A cookbook for GMOS-IFU data reduction

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This topic contains 6 replies, has 2 voices, and was last updated by  davidelena 3 years ago.

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  • #507

    davidelena
    Participant

    Dear IFUsers,
    at this link you can find some notes that I am putting together for the reduction of GMOS-IFU data.

    Suggestions for improvements and comments are very welcome.
    Cheers

    Davide Lena

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    #532

    smriti
    Participant

    Dear Davide,

    Thanks a lot for putting this document together; for a novice like me it has just proven immensely resourceful! Thanks a lot!

    I have a few questions/suggestion though:

    1. I have been advised in the past that since the processed bias is not overscan subtracted, if using that I should reduce all data without overscan subtraction. What are your thoughts on the issue? (I am currently working with 1 slit IFU data from Gemini-South).

    2. On a similar note, you overscan subtract the flat in S2.1 but not the twilight frame in 2.2; why is that?

    3. S 2.5: Other folks may be smarter than me, but its worth noting that gftransform gives an error if “.fits” is used in the file name.

    4. S2.6.1 : it might be worth noting that mdffile=default is the recommended option if unsure of the file name to use (for 1 slit example for instance).

    Regards, Smriti

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    #537

    davidelena
    Participant

    Dear Smriti,
    I am glad it was useful and thank you for writing back.
    After enquiring/discussing with some experts, these are my answers to your questions:

    1. Yes, processed bias files given in the GEMINI archive come with no overscan subtraction (see also point 4 in the GEMINI FAQ page http://www.gemini.edu/?q=node/11889). Apparently this was decided early in the history of GEMINI and for consistency it has not been changed (let’s complain all togheter!). Moreover the overscan is trimmed, therefore if we want to subtract the overscan from the bias then we have to find individual bias frames (see this page for further instructions: http://www.gemini.edu/sciops/data-and-results/science-archive/calibration-data-retrieval/instructions) and process them subtracting the overscan.
    If your bias is not overscan subtracted, then you shouldn’t subtract the overscan from the data. What if you do it? When you subtract a bias not overscan-subtracted from overscan-subtracted data then you will subtract too much from the data and e.g. the flux of your source will be underestimated (I don’t know how much important such an effect would be).
    Of course relative quantities (e.g. flux ratios) will not be affected.
    Thanks again for raising this point. I will update the document.

    2. In the commands that I gave in the cookbook I was overscan subtracting all my data. Then, as I mention in S2.1 at some point along the reduction pipeline I had a problem: all the fluxes through the fibers where zero and the only way I had this problem solved was not to overscan subtract the data.
    I don’t know what was going on. Probably the issue was related to the use of a bias that was indeed not overscan subtracted.
    As a rule, your data should either be all overscan subtracted (including the bias) or all not overscan subtracted.

    I hope this helps.
    Thanks again for your comments.
    Cheers

    P.S. Everyone is welcome to step in the discussion to complete or to correct my answers.

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    #569

    davidelena
    Participant

    One of my collaborators (Allan Schnorr-Muller) tested the effect of subtracting a bias without overscan subtraction from overscan-subtracted-data and compared the result with a datacube properly done (e.g. bias with no overscan subtraction applied on data with no overscan subtraction) and there is no noticeable difference.
    The residual between the two datacubes are at most of the order of 10e-19 (while the flux in the continuum is of the order of 10e-17 or 10e-18).

    Of course this does not mean that the reduction should be done improperly, but if it happened, then it seems that there shouldn’t be any serious problem.
    Cheers

    Davide

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    #599

    davidelena
    Participant

    I posted an updated version of the cookbook here.
    I will leave the old file linked at the top of this page just because the discussion above is related to it.

    For up-to-date versions, please refer to my webpage, currently this one.
    Regards

    Davide

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    • This reply was modified 3 years, 9 months ago by  davidelena.
    • This reply was modified 3 years, 9 months ago by  davidelena.
    #621

    davidelena
    Participant

    A correction to my Jan 15 post. I wrote:

    If your bias is not overscan subtracted, then you shouldn’t subtract the overscan from the data. What if you do it? …
    Of course relative quantities (e.g. flux ratios) will not be affected.

    The sad truth is that relative quantities (e.g. flux ratios) will be affected as well.
    Cheers

    Davide

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    • This reply was modified 3 years, 8 months ago by  davidelena.
    • This reply was modified 3 years, 8 months ago by  davidelena.
    #747

    davidelena
    Participant

    Dear IFUsers, I posted the cookbook on arXiv.
    This should provide a permanent link and bypass the problem of previous links gone dead. Feedback on the content will always be welcome.
    Cheers,

    Davide

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