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-rw-r--r--src/im-sandbox.c956
-rw-r--r--src/im-sandbox.h86
-rw-r--r--src/indexamajig.c540
-rw-r--r--src/partial_sim.c4
4 files changed, 1098 insertions, 488 deletions
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
new file mode 100644
index 00000000..b2f14bbb
--- /dev/null
+++ b/src/im-sandbox.c
@@ -0,0 +1,956 @@
+/*
+ * im-sandbox.c
+ *
+ * Sandbox for indexing
+ *
+ * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ * Copyright © 2012 Richard Kirian
+ * Copyright © 2012 Lorenzo Galli
+ *
+ * Authors:
+ * 2010-2012 Thomas White <taw@physics.org>
+ * 2011 Richard Kirian
+ * 2012 Lorenzo Galli
+ * 2012 Chunhong Yoon
+ *
+ * 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 <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#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>
+#include <signal.h>
+
+#ifdef HAVE_CLOCK_GETTIME
+#include <time.h>
+#else
+#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"
+
+
+/* Write statistics at APPROXIMATELY this interval */
+#define STATS_EVERY_N_SECONDS (5)
+
+
+struct sandbox
+{
+ pthread_mutex_t lock;
+
+ int n_indexable;
+ int n_processed;
+ int n_indexable_last_stats;
+ int n_processed_last_stats;
+ int t_last_stats;
+
+ struct index_args *iargs;
+
+ int n_proc;
+ pid_t *pids;
+ FILE *ofh;
+ FILE **fhs;
+
+ int *running;
+ FILE **result_fhs;
+ int *filename_pipes;
+ int *stream_pipe_read;
+ int *stream_pipe_write;
+ char **last_filename;
+};
+
+
+/* Horrible global variable for signal handler */
+int signal_pipe[2];
+
+
+static void lock_sandbox(struct sandbox *sb)
+{
+ pthread_mutex_lock(&sb->lock);
+}
+
+
+static void unlock_sandbox(struct sandbox *sb)
+{
+ pthread_mutex_unlock(&sb->lock);
+}
+
+
+static char *get_pattern(FILE *fh, char **use_this_one_instead,
+ int config_basename, const char *prefix)
+{
+ char *line;
+ char *filename;
+
+ do {
+
+ /* Get the next filename */
+ if ( *use_this_one_instead != NULL ) {
+
+ line = *use_this_one_instead;
+ *use_this_one_instead = NULL;
+
+ } else {
+
+ char *rval;
+
+ line = malloc(1024*sizeof(char));
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) {
+ free(line);
+ return NULL;
+ }
+
+ }
+
+ chomp(line);
+
+ } while ( strlen(line) == 0 );
+
+ if ( config_basename ) {
+ char *tmp;
+ tmp = safe_basename(line);
+ free(line);
+ line = tmp;
+ }
+
+ filename = malloc(strlen(prefix)+strlen(line)+1);
+
+ snprintf(filename, 1023, "%s%s", prefix, line);
+
+ free(line);
+
+ return filename;
+}
+
+
+static void process_image(const struct index_args *iargs,
+ struct pattern_args *pargs, FILE *ofh,
+ 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;
+ struct beam_params *beam = iargs->beam;
+ int r, check;
+ struct hdfile *hdfile;
+ struct image image;
+
+ image.features = NULL;
+ image.data = NULL;
+ image.flags = NULL;
+ image.indexed_cell = NULL;
+ image.det = copy_geom(iargs->det);
+ image.copyme = iargs->copyme;
+ image.reflections = NULL;
+ image.id = cookie;
+ image.filename = pargs->filename;
+ image.beam = beam;
+
+ hdfile = hdfile_open(image.filename);
+ if ( hdfile == NULL ) return;
+
+ 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);
+ free_detector_geometry(image.det);
+ return;
+ }
+
+ if ( image.lambda < 0.0 ) {
+ if ( beam != NULL ) {
+ ERROR("Using nominal photon energy of %.2f eV\n",
+ beam->photon_energy);
+ image.lambda = ph_en_to_lambda(
+ eV_to_J(beam->photon_energy));
+ } else {
+ ERROR("No wavelength in file, so you need to give "
+ "a beam parameters file with -b.\n");
+ hdfile_close(hdfile);
+ free_detector_geometry(image.det);
+ return;
+ }
+ }
+ fill_in_values(image.det, hdfile);
+
+ 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 {
+ 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");
+ }
+ break;
+
+ case PEAK_ZAEF:
+ search_peaks(&image, iargs->threshold,
+ iargs->min_gradient, iargs->min_snr,
+ iargs->ir_inn, iargs->ir_mid, iargs->ir_out);
+ 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;
+
+ /* Calculate orientation matrix (by magic) */
+ image.div = beam->divergence;
+ image.bw = beam->bandwidth;
+ image.profile_radius = 0.0001e9;
+
+ index_pattern(&image, cell, indm, iargs->cellr,
+ config_verbose, iargs->ipriv,
+ iargs->config_insane, iargs->tols);
+
+ if ( image.indexed_cell != NULL ) {
+ pargs->indexable = 1;
+ image.reflections = find_intersections(&image,
+ image.indexed_cell);
+ if (image.reflections != NULL) {
+ integrate_reflections(&image,
+ iargs->config_closer,
+ iargs->config_bgsub,
+ iargs->min_int_snr,
+ iargs->ir_inn,
+ iargs->ir_mid,
+ iargs->ir_out);
+ }
+ } else {
+ image.reflections = NULL;
+ }
+
+ write_chunk(ofh, &image, hdfile, iargs->stream_flags);
+ fprintf(ofh, "END\n");
+ fflush(ofh);
+
+ /* Only free cell if found */
+ cell_free(image.indexed_cell);
+
+ reflist_free(image.reflections);
+ free(image.data);
+ if ( image.flags != NULL ) free(image.flags);
+ image_feature_list_free(image.features);
+ hdfile_close(hdfile);
+ free_detector_geometry(image.det);
+}
+
+
+static void run_work(const struct index_args *iargs,
+ int filename_pipe, int results_pipe, FILE *ofh,
+ int cookie)
+{
+ int allDone = 0;
+ FILE *fh;
+ int w;
+
+ fh = fdopen(filename_pipe, "r");
+ if ( fh == NULL ) {
+ ERROR("Failed to fdopen() the filename pipe!\n");
+ return;
+ }
+
+ w = write(results_pipe, "\n", 1);
+ if ( w < 0 ) {
+ ERROR("Failed to send request for first filename.\n");
+ }
+
+ while ( !allDone ) {
+
+ struct pattern_args pargs;
+ int c;
+ char *line;
+ char *rval;
+ char buf[1024];
+
+ line = malloc(1024*sizeof(char));
+ rval = fgets(line, 1023, fh);
+ if ( rval == NULL ) {
+
+ ERROR("Read error!\n");
+ free(line);
+ allDone = 1;
+ continue;
+
+ }
+
+ chomp(line);
+
+ if ( strlen(line) == 0 ) {
+
+ allDone = 1;
+
+ } else {
+
+ pargs.filename = line;
+ pargs.indexable = 0;
+
+ process_image(iargs, &pargs, ofh, cookie);
+
+ /* Request another image */
+ c = sprintf(buf, "%i\n", pargs.indexable);
+ w = write(results_pipe, buf, c);
+ if ( w < 0 ) {
+ ERROR("write P0\n");
+ }
+
+ }
+
+ free(line);
+
+ }
+
+ cleanup_indexing(iargs->ipriv);
+ free(iargs->indm);
+ free(iargs->ipriv);
+ free_detector_geometry(iargs->det);
+ free(iargs->beam);
+ free(iargs->element);
+ free(iargs->hdf5_peak_path);
+ free_copy_hdf5_field_list(iargs->copyme);
+ cell_free(iargs->cell);
+ fclose(fh);
+}
+
+
+#ifdef HAVE_CLOCK_GETTIME
+
+static time_t get_monotonic_seconds()
+{
+ struct timespec tp;
+ clock_gettime(CLOCK_MONOTONIC, &tp);
+ return tp.tv_sec;
+}
+
+#else
+
+/* Fallback version of the above. The time according to gettimeofday() is not
+ * monotonic, so measuring intervals based on it will screw up if there's a
+ * timezone change (e.g. daylight savings) while the program is running. */
+static time_t get_monotonic_seconds()
+{
+ struct timeval tp;
+ gettimeofday(&tp, NULL);
+ return tp.tv_sec;
+}
+
+#endif
+
+static int pump_chunk(FILE *fh, FILE *ofh)
+{
+ int chunk_started = 0;
+ int chunk_finished = 0;
+
+ do {
+
+ char line[1024];
+ char *rval;
+
+ rval = fgets(line, 1024, fh);
+ if ( rval == NULL ) {
+
+ if ( feof(fh) ) {
+ /* Process died */
+ if ( chunk_started ) {
+ ERROR("EOF during chunk!\n");
+ fprintf(ofh, "Chunk is unfinished!\n");
+ }
+ return 1;
+ } else {
+ ERROR("fgets() failed: %s\n", strerror(errno));
+ }
+ chunk_finished = 1;
+ continue;
+
+ }
+
+ if ( strcmp(line, "END\n") == 0 ) {
+ chunk_finished = 1;
+ } else {
+ chunk_started = 1;
+ fprintf(ofh, "%s", line);
+ }
+
+ } while ( !chunk_finished );
+
+ return 0;
+}
+
+
+static void *run_reader(void *sbv)
+{
+ struct sandbox *sb = sbv;
+ int done = 0;
+
+ while ( !done ) {
+
+ int r, i;
+ struct timeval tv;
+ fd_set fds;
+ int fdmax;
+
+ tv.tv_sec = 5;
+ tv.tv_usec = 0;
+
+ FD_ZERO(&fds);
+ fdmax = 0;
+ lock_sandbox(sb);
+ for ( i=0; i<sb->n_proc; i++ ) {
+
+ int fd;
+
+ if ( !sb->running[i] ) continue;
+
+ fd = sb->stream_pipe_read[i];
+
+ FD_SET(fd, &fds);
+ if ( fd > fdmax ) fdmax = fd;
+
+ }
+
+ unlock_sandbox(sb);
+
+ r = select(fdmax+1, &fds, NULL, NULL, &tv);
+
+ if ( r == -1 ) {
+ if ( errno != EINTR ) {
+ ERROR("select() failed: %s\n", strerror(errno));
+ } /* Otherwise no big deal */
+ continue;
+ }
+
+ if ( r == 0 ) continue; /* Nothing this time. Try again */
+
+ lock_sandbox(sb);
+ for ( i=0; i<sb->n_proc; i++ ) {
+
+ if ( !sb->running[i] ) continue;
+
+ if ( !FD_ISSET(sb->stream_pipe_read[i], &fds) ) continue;
+
+ if ( pump_chunk(sb->fhs[i], sb->ofh) ) {
+ sb->running[i] = 0;
+ }
+
+ }
+
+ done = 1;
+ for ( i=0; i<sb->n_proc; i++ ) {
+ if ( sb->running[i] ) done = 0;
+ }
+ unlock_sandbox(sb);
+
+ }
+
+ return NULL;
+}
+
+
+static void start_worker_process(struct sandbox *sb, int slot)
+{
+ pid_t p;
+ int filename_pipe[2];
+ int result_pipe[2];
+
+ if ( pipe(filename_pipe) == - 1 ) {
+ ERROR("pipe() failed!\n");
+ return;
+ }
+
+ if ( pipe(result_pipe) == - 1 ) {
+ ERROR("pipe() failed!\n");
+ return;
+ }
+
+ p = fork();
+ if ( p == -1 ) {
+ ERROR("fork() failed!\n");
+ return;
+ }
+
+ if ( p == 0 ) {
+
+ FILE *sfh;
+ int j;
+ struct sigaction sa;
+ int r;
+
+ /* First, disconnect the signal handler */
+ sa.sa_flags = 0;
+ sigemptyset(&sa.sa_mask);
+ sa.sa_handler = SIG_DFL;
+ r = sigaction(SIGCHLD, &sa, NULL);
+ if ( r == -1 ) {
+ ERROR("Failed to set signal handler!\n");
+ return;
+ }
+
+ /* Free resources which will not be needed by worker */
+ for ( j=0; j<sb->n_proc; j++ ) {
+ if ( (j != slot) && (sb->running[j]) ) {
+ close(sb->stream_pipe_write[j]);
+ }
+ }
+ for ( j=0; j<sb->n_proc; j++ ) {
+ if ( (j != slot) && (sb->running[j]) ) {
+ fclose(sb->result_fhs[j]);
+ close(sb->filename_pipes[j]);
+ }
+ }
+ free(sb->filename_pipes);
+ free(sb->result_fhs);
+ free(sb->pids);
+ /* Also prefix, use_this_one_instead and fh */
+
+ /* Child process gets the 'read' end of the filename
+ * pipe, and the 'write' end of the result pipe. */
+ close(filename_pipe[1]);
+ close(result_pipe[0]);
+
+ sfh = fdopen(sb->stream_pipe_write[slot], "w");
+ run_work(sb->iargs, filename_pipe[0], result_pipe[1],
+ sfh, slot);
+ fclose(sfh);
+
+ //close(filename_pipe[0]);
+ close(result_pipe[1]);
+
+ exit(0);
+
+ }
+
+ /* Parent process gets the 'write' end of the filename pipe
+ * and the 'read' end of the result pipe. */
+ sb->pids[slot] = p;
+ sb->running[slot] = 1;
+ close(filename_pipe[0]);
+ close(result_pipe[1]);
+ sb->filename_pipes[slot] = filename_pipe[1];
+ sb->fhs[slot] = fdopen(sb->stream_pipe_read[slot], "r");
+ if ( sb->fhs[slot] == NULL ) {
+ ERROR("Couldn't fdopen() stream!\n");
+ return;
+ }
+
+ sb->result_fhs[slot] = fdopen(result_pipe[0], "r");
+ if ( sb->result_fhs[slot] == NULL ) {
+ ERROR("fdopen() failed.\n");
+ return;
+ }
+}
+
+
+static void signal_handler(int sig, siginfo_t *si, void *uc_v)
+{
+ write(signal_pipe[1], "\n", 1);
+}
+
+
+static void handle_zombie(struct sandbox *sb)
+{
+ int i;
+
+ lock_sandbox(sb);
+ for ( i=0; i<sb->n_proc; i++ ) {
+
+ int status, p;
+
+ if ( !sb->running[i] ) continue;
+
+ p = waitpid(sb->pids[i], &status, WNOHANG);
+
+ if ( p == -1 ) {
+ ERROR("waitpid() failed.\n");
+ continue;
+ }
+
+ if ( p == sb->pids[i] ) {
+
+ sb->running[i] = 0;
+
+ if ( WIFEXITED(status) ) {
+ STATUS("Worker %i exited normally.\n", i);
+ continue;
+ }
+
+ if ( WIFSIGNALED(status) ) {
+ STATUS("Worker %i was killed by signal %i\n",
+ i, WTERMSIG(status));
+ STATUS("Last filename was: %s\n",
+ sb->last_filename[i]);
+ start_worker_process(sb, i);
+ }
+
+ }
+
+ }
+ unlock_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)
+{
+ int i;
+ int allDone;
+ struct sigaction sa;
+ int r;
+ pthread_t reader_thread;
+ struct sandbox *sb;
+
+ sb = calloc(1, sizeof(struct sandbox));
+ if ( sb == NULL ) {
+ ERROR("Couldn't allocate memory for sandbox.\n");
+ return;
+ }
+
+ sb->n_indexable = 0;
+ sb->n_processed = 0;
+ sb->n_indexable_last_stats = 0;
+ sb->n_processed_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);
+
+ sb->stream_pipe_read = calloc(n_proc, sizeof(int));
+ sb->stream_pipe_write = calloc(n_proc, sizeof(int));
+ if ( sb->stream_pipe_read == NULL ) {
+ ERROR("Couldn't allocate memory for pipes.\n");
+ return;
+ }
+ if ( sb->stream_pipe_write == NULL ) {
+ ERROR("Couldn't allocate memory for pipes.\n");
+ return;
+ }
+
+ for ( i=0; i<n_proc; i++ ) {
+
+ int stream_pipe[2];
+
+ if ( pipe(stream_pipe) == - 1 ) {
+ ERROR("pipe() failed!\n");
+ return;
+ }
+
+ sb->stream_pipe_read[i] = stream_pipe[0];
+ sb->stream_pipe_write[i] = stream_pipe[1];
+
+ }
+
+ lock_sandbox(sb);
+ sb->filename_pipes = calloc(n_proc, sizeof(int));
+ sb->result_fhs = calloc(n_proc, sizeof(FILE *));
+ sb->pids = calloc(n_proc, sizeof(pid_t));
+ sb->running = calloc(n_proc, sizeof(int));
+ sb->fhs = calloc(sb->n_proc, sizeof(FILE *));
+ if ( sb->filename_pipes == NULL ) {
+ ERROR("Couldn't allocate memory for pipes.\n");
+ return;
+ }
+ if ( sb->result_fhs == NULL ) {
+ ERROR("Couldn't allocate memory for pipe file handles.\n");
+ return;
+ }
+ if ( sb->pids == NULL ) {
+ ERROR("Couldn't allocate memory for PIDs.\n");
+ return;
+ }
+ if ( sb->running == NULL ) {
+ ERROR("Couldn't allocate memory for process flags.\n");
+ return;
+ }
+
+ sb->last_filename = calloc(n_proc, sizeof(char *));
+ if ( sb->last_filename == NULL ) {
+ ERROR("Couldn't allocate memory for last filename list.\n");
+ return;
+ }
+ if ( sb->fhs == NULL ) {
+ ERROR("Couldn't allocate memory for file handles!\n");
+ return;
+ }
+ unlock_sandbox(sb);
+
+ if ( pthread_create(&reader_thread, NULL, run_reader, (void *)sb) ) {
+ ERROR("Failed to create reader thread.\n");
+ return;
+ }
+
+ if ( pipe(signal_pipe) == -1 ) {
+ ERROR("Failed to create signal pipe.\n");
+ return;
+ }
+
+ /* Set up signal handler to take action if any children die */
+ sa.sa_flags = SA_SIGINFO | SA_NOCLDSTOP;
+ sigemptyset(&sa.sa_mask);
+ sa.sa_sigaction = signal_handler;
+ r = sigaction(SIGCHLD, &sa, NULL);
+ if ( r == -1 ) {
+ ERROR("Failed to set signal handler!\n");
+ return;
+ }
+
+ /* Fork the right number of times */
+ lock_sandbox(sb);
+ for ( i=0; i<n_proc; i++ ) {
+ start_worker_process(sb, i);
+ }
+ unlock_sandbox(sb);
+
+ allDone = 0;
+ while ( !allDone ) {
+
+ int r, i;
+ struct timeval tv;
+ fd_set fds;
+ double tNow;
+ int fdmax;
+
+ tv.tv_sec = 1;
+ tv.tv_usec = 0;
+
+ FD_ZERO(&fds);
+ fdmax = 0;
+ lock_sandbox(sb);
+ for ( i=0; i<n_proc; i++ ) {
+
+ int fd;
+
+ if ( !sb->running[i] ) {
+ continue;
+ }
+
+ fd = fileno(sb->result_fhs[i]);
+ FD_SET(fd, &fds);
+ if ( fd > fdmax ) fdmax = fd;
+
+ }
+ unlock_sandbox(sb);
+
+ FD_SET(signal_pipe[0], &fds);
+ if ( signal_pipe[0] > fdmax ) fdmax = signal_pipe[0];
+
+ r = select(fdmax+1, &fds, NULL, NULL, &tv);
+ if ( r == -1 ) {
+ if ( errno != EINTR ) {
+ ERROR("select() failed: %s\n", strerror(errno));
+ }
+ continue;
+ }
+
+ if ( r == 0 ) continue; /* No progress this time. Try again */
+
+ if ( FD_ISSET(signal_pipe[0], &fds) ) {
+
+ char d;
+ read(signal_pipe[0], &d, 1);
+ handle_zombie(sb);
+
+ }
+
+ lock_sandbox(sb);
+ for ( i=0; i<n_proc; i++ ) {
+
+ char *nextImage;
+ char results[1024];
+ char *rval;
+ int fd;
+ int n;
+ char *eptr;
+
+ if ( !sb->running[i] ) {
+ continue;
+ }
+
+ fd = fileno(sb->result_fhs[i]);
+ if ( !FD_ISSET(fd, &fds) ) {
+ continue;
+ }
+
+ rval = fgets(results, 1024, sb->result_fhs[i]);
+ if ( rval == NULL ) {
+ if ( !feof(sb->result_fhs[i]) ) {
+ ERROR("fgets() failed: %s\n",
+ strerror(errno));
+ }
+ continue;
+ }
+
+ chomp(results);
+
+ n = strtol(results, &eptr, 10);
+ if ( eptr == results ) {
+ if ( strlen(results) > 0 ) {
+ ERROR("Invalid result '%s'\n", results);
+ }
+ } else {
+ sb->n_indexable += atoi(results);
+ sb->n_processed++;
+ }
+
+ /* Send next filename */
+ nextImage = get_pattern(fh, &use_this_one_instead,
+ config_basename, prefix);
+
+ free(sb->last_filename[i]);
+ sb->last_filename[i] = nextImage;
+
+ if ( nextImage == NULL ) {
+ /* No more images */
+ r = write(sb->filename_pipes[i], "\n", 1);
+ if ( r < 0 ) {
+ ERROR("Write pipe\n");
+ }
+ } else {
+ r = write(sb->filename_pipes[i], nextImage,
+ strlen(nextImage));
+ r -= write(sb->filename_pipes[i], "\n", 1);
+ if ( r < 0 ) {
+ ERROR("write pipe\n");
+ }
+ }
+
+ }
+ unlock_sandbox(sb);
+
+ /* Update progress */
+ lock_sandbox(sb);
+ 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);
+
+ sb->n_indexable_last_stats = sb->n_indexable;
+ sb->n_processed_last_stats = sb->n_processed;
+ sb->t_last_stats = tNow;
+
+ }
+ unlock_sandbox(sb);
+
+ allDone = 1;
+ lock_sandbox(sb);
+ for ( i=0; i<n_proc; i++ ) {
+ if ( sb->running[i] ) allDone = 0;
+ }
+
+ unlock_sandbox(sb);
+
+ }
+
+ fclose(fh);
+
+ pthread_mutex_destroy(&sb->lock);
+
+ for ( i=0; i<n_proc; i++ ) {
+ int status;
+ waitpid(sb->pids[i], &status, 0);
+ }
+
+ for ( i=0; i<n_proc; i++ ) {
+ close(sb->filename_pipes[i]);
+ fclose(sb->result_fhs[i]);
+ }
+
+ for ( i=0; i<sb->n_proc; i++ ) {
+ fclose(sb->fhs[i]);
+ }
+ free(sb->fhs);
+ free(sb->filename_pipes);
+ free(sb->result_fhs);
+ 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);
+
+}
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
new file mode 100644
index 00000000..8ad9fd90
--- /dev/null
+++ b/src/im-sandbox.h
@@ -0,0 +1,86 @@
+/*
+ * im-sandbox.h
+ *
+ * Sandbox for indexing
+ *
+ * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ * Copyright © 2012 Richard Kirian
+ * Copyright © 2012 Lorenzo Galli
+ *
+ * Authors:
+ * 2010-2012 Thomas White <taw@physics.org>
+ * 2011 Richard Kirian
+ * 2012 Lorenzo Galli
+ * 2012 Chunhong Yoon
+ *
+ * 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/>.
+ *
+ */
+
+enum {
+ PEAK_ZAEF,
+ PEAK_HDF5,
+};
+
+
+/* Information about the indexing process which is common to all patterns */
+struct index_args
+{
+ UnitCell *cell;
+ int config_cmfilter;
+ int config_noisefilter;
+ int config_verbose;
+ int stream_flags; /* What goes into the output? */
+ int config_satcorr;
+ int config_closer;
+ int config_insane;
+ int config_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 */
+ int cellr;
+ float tols[4];
+ struct beam_params *beam;
+ char *element;
+ char *hdf5_peak_path;
+ double ir_inn;
+ double ir_mid;
+ double ir_out;
+ struct copy_hdf5_field *copyme;
+};
+
+
+
+
+/* Information about the indexing process for one pattern */
+struct pattern_args
+{
+ /* "Input" */
+ char *filename;
+
+ /* "Output" */
+ int indexable;
+};
+
+extern void create_sandbox(struct index_args *iargs, int n_proc, char *prefix,
+ int config_basename, FILE *fh,
+ char *use_this_one_instead, FILE *ofh);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 1ff392e9..294bce1d 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -12,6 +12,7 @@
* 2010-2012 Thomas White <taw@physics.org>
* 2011 Richard Kirian
* 2012 Lorenzo Galli
+ * 2012 Chunhong Yoon
*
* This file is part of CrystFEL.
*
@@ -43,7 +44,6 @@
#include <getopt.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
-#include <pthread.h>
#ifdef HAVE_CLOCK_GETTIME
#include <time.h>
@@ -63,81 +63,7 @@
#include "stream.h"
#include "reflist-utils.h"
-
-/* Write statistics at APPROXIMATELY this interval */
-#define STATS_EVERY_N_SECONDS (5)
-
-
-enum {
- PEAK_ZAEF,
- PEAK_HDF5,
-};
-
-
-/* Information about the indexing process which is common to all patterns */
-struct static_index_args
-{
- UnitCell *cell;
- int config_cmfilter;
- int config_noisefilter;
- int config_verbose;
- int stream_flags; /* What goes into the output? */
- int config_satcorr;
- int config_closer;
- int config_insane;
- int config_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 */
- int cellr;
- float tols[4];
- struct beam_params *beam;
- const char *element;
- const char *hdf5_peak_path;
- double ir_inn;
- double ir_mid;
- double ir_out;
-
- /* Output stream */
- pthread_mutex_t *output_mutex; /* Protects the output stream */
- FILE *ofh;
- const struct copy_hdf5_field *copyme;
-};
-
-
-/* Information about the indexing process for one pattern */
-struct index_args
-{
- /* "Input" */
- char *filename;
- struct static_index_args static_args;
-
- /* "Output" */
- int indexable;
-};
-
-
-/* Information needed to choose the next task and dispatch it */
-struct queue_args
-{
- FILE *fh;
- char *prefix;
- int config_basename;
- struct static_index_args static_args;
-
- char *use_this_one_instead;
-
- int n_indexable;
- int n_processed;
- int n_indexable_last_stats;
- int n_processed_last_stats;
- int t_last_stats;
-};
+#include "im-sandbox.h"
static void show_help(const char *s)
@@ -234,294 +160,10 @@ static void show_help(const char *s)
" least 10%% of the located peaks.\n"
" --no-bg-sub Don't subtract local background estimates from\n"
" integrated intensities.\n"
-"\n"
-"\nYou can tune the CPU affinities for enhanced performance on NUMA machines:\n"
-"\n"
-" --cpus=<n> Specify number of CPUs. This is NOT the same as\n"
-" giving the number of analyses to run in parallel.\n"
-" --cpugroup=<n> Batch threads in groups of this size.\n"
-" --cpuoffset=<n> Start using CPUs at this group number.\n"
);
}
-static void process_image(void *pp, int cookie)
-{
- struct index_args *pargs = pp;
- struct hdfile *hdfile;
- struct image image;
- float *data_for_measurement;
- size_t data_size;
- char *filename = pargs->filename;
- UnitCell *cell = pargs->static_args.cell;
- int config_cmfilter = pargs->static_args.config_cmfilter;
- int config_noisefilter = pargs->static_args.config_noisefilter;
- int config_verbose = pargs->static_args.config_verbose;
- IndexingMethod *indm = pargs->static_args.indm;
- struct beam_params *beam = pargs->static_args.beam;
-
- image.features = NULL;
- image.data = NULL;
- image.flags = NULL;
- image.indexed_cell = NULL;
- image.reflections = NULL;
- image.id = cookie;
- image.filename = filename;
- image.det = copy_geom(pargs->static_args.det);
- image.copyme = pargs->static_args.copyme;
- image.beam = beam;
-
- pargs->indexable = 0;
-
- hdfile = hdfile_open(filename);
- if ( hdfile == NULL ) return;
-
- if ( pargs->static_args.element != NULL ) {
-
- int r;
- r = hdfile_set_image(hdfile, pargs->static_args.element);
- if ( r ) {
- ERROR("Couldn't select path '%s'\n",
- pargs->static_args.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;
- }
-
- }
-
- hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
-
- 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);
- free_detector_geometry(image.det);
- return;
- }
-
- if ( image.lambda < 0.0 ) {
- if ( beam != NULL ) {
- ERROR("Using nominal photon energy of %.2f eV\n",
- beam->photon_energy);
- image.lambda = ph_en_to_lambda(
- eV_to_J(beam->photon_energy));
- } else {
- ERROR("No wavelength in file, so you need to give "
- "a beam parameters file with -b.\n");
- hdfile_close(hdfile);
- free_detector_geometry(image.det);
- return;
- }
- }
- fill_in_values(image.det, hdfile);
-
- 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 {
- memcpy(data_for_measurement, image.data, data_size);
- }
-
- switch ( pargs->static_args.peaks )
- {
- case PEAK_HDF5 :
- /* Get peaks from HDF5 */
- if ( get_peaks(&image, hdfile,
- pargs->static_args.hdf5_peak_path) )
- {
- ERROR("Failed to get peaks from HDF5 file.\n");
- }
- break;
-
- case PEAK_ZAEF :
- search_peaks(&image, pargs->static_args.threshold,
- pargs->static_args.min_gradient,
- pargs->static_args.min_snr,
- pargs->static_args.ir_inn,
- pargs->static_args.ir_mid,
- pargs->static_args.ir_out);
- 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;
-
- /* Calculate orientation matrix (by magic) */
- image.div = beam->divergence;
- image.bw = beam->bandwidth;
- image.profile_radius = 0.0001e9;
- index_pattern(&image, cell, indm, pargs->static_args.cellr,
- config_verbose, pargs->static_args.ipriv,
- pargs->static_args.config_insane,
- pargs->static_args.tols);
-
- if ( image.indexed_cell != NULL ) {
-
- pargs->indexable = 1;
-
- image.reflections = find_intersections(&image,
- image.indexed_cell);
-
- if ( image.reflections != NULL ) {
-
- integrate_reflections(&image,
- pargs->static_args.config_closer,
- pargs->static_args.config_bgsub,
- pargs->static_args.min_int_snr,
- pargs->static_args.ir_inn,
- pargs->static_args.ir_mid,
- pargs->static_args.ir_out);
-
- }
-
- } else {
-
- image.reflections = NULL;
-
- }
-
- pthread_mutex_lock(pargs->static_args.output_mutex);
- write_chunk(pargs->static_args.ofh, &image, hdfile,
- pargs->static_args.stream_flags);
- pthread_mutex_unlock(pargs->static_args.output_mutex);
-
- /* Only free cell if found */
- cell_free(image.indexed_cell);
-
- reflist_free(image.reflections);
- free(image.data);
- if ( image.flags != NULL ) free(image.flags);
- image_feature_list_free(image.features);
- hdfile_close(hdfile);
- free_detector_geometry(image.det);
-}
-
-
-static void *get_image(void *qp)
-{
- char *line;
- struct index_args *pargs;
- char *rval;
- struct queue_args *qargs = qp;
-
- /* Initialise new task arguments */
- pargs = malloc(sizeof(struct index_args));
- memcpy(&pargs->static_args, &qargs->static_args,
- sizeof(struct static_index_args));
-
- /* Get the next filename */
- if ( qargs->use_this_one_instead != NULL ) {
-
- line = qargs->use_this_one_instead;
- qargs->use_this_one_instead = NULL;
-
- } else {
-
- line = malloc(1024*sizeof(char));
- rval = fgets(line, 1023, qargs->fh);
- if ( rval == NULL ) {
- free(pargs);
- free(line);
- return NULL;
- }
- chomp(line);
-
- }
-
- if ( qargs->config_basename ) {
- char *tmp;
- tmp = safe_basename(line);
- free(line);
- line = tmp;
- }
-
- pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
-
- snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);
-
- free(line);
-
- return pargs;
-}
-
-
-#ifdef HAVE_CLOCK_GETTIME
-
-static time_t get_monotonic_seconds()
-{
- struct timespec tp;
- clock_gettime(CLOCK_MONOTONIC, &tp);
- return tp.tv_sec;
-}
-
-#else
-
-/* Fallback version of the above. The time according to gettimeofday() is not
- * monotonic, so measuring intervals based on it will screw up if there's a
- * timezone change (e.g. daylight savings) while the program is running. */
-static time_t get_monotonic_seconds()
-{
- struct timeval tp;
- gettimeofday(&tp, NULL);
- return tp.tv_sec;
-}
-
-#endif
-
-static void finalise_image(void *qp, void *pp)
-{
- struct queue_args *qargs = qp;
- struct index_args *pargs = pp;
- time_t monotonic_seconds;
-
- qargs->n_indexable += pargs->indexable;
- qargs->n_processed++;
-
- monotonic_seconds = get_monotonic_seconds();
- if ( monotonic_seconds >= qargs->t_last_stats+STATS_EVERY_N_SECONDS ) {
-
- STATUS("%i out of %i indexed so far,"
- " %i out of %i since the last message.\n",
- qargs->n_indexable, qargs->n_processed,
- qargs->n_indexable - qargs->n_indexable_last_stats,
- qargs->n_processed - qargs->n_processed_last_stats);
-
- qargs->n_processed_last_stats = qargs->n_processed;
- qargs->n_indexable_last_stats = qargs->n_indexable;
- qargs->t_last_stats = monotonic_seconds;
-
- }
-
- free(pargs->filename);
- free(pargs);
-}
-
-
static int parse_cell_reduction(const char *scellr, int *err,
int *reduction_needs_cell)
{
@@ -554,7 +196,6 @@ int main(int argc, char *argv[])
FILE *fh;
FILE *ofh;
char *rval = NULL;
- int n_images;
int config_noindex = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
@@ -585,19 +226,15 @@ int main(int argc, char *argv[])
float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
int cellr;
int peaks;
- int nthreads = 1;
- pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
+ int n_proc = 1;
char *prepare_line;
char prepare_filename[1024];
- struct queue_args qargs;
+ char *use_this_one_instead;
+ struct index_args iargs;
struct beam_params *beam = NULL;
char *element = NULL;
double nominal_photon_energy;
int stream_flags = STREAM_INTEGRATED;
- int cpu_num = 0;
- int cpu_groupsize = 1;
- int cpu_offset = 0;
- char *endptr;
char *hdf5_peak_path = NULL;
struct copy_hdf5_field *copyme;
char *intrad = NULL;
@@ -684,7 +321,7 @@ int main(int argc, char *argv[])
break;
case 'j' :
- nthreads = atoi(optarg);
+ n_proc = atoi(optarg);
break;
case 'g' :
@@ -726,39 +363,10 @@ int main(int argc, char *argv[])
break;
case 6 :
- cpu_num = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid number of CPUs ('%s')\n",
- optarg);
- return 1;
- }
- break;
-
case 7 :
- cpu_groupsize = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid CPU group size ('%s')\n",
- optarg);
- return 1;
- }
- if ( cpu_groupsize < 1 ) {
- ERROR("CPU group size cannot be"
- " less than 1.\n");
- return 1;
- }
- break;
-
case 8 :
- cpu_offset = strtol(optarg, &endptr, 10);
- if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') ) ) {
- ERROR("Invalid CPU offset ('%s')\n",
- optarg);
- return 1;
- }
- if ( cpu_offset < 0 ) {
- ERROR("CPU offset must be positive.\n");
- return 1;
- }
+ ERROR("The options --cpus, --cpugroup and --cpuoffset"
+ " are no longer used by indexamajig.\n");
break;
case 9 :
@@ -795,12 +403,6 @@ int main(int argc, char *argv[])
}
- if ( (cpu_num > 0) && (cpu_num % cpu_groupsize != 0) ) {
- ERROR("Number of CPUs must be divisible by"
- " the CPU group size.\n");
- return 1;
- }
-
if ( filename == NULL ) {
filename = strdup("-");
}
@@ -816,18 +418,15 @@ int main(int argc, char *argv[])
free(filename);
if ( outfile == NULL ) {
- outfile = strdup("-");
- }
- if ( strcmp(outfile, "-") == 0 ) {
ofh = stdout;
} else {
ofh = fopen(outfile, "w");
+ if ( ofh == NULL ) {
+ ERROR("Failed to open output file '%s'\n", outfile);
+ return 1;
+ }
+ free(outfile);
}
- if ( ofh == NULL ) {
- ERROR("Failed to open output file '%s'\n", outfile);
- return 1;
- }
- free(outfile);
if ( hdf5_peak_path == NULL ) {
hdf5_peak_path = strdup("/processing/hitfinder/peakinfo");
@@ -860,8 +459,8 @@ int main(int argc, char *argv[])
}
}
- if ( nthreads == 0 ) {
- ERROR("Invalid number of threads.\n");
+ if ( n_proc == 0 ) {
+ ERROR("Invalid number of processes.\n");
return 1;
}
@@ -929,6 +528,7 @@ int main(int argc, char *argv[])
ERROR("Invalid parameters for '--int-radius'\n");
return 1;
}
+ free(intrad);
} else {
STATUS("WARNING: You did not specify --int-radius.\n");
STATUS("WARNING: I will use the default values, which are"
@@ -967,22 +567,20 @@ int main(int argc, char *argv[])
} else {
STATUS("No beam parameters file was given, so I'm taking the"
" nominal photon energy to be 2 keV.\n");
+ ERROR("I'm also going to assume 1 ADU per photon, which is");
+ ERROR(" almost certainly wrong. Peak sigmas will be"
+ " incorrect.\n");
nominal_photon_energy = 2000.0;
}
- if ( beam == NULL ) {
- ERROR("Warning: no beam parameters file.\n");
- ERROR("I'm going to assume 1 ADU per photon, which is almost");
- ERROR(" certainly wrong. Peak sigmas will be incorrect.\n");
- }
-
/* Get first filename and use it to set up the indexing */
- prepare_line = malloc(1024*sizeof(char));
+ prepare_line = malloc(1024);
rval = fgets(prepare_line, 1023, fh);
if ( rval == NULL ) {
ERROR("Failed to get filename to prepare indexing.\n");
return 1;
}
+ use_this_one_instead = strdup(prepare_line);
chomp(prepare_line);
if ( config_basename ) {
char *tmp;
@@ -991,7 +589,7 @@ int main(int argc, char *argv[])
prepare_line = tmp;
}
snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
- qargs.use_this_one_instead = prepare_line;
+ free(prepare_line);
/* Prepare the indexer */
if ( indm != NULL ) {
@@ -1007,67 +605,41 @@ int main(int argc, char *argv[])
gsl_set_error_handler_off();
- qargs.static_args.cell = cell;
- qargs.static_args.config_cmfilter = config_cmfilter;
- qargs.static_args.config_noisefilter = config_noisefilter;
- qargs.static_args.config_verbose = config_verbose;
- qargs.static_args.config_satcorr = config_satcorr;
- qargs.static_args.config_closer = config_closer;
- qargs.static_args.config_insane = config_insane;
- qargs.static_args.config_bgsub = config_bgsub;
- qargs.static_args.cellr = cellr;
- qargs.static_args.tols[0] = tols[0];
- qargs.static_args.tols[1] = tols[1];
- qargs.static_args.tols[2] = tols[2];
- qargs.static_args.tols[3] = tols[3];
- qargs.static_args.threshold = threshold;
- qargs.static_args.min_gradient = min_gradient;
- qargs.static_args.min_snr = min_snr;
- qargs.static_args.min_int_snr = min_int_snr;
- qargs.static_args.det = det;
- qargs.static_args.indm = indm;
- qargs.static_args.ipriv = ipriv;
- qargs.static_args.peaks = peaks;
- qargs.static_args.output_mutex = &output_mutex;
- qargs.static_args.ofh = ofh;
- qargs.static_args.beam = beam;
- qargs.static_args.element = element;
- qargs.static_args.stream_flags = stream_flags;
- qargs.static_args.hdf5_peak_path = hdf5_peak_path;
- qargs.static_args.copyme = copyme;
- qargs.static_args.ir_inn = ir_inn;
- qargs.static_args.ir_mid = ir_mid;
- qargs.static_args.ir_out = ir_out;
-
- qargs.fh = fh;
- qargs.prefix = prefix;
- qargs.config_basename = config_basename;
- qargs.n_indexable = 0;
- qargs.n_processed = 0;
- qargs.n_indexable_last_stats = 0;
- qargs.n_processed_last_stats = 0;
- qargs.t_last_stats = get_monotonic_seconds();
-
- n_images = run_threads(nthreads, process_image, get_image,
- finalise_image, &qargs, 0,
- cpu_num, cpu_groupsize, cpu_offset);
-
- cleanup_indexing(ipriv);
-
- free(indm);
- free(ipriv);
+ /* Static worker args */
+ iargs.cell = cell;
+ iargs.config_cmfilter = config_cmfilter;
+ iargs.config_noisefilter = config_noisefilter;
+ iargs.config_verbose = config_verbose;
+ iargs.config_satcorr = config_satcorr;
+ iargs.config_closer = config_closer;
+ iargs.config_insane = config_insane;
+ iargs.config_bgsub = config_bgsub;
+ iargs.cellr = cellr;
+ iargs.tols[0] = tols[0];
+ iargs.tols[1] = tols[1];
+ iargs.tols[2] = tols[2];
+ iargs.tols[3] = tols[3];
+ iargs.threshold = threshold;
+ iargs.min_gradient = min_gradient;
+ iargs.min_snr = min_snr;
+ iargs.min_int_snr = min_int_snr;
+ iargs.det = det;
+ iargs.indm = indm;
+ iargs.ipriv = ipriv;
+ iargs.peaks = peaks;
+ iargs.beam = beam;
+ iargs.element = element;
+ iargs.stream_flags = stream_flags;
+ iargs.hdf5_peak_path = hdf5_peak_path;
+ iargs.copyme = copyme;
+ iargs.ir_inn = ir_inn;
+ iargs.ir_mid = ir_mid;
+ iargs.ir_out = ir_out;
+
+ create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
+ use_this_one_instead, ofh);
+
free(prefix);
- free_detector_geometry(det);
- free(beam);
- free(element);
- free(hdf5_peak_path);
- free_copy_hdf5_field_list(copyme);
- cell_free(cell);
- if ( fh != stdin ) fclose(fh);
- if ( ofh != stdout ) fclose(ofh);
-
- STATUS("There were %i images, of which %i could be indexed.\n",
- n_images, qargs.n_indexable);
return 0;
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 899b9154..3cfb94a2 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -178,8 +178,6 @@ static void show_help(const char *s)
" -c, --cnoise=<val> Add random noise, with a flat distribution, to the\n"
" reciprocal lattice vector components given in the\n"
" stream, with maximum error +/- <val> percent.\n"
-" --pgraph=<file> Write reflection counts and partiality statistics\n"
-" to <file>.\n"
"\n"
);
}
@@ -549,8 +547,6 @@ int main(int argc, char *argv[])
if ( fh != NULL ) {
- fprintf(fh, "1/d_nm #refl pmean pmax\n");
-
for ( i=0; i<NBINS; i++ ) {
double rcen;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 14:02:06 +0000