GMOS IFU data reduction scripts (updated Oct 2016)

Home Forums Gemini Data Reduction GMOS IFU data reduction scripts (updated Oct 2016)

This topic contains 24 replies, has 4 voices, and was last updated by  jturner 1 year ago.

Viewing 10 posts - 16 through 25 (of 25 total)
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  • #863

    jturner
    Keymaster

    I have now posted a data reduction example (illustrating most of the new options in this package version) at http://drforum.gemini.edu/topic/gmos-ifu-data-reduction-example-2/.

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    #953
    Guille
    Guille
    Participant

    Hi James,

    Thanks for the huge work. We have previously (ifuproc_mod) reduced IFU data with flux variations among cubes and I am trying to re-reduce everything with the new scripts, to check for improvements.

    I did adapt the script for our IFU data (file names) and started to work on them, but faced a problem at the very beginning.

    I paste the end of the logfile when the problem is flagged, but I can send you the complete script and file if needed.

    ===============

    Aug 6 11:46: IMCOMBINE
    combine = average, scale = none, zero = none, weight = none
    reject = avsigclip, mclip = yes, nkeep = 1
    lsigma = 2., hsigma = 2.
    blank = 0.
    statsec = Aug 6 11:46
    Images Exp
    tmpfile7975ggS20110906S0200.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0201.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0203.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0204.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0205.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0206.fits[SCI,1] 0.0
    tmpfile7975ggS20110906S0207.fits[SCI,1] 0.0
    tmpfile7975ggS20110907S0354.fits[SCI,1] 0.0
    tmpfile7975ggS20110907S0355.fits[SCI,1] 0.0
    tmpfile7975ggS20110907S0356.fits[SCI,1] 0.0
    tmpfile7975ggS20110907S0357.fits[SCI,1] 0.0
    tmpfile7975ggS20110907S0358.fits[SCI,1] 0.0

    Output image = tmpcombout7975oj, ncombine = 12
    Number rejected mask = tmpcombdq7975pj.pl
    Sigma image = tmpcombsig7975qj
    ERROR – GEMCOMBINE: Could not access tmpfile7975ggS20110906S0205.fits[SCI,2]

    GEMCOMBINE — Finished: Thu Aug 6 11:46:34 ART 2015

    GEMCOMBINE — Exit status: ERROR

    =======

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    #958

    jturner
    Keymaster

    Hi Guillermo,

    Is this coming from gbias? That’s an odd one. I wonder whether you might have some malformed images sitting around from a previous gprepare run that got interrupted — what does “fxheader gS20110906S0205.fits” tell you? Could you delete any already-prepared (gS…) biases and try re-running it? Or maybe it’s a problem on Apple machines with the way I’m using gbias in the example (what platform is this?).

    If that doesn’t give you any clues, you’re welcome to send me your script and input files. I can set up an SFTP account if needed (but it might take a day or two as I’m waiting for our IS group to mend that service).

    Saludos,

    James.

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    #959
    Guille
    Guille
    Participant

    Hi James

    You did point me in the right direction. Found that S20110906S0205, 206, 207 only show one “section” in the raw data. fxheader yields:

    0 S20110906S0205.fits 16 Bias
    1 IMAGE -1 2080×4608 16 F

    0 S20110906S0206.fits 16 Bias
    1 IMAGE -1 2080×4608 16 F

    0 S20110906S0207.fits 16 Bias
    1 IMAGE -1 2080×4608 16 F

    I cannot check right now the GSA as it is giving some weird reply messages. In the meantime, deleting these 3 files avoided this problem

    GEMCOMBINE — Finished: Sat Aug 15 14:42:31 ART 2015

    GEMCOMBINE — Exit status: GOOD
    ——————————————————————————–

    GBIAS: Exit status: GOOD.
    —————————————————————————-

    🙂

    Cheers,

    Guillermo

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    #960

    jturner
    Keymaster

    Great :-).

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    • This reply was modified 2 years, 2 months ago by  jturner. Reason: Add critical smiley
    #1402

    jturner
    Keymaster

    Here’s a new ifudrgmos version that has been re-based on the public v1.13.1 update, with a few additional fixes (for Hamamatsu gap interpolation, extracting data with a central wavelength that doesn’t quite match the reference and to help support automation in Python).

    Sorry this has taken a while, but everything except my flat fielding had already been merged into the last official release anyway and I was still completing minor fixes to avoid requiring user intervention at a few steps that had peculiar behaviour when attempting to abstract the process a bit (more on that at a later date).

    Cheers,

    James.

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    #1417

    mmarinello
    Participant

    Hi James,

    Is there a “demo data” for GMOS?
    I would like to start to reduce GMOS data and a demo data is usually very helpful to learn the steps and tricks of data reduction.

    Cheers,
    Murilo.

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    #1422

    jturner
    Keymaster

    Not really (do you mean for the IFU?), but if you look at my post from 8 April 2015 above, I have posted a link to an example reduction script, for which you should be able to obtain the data from the Gemini archive. (Sorry that script is quite laborious to adapt — I’ve been rewriting it in Python and the new one gets the data for you etc. etc.) You can also type “gmosexamples” in the Gemini package to see some simpler example reduction scripts for the other modes.

    Cheers,

    James.

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    #1423

    dara norman
    Participant

    Hi, there are also examples for data reduction in the GMOS Cookbook available from the NOAO National Gemini Office. You can find the Cookbook under ‘GMOS’ on USNGO page ( http://ast.noao.edu/nssc/usngo ).
    Example reductions for the various GMOS modes are available under the ‘Processing Science Data’ sections. Questions about anything here would be most efficiently answered through the Gemini help desk.
    DARA

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    #1424

    jturner
    Keymaster

    Sorry, I completely forgot to mention that. Do you have a package of data to go with that tutorial (it looks quite comprehensive but I have trouble getting my bearings from the description there without enough time to sit down and work all the way through it)?

    James.

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