aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--libcrystfel/src/detector.c14
-rw-r--r--libcrystfel/src/image.h2
-rw-r--r--libcrystfel/src/index.c12
-rw-r--r--libcrystfel/src/index.h3
-rw-r--r--libcrystfel/src/pinkindexer.c30
-rw-r--r--libcrystfel/src/pinkindexer.h11
-rw-r--r--src/indexamajig.c10
7 files changed, 47 insertions, 35 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 201b9041..aab72341 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -1070,6 +1070,19 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam,
}
}
+ } else if ( strcmp(key, "photon_energy_bandwidth") == 0 ) {
+ if ( beam != NULL ) {
+ double v;
+ char *end;
+ v = strtod(val, &end);
+ if ( (val[0] != '\0') && (end[0] == '\0') ) {
+ beam->bandwidth = v;
+ } else {
+ ERROR("Invalid value for "
+ "photon_energy_bandwidth\n");
+ }
+ }
+
} else if ( strcmp(key, "photon_energy_scale") == 0 ) {
if ( beam != NULL ) {
beam->photon_energy_scale = atof(val);
@@ -1202,6 +1215,7 @@ struct detector *get_detector_geometry_from_string(const char *string,
beam->photon_energy = 0.0;
beam->photon_energy_from = NULL;
beam->photon_energy_scale = 1.0;
+ beam->bandwidth = 0.0;
}
det->n_panels = 0;
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 706b06b1..04fb18a0 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -110,6 +110,8 @@ struct beam_params
char *photon_energy_from; /**< HDF5 dataset name */
double photon_energy_scale; /**< Scale factor for photon energy, if it
* comes from an image header */
+ double bandwidth; /**< FWHM bandwidth as a fraction of
+ * wavelength */
};
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 80a773ab..d48a6634 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -238,6 +238,7 @@ static char *friendly_indexer_name(IndexingMethod m)
static void *prepare_method(IndexingMethod *m, UnitCell *cell,
+ struct detector *det, struct beam_params *beam,
struct xgandalf_options *xgandalf_opts,
struct pinkIndexer_options* pinkIndexer_opts,
struct felix_options *felix_opts)
@@ -285,7 +286,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
break;
case INDEXING_PINKINDEXER :
- priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts);
+ priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts,
+ det, beam);
break;
default :
@@ -316,8 +318,8 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell,
IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
- struct detector *det, float *tols,
- IndexingFlags flags,
+ struct detector *det, struct beam_params *beam,
+ float *tols, IndexingFlags flags,
struct taketwo_options *ttopts,
struct xgandalf_options *xgandalf_opts,
struct pinkIndexer_options *pinkIndexer_opts,
@@ -415,7 +417,9 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell,
int j;
ipriv->engine_private[i] = prepare_method(&methods[i], cell,
- xgandalf_opts, pinkIndexer_opts,
+ det, beam,
+ xgandalf_opts,
+ pinkIndexer_opts,
felix_opts);
if ( ipriv->engine_private[i] == NULL ) return NULL;
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index ab38016f..883df4a3 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -153,7 +153,8 @@ extern IndexingMethod get_indm_from_string_2(const char *method, int *err);
#include "felix.h"
extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell,
- struct detector *det, float *ltl,
+ struct detector *det,
+ struct beam_params *beam, float *ltl,
IndexingFlags flags,
struct taketwo_options *ttopts,
struct xgandalf_options *xgandalf_opts,
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c
index fe3b1625..eb8ec05e 100644
--- a/libcrystfel/src/pinkindexer.c
+++ b/libcrystfel/src/pinkindexer.c
@@ -154,26 +154,19 @@ int run_pinkIndexer(struct image *image, void *ipriv)
}
void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
- struct pinkIndexer_options *pinkIndexer_opts)
+ struct pinkIndexer_options *pinkIndexer_opts,
+ struct detector *det, struct beam_params *beam)
{
- if (pinkIndexer_opts->beamEnergy == 0.0) {
+ if ( beam->photon_energy_from != NULL ) {
ERROR("For pinkIndexer, the photon_energy must be defined as a "
"constant in the geometry file\n");
return NULL;
}
- if (pinkIndexer_opts->beamBandwidth == 0.0) {
- STATUS("Using default bandwidth of 0.01 for pinkIndexer\n");
- pinkIndexer_opts->beamBandwidth = 0.01;
- }
- if (pinkIndexer_opts->detectorDistance == 0.0 && pinkIndexer_opts->refinement_type ==
+ if ( (det->panels[0].clen_from != NULL) && pinkIndexer_opts->refinement_type ==
REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed) {
ERROR("Using center refinement makes it necessary to have the detector distance fixed in the geometry file!");
}
- if(pinkIndexer_opts->detectorDistance <= 0.0){
- pinkIndexer_opts->detectorDistance = 0.25; //fake value
- }
-
struct pinkIndexer_private_data* pinkIndexer_private_data = malloc(sizeof(struct pinkIndexer_private_data));
allocReciprocalPeaks(&(pinkIndexer_private_data->reciprocalPeaks_1_per_A));
pinkIndexer_private_data->intensities = malloc(MAX_PEAK_COUNT_FOR_INDEXER * sizeof(float));
@@ -199,9 +192,15 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
.bx = bsz * 1e-10, .by = bsx * 1e-10, .bz = bsy * 1e-10,
.cx = csz * 1e-10, .cy = csx * 1e-10, .cz = csy * 1e-10 };
- float detectorDistance_m = pinkIndexer_opts->detectorDistance;
- float beamEenergy_eV = pinkIndexer_opts->beamEnergy;
- float nonMonochromaticity = pinkIndexer_opts->beamBandwidth;
+ float detectorDistance_m;
+ if ( det->panels[0].clen_from != NULL ) {
+ detectorDistance_m = 0.25; /* fake value */
+ } else {
+ detectorDistance_m = det->panels[0].clen + det->panels[0].coffset;
+ }
+
+ float beamEenergy_eV = beam->photon_energy;
+ float nonMonochromaticity = beam->bandwidth;
float reflectionRadius_1_per_A;
if (pinkIndexer_opts->reflectionRadius < 0) {
reflectionRadius_1_per_A = 0.02
@@ -350,7 +349,8 @@ int run_pinkIndexer(struct image *image, void *ipriv)
}
extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
- struct pinkIndexer_options *pinkIndexer_opts)
+ struct pinkIndexer_options *pinkIndexer_opts,
+ struct detector *det, struct beam_params *beam)
{
ERROR("This copy of CrystFEL was compiled without PINKINDEXER support.\n");
ERROR("To use PINKINDEXER indexing, recompile with PINKINDEXER.\n");
diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h
index 5be2c1e7..1fcb3711 100644
--- a/libcrystfel/src/pinkindexer.h
+++ b/libcrystfel/src/pinkindexer.h
@@ -42,14 +42,8 @@ struct pinkIndexer_options {
int multi;
int thread_count;
int min_peaks;
-
int no_check_indexed;
-
- float beamEnergy; //in eV
- float beamBandwidth; //(delta lambda)/lambda
- float detectorDistance; //in m
-
- float reflectionRadius; //in 1/A
+ float reflectionRadius; /* In m^-1 */
};
#include <stddef.h>
@@ -58,7 +52,8 @@ struct pinkIndexer_options {
extern int run_pinkIndexer(struct image *image, void *ipriv);
extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell,
- struct pinkIndexer_options *pinkIndexer_opts);
+ struct pinkIndexer_options *pinkIndexer_opts,
+ struct detector *det, struct beam_params *beam);
extern void pinkIndexer_cleanup(void *pp);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 9aef3f2e..9fe14c65 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -1048,6 +1048,8 @@ int main(int argc, char *argv[])
"--pinkIndexer-reflection-radius\n");
return 1;
}
+ /* A^-1 to m^-1 */
+ iargs.pinkIndexer_opts.reflectionRadius /= 1e10;
break;
case 0 :
@@ -1149,12 +1151,6 @@ int main(int argc, char *argv[])
return 1;
}
add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam);
- iargs.pinkIndexer_opts.beamEnergy = iargs.beam->photon_energy;
- iargs.pinkIndexer_opts.beamBandwidth = 0.01;
- iargs.pinkIndexer_opts.detectorDistance = iargs.det->panels[0].clen;
- if(iargs.det->panels[0].clen_from != NULL){
- iargs.pinkIndexer_opts.detectorDistance = 0;
- }
/* If no peak path from geometry file, use these (but see later) */
if ( iargs.hdf5_peak_path == NULL ) {
@@ -1394,7 +1390,7 @@ int main(int argc, char *argv[])
}
iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det,
- iargs.tols, flags,
+ iargs.beam, iargs.tols, flags,
&iargs.taketwo_opts,
&iargs.xgandalf_opts,
&iargs.pinkIndexer_opts,
generated by cgit v1.2.3 (git 2.25.1) at 2024-10-31 04:29:37 +0000