diff options
| author | Thomas White <taw@physics.org> | 2010-09-07 11:08:28 +0200 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2012-02-22 15:26:56 +0100 |
| commit | 58149b59cd8d1ec119b4c99a9923c52be982ab75 (patch) | |
| tree | 27c9721b272a54d359924d1de2065f568c7e6df3 /src/indexamajig.c | |
| parent | ccfe74160b87c28a5e800102f5fd2265a64a174d (diff) | |
indexamajig: Reformat --help
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 29 |
1 files changed, 17 insertions, 12 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index eee4c009..b8d3df88 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -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" |