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-rw-r--r--src/process_image.c107
1 files changed, 58 insertions, 49 deletions
diff --git a/src/process_image.c b/src/process_image.c
index 2f856594..c26842c3 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -57,6 +57,8 @@
#include "im-sandbox.h"
#include "im-zmq.h"
#include "im-asapo.h"
+#include "peaks.h"
+#include "peakfinder8.h"
static float **backup_image_data(float **dp, struct detgeom *det)
{
@@ -292,35 +294,42 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
profile_start("peak-search");
switch ( iargs->peak_search.method ) {
+ ImageFeatureList *peaks;
+
case PEAK_HDF5:
case PEAK_CXI:
set_last_task(last_task, "peaksearch:hdf5orcxi");
- image->features = image_read_peaks(iargs->dtempl,
- pargs->filename,
- pargs->event,
- iargs->peak_search.half_pixel_shift);
- if ( image->features == NULL ) {
- ERROR("Failed to get peaks from HDF5 file.\n");
- }
+ peaks = image_read_peaks(iargs->dtempl,
+ pargs->filename,
+ pargs->event,
+ iargs->peak_search.half_pixel_shift);
if ( iargs->peak_search.revalidate ) {
- validate_peaks(image, iargs->peak_search.min_snr,
- iargs->peak_search.pk_inn, iargs->peak_search.pk_mid,
- iargs->peak_search.pk_out, iargs->peak_search.use_saturated,
- iargs->peak_search.check_hdf5_snr);
+ ImageFeatureList *npeaks = validate_peaks(image, peaks,
+ iargs->peak_search.min_snr,
+ iargs->peak_search.pk_inn,
+ iargs->peak_search.pk_mid,
+ iargs->peak_search.pk_out,
+ iargs->peak_search.use_saturated,
+ iargs->peak_search.check_hdf5_snr);
+ image_feature_list_free(peaks);
+ image->features = npeaks;
}
break;
case PEAK_ZAEF:
set_last_task(last_task, "peaksearch:zaef");
- search_peaks(image, iargs->peak_search.threshold,
- iargs->peak_search.min_sq_gradient, iargs->peak_search.min_snr,
- iargs->peak_search.pk_inn, iargs->peak_search.pk_mid, iargs->peak_search.pk_out,
- iargs->peak_search.use_saturated);
+ image->features = search_peaks(image, iargs->peak_search.threshold,
+ iargs->peak_search.min_sq_gradient,
+ iargs->peak_search.min_snr,
+ iargs->peak_search.pk_inn,
+ iargs->peak_search.pk_mid,
+ iargs->peak_search.pk_out,
+ iargs->peak_search.use_saturated);
break;
case PEAK_PEAKFINDER8:
set_last_task(last_task, "peaksearch:pf8");
- if ( search_peaks_peakfinder8(image, 2048,
+ image->features = peakfinder8(image, 2048,
iargs->peak_search.threshold,
iargs->peak_search.min_snr,
iargs->peak_search.min_pix_count,
@@ -329,40 +338,36 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
iargs->peak_search.min_res,
iargs->peak_search.max_res,
iargs->peak_search.use_saturated,
- iargs->peak_search.peakfinder8_fast,
- iargs->pf_private) ) {
- ERROR("Failed to find peaks in image %s"
- "(event %s).\n",
- image->filename, image->ev);
- }
+ iargs->peak_search.peakfinder8_fast,
+ iargs->pf_private);
break;
case PEAK_PEAKFINDER9:
set_last_task(last_task, "peaksearch:pf9");
- if ( search_peaks_peakfinder9(image,
- iargs->peak_search.min_snr_biggest_pix,
- iargs->peak_search.min_snr_peak_pix,
- iargs->peak_search.min_snr,
- iargs->peak_search.min_sig,
- iargs->peak_search.min_peak_over_neighbour,
- iargs->peak_search.local_bg_radius) )
- {
- ERROR("Failed to find peaks in image %s"
- "(event %s).\n",
- image->filename, image->ev);
- }
+ image->features = search_peaks_peakfinder9(image,
+ iargs->peak_search.min_snr_biggest_pix,
+ iargs->peak_search.min_snr_peak_pix,
+ iargs->peak_search.min_snr,
+ iargs->peak_search.min_sig,
+ iargs->peak_search.min_peak_over_neighbour,
+ iargs->peak_search.local_bg_radius);
break;
case PEAK_MSGPACK:
- image->features = image_msgpack_read_peaks(iargs->dtempl,
- pargs->zmq_data,
- pargs->zmq_data_size,
- iargs->peak_search.half_pixel_shift);
+ peaks = image_msgpack_read_peaks(iargs->dtempl,
+ pargs->zmq_data,
+ pargs->zmq_data_size,
+ iargs->peak_search.half_pixel_shift);
if ( iargs->peak_search.revalidate ) {
- validate_peaks(image, iargs->peak_search.min_snr,
- iargs->peak_search.pk_inn, iargs->peak_search.pk_mid,
- iargs->peak_search.pk_out, iargs->peak_search.use_saturated,
- iargs->peak_search.check_hdf5_snr);
+ ImageFeatureList *npeaks = validate_peaks(image, peaks,
+ iargs->peak_search.min_snr,
+ iargs->peak_search.pk_inn,
+ iargs->peak_search.pk_mid,
+ iargs->peak_search.pk_out,
+ iargs->peak_search.use_saturated,
+ iargs->peak_search.check_hdf5_snr);
+ image_feature_list_free(peaks);
+ image->features = npeaks;
}
break;
@@ -371,6 +376,10 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
break;
}
+ if ( image->features == NULL ) {
+ ERROR("Peaksearch failed for image %s" "(event %s).\n",
+ image->filename, image->ev);
+ }
profile_end("peak-search");
image->peak_resolution = estimate_peak_resolution(image->features,
@@ -434,20 +443,20 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
set_last_task(last_task, "prediction params");
if ( iargs->fix_profile_r >= 0.0 ) {
for ( i=0; i<image->n_crystals; i++ ) {
- crystal_set_profile_radius(image->crystals[i],
+ crystal_set_profile_radius(image->crystals[i].cr,
iargs->fix_profile_r);
- crystal_set_mosaicity(image->crystals[i], 0.0);
+ crystal_set_mosaicity(image->crystals[i].cr, 0.0);
}
} else {
for ( i=0; i<image->n_crystals; i++ ) {
- crystal_set_profile_radius(image->crystals[i], 0.02e9);
- crystal_set_mosaicity(image->crystals[i], 0.0);
+ crystal_set_profile_radius(image->crystals[i].cr, 0.02e9);
+ crystal_set_mosaicity(image->crystals[i].cr, 0.0);
}
}
if ( iargs->fix_profile_r < 0.0 ) {
for ( i=0; i<image->n_crystals; i++ ) {
- if ( refine_radius(image->crystals[i], image) ) {
+ if ( refine_radius(image->crystals[i].cr, image) ) {
ERROR("WARNING: Radius determination failed\n");
}
}
@@ -479,7 +488,7 @@ streamwrite:
int n = 0;
for ( i=0; i<image->n_crystals; i++ ) {
- n += crystal_get_num_implausible_reflections(image->crystals[i]);
+ n += crystal_get_num_implausible_reflections(image->crystals[i].cr);
}
if ( n > 0 ) {
STATUS("WARNING: %i implausibly negative reflection%s in %s "
@@ -495,7 +504,7 @@ out:
pthread_mutex_lock(&sb_shared->totals_lock);
any_crystals = 0;
for ( i=0; i<image->n_crystals; i++ ) {
- if ( crystal_get_user_flag(image->crystals[i]) == 0 ) {
+ if ( crystal_get_user_flag(image->crystals[i].cr) == 0 ) {
sb_shared->n_crystals++;
any_crystals = 1;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-17 05:27:25 +0000