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authorThomas White <taw@physics.org>2010-09-07 11:08:28 +0200
committerThomas White <taw@physics.org>2012-02-22 15:26:56 +0100
commit58149b59cd8d1ec119b4c99a9923c52be982ab75 (patch)
tree27c9721b272a54d359924d1de2065f568c7e6df3 /src
parentccfe74160b87c28a5e800102f5fd2265a64a174d (diff)
indexamajig: Reformat --help
Diffstat (limited to 'src')
-rw-r--r--src/indexamajig.c29
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"