February 4, 2016 at 11:17 pm #1104
Here is the latest version of the XDGNIRS script for reducing GNIRS cross-dispersed data. The tar file contains a manual, but here’s a direct link to it in case you’d like to take a look and see if the code might be useful to you:
XDGNIRS has been fairly well tested on a range of data but it’s the kind of code that astronomers write and I’m afraid I’m not going to be around to support it. Good luck!
Attachments:August 18, 2016 at 12:39 am #1344
The links to dropbox in the pdf document are broken. Though they link to the same files that are attached to the original post.May 10, 2017 at 7:56 pm #1517
For reference, the original post is at http://drforum.gemini.edu/topic/gnirs-xd-reduction-script/May 10, 2017 at 8:05 pm #1518
Could not import aqutil, please see the online PyRAF FAQ
Limited graphics available (aqutil not loaded)
This problem occurs at Step 10, and it is related to the display. As stated in the XDGNIRS manual:
“Most likely things to go wrong: This step is intended to help the Palomar XD group interpret the reduced data and may not work well on other data sets. If this step causes problems, simply run the code with “stop=9” and use your own routines to plot the .txt files output in the previous step. The total counts and FWHM recorded in the data sheet may not be correct for all data sets.”
Therefore, Gemini recommend that you follow that advice and use your own plotting routines.
Also, we would like to point out, also from that manual, Section 7:
“XDGNIRS is not officially supported by Gemini. File a helpdesk request for general questions about GNIRS data and reduction. XDGNIRS-specific questions can be addressed to Rachel Mason, who will attempt to answer on a best-efforts basis, other commitments permitting.”
This software is essentially a community-supported software, especially now that Rachel Mason has left Gemini, and the field. We recommend that you post your questions here on the DR Forum. Maybe someone in the community has solved this problem already and will be able to help.
A colleague suggested that it might still be worth asking the question to help@stsci. While they are no longer supporting Ureka, they try to help with those things on a best effort basis. “aqutil” is a pyraf module, therefore belongs to STScI.
I hope these clarifications help. If you do have a solution, please do post it here!May 10, 2017 at 8:15 pm #1519
I’ve had aqutil problems a couple of times. The last time a reboot of the machine fixed it.June 19, 2017 at 7:57 pm #1526
A few years ago there were several useful examples. I think about
(they are also given in the doc XDGNIRS_v226.pdf in the latest version of XDGNIRS)
But these links are broken now. Do you know where may I find them?
SimonJune 20, 2017 at 1:16 am #1529
All these dropbox links (not owned by Gemini) died recently, unfortunately.
You can access the data with the Gemini Observatory Archive:
The tar ball example_reduction.tar.gz would only have the intermediate files that the script produce. You may recreate them from the example data and the script.
Hope this works! Please, let us know.
June 20, 2017 at 7:27 pm #1531
- This reply was modified 2 years ago by achene.
Thanks a lot for your answer
Yes that is correctly working, until the step 10
I have to use AstroQuery, but it doesn’t find it (see bellow).
I use Ureka 1.5.2. And yes AstroQuery is not usable with Ureka
I can find AstroQuery in manual line from consol (with Anaconda) but not with the script of xdgnirs (with xdpiped.csh) which uses Ureka.
I don’t know what I am suppose to do. Do I have to force the script to use Anaconda (but this doesn’t have Pyraf)? Do I have to install AstroQuery in Ureka? Other?
Thank you so much for your help
************************************* ** Flux Calibration ** ************************************* ##### identifying the standard star and getting magnitudes .... Traceback (most recent call last): File "/Users/admin/Desktop/TOOLS/XDGNIRS_V2.2.6//mag2mass.py", line 11, in <module> from astroquery.simbad import Simbad ImportError: No module named astroquery.simbad >>>>>>>>>>>XDGNIRS has encountered a problem: >>>>>>>>>>>ImportError: No module named astroquery.simbad >>>>>>>>>>>Check LISTS/Status_inputfiles.txt >>>>>>>>>>>Stopping the script.June 22, 2017 at 12:11 am #1533
Specifically regarding Anaconda and IRAF, I would like to make you aware that IRAF, and Gemini IRAF v1.13.1, have recently been added to the AstroConda channel. Maybe that will help. See the instructions at http://www.gemini.edu/node/12665
KathleenJune 23, 2017 at 6:39 pm #1534
Thank you for your answer Kathleen.
I finally fix my problem with a modification of the GNIRS script. I added a custom line to import modules in anaconda, in the script which needed (mag2mass.py and redshift.py)
With that the script is available to find the astroauery module in the modules list of anaconda.
SimonJune 23, 2017 at 6:43 pm #1535
I’m really happy to hear that you found a solution. Thank you for sharing it with the community.June 30, 2017 at 3:59 pm #1544
I managed to reduce the GNIRS data following the script until nsfransform. So I have wavelength calibrated 2-D spectra. I would like to get rid of hot pixels and cosmic rays now. Andre-Nicolas suggested a few methods. I like crmedian but I found that my output files are not MEF anymore. In result I cannot use nsextract to get 1-D spectra. Am I doing something wrong?
The command I used is:
crmedian tel_com[sci,1] output=ctel_com[sci,1]
I would appreciate any tips for cosmic ray removal.
Here is the error message:
NSEXTRACT — Fri Jun 30 17:29:56 AEST 2017
FAIL: ctel_com[sci,1] – Extension not readable or absent
ERROR – NSEXTRACT: Problem with input images (missing or not MEF).
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