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authorThomas White <taw@physics.org>2021-03-11 14:48:18 +0100
committerThomas White <taw@physics.org>2021-03-11 16:10:54 +0100
commitd47c903416fb98701cda2c90e755c4b3e30d9478 (patch)
treed8c51dd48b3d71ed50c8d08b8df71eea10798ee6 /libcrystfel/src
parentb76a954f1ff1808b4cfec080e4c74ef21a8d3359 (diff)
PinkIndexer: Allocate peak lists when indexing
There doesn't seem to be any point in allocating them earlier, except to make space for some nice bugs.
Diffstat (limited to 'libcrystfel/src')
-rw-r--r--libcrystfel/src/indexers/pinkindexer.c56
1 files changed, 31 insertions, 25 deletions
diff --git a/libcrystfel/src/indexers/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c
index c831cb26..db4da101 100644
--- a/libcrystfel/src/indexers/pinkindexer.c
+++ b/libcrystfel/src/indexers/pinkindexer.c
@@ -65,8 +65,6 @@ struct pinkIndexer_options {
struct pinkIndexer_private_data {
PinkIndexer *pinkIndexer;
- reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A;
- float *intensities;
IndexingMethod indm;
UnitCell *cellTemplate;
@@ -120,17 +118,26 @@ static void scale_detector_shift(double fake_clen,
int run_pinkIndexer(struct image *image, void *ipriv)
{
struct pinkIndexer_private_data *pinkIndexer_private_data = ipriv;
- reciprocalPeaks_1_per_A_t* reciprocalPeaks_1_per_A = &(pinkIndexer_private_data->reciprocalPeaks_1_per_A);
- float *intensities = pinkIndexer_private_data->intensities;
+ reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A;
+ float *intensities;
+ int npk;
+ int i;
/* FIXME: Check if wavelength is too far from estimate */
- int peakCountMax = image_feature_count(image->features);
- if (peakCountMax < 5) {
- int goodLatticesCount = 0;
- return goodLatticesCount;
+
+ npk = image_feature_count(image->features);
+ if ( npk < 5 ) return 0;
+
+ if ( npk > MAX_PEAK_COUNT_FOR_INDEXER ) {
+ npk = MAX_PEAK_COUNT_FOR_INDEXER;
}
- reciprocalPeaks_1_per_A->peakCount = 0;
- for (int i = 0; i < peakCountMax && i < MAX_PEAK_COUNT_FOR_INDEXER; i++) {
+
+ reciprocalPeaks_1_per_A.peakCount = 0;
+ intensities = malloc(npk*sizeof(float));
+ allocReciprocalPeaks(&reciprocalPeaks_1_per_A);
+ if ( intensities == NULL ) return 0;
+
+ for ( i=0; i<npk; i++ ) {
struct imagefeature *f;
double r[3];
@@ -141,23 +148,26 @@ int run_pinkIndexer(struct image *image, void *ipriv)
detgeom_transform_coords(&image->detgeom->panels[f->pn],
f->fs, f->ss, image->lambda,
0.0, 0.0, r);
- reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = r[2] * 1e-10;
- reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = r[0] * 1e-10;
- reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = r[1] * 1e-10;
- intensities[reciprocalPeaks_1_per_A->peakCount] = (float) (f->intensity);
- reciprocalPeaks_1_per_A->peakCount++;
+ reciprocalPeaks_1_per_A.coordinates_x[reciprocalPeaks_1_per_A.peakCount] = r[2] * 1e-10;
+ reciprocalPeaks_1_per_A.coordinates_y[reciprocalPeaks_1_per_A.peakCount] = r[0] * 1e-10;
+ reciprocalPeaks_1_per_A.coordinates_z[reciprocalPeaks_1_per_A.peakCount] = r[1] * 1e-10;
+ intensities[reciprocalPeaks_1_per_A.peakCount] = f->intensity;
+ reciprocalPeaks_1_per_A.peakCount++;
}
int indexed = 0;
float center_shift[2];
Lattice_t indexedLattice;
int matchedPeaksCount = PinkIndexer_indexPattern(pinkIndexer_private_data->pinkIndexer,
- &indexedLattice,
- center_shift,
- reciprocalPeaks_1_per_A,
- intensities,
- pinkIndexer_private_data->maxRefinementDisbalance,
- pinkIndexer_private_data->threadCount);
+ &indexedLattice,
+ center_shift,
+ &reciprocalPeaks_1_per_A,
+ intensities,
+ pinkIndexer_private_data->maxRefinementDisbalance,
+ pinkIndexer_private_data->threadCount);
+
+ free(intensities);
+ freeReciprocalPeaks(reciprocalPeaks_1_per_A);
if ( matchedPeaksCount == -1 ) {
@@ -245,8 +255,6 @@ void *pinkIndexer_prepare(IndexingMethod *indm,
}
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));
pinkIndexer_private_data->indm = *indm;
pinkIndexer_private_data->cellTemplate = cell;
pinkIndexer_private_data->threadCount = pinkIndexer_opts->thread_count;
@@ -396,8 +404,6 @@ void pinkIndexer_cleanup(void *pp)
{
struct pinkIndexer_private_data* pinkIndexer_private_data = (struct pinkIndexer_private_data*) pp;
- freeReciprocalPeaks(pinkIndexer_private_data->reciprocalPeaks_1_per_A);
- free(pinkIndexer_private_data->intensities);
intmat_free(pinkIndexer_private_data->centeringTransformation);
PinkIndexer_delete(pinkIndexer_private_data->pinkIndexer);
}