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-rw-r--r--src/indexamajig.c237
1 files changed, 128 insertions, 109 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 4d3c213c..c32657d9 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -170,6 +170,127 @@ static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
}
+static int process_pattern(const char *filename, UnitCell *cell,
+ int config_cmfilter, int config_noisefilter,
+ int config_writedrx, int config_dumpfound,
+ int config_verbose, int config_alternate,
+ int config_nearbragg, int config_gpu,
+ int config_simulate, int config_nomatch,
+ IndexingMethod indm, double *intensities,
+ unsigned int *counts, struct gpu_context *gctx)
+{
+ struct hdfile *hdfile;
+ struct image image;
+ struct image *simage;
+ float *data_for_measurement;
+ size_t data_size;
+
+ image.features = NULL;
+ image.data = NULL;
+ image.indexed_cell = NULL;
+
+ #include "geometry-lcls.tmp"
+
+ STATUS("Processing '%s'\n", filename);
+
+ hdfile = hdfile_open(filename);
+ if ( hdfile == NULL ) {
+ return 0;
+ } else if ( hdfile_set_first_image(hdfile, "/") ) {
+ ERROR("Couldn't select path\n");
+ return 0;
+ }
+
+ hdf5_read(hdfile, &image);
+
+ if ( config_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 ( config_noisefilter ) {
+ filter_noise(&image, data_for_measurement);
+ } else {
+
+ int x, y;
+
+ for ( x=0; x<image.width; x++ ) {
+ for ( y=0; y<image.height; y++ ) {
+ float val;
+ val = image.data[x+image.width*y];
+ data_for_measurement[x+image.width*y] = val;
+ }
+ }
+
+ }
+
+ /* Perform 'fine' peak search */
+ search_peaks(&image);
+ if ( image_feature_count(image.features) < 5 ) goto done;
+
+ if ( config_dumpfound ) dump_peaks(&image);
+
+ /* Not indexing nor writing xfel.drx?
+ * Then there's nothing left to do. */
+ if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
+ goto done;
+ }
+
+ /* Calculate orientation matrix (by magic) */
+ if ( config_writedrx || (indm != INDEXING_NONE) ) {
+ index_pattern(&image, cell, indm, config_nomatch,
+ config_verbose);
+ }
+
+ /* No cell at this point? Then we're done. */
+ if ( image.indexed_cell == NULL ) goto done;
+
+ simage = get_simage(&image, config_alternate);
+
+ /* Measure intensities if requested */
+ if ( config_nearbragg ) {
+ /* Use original data (temporarily) */
+ simage->data = data_for_measurement;
+ output_intensities(simage, image.indexed_cell);
+ simage->data = NULL;
+ }
+
+ /* Simulate if requested */
+ if ( config_simulate ) {
+ if ( config_gpu ) {
+ simulate_and_write(simage, &gctx, intensities,
+ counts, cell);
+ } else {
+ simulate_and_write(simage, NULL, intensities,
+ counts, cell);
+ }
+ }
+
+ /* Finished with alternate image */
+ if ( simage->twotheta != NULL ) free(simage->twotheta);
+ if ( simage->data != NULL ) free(simage->data);
+ free(simage);
+
+ /* Only free cell if found */
+ free(image.indexed_cell);
+
+done:
+ free(image.data);
+ free(image.det.panels);
+ image_feature_list_free(image.features);
+ free(data_for_measurement);
+ hdfile_close(hdfile);
+ H5close();
+
+ if ( image.indexed_cell == NULL ) return 0;
+ return 1;
+}
+
+
int main(int argc, char *argv[])
{
int c;
@@ -192,7 +313,6 @@ int main(int argc, char *argv[])
int config_alternate = 0;
IndexingMethod indm;
char *indm_str = NULL;
- struct image image;
UnitCell *cell;
double *intensities = NULL;
char *intfile = NULL;
@@ -326,123 +446,22 @@ int main(int argc, char *argv[])
do {
char line[1024];
- struct hdfile *hdfile;
- struct image *simage;
- float *data_for_measurement;
- size_t data_size;
char prefixed[1024];
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
-
- image.features = NULL;
- image.data = NULL;
- image.indexed_cell = NULL;
-
- #include "geometry-lcls.tmp"
-
snprintf(prefixed, 1023, "%s%s", prefix, line);
- STATUS("Processing '%s'\n", prefixed);
-
n_images++;
- hdfile = hdfile_open(prefixed);
- if ( hdfile == NULL ) {
- continue;
- } else if ( hdfile_set_first_image(hdfile, "/") ) {
- ERROR("Couldn't select path\n");
- continue;
- }
-
- hdf5_read(hdfile, &image);
-
- if ( config_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 ( config_noisefilter ) {
- filter_noise(&image, data_for_measurement);
- } else {
-
- int x, y;
-
- for ( x=0; x<image.width; x++ ) {
- for ( y=0; y<image.height; y++ ) {
- float val;
- val = image.data[x+image.width*y];
- data_for_measurement[x+image.width*y] = val;
- }
- }
-
- }
-
- /* Perform 'fine' peak search */
- search_peaks(&image);
-
- if ( image_feature_count(image.features) < 5 ) goto done;
-
- if ( config_dumpfound ) dump_peaks(&image);
-
- /* Not indexing nor writing xfel.drx?
- * Then there's nothing left to do. */
- if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
- goto done;
- }
-
- /* Calculate orientation matrix (by magic) */
- if ( config_writedrx || (indm != INDEXING_NONE) ) {
- index_pattern(&image, cell, indm, config_nomatch,
- config_verbose);
- }
-
- /* No cell at this point? Then we're done. */
- if ( image.indexed_cell == NULL ) goto done;
-
- n_hits++;
-
- simage = get_simage(&image, config_alternate);
-
- /* Measure intensities if requested */
- if ( config_nearbragg ) {
- /* Use original data (temporarily) */
- simage->data = data_for_measurement;
- output_intensities(simage, image.indexed_cell);
- simage->data = NULL;
- }
-
- /* Simulate if requested */
- if ( config_simulate ) {
- if ( config_gpu ) {
- simulate_and_write(simage, &gctx, intensities,
- counts, cell);
- } else {
- simulate_and_write(simage, NULL, intensities,
- counts, cell);
- }
- }
-
- /* Finished with alternate image */
- if ( simage->twotheta != NULL ) free(simage->twotheta);
- if ( simage->data != NULL ) free(simage->data);
- free(simage);
-
- /* Only free cell if found */
- free(image.indexed_cell);
-
-done:
- free(image.data);
- free(image.det.panels);
- image_feature_list_free(image.features);
- free(data_for_measurement);
- hdfile_close(hdfile);
- H5close();
+ n_hits += process_pattern(line, cell, config_cmfilter,
+ config_noisefilter,
+ config_writedrx, config_dumpfound,
+ config_verbose, config_alternate,
+ config_nearbragg, config_gpu,
+ config_simulate, config_nomatch, indm,
+ intensities, counts, gctx);
} while ( rval != NULL );
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-18 02:42:28 +0000