This section is intended to provide an overview over comman line arguments
accepted by commie. For more information on the /verbose output
see Sec. 3.3.5.
At the moment commie supports the following command line arguments
/verbose: As the name suggests this will print out details of the
assembly process onto the screen or into a file/folder if a a filename is
supplied, e.g.
/show_final: This will only display the final assembled array once
commie is finished.
/merge_first : This CLA will cause commie to first
merge sample and no_sample files separately and then subtract
no_sample in the very end. The default is to subtract no_sample
for each position.
/no_background: Choose this option if you do not want commie
to subtract any no_sample files. It will still subtract the dark current though
/dk_by_pix: If this option is selected commie will subtract the dark
current on a pixel-by-pixel basis. It will also initialize the error arrays by looking
at the variance of each individual pixel in the dark current files. Note that this
option requires dark current files for each exposure time that the data has been
recorded with.
/use_saved_merged_pos: Run commie with this option if you
wish to read previously saved merged positions from disk. This comes in handy
when all you did is update the beamstop mask and wish to have the new mask
applied before adding all merged positions together - it will save you a lot of time.
Note that the program will check against all CLAs that could potentially modify
the outcome of the merging-by-position process (i.e.dk_by_pix,
merge_first, and no_background) to make sure that they are the same
as those that were set when the merged positions were saved to disk.
