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-rw-r--r--src/im-sandbox.c129
1 files changed, 77 insertions, 52 deletions
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index c8cceb2b..825f2d6a 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -73,14 +73,27 @@
#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 sandbox
{
pthread_mutex_t lock;
- int n_indexable;
int n_processed;
- int n_indexable_last_stats;
+ int n_hadcrystals;
+ int n_crystals;
int n_processed_last_stats;
+ int n_hadcrystals_last_stats;
+ int n_crystals_last_stats;
int t_last_stats;
struct index_args *iargs;
@@ -164,31 +177,29 @@ static char *get_pattern(FILE *fh, char **use_this_one_instead,
static void process_image(const struct index_args *iargs,
- struct pattern_args *pargs, FILE *ofh,
+ struct pattern_args *pargs, Stream *st,
int cookie)
{
float *data_for_measurement;
size_t data_size;
- UnitCell *cell = iargs->cell;
int config_cmfilter = iargs->config_cmfilter;
int config_noisefilter = iargs->config_noisefilter;
- int config_verbose = iargs->config_verbose;
IndexingMethod *indm = iargs->indm;
int check;
struct hdfile *hdfile;
struct image image;
+ int i;
image.features = NULL;
image.data = NULL;
image.flags = NULL;
- image.indexed_cell = NULL;
image.copyme = iargs->copyme;
- image.reflections = NULL;
- image.n_saturated = 0;
image.id = cookie;
image.filename = pargs->filename;
image.beam = iargs->beam;
image.det = iargs->det;
+ image.crystals = NULL;
+ image.n_crystals = 0;
hdfile = hdfile_open(image.filename);
if ( hdfile == NULL ) return;
@@ -291,28 +302,34 @@ static void process_image(const struct index_args *iargs,
free(image.data);
image.data = data_for_measurement;
- /* Calculate orientation matrix (by magic) */
+ /* Index the pattern */
+ index_pattern(&image, indm, iargs->ipriv);
+
+ /* Default beam parameters */
image.div = image.beam->divergence;
image.bw = image.beam->bandwidth;
- image.profile_radius = image.beam->profile_radius;
- index_pattern(&image, cell, indm, iargs->cellr,
- config_verbose, iargs->ipriv,
- iargs->config_insane, iargs->tols);
+ /* Integrate each crystal's diffraction spots */
+ for ( i=0; i<image.n_crystals; i++ ) {
- if ( image.indexed_cell != NULL ) {
+ RefList *reflections;
- pargs->indexable = 1;
+ /* Set default crystal parameter(s) */
+ crystal_set_profile_radius(image.crystals[i],
+ image.beam->profile_radius);
if ( iargs->integrate_found ) {
- image.reflections = select_intersections(&image,
- image.indexed_cell);
+ reflections = select_intersections(&image,
+ image.crystals[i]);
} else {
- image.reflections = find_intersections(&image,
- image.indexed_cell);
+ reflections = find_intersections(&image,
+ image.crystals[i]);
}
- if (image.reflections != NULL) {
+ crystal_set_reflections(image.crystals[i], reflections);
+
+ if ( reflections != NULL ) {
+
integrate_reflections(&image,
iargs->config_closer,
iargs->config_bgsub,
@@ -323,18 +340,15 @@ static void process_image(const struct index_args *iargs,
iargs->integrate_saturated);
}
- } else {
- image.reflections = NULL;
}
- write_chunk(ofh, &image, hdfile, iargs->stream_flags);
- fprintf(ofh, "END\n");
- fflush(ofh);
+ write_chunk(st, &image, hdfile, iargs->include_peaks,
+ iargs->include_reflections);
- /* Only free cell if found */
- cell_free(image.indexed_cell);
+ for ( i=0; i<image.n_crystals; i++ ) {
+ crystal_free(image.crystals[i]);
+ }
- reflist_free(image.reflections);
free(image.data);
if ( image.flags != NULL ) free(image.flags);
image_feature_list_free(image.features);
@@ -343,7 +357,7 @@ static void process_image(const struct index_args *iargs,
static void run_work(const struct index_args *iargs,
- int filename_pipe, int results_pipe, FILE *ofh,
+ int filename_pipe, int results_pipe, Stream *st,
int cookie)
{
int allDone = 0;
@@ -389,12 +403,12 @@ static void run_work(const struct index_args *iargs,
} else {
pargs.filename = line;
- pargs.indexable = 0;
+ pargs.n_crystals = 0;
- process_image(iargs, &pargs, ofh, cookie);
+ process_image(iargs, &pargs, st, cookie);
/* Request another image */
- c = sprintf(buf, "%i\n", pargs.indexable);
+ c = sprintf(buf, "%i\n", pargs.n_crystals);
w = write(results_pipe, buf, c);
if ( w < 0 ) {
ERROR("write P0\n");
@@ -406,7 +420,7 @@ static void run_work(const struct index_args *iargs,
}
- cleanup_indexing(iargs->ipriv);
+ cleanup_indexing(iargs->indm, iargs->ipriv);
free(iargs->indm);
free(iargs->ipriv);
free_detector_geometry(iargs->det);
@@ -577,7 +591,7 @@ static void start_worker_process(struct sandbox *sb, int slot)
if ( p == 0 ) {
- FILE *sfh;
+ Stream *st;
int j;
struct sigaction sa;
int r;
@@ -614,10 +628,10 @@ static void start_worker_process(struct sandbox *sb, int slot)
close(filename_pipe[1]);
close(result_pipe[0]);
- sfh = fdopen(sb->stream_pipe_write[slot], "w");
+ st = open_stream_fd_for_write(sb->stream_pipe_write[slot]);
run_work(sb->iargs, filename_pipe[0], result_pipe[1],
- sfh, slot);
- fclose(sfh);
+ st, slot);
+ close_stream(st);
//close(filename_pipe[0]);
close(result_pipe[1]);
@@ -697,7 +711,7 @@ static void handle_zombie(struct sandbox *sb)
void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
int config_basename, FILE *fh, char *use_this_one_instead,
- FILE *ofh)
+ Stream *st)
{
int i;
int allDone;
@@ -712,13 +726,14 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
return;
}
- sb->n_indexable = 0;
sb->n_processed = 0;
- sb->n_indexable_last_stats = 0;
+ sb->n_hadcrystals = 0;
+ sb->n_crystals = 0;
sb->n_processed_last_stats = 0;
+ sb->n_hadcrystals_last_stats = 0;
+ sb->n_crystals_last_stats = 0;
sb->t_last_stats = get_monotonic_seconds();
sb->n_proc = n_proc;
- sb->ofh = ofh;
sb->iargs = iargs;
pthread_mutex_init(&sb->lock, NULL);
@@ -895,8 +910,14 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
ERROR("Invalid result '%s'\n", results);
}
} else {
- sb->n_indexable += atoi(results);
+
+ int nc = atoi(results);
+ sb->n_crystals += nc;
+ if ( nc > 0 ) {
+ sb->n_hadcrystals++;
+ }
sb->n_processed++;
+
}
/* Send next filename */
@@ -929,14 +950,19 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
tNow = get_monotonic_seconds();
if ( tNow >= sb->t_last_stats+STATS_EVERY_N_SECONDS ) {
- STATUS("%i out of %i indexed so far,"
- " %i out of %i since the last message.\n",
- sb->n_indexable, sb->n_processed,
- sb->n_indexable - sb->n_indexable_last_stats,
- sb->n_processed - sb->n_processed_last_stats);
+ STATUS("Total so far: %i images processed, "
+ "%i had crystals, %i crystals overall. "
+ "Since the last message: %i images processed,"
+ "%i had crystals, %i crystals overall.\n",
+ sb->n_processed, sb->n_hadcrystals,
+ sb->n_crystals,
+ sb->n_processed - sb->n_processed_last_stats,
+ sb->n_hadcrystals - sb->n_hadcrystals_last_stats,
+ sb->n_crystals - sb->n_crystals_last_stats);
- sb->n_indexable_last_stats = sb->n_indexable;
sb->n_processed_last_stats = sb->n_processed;
+ sb->n_hadcrystals_last_stats = sb->n_hadcrystals;
+ sb->n_crystals_last_stats = sb->n_crystals;
sb->t_last_stats = tNow;
}
@@ -975,9 +1001,8 @@ void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
free(sb->pids);
free(sb->running);
- if ( ofh != stdout ) fclose(ofh);
-
- STATUS("There were %i images, of which %i could be indexed.\n",
- sb->n_processed, sb->n_indexable);
+ STATUS("Final:"
+ " %i images processed, %i had crystals, %i crystals overall.\n",
+ sb->n_processed, sb->n_hadcrystals, sb->n_crystals);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-30 13:41:40 +0000