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Unfortunately, there is not any standard how to save a date and time of observation to FITS file, so every program uses its own special format. Although current version of C-Munipack can read many different formats, it may happens, that your program uses the another one. Send me one frame or two as sample (see email address above) and I will add it to the sources promptly.
FWHM is an abbreviation of Full Width at Half Maximum. Although stars can be theoretically considered as ideal spot light sources, when their light arrives on a detector, it has a shape of point spread function mostly due to the atmospheric seeing and wave nature of the light going through the telescope. FWHM value of a star tells the diameter of the star's image.
In the Muniwin program, the FWHM value is derived by finding the maximum pixels of a star (H) and mean level of background (B). Half maximum is set to 0.5*(H+B). Then, the profile of a star is tracked down from the pixel with highest value to all four directions (up, down, right and left). The distance from the center to the point when the profile first crosses the half maximum is partial FWHM in that direction. The linear interpolation is used to get subpixel precision. The average of the four values is the FWHM estimation. Its value is always displayed in pixels.