SER, FITS and Octave

While capturing a series of images in an autocorrelation experiment using a QHY5L-II and Sharpcap, instead of capturing as a series of PNG files, captured as SER files by mistake. From the experience of trying to use that data, found the following.

1. SER capture is faster than PNG sequence capture - PNG was capturing at 20 fps or so, but dropping frames after 80 frames or so, and was taking the last 20 frames at around 5 fps. SER was not dropping frames at all. All this on the Menlo systems Lenovo laptop. 
2. Octave and Matlab don't open SER files without conversion, the definitive site for SER files seems to be http://www.grischa-hahn.homepage.t-online.de/astro/ser/
3. After some back and forth on this thread, found that Siril can export SER to a sequence of FITS images without losing the 16-bit resolution. 
4. Imagemagick can be used to convert the FITS images to 16-bit TIFF using
   mogrify -format tif *.fits
5. Alternately, the fits octave package can be used to read the data into Octave from the FITS files. Although Octave uses Imagemagick to implement imread, imread doesn't seem to work with the FITS files from Siril, complaining
   error: Magick++ exception: Magick: Unexpected end-of-file (/media/mac/SAM2TB/Autocorr/2017-10-16/Capture/14_10_49/Capture_00002.fit) reported by coders/fits.c:370 (ReadFITSImage)
6. In order to install the fits package, had to install its dependency, with
   sudo apt-get install libcfitsio*
   and then run octave as root,
   sudo octave
   and within octave, run
   pkg install -forge fits
7. Reading using the fits package and imread give different results.
   imread returns uint16 rows x columns
   read_fits_image returns double columns x rows, upside down.
   So, for equivalence with imread, we need to use flipud.
   b=read_fits_image('im.fits')
   b=b';
   b=flipud(b);
   imagesc(b)
   gives the same numbers as
   a=imread('im.tif')
8. identify Capture_0035.png
   can be used to check whether the png is 8-bit or 16-bit. 
9. Installing ISIS and SER Player turned out to be dead-ends, since they did not convert SER to PNG without converting to 8-bit.

Edit - more on siril's stackall here.