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authorYaroslav Gevorkov <yaroslav.gevorkov@desy.de>2019-10-29 15:19:30 +0100
committerYaroslav Gevorkov <yaroslav.gevorkov@desy.de>2019-10-29 15:19:30 +0100
commit858e20d551bbb0912d9c8fba0d6d0ceb54b76c1a (patch)
tree90a4635a1f2fb6ab04569cf19a93bb35e7c674b0 /libcrystfel
parent6991bfee645de722e28a3305dcbc6d4264f80b65 (diff)
add "override" beam options to pinkIndexer
Diffstat (limited to 'libcrystfel')
-rw-r--r--libcrystfel/src/pinkindexer.c43
-rw-r--r--libcrystfel/src/pinkindexer.h2
2 files changed, 40 insertions, 5 deletions
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index 811aa3c8..b8833847 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -157,9 +157,9 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
struct pinkIndexer_options *pinkIndexer_opts,
struct detector *det, struct beam_params *beam)
{
- if ( beam->photon_energy_from != NULL ) {
+ if ( beam->photon_energy_from != NULL && pinkIndexer_opts->overridenPhotonEnergy > 0) {
ERROR("For pinkIndexer, the photon_energy must be defined as a "
- "constant in the geometry file\n");
+ "constant in the geometry file or a parameter\n");
return NULL;
}
if ( (det->panels[0].clen_from != NULL) && pinkIndexer_opts->refinement_type ==
@@ -201,13 +201,20 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
float beamEenergy_eV = beam->photon_energy;
float nonMonochromaticity = beam->bandwidth;
+ if(pinkIndexer_opts->overridenPhotonEnergy > 0){
+ beamEenergy_eV = pinkIndexer_opts->overridenPhotonEnergy;
+ }
+ if(pinkIndexer_opts->overridenBandwidth >= 0){
+ nonMonochromaticity = pinkIndexer_opts->overridenBandwidth;
+ }
+
float reflectionRadius_1_per_A;
if (pinkIndexer_opts->reflectionRadius < 0) {
reflectionRadius_1_per_A = 0.02
* sqrt(lattice.ax * lattice.ax + lattice.ay * lattice.ay + lattice.az * lattice.az);
}
else {
- reflectionRadius_1_per_A = pinkIndexer_opts->reflectionRadius;
+ reflectionRadius_1_per_A = pinkIndexer_opts->reflectionRadius * 1e10; /* m^-1 to A^-1*/
}
float divergenceAngle_deg = 0.01; //fake
@@ -370,7 +377,8 @@ const char *pinkIndexer_probe(UnitCell *cell)
static void show_help()
{
- printf("Parameters for the PinkIndexer indexing algorithm:\n"
+ printf(
+"Parameters for the PinkIndexer indexing algorithm:\n"
" --pinkIndexer-considered-peaks-count\n"
" Considered peaks count, 0 (fewest) to 4 (most)\n"
" Default: 4\n"
@@ -395,7 +403,11 @@ static void show_help()
" --pinkIndexer-no-check-indexed\n"
" Disable internal check for correct indexing\n"
" solutions\n"
-);
+" --pinkIndexer-override-photon-energy\n"
+" Mean wavelength in A to use for indexing.\n"
+" --pinkIndexer-override-bandwidth\n"
+" Bandwidth in (delta lambda)/(lambda) to use for indexing.\n"
+ );
}
@@ -419,6 +431,8 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
(*opts_ptr)->no_check_indexed = 0;
(*opts_ptr)->min_peaks = 2;
(*opts_ptr)->reflectionRadius = -1;
+ (*opts_ptr)->overridenPhotonEnergy = -1;
+ (*opts_ptr)->overridenBandwidth = -1;
break;
case 1 :
@@ -493,6 +507,21 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
(*opts_ptr)->reflectionRadius = tmp / 1e10; /* A^-1 to m^-1 */
break;
+ case 11 :
+ if (sscanf(arg, "%f", &(*opts_ptr)->overridenPhotonEnergy) != 1)
+ {
+ ERROR("Invalid value for --pinkIndexer-override-photon-energy\n");
+ return EINVAL;
+ }
+ break;
+
+ case 12 :
+ if (sscanf(arg, "%f", &(*opts_ptr)->overridenBandwidth) != 1)
+ {
+ ERROR("Invalid value for --pinkIndexer-override-bandwidth\n");
+ return EINVAL;
+ }
+ break;
}
return 0;
@@ -528,6 +557,10 @@ static struct argp_option options[] = {
{"pinkIndexer-reflection-radius", 10, "r", OPTION_HIDDEN, NULL},
+ {"pinkIndexer-override-photon-energy", 11, "overriddenPhotonEnergy", OPTION_HIDDEN, NULL},
+
+ {"pinkIndexer-override-bandwidth", 12, "overridenBandwidth", OPTION_HIDDEN, NULL},
+
{0}
};
diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h
index 0169d028..8c2d4cb6 100644
--- a/libcrystfel/src/pinkindexer.h
+++ b/libcrystfel/src/pinkindexer.h
@@ -47,6 +47,8 @@ struct pinkIndexer_options {
int min_peaks;
int no_check_indexed;
float reflectionRadius; /* In m^-1 */
+ float overridenPhotonEnergy;
+ float overridenBandwidth;
};
#include <stddef.h>