PinkIndexer documentation

2 files changed, 20 insertions, 11 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 2e9e4e76..3a87488e 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -448,6 +448,9 @@ These set low-level parameters for the XGANDALF indexing algorithm.
 .IP \fB--pinkIndexer-multi=\fIn\fR
 .IP \fB--pinkIndexer-thread-count=\fIn\fR
 .IP \fB--pinkIndexer-no-check-indexed=\fIn\fR
+.IP \fB--pinkIndexer-override-photon-energy=\fIn\fR
+.IP \fB--pinkIndexer-override-bandwidth=\fIn\fR
+.IP \fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR
 
 .PD
 These set low-level parameters for the XGANDALF indexing algorithm.
@@ -469,6 +472,12 @@ These set low-level parameters for the XGANDALF indexing algorithm.
 \fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFELs parallelization does. For HPCs typically a mixture of both parallelizations leads to best results.
 .IP
 \fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFELs prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented.
+.IP
+\fB--pinkIndexer-override-photon-energy=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is difined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR
+.IP
+\fB--pinkIndexer-override-bandwidth=\fIn\fR Overrides the mean energy in eV to use for indexing (which usually is difined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR
+.IP
+\fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR Overrides photon energy and bandwidth according to a range of energies that have high enough intensity to produce visible Bragg spots on the detector. min and max range borders are separated by a minus sign (no whitespace).
 
 .SH INTEGRATION OPTIONS
 .PD 0
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index cf3ecc94..be48ecff 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -384,39 +384,39 @@ static void show_help()
 {
 	printf(
 "Parameters for the PinkIndexer indexing algorithm:\n"
-"     --pinkIndexer-considered-peaks-count\n"
+"     --pinkIndexer-considered-peaks-count=n\n"
 "                           Considered peaks count, 0 (fewest) to 4 (most)\n"
 "                            Default: 4\n"
-"     --pinkIndexer-angle-resolution\n"
+"     --pinkIndexer-angle-resolution=n\n"
 "                           Angle resolution, 0 (loosest) to 4 (most dense)\n"
 "                            Default: 2\n"
-"     --pinkIndexer-refinement-type\n"
+"     --pinkIndexer-refinement-type=n\n"
 "                           Refinement type, 0 (none) to 5 (most accurate)\n"
 "                            Default: 1\n"
-"     --pinkIndexer-tolerance\n"
+"     --pinkIndexer-tolerance=n\n"
 "                           Relative tolerance of the lattice vectors.\n"
 "                            Default 0.06\n"
-"     --pinkIndexer-reflection-radius\n"
+"     --pinkIndexer-reflection-radius=n\n"
 "                           Radius of the reflections in reciprocal space.\n"
 "                            Specified in 1/A.  Default is 2%% of a*.\n"
-"     --pinkIndexer-max-resolution-for-indexing\n"
+"     --pinkIndexer-max-resolution-for-indexing=n\n"
 "                           Measured in 1/A\n"
 "     --pinkIndexer-multi   Use pinkIndexers own multi indexing.\n"
-"     --pinkIndexer-thread-count\n"
+"     --pinkIndexer-thread-count=n\n"
 "                           Thread count for internal parallelization \n"
 "                            Default: 1\n"
 "     --pinkIndexer-no-check-indexed\n"
 "                           Disable internal check for correct indexing\n"
 "                            solutions\n"
-"     --pinkIndexer-override-photon-energy\n"
+"     --pinkIndexer-override-photon-energy=ev\n"
 "                           Mean energy in eV to use for indexing.\n"
-"     --pinkIndexer-override-bandwidth\n"
+"     --pinkIndexer-override-bandwidth=n\n"
 "                           Bandwidth in (delta energy)/(mean energy) to use for indexing.\n"
-"     --pinkIndexer-override-visible-energy-range=n1-n2\n"
+"     --pinkIndexer-override-visible-energy-range=min-max\n"
 "                           Overrides photon energy and bandwidth according to a range of \n"
 "                           energies that have high enough intensity to produce \"visible\" \n"
 "                           Bragg spots on the detector.\n"
-"                           Lower and higher range are separated by a minus sign (no whitespace).\n"
+"                           Min and max range borders are separated by a minus sign (no whitespace).\n"
 	);
 }