diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 48 |
1 files changed, 24 insertions, 24 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index b118593e..89b297c0 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -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" ); } |