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Preref: pre-refine detector position

The exact detector position can differ between scans. Especially "dx" is sometimes slightly off from the desired position. To be able to predict the reflection positions accurately, the shoe box generation can be preceded by a refinement of the detector position based on peak locations.

Usage

The preref program can be automatically called from the makeshoe program. Just activate the flag under "More options".

If you want to run preref yourself from the command line, it can be called as follows:

preref [options] [kcdfilenames or scan prefix] [rmat file]

The "kcdfilenames" can be standard KCD files or compressed KCD files (recognized by the extension .Z, .gz, or .bz2) or any mixture. Alternatively, a scan prefix can be given, and a subset of the frames in that scan will be used for the pre-refinement.

The unit cell in the specified rmat file will be used to predict reflection positions. If no rmat file is specified, the newest .rmat file from the current directory will be used automatically. Command line options are:

imin=x: Sets the minimum intensity for reflections to be searched to "x".
kill=x: Sets the "kill level" of the peak search algorithm. The default is 3.8. Increasing this number makes the peak search less sensitive.
accurate: Use a more accurate peak integration. This takes a lot of CPU time and does not improve the refinement results dramatically.
nofilters: Do not use badpixel and dark current correction filters on the images.
subset: Use only an intelligent subset of the kcd files specified.
allfiles: Use all of the kcd files specified. This is the default.
pat=xxx: Use "xxx" as the file name pattern, i.e. make files "xxx.pk", "xxx.det" and "peakref-xxx.log". Default value is the kcd-filename prefix given, or, if the individual kcd files are given, "preref.pk", "preref.det" and "peakref.log".

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Next: makeshoe: Make shoeboxes to prepare integration