propagation in the GMOS package have undergone limited testing; the accuracy of the results should still be verified at each step by the scientist, particularly for spectroscopic data reduction tasks.


gdisplay, gprepare, gmosaic, ggain, gbias, gbpm, gmosinfoimag, gmosinfospec, gmosinfoifu, gmosexamples