Commit 1228c4b4 authored by Yaroslav Gevorkov's avatar Yaroslav Gevorkov Committed by Thomas White
Browse files

PinkIndexer documentation

parent 747ef478
...@@ -448,6 +448,9 @@ These set low-level parameters for the XGANDALF indexing algorithm. ...@@ -448,6 +448,9 @@ These set low-level parameters for the XGANDALF indexing algorithm.
.IP \fB--pinkIndexer-multi=\fIn\fR .IP \fB--pinkIndexer-multi=\fIn\fR
.IP \fB--pinkIndexer-thread-count=\fIn\fR .IP \fB--pinkIndexer-thread-count=\fIn\fR
.IP \fB--pinkIndexer-no-check-indexed=\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 .PD
These set low-level parameters for the XGANDALF indexing algorithm. These set low-level parameters for the XGANDALF indexing algorithm.
...@@ -469,6 +472,12 @@ 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. \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 .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. \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 .SH INTEGRATION OPTIONS
.PD 0 .PD 0
......
...@@ -384,39 +384,39 @@ static void show_help() ...@@ -384,39 +384,39 @@ static void show_help()
{ {
printf( printf(
"Parameters for the PinkIndexer indexing algorithm:\n" "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" " Considered peaks count, 0 (fewest) to 4 (most)\n"
" Default: 4\n" " Default: 4\n"
" --pinkIndexer-angle-resolution\n" " --pinkIndexer-angle-resolution=n\n"
" Angle resolution, 0 (loosest) to 4 (most dense)\n" " Angle resolution, 0 (loosest) to 4 (most dense)\n"
" Default: 2\n" " Default: 2\n"
" --pinkIndexer-refinement-type\n" " --pinkIndexer-refinement-type=n\n"
" Refinement type, 0 (none) to 5 (most accurate)\n" " Refinement type, 0 (none) to 5 (most accurate)\n"
" Default: 1\n" " Default: 1\n"
" --pinkIndexer-tolerance\n" " --pinkIndexer-tolerance=n\n"
" Relative tolerance of the lattice vectors.\n" " Relative tolerance of the lattice vectors.\n"
" Default 0.06\n" " Default 0.06\n"
" --pinkIndexer-reflection-radius\n" " --pinkIndexer-reflection-radius=n\n"
" Radius of the reflections in reciprocal space.\n" " Radius of the reflections in reciprocal space.\n"
" Specified in 1/A. Default is 2%% of a*.\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" " Measured in 1/A\n"
" --pinkIndexer-multi Use pinkIndexers own multi indexing.\n" " --pinkIndexer-multi Use pinkIndexers own multi indexing.\n"
" --pinkIndexer-thread-count\n" " --pinkIndexer-thread-count=n\n"
" Thread count for internal parallelization \n" " Thread count for internal parallelization \n"
" Default: 1\n" " Default: 1\n"
" --pinkIndexer-no-check-indexed\n" " --pinkIndexer-no-check-indexed\n"
" Disable internal check for correct indexing\n" " Disable internal check for correct indexing\n"
" solutions\n" " solutions\n"
" --pinkIndexer-override-photon-energy\n" " --pinkIndexer-override-photon-energy=ev\n"
" Mean energy in eV to use for indexing.\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" " 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" " Overrides photon energy and bandwidth according to a range of \n"
" energies that have high enough intensity to produce \"visible\" \n" " energies that have high enough intensity to produce \"visible\" \n"
" Bragg spots on the detector.\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"
); );
} }
......
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