GMOS-S IFU – Aperture numbers changing while reducing

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    The error I get when using gfcube is number of rows in image does not equal the number of good fibres in MDF — Which I believe translates to the number of fibres extracted does not equal the number of fibres in the MDF.

    This is tricky, as the problem manifests itself in the middle of the pipeline somewhere. At the (erg+filename) step, the two flats have 1488 apertures, which matches the default MDF given. From there on, it seems the mdf and the flats then have different number of apertures later on. For reference, at the (eqxbprg+filename) step [meaning the flats have then been qecorr, cosmic ray removed, background light modeled and subtracted, and bad pixel repaired] the number of apertures becomes something different. For the two spatial dithers flats earlier there were 745 and 743 apertures, but now it seems to be 745 and 729 for one flat and 745 and 735 for the other.

    So then in the datacube step, gfcube sees that the mdf is still 743 and 745 while the two flats are different(!) meaning I don not think I could just simply change the mdf to fit both of them.

    Any ideas how to solve this problem? It may also be worth mentioning that our pipeline works well and I have ran it for 10 other galaxies just fine, but this particular object is problematic. I theorize some apertures are accidentally removed in the background subtraction step, but am not sure of how to remedy that situation anyways…. that’s not just not doing that step.

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