Commit 58149b59 authored by Thomas White's avatar Thomas White
Browse files

indexamajig: Reformat --help

parent ccfe7416
......@@ -100,8 +100,9 @@ static void show_help(const char *s)
" dirax : invoke DirAx\n"
" template : index by template matching\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
"\n\nWith just the above options, this program does not do much of practical "
"use.\nYou should also enable some of the following:\n\n"
"\n"
"\nWith just the above options, this program does not do much of practical use."
"\nYou should also enable some of the following:\n\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
" When pixels with fractional indices within 0.1 of\n"
" integer values (the Bragg condition) are found,\n"
......@@ -118,13 +119,6 @@ static void show_help(const char *s)
" as \"simulated.h5\". You can TRY to combine this\n"
" with \"-j <n>\" with n greater than 1, but it's\n"
" not a good idea.\n"
" --filter-cm Perform common-mode noise subtraction on images\n"
" before proceeding. Intensities will be extracted\n"
" from the image as it is after this processing.\n"
" --filter-noise Apply an aggressive noise filter which sets all\n"
" pixels in each 3x3 region to zero if any of them\n"
" have negative values. Intensity measurement will\n"
" be performed on the image as it was before this.\n"
" --write-drx Write 'xfel.drx' for visualisation of reciprocal\n"
" space. Implied by any indexing method other than\n"
" 'none'. Beware: the units in this file are\n"
......@@ -132,21 +126,32 @@ static void show_help(const char *s)
" --dump-peaks Write the results of the peak search to stdout.\n"
" The intensities in this list are from the\n"
" centroid/integration procedure.\n"
"\n"
"\nFor more control over the process, you might need:\n\n"
" --no-match Don't attempt to match the indexed cell to the\n"
" model, just proceed with the one generated by the\n"
" auto-indexing procedure.\n"
" --unpolarized Don't correct for the polarisation of the X-rays.\n"
" --check-sanity Check that indexed locations approximately correspond\n"
" with detected peaks.\n"
" --filter-cm Perform common-mode noise subtraction on images\n"
" before proceeding. Intensities will be extracted\n"
" from the image as it is after this processing.\n"
" --filter-noise Apply an aggressive noise filter which sets all\n"
" pixels in each 3x3 region to zero if any of them\n"
" have negative values. Intensity measurement will\n"
" be performed on the image as it was before this.\n"
" --unpolarized Don't correct for the polarisation of the X-rays.\n"
" --sat-corr Correct values of saturated peaks using a table\n"
" included in the HDF5 file.\n"
" --no-sa Don't correct for the differing solid angles of\n"
" the pixels.\n"
"\n\nOptions for greater performance or verbosity:\n\n"
"\n"
"\nOptions for greater performance or verbosity:\n\n"
" --verbose Be verbose about indexing.\n"
" --gpu Use the GPU to speed up the simulation.\n"
" -j <n> Run <n> analyses in parallel. Default 1.\n"
"\n\nControl of model and data input:\n\n"
"\n"
"\nControl of model and data input:\n\n"
" --intensities=<file> Specify file containing reflection intensities\n"
" to use when simulating.\n"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.\n"
......
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