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Phase III: Retrieving & Reducing Data

Submitting a HelpDesk Ticket

When having data reduction issues, it is recommended to first ensure that you are using the latest version of the software, be it DRAGONS or Gemini IRAF.  If for some reason you cannot update, please raise this in your ticket as it might be relevant.

When you submit a helpdesk ticket about an issue related to DRAGONS, please describe your issue as clearly as possible and  include the information below.  Adding all the information in the initial ticket will save valuable time, skipping the back and forth because there’s a high likelihood that we will be asking for that information anyway.

Once you have gathered all the info, go to the Helpdesk portal to submit your ticket.  For "Topic", select "DRAGONS" or "Gemini IRAF" as appropriate

What to include in your...
DRAGONS ticket Gemini IRAF ticket
  1. Description of the issue, as detailed and clearly as possible.
  2. The command(s) you ran.
  3. For each command run on a file list, the content of that list.
  4. The error message, in full.
  5. Attach a copy of the reduce.log file.
  6. Program Number.
  7. Observation ID.
  8. The content of your calibration database.
    Run:  caldb list.
  9. Then, the output of the following commands:
    ($ is the shell prompt, >>> the python prompt)
    • $ uname -a
    • $ export
    • $ cat ~/.condarc
    • $ which conda
    • $ conda --version
    • $ which python
    • $ python --version
    • $ which reduce
    • $ reduce --version
      $ conda list dragons
      $ conda list gemini_calmgr
      $ cat ~/.dragons/dragonsrc
      $ which caldb
      $ caldb config
      $ python
      >>> import astrodata
      >>> astrodata.__file__
      >>> astrodata.__version__
      >>> import gemini_calmgr
      >>> gemini_calmgr.__file__
      >>> gemini_calmgr.__version__
    • >>> import gemini_obs_db
    • >>> gemini_obs_db.__file__
    • >>> gemini_obs_db.__version__
  1. Description of the issue, as detailed and clearly as possible. 
  2. The command you ran.
  3. For each command run on a file list, the content of that list.
  4. The error message, in full.
  5. Attach a copy of the log file.
  6. Program Number.
  7. Observation ID.
  8. Then, the output of the following commands:
    ($ is the shell prompt, >>> the python prompt)
    • $ uname -a
    • $ export
    If on Linux, continue. If on Mac, do this in the VM:
    • $ cat ~/.condarc
    • $ which conda
    • $ conda --version
    • $ which python
    • $ python --version
    • $ which pyraf
    • $ pyraf --version
    • $ pyraf
    • --> gemini
      --> show gemini
      --> lpar gemini

For example of what you will be asked for and to see what procedure your First Responder might follow, check this document:  Data Reduction Helpdesk First Responder Guidelines.

A Few IRAF Pointers

 1) Is the Gemini IRAF package compatible with PyRAF?
  • Yes. Version 1.10 (and all subsequent releases) of the Gemini IRAF package is fully compatible with PyRAF.
 2) I have just installed the latest version of the Gemini IRAF package and now I am getting "ERROR: parameter `some-parameter' not found" messages. What am I doing wrong?
  • Some tasks in the version that you have just installed may have new parameters that do not exist in the old parameter files, which are found in the uparm directory. The solution to this problem is to initialise the uparm directory by typing "rm uparm/*" in your iraf home directory (i.e., where you ran mkiraf / where your login.cl file is located). This will remove any old Gemini parameter files that may be causing the problem. NOTE: if you wish to make a note of any stored parameters, please do so before running this command.
 3) How can I use regular IRAF tasks with my Gemini data?
  • The fitsutil package provides some helpful tasks that can be used to manipulate Multi-Extension Fits (MEF) files.
4) I am using gsreduce with fl_over+ to reduce my GMOS data but the output image contains negative pixel values. What am I doing wrong?
  • The processed biases in the archive are created using gbias with the fl_over parameter set to no. This means that the overscan level has not been subtracted from the processed biases. The solution to this problem is to either use the processed biases in the archive and then process all of your data with the fl_over parameter set to no OR do not use the processed biases in the archive; download the raw biases and reduce them using gbias with the fl_over parameter set to yes.
 5) I am using imcoadd to combine NIRI data, but I am getting "ERROR: Non-boolean operand used where boolean expected" messages. What am I doing wrong?
  • This error is due to a corrupted parameter file. The solution to this problem is to initialise the uparm directory by typing "rm uparm/*" in your iraf home directory (i.e., where you ran mkiraf / where your login.cl file is located). NOTE: if you wish to make a note of any stored parameters, please do so before running this command.
 6) I am following the GMOS Long-Slit / Multi-Slit Tutorial from the NOAO Gemini Data Workshop held in Tucson in 2010, but I can't find the gscrspec task that calls the Laplacian Cosmic Ray Identification routine (lacos_spec; written by Pieter G. van Dokkum) that is mentioned in the tutorial. Can I get a copy of this task?
  • The task gscrspec was originally written by Bryan MIller and is not supported as part of the Gemini IRAF package. It comes with no guarantees but you can download a copy here (updated May 14, 2013).
 7) I am unable to determine a wavelength solution for my NIFS arc (I see e.g., "No solution found" messages). What am I doing wrong?
  • This problem can occur when using a non-default central wavelength with NIFS. The nsappwave task adds a starting guess for the central wavelength to the header of the data using, by default, a value determined from a lookup table (the starting guess values are 1.05 for the Z grating, 1.25 for the J, 1.65 for H and 2.2 for K). Unfortunately, these values do not reflect the central wavelength actually used when not using the default position and can fail to provide a robust solution. To circumvent this problem, use the "crval" parameter in nsreduce (which is internally passed to nsappwave) to provide the actual central wavelength that was used (in Angstrom). The central wavelength value specified for the observation is stored in the header keyword "GRATWAVE" (nsappwave will only use this keyword if there is no value in the lookup table).
 8)  Where can I find more information?
  • Each task in the Gemini IRAF package has an associated help file. You can read this file by typing "help <taskname>" at the IRAF prompt, where <taskname> is the name of the task, e.g., nsprepare.
  • Each instrument specific package in the Gemini IRAF package has an associated "information" file. You can read this file by typing "<instrument>info" at the IRAF prompt, where <instrument> is the instrument, e.g., gmos.
  • There are a number of example reductions in the Gemini IRAF package. You can look at these examples by typing "<instrument>examples" at the IRAF prompt, where <instrument> is the instrument, e.g., niri.
  • Finally, for general IRAF issues, iraf.net is a good resource.
Getting Help | Gemini Observatory

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