indexamajig: Clarify behaviour of intensity extraction

1 files changed, 7 insertions, 0 deletions

diff --git a/src/indexamajig.c b/src/indexamajig.c
index 9bdfa5e0..5a47254f 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -52,6 +52,11 @@ static void show_help(const char *s)
 "      --gpu               Use the GPU to speed up the simulation.\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"
 "      --simulate          Simulate the diffraction pattern using the indexed\n"
 "                           unit cell.\n"
 "      --filter-cm         Perform common-mode noise subtraction on images\n"
@@ -67,6 +72,8 @@ static void show_help(const char *s)
 "                           'none'.  Beware: the units in this file are\n"
 "                           reciprocal Angstroms.\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"
 "      --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"