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I'm having issues combining my flats (already separated by filter) using flatcombine. For full disclosure the motivation for this is my A305 class and we are supposed to be "getting our feet wet" by reducing some data. I have brought this to my AI's and they haven't a clue and have polled several other grad's in the dept who also have seen this before. My login.cl files has imtype set for "fits" and the line is uncommented. When I run flat combine on say the B-filter flats it spits out one flatB.imh and one flatB.pix. The goal is to get a ".fits" file similar to when I used zercombine for the bias images (worked perfectly). Any thoughts on why this would be occurring?
My parameters for flat combine and ccdproc are:
PACKAGE = ccdred
TASK = flatcombine
input = List of flat field images to combine
(output = ) Output flat field root name
(combine= average) Type of combine operation
(reject = avsigclip) Type of rejection
(ccdtype= ) CCD image type to combine
(process= no) Process images before combining?
(subsets= yes) Combine images by subset parameter?
(delete = no) Delete input images after combining?
(clobber= no) Clobber existing output image?
(scale = mode) Image scaling
(statsec= ) Image section for computing statistics
(nlow = 1) minmax: Number of low pixels to reject
(nhigh = 1) minmax: Number of high pixels to reject
(nkeep = 1) Minimum to keep (pos) or maximum to reject (neg)
(mclip = yes) Use median in sigma clipping algorithms?
(lsigma = 3.) Lower sigma clipping factor
(hsigma = 3.) Upper sigma clipping factor
(rdnoise= 0.) ccdclip: CCD readout noise (electrons)
(gain = 1.) ccdclip: CCD gain (electrons/DN)
(snoise = 0.) ccdclip: Sensitivity noise (fraction)
(pclip = -0.5) pclip: Percentile clipping parameter
(blank = 1.) Value if there are no pixels
(mode = ql)

PACKAGE = ccdred
TASK = ccdproc

images = List of CCD images to correct
(output = ) List of output CCD images
(ccdtype= ) CCD image type to correct
(max_cac= 0) Maximum image caching memory (in Mbytes)
(noproc = no) List processing steps only?

(fixpix = no) Fix bad CCD lines and columns?
(oversca= yes) Apply overscan strip correction?
(trim = yes) Trim the image?
(zerocor= no) Apply zero level correction?
(darkcor= no) Apply dark count correction?
(flatcor= no) Apply flat field correction?
(illumco= no) Apply illumination correction?
(fringec= no) Apply fringe correction?
(readcor= no) Convert zero level image to readout correction?
(scancor= no) Convert flat field image to scan correction?

(readaxi= line) Read out axis (column|line)
(fixfile= ) File describing the bad lines and columns
(biassec= image) Overscan strip image section
(trimsec= image) Trim data section
(zero = ) Zero level calibration image
(dark = ) Dark count calibration image
(flat = ) Flat field images
(illum = ) Illumination correction images
(fringe = ) Fringe correction images
(minrepl= 1.) Minimum flat field value
(scantyp= shortscan) Scan type (shortscan|longscan)
(nscan = 1) Number of short scan lines

(interac= no) Fit overscan interactively?
(functio= legendre) Fitting function
(order = 1) Number of polynomial terms or spline pieces
(sample = *) Sample points to fit
(naverag= 1) Number of sample points to combine
(niterat= 1) Number of rejection iterations
(low_rej= 3.) Low sigma rejection factor
(high_re= 3.) High sigma rejection factor
(grow = 0.) Rejection growing radius
(mode = ql)

The default image type is set in the $iraf/unix/hlib/zzsetenv.def file so a crude method to force the fits type is to edit this file. If you still see imh images then the 'imtype' environment variable is being reset somewhere, e.g. in a loginuser.cl file that is sourced after the login.cl definitions, or in some package loading script. You can do a "show imtype" before you run the task to see whether it's been changed, then start looking at the packages you've loaded automatically to see which might have changed it. FITS has been the default type for a while (since v2.13) so I would suspect and older package is the cause.

So I did show imtype and it spat out âfitsâ as the answer. I'm assuming the odd "a" has something to do with the quotes (but just a guess). Regardless I use set imtype=fits and then redid the show imtype. Its gave the regular fits without the odd "a." I reran flatcombine and it processed the B flat and HA flat correctly so far. As it stands now I would say the issue is resolved but any ideas on why that worked?

I would guess maybe an unprintable character in your login.cl file when you edited it? You can do a new MKIRAF to recreate the login.cl and see if that clears it up. Do you use an editor that uses "\r\n" as the end-of-line instead of just "\n", that sometimes messes things up.

So I finally got a valid answer from my AI who has been running around the dept asking people essentially WT_! When I did the mkiraf and subsequently edited my login.cl I used the command !open -e login.cl to open and edit the file. Turns out text editor doesn't play well with IRAF so his suggestion was to use emacs to open and edit. Once I opened the file I showed the imtype as ?fits? which I think is why the thing was acting so wonky.
Fixed everything, logged out, logged in, loaded packages, and no I'm happily chugging through the reduction steps.
Thanks for the assistance fitz.

Good to hear. Be aware though that emacs also has the potential of not putting a EOF on an edited file (or a final '\n" on the last line). If you see a "parser gagged" or have trouble reading an @file list, check the last line of the file.