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authorThomas White <taw@physics.org>2013-02-22 11:57:26 +0100
committerThomas White <taw@physics.org>2013-02-22 11:57:26 +0100
commit8a1898f66575495b9dbb75a7ce1bc6ea26c05cb3 (patch)
tree1f3113a22df42f55f362bd70e446d2d9d743e85b
parent9dd569008c6190b697d64c77a96e50a59e65fbf0 (diff)
Move processing pipeline to separate file
-rw-r--r--Makefile.am2
-rw-r--r--libcrystfel/src/index.h11
-rw-r--r--src/im-sandbox.c210
-rw-r--r--src/im-sandbox.h44
-rw-r--r--src/process_image.c231
-rw-r--r--src/process_image.h94
6 files changed, 335 insertions, 257 deletions
diff --git a/Makefile.am b/Makefile.am
index 422a34fb..961135a3 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -48,7 +48,7 @@ endif
src_process_hkl_SOURCES = src/process_hkl.c
-src_indexamajig_SOURCES = src/indexamajig.c src/im-sandbox.c
+src_indexamajig_SOURCES = src/indexamajig.c src/im-sandbox.c src/process_image.c
if BUILD_HDFSEE
src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/hdfsee-render.c
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index f60bb18f..f8f6e55b 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -38,12 +38,6 @@
#endif
-#include "beam-parameters.h"
-#include "cell.h"
-#include "image.h"
-#include "detector.h"
-
-
#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS)
@@ -110,6 +104,11 @@ typedef void *IndexingPrivate;
extern IndexingMethod *build_indexer_list(const char *str);
extern char *indexer_str(IndexingMethod indm);
+#include "beam-parameters.h"
+#include "detector.h"
+#include "cell.h"
+#include "image.h"
+
extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
const char *filename,
struct detector *det,
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 504c52c4..290f811f 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -41,8 +41,6 @@
#include <string.h>
#include <unistd.h>
#include <getopt.h>
-#include <hdf5.h>
-#include <gsl/gsl_errno.h>
#include <pthread.h>
#include <sys/wait.h>
#include <fcntl.h>
@@ -55,36 +53,14 @@
#include <sys/time.h>
#endif
-#include "utils.h"
-#include "hdf5-file.h"
-#include "index.h"
-#include "peaks.h"
-#include "detector.h"
-#include "filters.h"
-#include "thread-pool.h"
-#include "beam-parameters.h"
-#include "geometry.h"
-#include "stream.h"
-#include "reflist-utils.h"
-
#include "im-sandbox.h"
+#include "process_image.h"
/* Write statistics at APPROXIMATELY this interval */
#define STATS_EVERY_N_SECONDS (5)
-/* Information about the indexing process for one pattern */
-struct pattern_args
-{
- /* "Input" */
- char *filename;
-
- /* "Output" */
- int n_crystals;
-};
-
-
struct sb_reader
{
pthread_mutex_t lock;
@@ -194,190 +170,6 @@ static char *get_pattern(FILE *fh, char **use_this_one_instead,
}
-static void process_image(const struct index_args *iargs,
- struct pattern_args *pargs, Stream *st,
- int cookie)
-{
- float *data_for_measurement;
- size_t data_size;
- int check;
- struct hdfile *hdfile;
- struct image image;
- int i;
- char filename[1024];
-
- /* Prefix to jump out of temporary folder */
- if ( pargs->filename[0] != '/' ) {
- snprintf(filename, 1023, "../../%s", pargs->filename);
- } else {
- snprintf(filename, 1023, "%s", pargs->filename);
- }
-
- image.features = NULL;
- image.data = NULL;
- image.flags = NULL;
- image.copyme = iargs->copyme;
- image.id = cookie;
- image.filename = pargs->filename; /* Relative to top level */
- image.beam = iargs->beam;
- image.det = iargs->det;
- image.crystals = NULL;
- image.n_crystals = 0;
-
- hdfile = hdfile_open(filename); /* Relative to temporary folder */
- if ( hdfile == NULL ) return;
-
- if ( iargs->element != NULL ) {
-
- int r;
- r = hdfile_set_image(hdfile, iargs->element);
- if ( r ) {
- ERROR("Couldn't select path '%s'\n", iargs->element);
- hdfile_close(hdfile);
- return;
- }
-
- } else {
-
- int r;
- r = hdfile_set_first_image(hdfile, "/");
- if ( r ) {
- ERROR("Couldn't select first path\n");
- hdfile_close(hdfile);
- return;
- }
-
- }
-
- check = hdf5_read(hdfile, &image, 1);
- if ( check ) {
- hdfile_close(hdfile);
- return;
- }
-
- if ( (image.width != image.det->max_fs + 1 )
- || (image.height != image.det->max_ss + 1))
- {
- ERROR("Image size doesn't match geometry size"
- " - rejecting image.\n");
- ERROR("Image size: %i,%i. Geometry size: %i,%i\n",
- image.width, image.height,
- image.det->max_fs + 1, image.det->max_ss + 1);
- hdfile_close(hdfile);
- return;
- }
-
- fill_in_values(image.det, hdfile);
- fill_in_beam_parameters(image.beam, hdfile);
-
- image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
-
- if ( (image.beam->photon_energy < 0.0) || (image.lambda > 1000) ) {
- /* Error message covers a silly value in the beam file or in
- * the HDF5 file. */
- ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n",
- image.lambda, image.beam->photon_energy, image.filename);
- hdfile_close(hdfile);
- return;
- }
-
- if ( iargs->cmfilter ) filter_cm(&image);
-
- /* Take snapshot of image after CM subtraction but before
- * the aggressive noise filter. */
- data_size = image.width * image.height * sizeof(float);
- data_for_measurement = malloc(data_size);
-
- if ( iargs->noisefilter ) {
- filter_noise(&image, data_for_measurement);
- } else {
- memcpy(data_for_measurement, image.data, data_size);
- }
-
- switch ( iargs->peaks ) {
-
- case PEAK_HDF5:
- // Get peaks from HDF5
- if (get_peaks(&image, hdfile,
- iargs->hdf5_peak_path)) {
- ERROR("Failed to get peaks from HDF5 file.\n");
- }
- if ( !iargs->no_revalidate ) {
- validate_peaks(&image, iargs->min_int_snr,
- iargs->ir_inn, iargs->ir_mid,
- iargs->ir_out, iargs->use_saturated);
- }
- break;
-
- case PEAK_ZAEF:
- search_peaks(&image, iargs->threshold,
- iargs->min_gradient, iargs->min_snr,
- iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
- iargs->use_saturated);
- break;
-
- }
-
- /* Get rid of noise-filtered version at this point
- * - it was strictly for the purposes of peak detection. */
- free(image.data);
- image.data = data_for_measurement;
-
- /* Index the pattern */
- index_pattern(&image, iargs->indm, iargs->ipriv);
-
- pargs->n_crystals = image.n_crystals;
-
- /* Default beam parameters */
- image.div = image.beam->divergence;
- image.bw = image.beam->bandwidth;
-
- /* Integrate each crystal's diffraction spots */
- for ( i=0; i<image.n_crystals; i++ ) {
-
- RefList *reflections;
-
- /* Set default crystal parameter(s) */
- crystal_set_profile_radius(image.crystals[i],
- image.beam->profile_radius);
-
- if ( iargs->integrate_found ) {
- reflections = select_intersections(&image,
- image.crystals[i]);
- } else {
- reflections = find_intersections(&image,
- image.crystals[i]);
- }
-
- crystal_set_reflections(image.crystals[i], reflections);
-
- }
-
- /* Integrate all the crystals at once - need all the crystals so that
- * overlaps can be detected. */
- integrate_reflections(&image, iargs->closer,
- iargs->bgsub,
- iargs->min_int_snr,
- iargs->ir_inn,
- iargs->ir_mid,
- iargs->ir_out,
- iargs->integrate_saturated,
- iargs->res_cutoff);
-
- write_chunk(st, &image, hdfile,
- iargs->stream_peaks, iargs->stream_refls);
-
- for ( i=0; i<image.n_crystals; i++ ) {
- crystal_free(image.crystals[i]);
- }
-
- free(image.data);
- if ( image.flags != NULL ) free(image.flags);
- image_feature_list_free(image.features);
- hdfile_close(hdfile);
-}
-
-
static void run_work(const struct index_args *iargs,
int filename_pipe, int results_pipe, Stream *st,
int cookie)
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index dfddabe6..7df41738 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -31,48 +31,10 @@
*
*/
+#include "index.h"
#include "stream.h"
-
-enum {
- PEAK_ZAEF,
- PEAK_HDF5,
-};
-
-
-/* Information about the indexing process which is common to all patterns */
-struct index_args
-{
- UnitCell *cell;
- int cmfilter;
- int noisefilter;
- int satcorr;
- int closer;
- int bgsub;
- float threshold;
- float min_gradient;
- float min_snr;
- double min_int_snr;
- struct detector *det;
- IndexingMethod *indm;
- IndexingPrivate **ipriv;
- int peaks; /* Peak detection method */
- float tols[4];
- struct beam_params *beam;
- char *element;
- char *hdf5_peak_path;
- float ir_inn;
- float ir_mid;
- float ir_out;
- struct copy_hdf5_field *copyme;
- int integrate_saturated;
- int use_saturated;
- int no_revalidate;
- int integrate_found;
- int stream_peaks;
- int stream_refls;
- int res_cutoff;
-};
-
+#include "cell.h"
+#include "process_image.h"
extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh,
diff --git a/src/process_image.c b/src/process_image.c
new file mode 100644
index 00000000..010054c8
--- /dev/null
+++ b/src/process_image.c
@@ -0,0 +1,231 @@
+/*
+ * process_image.c
+ *
+ * The processing pipeline for one image
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2010-2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <hdf5.h>
+#include <gsl/gsl_errno.h>
+
+#include "utils.h"
+#include "hdf5-file.h"
+#include "index.h"
+#include "peaks.h"
+#include "detector.h"
+#include "filters.h"
+#include "thread-pool.h"
+#include "beam-parameters.h"
+#include "geometry.h"
+#include "stream.h"
+#include "reflist-utils.h"
+#include "process_image.h"
+
+
+void process_image(const struct index_args *iargs, struct pattern_args *pargs,
+ Stream *st, int cookie)
+{
+ float *data_for_measurement;
+ size_t data_size;
+ int check;
+ struct hdfile *hdfile;
+ struct image image;
+ int i;
+ char filename[1024];
+
+ /* Prefix to jump out of temporary folder */
+ if ( pargs->filename[0] != '/' ) {
+ snprintf(filename, 1023, "../../%s", pargs->filename);
+ } else {
+ snprintf(filename, 1023, "%s", pargs->filename);
+ }
+
+ image.features = NULL;
+ image.data = NULL;
+ image.flags = NULL;
+ image.copyme = iargs->copyme;
+ image.id = cookie;
+ image.filename = pargs->filename; /* Relative to top level */
+ image.beam = iargs->beam;
+ image.det = iargs->det;
+ image.crystals = NULL;
+ image.n_crystals = 0;
+
+ hdfile = hdfile_open(filename); /* Relative to temporary folder */
+ if ( hdfile == NULL ) return;
+
+ if ( iargs->element != NULL ) {
+
+ int r;
+ r = hdfile_set_image(hdfile, iargs->element);
+ if ( r ) {
+ ERROR("Couldn't select path '%s'\n", iargs->element);
+ hdfile_close(hdfile);
+ return;
+ }
+
+ } else {
+
+ int r;
+ r = hdfile_set_first_image(hdfile, "/");
+ if ( r ) {
+ ERROR("Couldn't select first path\n");
+ hdfile_close(hdfile);
+ return;
+ }
+
+ }
+
+ check = hdf5_read(hdfile, &image, 1);
+ if ( check ) {
+ hdfile_close(hdfile);
+ return;
+ }
+
+ if ( (image.width != image.det->max_fs + 1 )
+ || (image.height != image.det->max_ss + 1))
+ {
+ ERROR("Image size doesn't match geometry size"
+ " - rejecting image.\n");
+ ERROR("Image size: %i,%i. Geometry size: %i,%i\n",
+ image.width, image.height,
+ image.det->max_fs + 1, image.det->max_ss + 1);
+ hdfile_close(hdfile);
+ return;
+ }
+
+ fill_in_values(image.det, hdfile);
+ fill_in_beam_parameters(image.beam, hdfile);
+
+ image.lambda = ph_en_to_lambda(eV_to_J(image.beam->photon_energy));
+
+ if ( (image.beam->photon_energy < 0.0) || (image.lambda > 1000) ) {
+ /* Error message covers a silly value in the beam file or in
+ * the HDF5 file. */
+ ERROR("Nonsensical wavelength (%e m or %e eV) value for %s.\n",
+ image.lambda, image.beam->photon_energy, image.filename);
+ hdfile_close(hdfile);
+ return;
+ }
+
+ if ( iargs->cmfilter ) filter_cm(&image);
+
+ /* Take snapshot of image after CM subtraction but before
+ * the aggressive noise filter. */
+ data_size = image.width * image.height * sizeof(float);
+ data_for_measurement = malloc(data_size);
+
+ if ( iargs->noisefilter ) {
+ filter_noise(&image, data_for_measurement);
+ } else {
+ memcpy(data_for_measurement, image.data, data_size);
+ }
+
+ switch ( iargs->peaks ) {
+
+ case PEAK_HDF5:
+ // Get peaks from HDF5
+ if (get_peaks(&image, hdfile,
+ iargs->hdf5_peak_path)) {
+ ERROR("Failed to get peaks from HDF5 file.\n");
+ }
+ if ( !iargs->no_revalidate ) {
+ validate_peaks(&image, iargs->min_int_snr,
+ iargs->ir_inn, iargs->ir_mid,
+ iargs->ir_out, iargs->use_saturated);
+ }
+ break;
+
+ case PEAK_ZAEF:
+ search_peaks(&image, iargs->threshold,
+ iargs->min_gradient, iargs->min_snr,
+ iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
+ iargs->use_saturated);
+ break;
+
+ }
+
+ /* Get rid of noise-filtered version at this point
+ * - it was strictly for the purposes of peak detection. */
+ free(image.data);
+ image.data = data_for_measurement;
+
+ /* Index the pattern */
+ index_pattern(&image, iargs->indm, iargs->ipriv);
+
+ pargs->n_crystals = image.n_crystals;
+
+ /* Default beam parameters */
+ image.div = image.beam->divergence;
+ image.bw = image.beam->bandwidth;
+
+ /* Integrate each crystal's diffraction spots */
+ for ( i=0; i<image.n_crystals; i++ ) {
+
+ RefList *reflections;
+
+ /* Set default crystal parameter(s) */
+ crystal_set_profile_radius(image.crystals[i],
+ image.beam->profile_radius);
+
+ if ( iargs->integrate_found ) {
+ reflections = select_intersections(&image,
+ image.crystals[i]);
+ } else {
+ reflections = find_intersections(&image,
+ image.crystals[i]);
+ }
+
+ crystal_set_reflections(image.crystals[i], reflections);
+
+ }
+
+ /* Integrate all the crystals at once - need all the crystals so that
+ * overlaps can be detected. */
+ integrate_reflections(&image, iargs->closer,
+ iargs->bgsub,
+ iargs->min_int_snr,
+ iargs->ir_inn,
+ iargs->ir_mid,
+ iargs->ir_out,
+ iargs->integrate_saturated,
+ iargs->res_cutoff);
+
+ write_chunk(st, &image, hdfile,
+ iargs->stream_peaks, iargs->stream_refls);
+
+ for ( i=0; i<image.n_crystals; i++ ) {
+ crystal_free(image.crystals[i]);
+ }
+
+ free(image.data);
+ if ( image.flags != NULL ) free(image.flags);
+ image_feature_list_free(image.features);
+ hdfile_close(hdfile);
+}
diff --git a/src/process_image.h b/src/process_image.h
new file mode 100644
index 00000000..f2f034d9
--- /dev/null
+++ b/src/process_image.h
@@ -0,0 +1,94 @@
+/*
+ * process_image.h
+ *
+ * The processing pipeline for one image
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2010-2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef PROCESS_IMAGE_H
+#define PROCESS_IMAGE_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+enum {
+ PEAK_ZAEF,
+ PEAK_HDF5,
+};
+
+
+/* Information about the indexing process which is common to all patterns */
+struct index_args
+{
+ UnitCell *cell;
+ int cmfilter;
+ int noisefilter;
+ int satcorr;
+ int closer;
+ int bgsub;
+ float threshold;
+ float min_gradient;
+ float min_snr;
+ double min_int_snr;
+ struct detector *det;
+ IndexingMethod *indm;
+ IndexingPrivate **ipriv;
+ int peaks; /* Peak detection method */
+ float tols[4];
+ struct beam_params *beam;
+ char *element;
+ char *hdf5_peak_path;
+ float ir_inn;
+ float ir_mid;
+ float ir_out;
+ struct copy_hdf5_field *copyme;
+ int integrate_saturated;
+ int use_saturated;
+ int no_revalidate;
+ int integrate_found;
+ int stream_peaks;
+ int stream_refls;
+ int res_cutoff;
+};
+
+
+/* Information about the indexing process for one pattern */
+struct pattern_args
+{
+ /* "Input" */
+ char *filename;
+
+ /* "Output" */
+ int n_crystals;
+};
+
+
+extern void process_image(const struct index_args *iargs,
+ struct pattern_args *pargs, Stream *st,
+ int cookie);
+
+
+#endif /* PROCESS_IMAGEs_H */