1) Untar the file in any directory (e.g., ~/pygmos/), then add this directory to your path by including, in your HOME$/.bashrc (or .tcshrc, etc.):

export PATH=$PATH:$HOME/pygmos

or

setenv PATH=$PATH:$HOME/pygmos

depending on your preferred environment.

2) Type

pygmos [object=]<object_name> [-p parameters_file] [ds9-] [cut-] [align+]
[mask=<mask_number(s)>] [program=<program_name>]

3) IRAF task parameters are set using the parameter file provided with PyGMOS (see below), which should be modified (parameters can be added following the given format) to fit the needs of the dataset to be reduced.

object (Mandatory)

The name of the object, as defined by the header keyword OBJECT. If the name in the OBJECT keyword contains spaces, these should be replaced by a "?" in the command line.

mask (Optional)

Default: "all"
Mask number(s) to be processed, as defined by the number after the "-" of the header keyword MASKNAME, or equivalently as listed in the <object>.assoc file written by inventory.py. Receives mask numbers separated by a comma (no spaces) or the strings "all" (which means that all MOS masks for the given object will be processed) and "longslit" (used for longslit spectra).

program (Optional)

Default: ""
If there are data for the same object in different Gemini programs (header keyword GEMPRGID), this is used to specify data from which program should be reduced.

align-suffix (Optional)

Default: "aligned"
Suffix for gstransformed files after being processed by align.cl. This suffix is removed from files generated further in the reduction process but all this files are still aligned. Need to set align+ in the command line.

cutdir (Optional)

Default: "spectra"
Directory where the single 1d spectra should be placed, if cut- is not set. The directory is created automatically by the pipeline. Previously cut spectra (in the same directory) are overwritten.

ds9

Default: enabled
PyGMOS will by default open a DS9 window when it starts and will display images on-the-fly as they are produced by the pipeline. Both the DS9 window and the displaying of images can be disabled by setting ds9- in the command-line.

cut

Default: enabled
Cut the 1d spectra into separate files. Can be disabled by including cut- in the command-line.

align

Default: disabled
Align the wavelength-transformed files. This task should be used for viewing purposes only and should not expected to be super-accurate. Can be enabled by including align- in the command-line.

pygmos <object> -i

Only run the inventory for a given object, without actually reducing the data.

pygmos -h

Display a short help message.

pygmos -d

Dump a parameters file.

pygmos -dd

Dump an extended parameters file.

pygmos -l

Dump a CuAr emission line table file, to be used for the wavelength calibration.

• This pipeline is intended for redshift measurements only. It provides a first-try reduction of raw data. As such, some masks, slits, or tasks may fail in pathological cases. By far, the IRAF task that fails the most is gsextract, the 1d spectrum extraction. This may happen on ~10% of the slits or less. Also, automatically gsextract extracts only one spectrum per slit, so slits with multiple apertures must be extracted manually.
• A processed bias file has to be provided in the parameter file for gsflat and gsreduce. The pipeline currently does not have the ability to identify the appropriate raw bias files, reduce them and use them.