Postrefine: refine unit cell and detector position
After the integration is complete, the optional "postrefine" step
can be used to improve the predictions of the reflection positions
for a second round of integration.
Usage
The postrefine program can be called as follows:
postrefine [options] [.rmat filename] <directory name>
Postrefine will read the specified .rmat file (or, if none was
specified, the .rmat file with the same name as the specified
directory) and all ".y" files in the named directory. It will
generate a new, refined, .rmat file.
There are three levels of refinement:
- default: an output file postref.rmat is written containing the
postrefined cell based on ALL data. Using the option
"write=xxx.rmat" the name of this output file can be changed.
- "detector": When the program is run specifying the "detector" option, a
subsequent refinement is done for each scan. This refines the
detector position. These will be saved under the name
postref_xxxx.vic (e.g. postref_s01f.vic). These will
AUTOMATICALLY be used by makeshoe.
- "xtalorient": In the run for each scan, the orientation of the crystal
(but not the cell parameters) are refined as well. They are saved
as xxxx_postref.rmat (e.g. s01f_postref.rmat). The output file
name also listens to the "write=xxx.rmat" option. These individual
rmat files are currently NOT AUTOMATICALLY used by makeshoe.
When the program is finished, new shoeboxes can be created. This will
automatically use the refined matrices and refined detector positions
found in the postref subdirectory. When the new shoeboxes are
integrated, the "shifts" as reported by "evalall" will be very small.
The program accepts all options for controlling the way the unit cell is treated.
If the option "gui" is specified on the command line, the program
will pop up query and progress windows.
