diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/im-sandbox.c | 889 | ||||
-rw-r--r-- | src/im-sandbox.h | 86 | ||||
-rw-r--r-- | src/indexamajig.c | 859 |
3 files changed, 978 insertions, 856 deletions
diff --git a/src/im-sandbox.c b/src/im-sandbox.c new file mode 100644 index 00000000..a5806734 --- /dev/null +++ b/src/im-sandbox.c @@ -0,0 +1,889 @@ +/* + * 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 +{ + +}; + + +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; + + fh = fdopen(filename_pipe, "r"); + if ( fh == NULL ) { + ERROR("Failed to fdopen() the filename pipe!\n"); + return; + } + + while ( !allDone ) { + + struct pattern_args pargs; + int w, c; + char buf[1024]; + char *line; + char *rval; + + line = malloc(1024*sizeof(char)); + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + free(line); + if ( feof(fh) ) { + allDone = 1; + continue; + } else { + ERROR("Read error!\n"); + break; + } + } + + 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); + + } + + /* close my pipes */ + fclose(fh); + + 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); +} + + +#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 pump_chunk(FILE *fh, int *finished, 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 */ + *finished = 1; + if ( chunk_started ) { + ERROR("EOF during chunk!\n"); + fprintf(ofh, "Chunk is unfinished!\n"); + } + } 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 ); +} + + +static void run_reader(int *stream_pipe_read, int n_proc, FILE *ofh) +{ + int done = 0; + int *finished; + FILE **fhs; + int i; + + finished = calloc(n_proc, sizeof(int)); + if ( finished == NULL ) { + ERROR("Couldn't allocate memory for flags!\n"); + exit(1); + } + + fhs = calloc(n_proc, sizeof(FILE *)); + if ( fhs == NULL ) { + ERROR("Couldn't allocate memory for file handles!\n"); + exit(1); + } + + for ( i=0; i<n_proc; i++ ) { + fhs[i] = fdopen(stream_pipe_read[i], "r"); + if ( fhs[i] == NULL ) { + ERROR("Couldn't fdopen() stream!\n"); + exit(1); + } + } + + 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; + for ( i=0; i<n_proc; i++ ) { + + int fd; + + if ( finished[i] ) continue; + + fd = stream_pipe_read[i]; + + FD_SET(fd, &fds); + if ( fd > fdmax ) fdmax = fd; + + } + + r = select(fdmax+1, &fds, NULL, NULL, &tv); + + if ( r == -1 ) { + ERROR("select() failed: %s\n", strerror(errno)); + continue; + } + + if ( r == 0 ) continue; /* Nothing this time. Try again */ + + for ( i=0; i<n_proc; i++ ) { + + if ( finished[i] ) continue; + + if ( !FD_ISSET(stream_pipe_read[i], &fds) ) continue; + + pump_chunk(fhs[i], &finished[i], ofh); + + } + + done = 1; + for ( i=0; i<n_proc; i++ ) { + if ( !finished[i] ) done = 0; + } + + } + + free(finished); + + for ( i=0; i<n_proc; i++ ) { + fclose(fhs[i]); + } + free(fhs); + + if ( ofh != stdout ) fclose(ofh); +} + + +static void signal_handler(int sig, siginfo_t *si, void *uc_v) +{ + struct ucontext_t *uc = uc_v; + + STATUS("Signal!\n"); +} + + +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 n_indexable, n_processed, n_indexable_last_stats; + int n_processed_last_stats; + int t_last_stats; + pid_t *pids; + int *filename_pipes; + int *stream_pipe_read; + int *stream_pipe_write; + FILE **result_fhs; + int i; + int allDone; + int *finished; + pid_t pr; + struct sigaction sa; + int r; + + n_indexable = 0; + n_processed = 0; + n_indexable_last_stats = 0; + n_processed_last_stats = 0; + t_last_stats = get_monotonic_seconds(); + + stream_pipe_read = calloc(n_proc, sizeof(int)); + stream_pipe_write = calloc(n_proc, sizeof(int)); + if ( stream_pipe_read == NULL ) { + ERROR("Couldn't allocate memory for pipes.\n"); + return; + } + if ( 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; + } + + stream_pipe_read[i] = stream_pipe[0]; + stream_pipe_write[i] = stream_pipe[1]; + + } + + pr = fork(); + if ( pr == - 1 ) { + ERROR("fork() failed (for reader process)\n"); + return; + } + + if ( pr == 0 ) { + + /* Free resources not needed by reader + * (but which will be needed by worker or master) */ + for ( i=0; i<n_proc; i++ ) { + close(stream_pipe_write[i]); + } + free(prefix); + free(use_this_one_instead); + free(stream_pipe_write); + 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); + + run_reader(stream_pipe_read, n_proc, ofh); + + free(stream_pipe_read); + + exit(0); + + } + + /* 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; + } + + /* Free resources needed by reader only */ + if ( ofh != stdout ) fclose(ofh); + for ( i=0; i<n_proc; i++ ) { + close(stream_pipe_read[i]); + } + free(stream_pipe_read); + + filename_pipes = calloc(n_proc, sizeof(int)); + result_fhs = calloc(n_proc, sizeof(FILE *)); + pids = calloc(n_proc, sizeof(pid_t)); + if ( filename_pipes == NULL ) { + ERROR("Couldn't allocate memory for pipes.\n"); + return; + } + if ( result_fhs == NULL ) { + ERROR("Couldn't allocate memory for pipe file handles.\n"); + return; + } + if ( pids == NULL ) { + ERROR("Couldn't allocate memory for PIDs.\n"); + return; + } + + /* Fork the right number of times */ + for ( i=0; i<n_proc; i++ ) { + + 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; + + /* Free resources which will not be needed by worker */ + for ( j=0; j<n_proc; j++ ) { + if ( i != j ) close(stream_pipe_write[j]); + } + for ( j=0; j<i-1; j++ ) { + fclose(result_fhs[j]); + close(filename_pipes[j]); + } + free(prefix); + free(use_this_one_instead); + free(filename_pipes); + free(result_fhs); + fclose(fh); + free(pids); + + /* 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(stream_pipe_write[i], "w"); + run_work(iargs, filename_pipe[0], result_pipe[1], + sfh, i); + fclose(sfh); + + free(stream_pipe_write); + 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. */ + pids[i] = p; + close(filename_pipe[0]); + close(result_pipe[1]); + filename_pipes[i] = filename_pipe[1]; + + result_fhs[i] = fdopen(result_pipe[0], "r"); + if ( result_fhs[i] == NULL ) { + ERROR("fdopen() failed.\n"); + return; + } + + } + + /* Free resources which will not be used by the main thread */ + 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); + for ( i=0; i<n_proc; i++ ) { + close(stream_pipe_write[i]); + } + free(stream_pipe_write); + + /* Send first image to all children */ + for ( i=0; i<n_proc; i++ ) { + + char *nextImage; + + nextImage = get_pattern(fh, &use_this_one_instead, + config_basename, prefix); + + if ( nextImage != NULL ) { + + write(filename_pipes[i], nextImage, strlen(nextImage)); + write(filename_pipes[i], "\n", 1); + + free(nextImage); + + } else { + + int r; + + /* No more files to process.. already? */ + r = write(filename_pipes[i], "\n", 1); + if ( r < 0 ) { + ERROR("Write pipe\n"); + } + + } + + } + + finished = calloc(n_proc, sizeof(int)); + if ( finished == NULL ) { + ERROR("Couldn't allocate memory for process flags.\n"); + return; + } + + allDone = 0; + while ( !allDone ) { + + int r, i; + struct timeval tv; + fd_set fds; + double tNow; + int fdmax; + + tv.tv_sec = 5; + tv.tv_usec = 0; + + FD_ZERO(&fds); + fdmax = 0; + for ( i=0; i<n_proc; i++ ) { + + int fd; + + if ( finished[i] ) continue; + + fd = fileno(result_fhs[i]); + FD_SET(fd, &fds); + if ( fd > fdmax ) fdmax = fd; + + } + + r = select(fdmax+1, &fds, NULL, NULL, &tv); + + if ( r == -1 ) { + ERROR("select() failed: %s\n", strerror(errno)); + continue; + } + + if ( r == 0 ) continue; /* No progress this time. Try again */ + + for ( i=0; i<n_proc; i++ ) { + + char *nextImage; + char results[1024]; + char *rval; + int fd; + + if ( finished[i] ) continue; + + fd = fileno(result_fhs[i]); + if ( !FD_ISSET(fd, &fds) ) continue; + + rval = fgets(results, 1024, result_fhs[i]); + if ( rval == NULL ) { + if ( feof(result_fhs[i]) ) { + /* Process died */ + finished[i] = 1; + } else { + ERROR("fgets() failed: %s\n", + strerror(errno)); + } + continue; + } + + chomp(results); + n_indexable += atoi(results); + n_processed++; + + /* Send next filename */ + nextImage = get_pattern(fh, &use_this_one_instead, + config_basename, prefix); + + if ( nextImage == NULL ) { + /* No more images */ + r = write(filename_pipes[i], "\n", 1); + if ( r < 0 ) { + ERROR("Write pipe\n"); + } + } else { + + r = write(filename_pipes[i], nextImage, + strlen(nextImage)); + r -= write(filename_pipes[i], "\n", 1); + if ( r < 0 ) { + ERROR("write pipe\n"); + } + free(nextImage); + } + + } + + /* Update progress */ + tNow = get_monotonic_seconds(); + if ( tNow >= t_last_stats+STATS_EVERY_N_SECONDS ) { + + STATUS("%i out of %i indexed so far," + " %i out of %i since the last message.\n", + n_indexable, n_processed, + n_indexable - n_indexable_last_stats, + n_processed - n_processed_last_stats); + + n_indexable_last_stats = n_indexable; + n_processed_last_stats = n_processed; + t_last_stats = tNow; + + } + + allDone = 1; + for ( i=0; i<n_proc; i++ ) { + if ( !finished[i] ) allDone = 0; + } + + } + + fclose(fh); + + for ( i=0; i<n_proc; i++ ) { + int status; + waitpid(pids[i], &status, 0); + } + + for ( i=0; i<n_proc; i++ ) { + close(filename_pipes[i]); + fclose(result_fhs[i]); + } + + free(filename_pipes); + free(result_fhs); + free(pids); + free(finished); + + STATUS("There were %i images, of which %i could be indexed.\n", + n_processed, 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 b8e57048..c2c9ed2c 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -44,10 +44,6 @@ #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> @@ -67,57 +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 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; -}; +#include "im-sandbox.h" static void show_help(const char *s) @@ -218,305 +164,6 @@ static void show_help(const char *s) } -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; - - fh = fdopen(filename_pipe, "r"); - if ( fh == NULL ) { - ERROR("Failed to fdopen() the filename pipe!\n"); - return; - } - - while ( !allDone ) { - - struct pattern_args pargs; - int w, c; - char buf[1024]; - char *line; - char *rval; - - line = malloc(1024*sizeof(char)); - rval = fgets(line, 1023, fh); - if ( rval == NULL ) { - free(line); - if ( feof(fh) ) { - allDone = 1; - continue; - } else { - ERROR("Read error!\n"); - break; - } - } - - 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); - - } - - /* close my pipes */ - fclose(fh); - - 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); -} - - -#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 parse_cell_reduction(const char *scellr, int *err, int *reduction_needs_cell) { @@ -541,142 +188,6 @@ static int parse_cell_reduction(const char *scellr, int *err, } -static void pump_chunk(FILE *fh, int *finished, 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 */ - *finished = 1; - if ( chunk_started ) { - ERROR("EOF during chunk!\n"); - fprintf(ofh, "Chunk is unfinished!\n"); - } - } 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 ); -} - - -static void run_reader(int *stream_pipe_read, int n_proc, FILE *ofh) -{ - int done = 0; - int *finished; - FILE **fhs; - int i; - - finished = calloc(n_proc, sizeof(int)); - if ( finished == NULL ) { - ERROR("Couldn't allocate memory for flags!\n"); - exit(1); - } - - fhs = calloc(n_proc, sizeof(FILE *)); - if ( fhs == NULL ) { - ERROR("Couldn't allocate memory for file handles!\n"); - exit(1); - } - - for ( i=0; i<n_proc; i++ ) { - fhs[i] = fdopen(stream_pipe_read[i], "r"); - if ( fhs[i] == NULL ) { - ERROR("Couldn't fdopen() stream!\n"); - exit(1); - } - } - - 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; - for ( i=0; i<n_proc; i++ ) { - - int fd; - - if ( finished[i] ) continue; - - fd = stream_pipe_read[i]; - - FD_SET(fd, &fds); - if ( fd > fdmax ) fdmax = fd; - - } - - r = select(fdmax+1, &fds, NULL, NULL, &tv); - - if ( r == -1 ) { - ERROR("select() failed: %s\n", strerror(errno)); - continue; - } - - if ( r == 0 ) continue; /* Nothing this time. Try again */ - - for ( i=0; i<n_proc; i++ ) { - - if ( finished[i] ) continue; - - if ( !FD_ISSET(stream_pipe_read[i], &fds) ) continue; - - pump_chunk(fhs[i], &finished[i], ofh); - - } - - done = 1; - for ( i=0; i<n_proc; i++ ) { - if ( !finished[i] ) done = 0; - } - - } - - free(finished); - - for ( i=0; i<n_proc; i++ ) { - fclose(fhs[i]); - } - free(fhs); - - if ( ofh != stdout ) fclose(ofh); -} - - -static void signal_handler(int sig, siginfo_t *si, void *uc_v) -{ - struct ucontext_t *uc = uc_v; - - STATUS("Signal!\n"); -} - - int main(int argc, char *argv[]) { int c; @@ -730,20 +241,6 @@ int main(int argc, char *argv[]) float ir_inn = 4.0; float ir_mid = 5.0; float ir_out = 7.0; - int n_indexable, n_processed, n_indexable_last_stats; - int n_processed_last_stats; - int t_last_stats; - pid_t *pids; - int *filename_pipes; - int *stream_pipe_read; - int *stream_pipe_write; - FILE **result_fhs; - int i; - int allDone; - int *finished; - pid_t pr; - struct sigaction sa; - int r; copyme = new_copy_hdf5_field_list(); if ( copyme == NULL ) { @@ -1139,360 +636,10 @@ int main(int argc, char *argv[]) iargs.ir_mid = ir_mid; iargs.ir_out = ir_out; - n_indexable = 0; - n_processed = 0; - n_indexable_last_stats = 0; - n_processed_last_stats = 0; - t_last_stats = get_monotonic_seconds(); - - stream_pipe_read = calloc(n_proc, sizeof(int)); - stream_pipe_write = calloc(n_proc, sizeof(int)); - if ( stream_pipe_read == NULL ) { - ERROR("Couldn't allocate memory for pipes.\n"); - return 1; - } - if ( stream_pipe_write == NULL ) { - ERROR("Couldn't allocate memory for pipes.\n"); - return 1; - } - - for ( i=0; i<n_proc; i++ ) { - - int stream_pipe[2]; - - if ( pipe(stream_pipe) == - 1 ) { - ERROR("pipe() failed!\n"); - return 1; - } - - stream_pipe_read[i] = stream_pipe[0]; - stream_pipe_write[i] = stream_pipe[1]; - - } - - pr = fork(); - if ( pr == - 1 ) { - ERROR("fork() failed (for reader process)\n"); - return 1; - } - - if ( pr == 0 ) { - - /* Free resources not needed by reader - * (but which will be needed by worker or master) */ - for ( i=0; i<n_proc; i++ ) { - close(stream_pipe_write[i]); - } - free(prefix); - free(use_this_one_instead); - free(stream_pipe_write); - cleanup_indexing(ipriv); - free(indm); - free(ipriv); - free_detector_geometry(det); - free(beam); - free(element); - free(hdf5_peak_path); - free_copy_hdf5_field_list(copyme); - cell_free(cell); - fclose(fh); - - run_reader(stream_pipe_read, n_proc, ofh); - - free(stream_pipe_read); - - exit(0); - - } - - /* 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 1; - } - - /* Free resources needed by reader only */ - if ( ofh != stdout ) fclose(ofh); - for ( i=0; i<n_proc; i++ ) { - close(stream_pipe_read[i]); - } - free(stream_pipe_read); - - filename_pipes = calloc(n_proc, sizeof(int)); - result_fhs = calloc(n_proc, sizeof(FILE *)); - pids = calloc(n_proc, sizeof(pid_t)); - if ( filename_pipes == NULL ) { - ERROR("Couldn't allocate memory for pipes.\n"); - return 1; - } - if ( result_fhs == NULL ) { - ERROR("Couldn't allocate memory for pipe file handles.\n"); - return 1; - } - if ( pids == NULL ) { - ERROR("Couldn't allocate memory for PIDs.\n"); - return 1; - } - - /* Fork the right number of times */ - for ( i=0; i<n_proc; i++ ) { - - pid_t p; - int filename_pipe[2]; - int result_pipe[2]; - - if ( pipe(filename_pipe) == - 1 ) { - ERROR("pipe() failed!\n"); - return 1; - } - - if ( pipe(result_pipe) == - 1 ) { - ERROR("pipe() failed!\n"); - return 1; - } - - p = fork(); - if ( p == -1 ) { - ERROR("fork() failed!\n"); - return 1; - } - - if ( p == 0 ) { - - FILE *sfh; - int j; - - /* Free resources which will not be needed by worker */ - for ( j=0; j<n_proc; j++ ) { - if ( i != j ) close(stream_pipe_write[j]); - } - for ( j=0; j<i-1; j++ ) { - fclose(result_fhs[j]); - close(filename_pipes[j]); - } - free(prefix); - free(use_this_one_instead); - free(filename_pipes); - free(result_fhs); - fclose(fh); - free(pids); - - /* 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(stream_pipe_write[i], "w"); - run_work(&iargs, filename_pipe[0], result_pipe[1], - sfh, i); - fclose(sfh); - - free(stream_pipe_write); - 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. */ - pids[i] = p; - close(filename_pipe[0]); - close(result_pipe[1]); - filename_pipes[i] = filename_pipe[1]; - - result_fhs[i] = fdopen(result_pipe[0], "r"); - if ( result_fhs[i] == NULL ) { - ERROR("fdopen() failed.\n"); - return 1; - } - - } - - /* Free resources which will not be used by the main thread */ - cleanup_indexing(ipriv); - free(indm); - free(ipriv); - free_detector_geometry(det); - free(beam); - free(element); - free(hdf5_peak_path); - free_copy_hdf5_field_list(copyme); - cell_free(cell); - for ( i=0; i<n_proc; i++ ) { - close(stream_pipe_write[i]); - } - free(stream_pipe_write); - - /* Send first image to all children */ - for ( i=0; i<n_proc; i++ ) { - - char *nextImage; - - nextImage = get_pattern(fh, &use_this_one_instead, - config_basename, prefix); - - if ( nextImage != NULL ) { - - write(filename_pipes[i], nextImage, strlen(nextImage)); - write(filename_pipes[i], "\n", 1); - - free(nextImage); - - } else { - - int r; - - /* No more files to process.. already? */ - r = write(filename_pipes[i], "\n", 1); - if ( r < 0 ) { - ERROR("Write pipe\n"); - } - - } - - } - - finished = calloc(n_proc, sizeof(int)); - if ( finished == NULL ) { - ERROR("Couldn't allocate memory for process flags.\n"); - return 1; - } - - allDone = 0; - while ( !allDone ) { - - int r, i; - struct timeval tv; - fd_set fds; - double tNow; - int fdmax; - - tv.tv_sec = 5; - tv.tv_usec = 0; - - FD_ZERO(&fds); - fdmax = 0; - for ( i=0; i<n_proc; i++ ) { - - int fd; - - if ( finished[i] ) continue; - - fd = fileno(result_fhs[i]); - FD_SET(fd, &fds); - if ( fd > fdmax ) fdmax = fd; - - } - - r = select(fdmax+1, &fds, NULL, NULL, &tv); - - if ( r == -1 ) { - ERROR("select() failed: %s\n", strerror(errno)); - continue; - } - - if ( r == 0 ) continue; /* No progress this time. Try again */ - - for ( i=0; i<n_proc; i++ ) { - - char *nextImage; - char results[1024]; - char *rval; - int fd; - - if ( finished[i] ) continue; - - fd = fileno(result_fhs[i]); - if ( !FD_ISSET(fd, &fds) ) continue; - - rval = fgets(results, 1024, result_fhs[i]); - if ( rval == NULL ) { - if ( feof(result_fhs[i]) ) { - /* Process died */ - finished[i] = 1; - } else { - ERROR("fgets() failed: %s\n", - strerror(errno)); - } - continue; - } - - chomp(results); - n_indexable += atoi(results); - n_processed++; - - /* Send next filename */ - nextImage = get_pattern(fh, &use_this_one_instead, - config_basename, prefix); - - if ( nextImage == NULL ) { - /* No more images */ - r = write(filename_pipes[i], "\n", 1); - if ( r < 0 ) { - ERROR("Write pipe\n"); - } - } else { - - r = write(filename_pipes[i], nextImage, - strlen(nextImage)); - r -= write(filename_pipes[i], "\n", 1); - if ( r < 0 ) { - ERROR("write pipe\n"); - } - free(nextImage); - } - - } - - /* Update progress */ - tNow = get_monotonic_seconds(); - if ( tNow >= t_last_stats+STATS_EVERY_N_SECONDS ) { - - STATUS("%i out of %i indexed so far," - " %i out of %i since the last message.\n", - n_indexable, n_processed, - n_indexable - n_indexable_last_stats, - n_processed - n_processed_last_stats); - - n_indexable_last_stats = n_indexable; - n_processed_last_stats = n_processed; - t_last_stats = tNow; - - } - - allDone = 1; - for ( i=0; i<n_proc; i++ ) { - if ( !finished[i] ) allDone = 0; - } - - } - - fclose(fh); - - for ( i=0; i<n_proc; i++ ) { - int status; - waitpid(pids[i], &status, 0); - } - - for ( i=0; i<n_proc; i++ ) { - close(filename_pipes[i]); - fclose(result_fhs[i]); - } + create_sandbox(&iargs, n_proc, prefix, config_basename, fh, + use_this_one_instead, ofh); free(prefix); - free(filename_pipes); - free(result_fhs); - free(pids); - free(finished); - - STATUS("There were %i images, of which %i could be indexed.\n", - n_processed, n_indexable); return 0; } |