If you continue to see what appear to be hot pixels or cosmic rays, even after processing your data with calstis, there are a couple of things you should check before contacting the Help Desk.
- Check that the data reduction was done using the best weekly dark files available for your observation. If you requested your data close to the time of the observation, you should make sure no new reference files applicable to your data have been made available since. If new files are available, it might be better to re-request your data from the archive again, so that they are automatically recalibrated using the best and current reference files.
- The standard dark file subtracted from STIS data is based on a combination of several long dark files taken over an entire week. They usually don't do a perfect job of subtracting hot pixels, both because the hot pixels can change on short time scales, and because some of the hotter pixels may have been saturated in the long dark images. For these reasons it will often be useful to construct a customized dark image for that particular day using short darks taken on the same day as your science image. Procedures for doing this are described at http://www.stsci.edu/hst/stis/software/analyzing/scripts/daydark/. After you create your new daydark file, you should set the DARKFILE keyword in the [0] extension of the _raw.fits files to reference this new dark file and then reprocess the data through calstis.
- Even using a daydark will not give perfect removal of all bad pixels. There is no routine available that will automatically find and fix the bad pixels. It will often be necessary to identify them by hand and create a bad pixel mask. Once such a mask has been made, the IRAF routine fixpix may be useful. This task interpolates over bad pixels, and allows the bad pixel mask to be defined with a text file rather than a fits image. It is probably best to find the bad pixels in the _crj.fits file, use fixpix to adjust the crj fluxes and errors, and then run subsequent calibration and reduction programs on the corrected _crj file. For data taken on the same day, most of the bad pixels will be in the same place in each image.