Commit 6e463f8b authored by Thomas White's avatar Thomas White
Browse files

indexamajig: More fussing over --help

parent fbb24f22
......@@ -91,20 +91,22 @@ static void show_help(const char *s)
printf(
"Process and index FEL diffraction images.\n"
"\n"
" -h, --help Display this help message.\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" '-' means stdin, which is the default.\n"
"\n"
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" none : no indexing\n"
" dirax : invoke DirAx\n"
" template : index by template matching\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.\n"
" -x, --prefix=<p> Prefix filenames from input file with <p>.\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"
" --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"
" the integral of pixels within a ten pixel radius\n"
......@@ -115,49 +117,47 @@ static void show_help(const char *s)
" was located by the initial peak search close to\n"
" the \"near Bragg\" location, its coordinates will\n"
" be taken as the centre instead.\n"
" --simulate Simulate the diffraction pattern using the indexed\n"
" --simulate Simulate the diffraction pattern using the indexed\n"
" unit cell. The simulated pattern will be saved\n"
" 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"
" --write-drx Write 'xfel.drx' for visualisation of reciprocal\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"
" reciprocal Angstroms.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" --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"
" --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"
" --check-sanity Check that indexed locations approximately correspond\n"
" --check-sanity Check that indexed locations approximately correspond\n"
" with detected peaks.\n"
" --filter-cm Perform common-mode noise subtraction on images\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"
" --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"
" --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"
" --no-sa Don't correct for the differing solid angles of\n"
" the pixels.\n"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\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"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n"
"\n"
"\nControl of model and data input:\n\n"
"\nIf you used --simulate, you may also want:\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"
" -x, --prefix=<p> Prefix filenames from input file with 'p'.\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"
);
}
......
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