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I am using IRAF 2.14.1 on an Ubuntu 32 bit
machine. I am using fits files (data cubes) from Herschel/PACS. I am looking at
the [OI] (63microns) emission from the outflow of protostars. The cube has 5x5
spatial pixels (spaxels) in the x-y direction and 55 layers (0-54) in the lambda
(z-) direction. I want to obtain the line profile in the lambda (z-) direction,
and I assume to do this via integration.I have been advised to use the gemini/gmos package. I have attempted using tasks
such as gfextract, gfcube and gprepare but issues keep arising, such as:gfcube hd169142.fits outimage="dhd169142.fits"
ERROR: FXF: extname and/or extver value not found ('SCI,1')
***************************************************************
gfcube hd169142 outimage="dhd169142"
ERROR: gfcube: inimage does not exist
***************************************************************
gfcube hd169142 outimage="dhd169142"
ERROR: FXF: extname and/or extver value not found ('SCI,1')
***************************************************************
gfextract inimage "/home/afinn/15Oct/hd169142.fits/"
ERROR: too many positional arguments for `gfextract'GFEXTRACT -- Wed Oct 17 15:10:58 IST 2012inimage = /home/afinn/gemini/hd169142.fits
outimage =
outpref = e
title =
response =
reference =
trace = yes
function = chebyshev
order = 5
weights = variance
bpmfile = gmos$data/chipgaps.dat
gratingdb = gmos$data/GMOSgratings.dat
filterdb = gmos$data/GMOSfilters.dat
xoffset = INDEF
fl_vardq = noWarning: table not found in FITS file `/home/afinn/gemini/hd169142.fits'
Warning: Image header parameter not found (GRATING)
ERROR: FXF: extname and/or extver value not found ('sci,1')
"imgets(l_inimage//"[sci,1]","CCDSUM")"
line 264: gmos$gfextract.cl
called as: `gfextract ()'
gmos> gfextract /home/afinn/gemini/hd169142.fits
***************************************************************
gmos> cd /home/afinn/15Oct
gmos> gprepare hd169142.fits
-------------------------------------------------------------
GPREPARE -- Wed Oct 17 10:48:44 IST 2012Input list = hd169142.fits
Output list =
Output prefix = g
Raw path =
VAR/DQ planes = no
Add MDF = noInput hd169142.fits Output ghd169142.fits
ERROR: Cannot open connected subprocess (./x_fitsutil.e)
"fxhead (img, format_file="", long_head-, count_lines-, >& "dev$null" ..."
line 518: gmos$gprepare.cl
called as: `gprepare (inimages=hd169142.fits)'
***************************************************************
gmos> gprepare inimage rawpath="/home/afinn/15Oct/hd169142.fits/" fl_vardq-
----------------------------------------------------------------------------
GPREPARE -- Wed Oct 17 10:59:15 IST 2012Input list = inimage
Output list =
Output prefix = g
Raw path = /home/afinn/15Oct/hd169142.fits/
VAR/DQ planes = no
Add MDF = noERROR - GPREPARE: Input image /home/afinn/15Oct/hd169142.fits/inimage does not
exist
ERROR - GPREPARE: 1 input files do not exist, are the wrong type, or
are already GPREPAREdGPREPARE exit status: error.
*********************************************************************
I am unsure whether I am using the wrong routines, the fits file is not how it
should be or I'm defining the file wrong/giving the pathway via an incorrect
method. If there are other routines that you think best to use, please let me
know.
Best wishes,
Aiveen

Hello Aiveen,I'm not sure how well the Gemini IRAF package will handle reducing data that were not taken with the Gemini telescopes, but I will see if I can help you.Firstly, all data must be processed with gprepare before further processing. This is why you are seeing the " ERROR: FXF: extname and/or extver value not found ('SCI,1')" error. You can read more about the processing steps by typing "gmosinfo" at the IRAF prompt. Also, the information on the "Getting Started" web page might be useful to you (http://www.gemini.edu/sciops/data-and-results/processing-software/getting-started).The "Cannot open connected subprocess (./x_fitsutil.e)" error indicates that there is a problem with your installation of fitsutil. Is the fitsutil package properly defined in your extern.pkg file? There is an install_check.cl task in the Gemini IRAF package that can be used to check a Gemini IRAF installation. The task can be defined and executed by typing the following at the IRAF prompt:[code:1:8994866059]ecl> task $install_check=gemini$install_check.cl
ecl> install_check
[/code:1:8994866059]In your second call to gprepare, you are saying that you have an input image called "inimage" that is located in the directory "/home/afinn/15Oct/hd169142.fits/", which is incorrect ... I assume (from the first call to gprepare) that you have an input image called "hd169142.fits" that is located in the directory "/home/afinn/15Oct/". By specifying the values for these parameters correctly, the "GPREPARE: Input image /home/afinn/15Oct/hd169142.fits/inimage does not exist" should not occur. Please read the help file for gprepare for more information (type "help gprepare" at the IRAF prompt).The "too many positional arguments for `gfextract'" error occurs because gfextract only has one required parameter (the input images parameter), yet you have supplied two parameter values without specifying any parameter names (perhaps you forgot the equal sign between the "inimage" parameter name and the value for this parameter?). This is standard IRAF syntax and you can read more about IRAF in the "Docs" tab at the top of this page.Finally, you may want to speak to the person who recommended that you use the Gemini IRAF package to reduce your data, since is it expected that certain keywords and an MDF exist in the data ... perhaps that person has a way of dealing with these issues?Many thanks,Emma