indexamajig: Improve --help

1 files changed, 17 insertions, 11 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 46109a76..48833db2 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -82,17 +82,19 @@ static void show_help(const char *s)
 "      --indexing=<method> Use 'method' for indexing.  Choose from:\n"
 "                           none     : no indexing\n"
 "                           dirax    : invoke DirAx\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"
+"\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"
-"                           The intensities in this list are the sum of\n"
-"                           the values in a 7x7 square centered on the pixel\n"
-"                           closest to the Bragg condition.  Only pixels with\n"
-"                           fractional indices within 0.1 of the Bragg\n"
-"                           condition will be counted.\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"
+"                           of the nearest-to-Bragg pixel will be reported as\n"
+"                           the intensity.  The centroid of the pixels will\n"
+"                           be given as the coordinates, as well as the h,k,l\n"
+"                           (integer) indices of the reflection.  If a peak\n"
+"                           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"
 "                           unit cell.\n"
 "      --filter-cm         Perform common-mode noise subtraction on images\n"
@@ -102,7 +104,6 @@ static void show_help(const char *s)
 "                           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"
-"\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"
@@ -113,6 +114,11 @@ static void show_help(const char *s)
 "      --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"
+"\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"
 "     --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"