diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/geoptimiser.c | 2 | ||||
| -rw-r--r-- | src/im-sandbox.c | 153 | ||||
| -rw-r--r-- | src/im-zmq.c | 28 | ||||
| -rw-r--r-- | src/im-zmq.h | 17 | ||||
| -rw-r--r-- | src/indexamajig.c | 65 | ||||
| -rw-r--r-- | src/partial_sim.c | 5 | ||||
| -rw-r--r-- | src/partialator.c | 12 | ||||
| -rw-r--r-- | src/post-refinement.c | 8 | ||||
| -rw-r--r-- | src/process_hkl.c | 2 | ||||
| -rw-r--r-- | src/process_image.c | 314 | ||||
| -rw-r--r-- | src/process_image.h | 8 | ||||
| -rw-r--r-- | src/whirligig.c | 2 |
12 files changed, 186 insertions, 430 deletions
diff --git a/src/geoptimiser.c b/src/geoptimiser.c index 73e37249..cae2ae4e 100644 --- a/src/geoptimiser.c +++ b/src/geoptimiser.c @@ -789,7 +789,7 @@ static int compute_pixel_displacements(struct image *images, int n_images, "(panel %s), image %s %s\n", imfe->fs, imfe->ss, gp->p->name, images[cp].filename, - get_event_string(images[cp].event)); + images[cp].ev); return r; } diff --git a/src/im-sandbox.c b/src/im-sandbox.c index fb4a9674..c7840f94 100644 --- a/src/im-sandbox.c +++ b/src/im-sandbox.c @@ -113,7 +113,7 @@ struct get_pattern_ctx { FILE *fh; int use_basename; - struct detector *det; + const DataTemplate *dtempl; const char *prefix; char *filename; struct event_list *events; /* FIXME: Deprecated */ @@ -251,107 +251,51 @@ static char *read_prefixed_filename(struct get_pattern_ctx *gpctx, char **event) } -static struct filename_plus_event *get_pattern(struct get_pattern_ctx *gpctx) +/* Return 0 for "no more" */ +static int get_pattern(struct get_pattern_ctx *gpctx, + char **pfilename, char **pevent) { char *filename; char *evstr; - /* If single-event geometry, just return next filename */ - if ( !multi_event_geometry(gpctx->det) ) - { - struct filename_plus_event *fne; - fne = malloc(sizeof(struct filename_plus_event)); - if ( fne == NULL ) return NULL; - fne->filename = read_prefixed_filename(gpctx, NULL); - if ( fne->filename == NULL ) { - free(fne); - return NULL; - } - fne->ev = NULL; - return fne; - } - - /* Ok, multi-event geometry. Is an event available already? */ + /* Is an event available already? */ if ( (gpctx->events != NULL) && (gpctx->event_index < gpctx->events->num_events) ) { - struct filename_plus_event *fne; - fne = malloc(sizeof(struct filename_plus_event)); - fne->filename = strdup(gpctx->filename); - fne->ev = copy_event(gpctx->events->events[gpctx->event_index++]); - - return fne; + *pfilename = strdup(gpctx->filename); + *pevent = get_event_string(gpctx->events->events[gpctx->event_index++]); + return 1; } /* No events in list. Time to top it up */ filename = read_prefixed_filename(gpctx, &evstr); /* Nothing left in file -> we're done */ - if ( filename == NULL ) return NULL; - - /* Muppet check */ - if ( is_cbf_file(filename) == 1 ) { - ERROR("Your geometry file is for a multi-event format, but " - "this file is in CBF format.\n"); - ERROR("Your geometry file probably needs to be changed.\n"); - return NULL; - } + if ( filename == NULL ) return 0; /* Does the line from the input file contain an event ID? - * If so, just parse it and sent it straight back. */ + * If so, just send it straight back. */ if ( evstr != NULL ) { + *pfilename = strdup(filename); + *pevent = strdup(evstr); + return 1; + } - /* Make an event list with only one item */ - struct event *ev = get_event_from_event_string(evstr); - if ( ev == NULL ) { - ERROR("Bad event descriptor: '%s'\n", evstr); - return NULL; - } else { - struct filename_plus_event *fne; - fne = malloc(sizeof(struct filename_plus_event)); - fne->filename = filename; - fne->ev = ev; - return fne; - } - - } else { - - /* Enumerate all the events in the file and then send the - * first one back */ - struct hdfile *hdfile; - struct filename_plus_event *fne; - - hdfile = hdfile_open(filename); - if ( hdfile == NULL ) { - ERROR("Failed to open %s\n", filename); - return NULL; - } - - if ( gpctx->events != NULL ) { - free_event_list(gpctx->events); - } - - gpctx->events = fill_event_list(hdfile, gpctx->det); - if ( gpctx->events == NULL ) { - ERROR("Failed to get event list.\n"); - return NULL; - } - - hdfile_close(hdfile); - - /* Save filename for next time */ - if ( gpctx->filename != NULL ) { - free(gpctx->filename); - } - gpctx->filename = filename; + free_event_list(gpctx->events); + gpctx->events = image_expand_frames(gpctx->dtempl, filename); + if ( gpctx->events == NULL ) { + ERROR("Failed to get event list.\n"); + return 0; + } - gpctx->event_index = 0; - fne = malloc(sizeof(struct filename_plus_event)); - fne->filename = strdup(gpctx->filename); - fne->ev = copy_event(gpctx->events->events[gpctx->event_index++]); - return fne; + /* Save filename for next time */ + free(gpctx->filename); + gpctx->filename = filename; - } + gpctx->event_index = 0; + *pfilename = strdup(gpctx->filename); + *pevent = get_event_string(gpctx->events->events[gpctx->event_index++]); + return 1; } @@ -398,7 +342,6 @@ static int run_work(const struct index_args *iargs, Stream *st, char filename[MAX_EV_LEN]; char event_str[MAX_EV_LEN]; int ser; - struct event *ev; int r; if ( !sb->zmq ) { @@ -444,31 +387,16 @@ static int run_work(const struct index_args *iargs, Stream *st, if ( r != 3 ) continue; - pargs.filename_p_e = initialize_filename_plus_event(); - pargs.filename_p_e->filename = strdup(filename); - - if ( strcmp(event_str, "(none)") != 0 ) { - - ev = get_event_from_event_string(event_str); - if ( ev == NULL ) { - ERROR("Bad event string '%s'\n", event_str); - continue; - } - pargs.filename_p_e->ev = ev; - - } else { + pargs.filename = strdup(filename); + pargs.event = strdup(event_str); - pargs.filename_p_e->ev = NULL; - - } pargs.msgpack_obj = NULL; } else { pargs.msgpack_obj = im_zmq_fetch(zmqstuff); - pargs.filename_p_e = initialize_filename_plus_event(); - pargs.filename_p_e->filename = strdup("(from ZMQ)"); - pargs.filename_p_e->ev = NULL; + pargs.filename = strdup("(from ZMQ)"); + pargs.event = NULL; ser = 0; /* FIXME */ } @@ -477,9 +405,7 @@ static int run_work(const struct index_args *iargs, Stream *st, process_image(iargs, &pargs, st, cookie, tmpdir, ser, sb->shared, taccs, sb->shared->last_task[cookie]); - if ( !sb->zmq ) { - free_filename_plus_event(pargs.filename_p_e); - } else { + if ( sb->zmq ) { im_zmq_clean(zmqstuff); } @@ -489,8 +415,6 @@ static int run_work(const struct index_args *iargs, Stream *st, time_accounts_set(taccs, TACC_FINALCLEANUP); cleanup_indexing(iargs->ipriv); - free_detector_geometry(iargs->det); - free(iargs->hdf5_peak_path); free_imagefile_field_list(iargs->copyme); cell_free(iargs->cell); if ( sb->profile ) time_accounts_print(taccs); @@ -743,7 +667,6 @@ static void start_worker_process(struct sandbox *sb, int slot) close_stream(st); free(tmp); - free(sb->iargs->beam->photon_energy_from); munmap(sb->shared, sizeof(struct sb_shm)); @@ -861,19 +784,15 @@ static int fill_queue(struct get_pattern_ctx *gpctx, struct sandbox *sb) while ( sb->shared->n_events < QUEUE_SIZE ) { - struct filename_plus_event *ne; + char *filename; char *evstr; - ne = get_pattern(gpctx); - if ( ne == NULL ) return 1; /* No more */ + if ( !get_pattern(gpctx, &filename, &evstr) ) return 1; memset(sb->shared->queue[sb->shared->n_events], 0, MAX_EV_LEN); - evstr = get_event_string(ne->ev), snprintf(sb->shared->queue[sb->shared->n_events++], MAX_EV_LEN, - "%s %s %i", ne->filename, evstr, sb->serial++); - free(evstr); + "%s %s %i", filename, evstr, sb->serial++); sem_post(sb->queue_sem); - free_filename_plus_event(ne); } return 0; @@ -1103,7 +1022,7 @@ int create_sandbox(struct index_args *iargs, int n_proc, char *prefix, gpctx.fh = fh; gpctx.use_basename = config_basename; - gpctx.det = iargs->det; + gpctx.dtempl = iargs->dtempl; gpctx.prefix = prefix; gpctx.filename = NULL; gpctx.events = NULL; diff --git a/src/im-zmq.c b/src/im-zmq.c index da0a5fff..f8743dbb 100644 --- a/src/im-zmq.c +++ b/src/im-zmq.c @@ -408,7 +408,7 @@ static double *find_msgpack_data(msgpack_object *obj, int *width, int *height) } -static double *zero_array(struct detector *det, int *dw, int *dh) +static double *zero_array(DataTemplate *dtempl, int *dw, int *dh) { int max_fs = 0; int max_ss = 0; @@ -446,17 +446,14 @@ static double *zero_array(struct detector *det, int *dw, int *dh) * ... * } */ -int unpack_msgpack_data(msgpack_object *obj, struct image *image, - int no_image_data) +struct image *unpack_msgpack_data(msgpack_object *obj, + const DataTemplate *dtempl, + int no_image_data) { + struct image *image; int data_width, data_height; double *data; - if ( image->det == NULL ) { - ERROR("Geometry not available.\n"); - return 1; - } - if ( obj == NULL ) { ERROR("No MessagePack object!\n"); return 1; @@ -469,20 +466,21 @@ int unpack_msgpack_data(msgpack_object *obj, struct image *image, return 1; } } else { - data = zero_array(image->det, &data_width, &data_height); + data = zero_array(dtempl, &data_width, &data_height); } + image = image_new(); + if ( image == NULL ) return 1; + if ( unpack_slab(image, data, data_width, data_height) ) { ERROR("Failed to unpack data slab.\n"); return 1; } - if ( image->beam != NULL ) { - im_zmq_fill_in_beam_parameters(image->beam, image); - if ( image->lambda > 1000 ) { - ERROR("Warning: Missing or nonsensical wavelength " - "(%e m).\n", image->lambda); - } + im_zmq_fill_in_beam_parameters(image->beam, image); + if ( image->lambda > 1000 ) { + ERROR("Warning: Missing or nonsensical wavelength " + "(%e m).\n", image->lambda); } im_zmq_fill_in_clen(image->det); fill_in_adu(image); diff --git a/src/im-zmq.h b/src/im-zmq.h index bc6175af..270a7c3a 100644 --- a/src/im-zmq.h +++ b/src/im-zmq.h @@ -54,8 +54,9 @@ extern ImageFeatureList *get_peaks_msgpack(msgpack_object *obj, const DataTemplate *dtempl, int half_pixel_shift); -extern int unpack_msgpack_data(msgpack_object *obj, struct image *image, - int no_image_data); +extern struct image *unpack_msgpack_data(msgpack_object *obj, + DataTemplate *dtempl, + int no_image_data); #else /* defined(HAVE_MSGPACK) && defined(HAVE_ZMQ) */ @@ -67,11 +68,15 @@ static UNUSED void im_zmq_shutdown(struct im_zmq *z) { return; } static UNUSED void *im_zmq_fetch(struct im_zmq *z) { return NULL; } -static UNUSED int get_peaks_msgpack(void *obj, struct image *image, - int half_pixel_shift) { return 0; } +static UNUSED int get_peaks_msgpack(void *obj, + const DataTemplate *dtempl, + int half_pixel_shift) +{ return 0; } -static UNUSED int unpack_msgpack_data(void *obj, struct image *image, - int no_image_data) { return 1; } +static UNUSED struct image *unpack_msgpack_data(void *obj, + const DataTemplate *dtempl, + int no_image_data) +{ return 1; } #endif /* defined(HAVE_MSGPACK) && defined(HAVE_ZMQ) */ diff --git a/src/indexamajig.c b/src/indexamajig.c index e44f9576..f4c3af50 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -68,27 +68,6 @@ #include "datatemplate.h" -static void add_geom_beam_stuff_to_field_list(struct imagefile_field_list *copyme, - struct detector *det, - struct beam_params *beam) -{ - int i; - - for ( i=0; i<det->n_panels; i++ ) { - - struct panel *p = &det->panels[i]; - - if ( p->clen_from != NULL ) { - add_imagefile_field(copyme, p->clen_from); - } - } - - if ( beam->photon_energy_from != NULL ) { - add_imagefile_field(copyme, beam->photon_energy_from); - } -} - - struct indexamajig_arguments { struct index_args iargs; /* These are the options that will be @@ -107,7 +86,6 @@ struct indexamajig_arguments int no_image_data; int serial_start; char *temp_location; - char *command_line_peak_path; int if_refine; int if_checkcell; int if_peaks; @@ -251,8 +229,8 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) break; case 304 : - free(args->command_line_peak_path); - args->command_line_peak_path = strdup(arg); + ERROR("The option --hdf5-peak-path is no longer used.\n"); + ERROR("Set the peak path in the geometry file.\n"); break; case 305 : @@ -582,7 +560,6 @@ int main(int argc, char *argv[]) char *tmpdir; /* e.g. /tmp/indexamajig.12345 */ char *rn; /* e.g. /home/taw/indexing */ int r; - struct beam_params beam; char *zmq_address = NULL; int timeout = 240; TakeTwoOptions *taketwo_opts = NULL; @@ -604,7 +581,6 @@ int main(int argc, char *argv[]) args.basename = 0; args.zmq = 0; args.serial_start = 1; - args.command_line_peak_path = NULL; args.if_peaks = 1; args.if_multi = 0; args.if_retry = 1; @@ -639,10 +615,8 @@ int main(int argc, char *argv[]) args.iargs.min_sig = 11.0; args.iargs.min_peak_over_neighbour = -INFINITY; args.iargs.check_hdf5_snr = 0; - args.iargs.det = NULL; + args.iargs.dtempl = NULL; args.iargs.peaks = PEAK_ZAEF; - args.iargs.beam = &beam; - args.iargs.hdf5_peak_path = NULL; args.iargs.half_pixel_shift = 1; args.iargs.copyme = NULL; args.iargs.pk_inn = -1.0; @@ -849,18 +823,6 @@ int main(int argc, char *argv[]) return 1; } - /* Load detector geometry (old API) */ - args.iargs.det = get_detector_geometry_2(args.geom_filename, - args.iargs.beam, - &args.iargs.hdf5_peak_path); - if ( args.iargs.det == NULL ) { - ERROR("Failed to read detector geometry from '%s'\n", - args.geom_filename); - return 1; - } - add_geom_beam_stuff_to_field_list(args.iargs.copyme, args.iargs.det, - args.iargs.beam); - /* Load data template (new API) */ args.iargs.dtempl = data_template_new_from_file(args.geom_filename); if ( args.iargs.dtempl == NULL ) { @@ -869,21 +831,6 @@ int main(int argc, char *argv[]) return 1; } - /* If no peak path from geometry file, use these (but see later) */ - if ( args.iargs.hdf5_peak_path == NULL ) { - if ( args.iargs.peaks == PEAK_HDF5 ) { - args.iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo"); - } else if ( args.iargs.peaks == PEAK_CXI ) { - args.iargs.hdf5_peak_path = strdup("/entry_1/result_1"); - } - } - - /* If an HDF5 peak path was given on the command line, use it */ - if ( args.command_line_peak_path != NULL ) { - free(args.iargs.hdf5_peak_path); - args.iargs.hdf5_peak_path = args.command_line_peak_path; - } - /* If no integration radii were given, apply the defaults */ if ( args.iargs.ir_inn < 0 ) { STATUS("WARNING: You did not specify --int-radius.\n"); @@ -998,7 +945,7 @@ int main(int argc, char *argv[]) } args.iargs.ipriv = setup_indexing(args.indm_str, args.iargs.cell, - args.iargs.det, args.iargs.beam, + args.iargs.dtempl, args.iargs.tols, flags, taketwo_opts, xgandalf_opts, @@ -1063,12 +1010,10 @@ int main(int argc, char *argv[]) free_imagefile_field_list(args.iargs.copyme); cell_free(args.iargs.cell); - free(args.iargs.beam->photon_energy_from); free(args.prefix); free(args.temp_location); free(tmpdir); - free_detector_geometry(args.iargs.det); - free(args.iargs.hdf5_peak_path); + data_template_free(args.iargs.dtempl); close_stream(st); cleanup_indexing(args.iargs.ipriv); diff --git a/src/partial_sim.c b/src/partial_sim.c index 884032b5..32263cad 100644 --- a/src/partial_sim.c +++ b/src/partial_sim.c @@ -362,7 +362,6 @@ static void *create_job(void *vqargs) crystal_free(im.crystals[0]); free(im.filename); - free_event(im.event); } else { wargs->template_cell = NULL; @@ -465,7 +464,7 @@ static void finalise_job(void *vqargs, void *vwargs) int i; int ret; - ret = write_chunk(qargs->stream, &wargs->image, NULL, 0, 1, NULL); + ret = write_chunk(qargs->stream, &wargs->image, 0, 1); if ( ret != 0) { ERROR("WARNING: error writing stream file.\n"); } @@ -899,12 +898,12 @@ int main(int argc, char *argv[]) image.bw = bandwidth; image.spectrum = spectrum_generate_gaussian(image.lambda, image.bw); image.filename = "dummy.h5"; + image.ev = "(none)"; image.copyme = NULL; image.crystals = NULL; image.n_crystals = 0; image.indexed_by = INDEXING_SIMULATION; image.serial = 0; - image.event = NULL; image.hit = 0; image.n_indexing_tries = 1; image.features = NULL; diff --git a/src/partialator.c b/src/partialator.c index 246880da..47a752b0 100644 --- a/src/partialator.c +++ b/src/partialator.c @@ -254,14 +254,12 @@ static void write_custom_split(struct custom_split *csplit, int dsn, for ( i=0; i<n_crystals; i++ ) { const char *fn; - struct event *ev; char *evs; char *id; int dsn_crystal; fn = crystal_get_image(crystals[i])->filename; - ev = crystal_get_image(crystals[i])->event; - evs = get_event_string(ev); + evs = crystal_get_image(crystals[i])->ev; id = malloc(strlen(evs)+strlen(fn)+2); if ( id == NULL ) { @@ -349,14 +347,12 @@ static signed int find_first_crystal(Crystal **crystals, int n_crystals, for ( i=0; i<n_crystals; i++ ) { const char *fn; - struct event *ev; char *evs; char *id; int dsn_crystal; fn = crystal_get_image(crystals[i])->filename; - ev = crystal_get_image(crystals[i])->event; - evs = get_event_string(ev); + evs = crystal_get_image(crystals[i])->ev; id = malloc(strlen(evs)+strlen(fn)+2); if ( id == NULL ) { @@ -389,14 +385,12 @@ static void check_csplit(Crystal **crystals, int n_crystals, for ( i=0; i<n_crystals; i++ ) { const char *fn; - struct event *ev; char *evs; char *id; int dsn_crystal; fn = crystal_get_image(crystals[i])->filename; - ev = crystal_get_image(crystals[i])->event; - evs = get_event_string(ev); + evs = crystal_get_image(crystals[i])->ev; id = malloc(strlen(evs)+strlen(fn)+2); if ( id == NULL ) { diff --git a/src/post-refinement.c b/src/post-refinement.c index 16ab41ce..b3ce79c1 100644 --- a/src/post-refinement.c +++ b/src/post-refinement.c @@ -336,9 +336,7 @@ void write_test_logs(Crystal *crystal, const RefList *full, } if ( cycle == 0 ) { - char *evstr = get_event_string(image->event); - fprintf(fh, "Image: %s %s\n", image->filename, evstr); - free(evstr); + fprintf(fh, "Image: %s %s\n", image->filename, image->ev); } if ( cycle >= 0 ) { @@ -393,10 +391,8 @@ void write_specgraph(Crystal *crystal, const RefList *full, } if ( cycle == 0 ) { - char *evstr = get_event_string(image->event); - fprintf(fh, "Image: %s %s\n", image->filename, evstr); + fprintf(fh, "Image: %s %s\n", image->filename, image->ev); fprintf(fh, "khalf/m 1/d(m) pcalc pobs iteration h k l\n"); - free(evstr); } cell = crystal_get_cell(crystal); diff --git a/src/process_hkl.c b/src/process_hkl.c index 63c24912..5aadda47 100644 --- a/src/process_hkl.c +++ b/src/process_hkl.c @@ -300,7 +300,7 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr, if ( scale <= 0.0 ) return 1; if ( stat != NULL ) { fprintf(stat, "%s %s %f %f\n", image->filename, - get_event_string(image->event), scale, cc); + image->ev, scale, cc); } } else { diff --git a/src/process_image.c b/src/process_image.c index b71fbec3..d529a444 100644 --- a/src/process_image.c +++ b/src/process_image.c @@ -44,7 +44,6 @@ #include "hdf5-file.h" #include "index.h" #include "peaks.h" -#include "detector.h" #include "filters.h" #include "thread-pool.h" #include "geometry.h" @@ -59,7 +58,7 @@ #include "detgeom.h" -static float **backup_image_data(float **dp, struct detector *det) +static float **backup_image_data(float **dp, struct detgeom *det) { float **bu; int i; @@ -87,7 +86,7 @@ static float **backup_image_data(float **dp, struct detector *det) } -static void restore_image_data(float **dp, struct detector *det, float **bu) +static void restore_image_data(float **dp, struct detgeom *det, float **bu) { int i; @@ -101,16 +100,20 @@ static void restore_image_data(float **dp, struct detector *det, float **bu) } -static int file_wait_open_read(struct sb_shm *sb_shared, struct image *image, - TimeAccounts *taccs, char *last_task, - signed int wait_for_file, int cookie, - struct imagefile **pimfile) +static struct image *file_wait_open_read(const char *filename, + const char *event, + DataTemplate *dtempl, + struct sb_shm *sb_shared, + TimeAccounts *taccs, + char *last_task, + signed int wait_for_file, + int cookie) { signed int file_wait_time = wait_for_file; int wait_message_done = 0; int read_retry_done = 0; int r; - struct imagefile *imfile; + struct image *image; time_accounts_set(taccs, TACC_WAITFILE); set_last_task(last_task, "wait for file"); @@ -120,7 +123,7 @@ static int file_wait_open_read(struct sb_shm *sb_shared, struct image *image, struct stat statbuf; sb_shared->pings[cookie]++; - r = stat(image->filename, &statbuf); + r = stat(filename, &statbuf); if ( r ) { if ( (wait_for_file != 0) && (file_wait_time != 0) ) { @@ -139,8 +142,8 @@ static int file_wait_open_read(struct sb_shm *sb_shared, struct image *image, } - ERROR("File %s not found\n", image->filename); - return 1; + ERROR("File %s not found\n", filename); + return NULL; } } while ( r ); @@ -150,79 +153,28 @@ static int file_wait_open_read(struct sb_shm *sb_shared, struct image *image, sb_shared->pings[cookie]++; do { - imfile = imagefile_open(image->filename); - if ( imfile == NULL ) { - if ( wait_for_file && !read_retry_done ) { - read_retry_done = 1; - r = 1; - STATUS("File '%s' exists but could not be opened." - " Trying again after 10 seconds.\n", - image->filename); - sleep(10); - continue; - } - ERROR("Couldn't open file: %s\n", image->filename); - return 1; - } time_accounts_set(taccs, TACC_HDF5READ); set_last_task(last_task, "read file"); sb_shared->pings[cookie]++; - r = imagefile_read(imfile, image, image->event); - if ( r ) { + image = image_read(dtempl, filename, event); + if ( image == NULL ) { if ( wait_for_file && !read_retry_done ) { read_retry_done = 1; - imagefile_close(imfile); STATUS("File '%s' exists but could not be read." " Trying again after 10 seconds.\n", - image->filename); + filename); sleep(10); continue; } - ERROR("Couldn't open file: %s\n", image->filename); - return 1; + ERROR("Couldn't open file: %s\n", filename); + return NULL; } } while ( r ); - *pimfile = imfile; - return 0; -} - - -static struct detgeom *detgeom_from_olddet(struct detector *det) -{ - struct detgeom *dg; - int i; - - dg = malloc(sizeof(struct detgeom)); - if ( dg == NULL ) return NULL; - - dg->panels = malloc(det->n_panels*sizeof(struct detgeom_panel)); - if ( dg->panels == NULL ) return NULL; - - dg->n_panels = det->n_panels; - - for ( i=0; i<det->n_panels; i++ ) { - dg->panels[i].name = strdup(det->panels[i].name); - dg->panels[i].cnx = det->panels[i].cnx; - dg->panels[i].cny = det->panels[i].cny; - dg->panels[i].cnz = det->panels[i].clen; - dg->panels[i].pixel_pitch = 1.0/det->panels[i].res; - dg->panels[i].adu_per_photon = det->panels[i].adu_per_photon; - dg->panels[i].max_adu = det->panels[i].max_adu; - dg->panels[i].fsx = det->panels[i].fsx; - dg->panels[i].fsy = det->panels[i].fsy; - dg->panels[i].fsz = det->panels[i].fsz; - dg->panels[i].ssx = det->panels[i].ssx; - dg->panels[i].ssy = det->panels[i].ssy; - dg->panels[i].ssz = det->panels[i].ssz; - dg->panels[i].w = det->panels[i].w; - dg->panels[i].h = det->panels[i].h; - } - - return dg; + return image; } @@ -231,8 +183,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, int serial, struct sb_shm *sb_shared, TimeAccounts *taccs, char *last_task) { - struct imagefile *imfile = NULL; - struct image image; + struct image *image; int i; int r; int ret; @@ -240,27 +191,17 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, float **prefilter; int any_crystals; - image.features = NULL; - image.copyme = iargs->copyme; - image.id = cookie; - image.beam = iargs->beam; - image.det = copy_geom(iargs->det); - image.crystals = NULL; - image.n_crystals = 0; - image.serial = serial; - image.indexed_by = INDEXING_NONE; - - image.filename = pargs->filename_p_e->filename; - image.event = pargs->filename_p_e->ev; if ( pargs->msgpack_obj != NULL ) { set_last_task(last_task, "unpacking messagepack object"); - if ( unpack_msgpack_data(pargs->msgpack_obj, &image, - iargs->no_image_data) ) return; + image = unpack_msgpack_data(pargs->msgpack_obj, + iargs->no_image_data); + if ( image == NULL ) return; } else { - if ( file_wait_open_read(sb_shared, &image, taccs, last_task, - iargs->wait_for_file, cookie, - &imfile) ) - { + image = file_wait_open_read(pargs->filename, pargs->event, + iargs->dtempl, + sb_shared, taccs, last_task, + iargs->wait_for_file, cookie); + if ( image == NULL ) { if ( iargs->wait_for_file != 0 ) { pthread_mutex_lock(&sb_shared->totals_lock); sb_shared->should_shutdown = 1; @@ -270,66 +211,44 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, } } - /* Create detgeom structure after loading image, - * so we get the "filled in" clen values, etc. */ - image.detgeom = detgeom_from_olddet(iargs->det); - - image.bw = iargs->beam->bandwidth; + image->serial = serial; + image->copyme = iargs->copyme; /* Take snapshot of image before applying horrible noise filters */ time_accounts_set(taccs, TACC_FILTER); set_last_task(last_task, "image filter"); sb_shared->pings[cookie]++; - prefilter = backup_image_data(image.dp, image.det); + prefilter = backup_image_data(image->dp, image->detgeom); if ( iargs->median_filter > 0 ) { - filter_median(&image, iargs->median_filter); + filter_median(image, iargs->median_filter); } if ( iargs->noisefilter ) { - filter_noise(&image); + filter_noise(image); } time_accounts_set(taccs, TACC_RESRANGE); set_last_task(last_task, "resolution range"); sb_shared->pings[cookie]++; - mark_resolution_range_as_bad(&image, iargs->highres, +INFINITY); + mark_resolution_range_as_bad(image, iargs->highres, +INFINITY); time_accounts_set(taccs, TACC_PEAKSEARCH); sb_shared->pings[cookie]++; switch ( iargs->peaks ) { - struct hdfile *hdfile; - case PEAK_HDF5: - set_last_task(last_task, "peaksearch:hdf5"); - hdfile = imagefile_get_hdfile(imfile); - if ( (hdfile == NULL) - || (get_peaks_2(&image, hdfile, iargs->hdf5_peak_path, - iargs->half_pixel_shift)) ) - { - ERROR("Failed to get peaks from HDF5 file.\n"); - } - if ( !iargs->no_revalidate ) { - validate_peaks(&image, iargs->min_snr, - iargs->pk_inn, iargs->pk_mid, - iargs->pk_out, iargs->use_saturated, - iargs->check_hdf5_snr); - } - break; - case PEAK_CXI: - set_last_task(last_task, "peaksearch:cxi"); - hdfile = imagefile_get_hdfile(imfile); - if ( (hdfile == NULL) - || (get_peaks_cxi_2(&image, hdfile, iargs->hdf5_peak_path, - pargs->filename_p_e, - iargs->half_pixel_shift)) ) - { - ERROR("Failed to get peaks from CXI file.\n"); + set_last_task(last_task, "peaksearch:hdf5orcxi"); + image->features = image_read_peaks(iargs->dtempl, + pargs->filename, + pargs->event, + iargs->half_pixel_shift); + if ( image->features == NULL ) { + ERROR("Failed to get peaks from HDF5 file.\n"); } if ( !iargs->no_revalidate ) { - validate_peaks(&image, iargs->min_snr, + validate_peaks(image, iargs->min_snr, iargs->pk_inn, iargs->pk_mid, iargs->pk_out, iargs->use_saturated, iargs->check_hdf5_snr); @@ -338,7 +257,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, case PEAK_ZAEF: set_last_task(last_task, "peaksearch:zaef"); - search_peaks(&image, iargs->threshold, + search_peaks(image, iargs->threshold, iargs->min_sq_gradient, iargs->min_snr, iargs->pk_inn, iargs->pk_mid, iargs->pk_out, iargs->use_saturated); @@ -346,30 +265,24 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, case PEAK_PEAKFINDER8: set_last_task(last_task, "peaksearch:pf8"); - if ( search_peaks_peakfinder8(&image, 2048, - iargs->threshold, - iargs->min_snr, - iargs->min_pix_count, - iargs->max_pix_count, - iargs->local_bg_radius, - iargs->min_res, - iargs->max_res, - iargs->use_saturated) ) { - if ( image.event != NULL ) { - ERROR("Failed to find peaks in image %s" - "(event %s).\n", image.filename, - get_event_string(image.event)); - } else { - ERROR("Failed to find peaks in image %s.", - image.filename); - } - + if ( search_peaks_peakfinder8(image, 2048, + iargs->threshold, + iargs->min_snr, + iargs->min_pix_count, + iargs->max_pix_count, + iargs->local_bg_radius, + iargs->min_res, + iargs->max_res, + iargs->use_saturated) ) { + ERROR("Failed to find peaks in image %s" + "(event %s).\n", + image->filename, image->ev); } break; case PEAK_PEAKFINDER9: set_last_task(last_task, "peaksearch:pf9"); - if ( search_peaks_peakfinder9(&image, + if ( search_peaks_peakfinder9(image, iargs->min_snr_biggest_pix, iargs->min_snr_peak_pix, iargs->min_snr, @@ -377,21 +290,16 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, iargs->min_peak_over_neighbour, iargs->local_bg_radius) ) { - if ( image.event != NULL ) { - ERROR("Failed to find peaks in image %s" - "(event %s).\n", image.filename, - get_event_string(image.event)); - } else { - ERROR("Failed to find peaks in image %s.", - image.filename); - } + ERROR("Failed to find peaks in image %s" + "(event %s).\n", + image->filename, image->ev); } break; case PEAK_MSGPACK: - image.features = get_peaks_msgpack(pargs->msgpack_obj, - iargs->dtempl, - iargs->half_pixel_shift); + image->features = get_peaks_msgpack(pargs->msgpack_obj, + iargs->dtempl, + iargs->half_pixel_shift); break; case PEAK_NONE: @@ -400,11 +308,11 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, } - image.peak_resolution = estimate_peak_resolution(image.features, - image.lambda, - image.det); + image->peak_resolution = estimate_peak_resolution(image->features, + image->lambda, + image->det); - restore_image_data(image.dp, image.det, prefilter); + restore_image_data(image->dp, image->detgeom, prefilter); rn = getcwd(NULL, 0); @@ -412,33 +320,31 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, if ( r ) { ERROR("Failed to chdir to temporary folder: %s\n", strerror(errno)); - imagefile_close(imfile); return; } /* Set beam parameters */ if ( iargs->fix_divergence >= 0.0 ) { - image.div = iargs->fix_divergence; + image->div = iargs->fix_divergence; } else { - image.div = 0.0; + image->div = 0.0; } /* Set beam spectrum */ if ( iargs->spectrum != NULL ) { - image.spectrum = iargs->spectrum; + image->spectrum = iargs->spectrum; } else { - image.spectrum = spectrum_generate_gaussian(image.lambda, - image.bw); + image->spectrum = spectrum_generate_gaussian(image->lambda, + image->bw); } - if ( image_feature_count(image.features) < iargs->min_peaks ) { + if ( image_feature_count(image->features) < iargs->min_peaks ) { r = chdir(rn); if ( r ) { ERROR("Failed to chdir: %s\n", strerror(errno)); - imagefile_close(imfile); return; } free(rn); - image.hit = 0; + image->hit = 0; if ( iargs->stream_nonhits ) { goto streamwrite; @@ -446,18 +352,17 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, goto out; } } - image.hit = 1; + image->hit = 1; /* Index the pattern */ time_accounts_set(taccs, TACC_INDEXING); set_last_task(last_task, "indexing"); - index_pattern_3(&image, iargs->ipriv, &sb_shared->pings[cookie], + index_pattern_3(image, iargs->ipriv, &sb_shared->pings[cookie], last_task); r = chdir(rn); if ( r ) { ERROR("Failed to chdir: %s\n", strerror(errno)); - imagefile_close(imfile); return; } free(rn); @@ -466,21 +371,21 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, time_accounts_set(taccs, TACC_PREDPARAMS); set_last_task(last_task, "prediction params"); if ( iargs->fix_profile_r >= 0.0 ) { - for ( i=0; i<image.n_crystals; i++ ) { - crystal_set_profile_radius(image.crystals[i], + for ( i=0; i<image->n_crystals; i++ ) { + crystal_set_profile_radius(image->crystals[i], iargs->fix_profile_r); - crystal_set_mosaicity(image.crystals[i], 0.0); + crystal_set_mosaicity(image->crystals[i], 0.0); } } else { - for ( i=0; i<image.n_crystals; i++ ) { - crystal_set_profile_radius(image.crystals[i], 0.02e9); - crystal_set_mosaicity(image.crystals[i], 0.0); + for ( i=0; i<image->n_crystals; i++ ) { + crystal_set_profile_radius(image->crystals[i], 0.02e9); + crystal_set_mosaicity(image->crystals[i], 0.0); } } if ( iargs->fix_profile_r < 0.0 ) { - for ( i=0; i<image.n_crystals; i++ ) { - if ( refine_radius(image.crystals[i], &image) ) { + for ( i=0; i<image->n_crystals; i++ ) { + if ( refine_radius(image->crystals[i], image) ) { ERROR("WARNING: Radius determination failed\n"); } } @@ -490,7 +395,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, time_accounts_set(taccs, TACC_INTEGRATION); set_last_task(last_task, "integration"); sb_shared->pings[cookie]++; - integrate_all_5(&image, iargs->int_meth, PMODEL_XSPHERE, + integrate_all_5(image, iargs->int_meth, PMODEL_XSPHERE, iargs->push_res, iargs->ir_inn, iargs->ir_mid, iargs->ir_out, iargs->int_diag, iargs->int_diag_h, @@ -501,21 +406,19 @@ streamwrite: time_accounts_set(taccs, TACC_WRITESTREAM); set_last_task(last_task, "stream write"); sb_shared->pings[cookie]++; - ret = write_chunk(st, &image, imfile, - iargs->stream_peaks, iargs->stream_refls, - pargs->filename_p_e->ev); + ret = write_chunk(st, image, iargs->stream_peaks, + iargs->stream_refls); if ( ret != 0 ) { ERROR("Error writing stream file.\n"); } int n = 0; - for ( i=0; i<image.n_crystals; i++ ) { - n += crystal_get_num_implausible_reflections(image.crystals[i]); + for ( i=0; i<image->n_crystals; i++ ) { + n += crystal_get_num_implausible_reflections(image->crystals[i]); } if ( n > 0 ) { STATUS("WARNING: %i implausibly negative reflection%s in %s " - "%s\n", n, n>1?"s":"", image.filename, - get_event_string(image.event)); + "%s\n", n, n>1?"s":"", image->filename, image->ev); } out: @@ -525,40 +428,39 @@ out: sb_shared->pings[cookie]++; pthread_mutex_lock(&sb_shared->totals_lock); any_crystals = 0; - for ( i=0; i<image.n_crystals; i++ ) { - if ( crystal_get_user_flag(image.crystals[i]) == 0 ) { + for ( i=0; i<image->n_crystals; i++ ) { + if ( crystal_get_user_flag(image->crystals[i]) == 0 ) { sb_shared->n_crystals++; any_crystals = 1; } } sb_shared->n_processed++; - sb_shared->n_hits += image.hit; + sb_shared->n_hits += image->hit; sb_shared->n_hadcrystals += any_crystals; pthread_mutex_unlock(&sb_shared->totals_lock); - for ( i=0; i<image.n_crystals; i++ ) { - cell_free(crystal_get_cell(image.crystals[i])); - reflist_free(crystal_get_reflections(image.crystals[i])); - crystal_free(image.crystals[i]); + for ( i=0; i<image->n_crystals; i++ ) { + cell_free(crystal_get_cell(image->crystals[i])); + reflist_free(crystal_get_reflections(image->crystals[i])); + crystal_free(image->crystals[i]); } - free(image.crystals); + free(image->crystals); /* Free spectrum only if we generated it for this image */ if ( iargs->spectrum == NULL ) { - spectrum_free(image.spectrum); + spectrum_free(image->spectrum); } - for ( i=0; i<image.det->n_panels; i++ ) { - free(image.dp[i]); - free(image.bad[i]); - free(image.sat[i]); + for ( i=0; i<image->det->n_panels; i++ ) { + free(image->dp[i]); + free(image->bad[i]); + free(image->sat[i]); } - free(image.dp); - free(image.bad); - free(image.sat); + free(image->dp); + free(image->bad); + free(image->sat); - image_feature_list_free(image.features); - free_detector_geometry(image.det); - if ( imfile != NULL ) imagefile_close(imfile); + image_feature_list_free(image->features); + free_detector_geometry(image->det); set_last_task(last_task, "sandbox"); } diff --git a/src/process_image.h b/src/process_image.h index debae92e..908a2e06 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -58,13 +58,10 @@ struct index_args float min_sq_gradient; float min_snr; int check_hdf5_snr; - struct detector *det; - const DataTemplate *dtempl; + DataTemplate *dtempl; IndexingPrivate *ipriv; enum peak_search_method peaks; float tols[6]; - struct beam_params *beam; - char *hdf5_peak_path; int half_pixel_shift; float pk_inn; float pk_mid; @@ -110,7 +107,8 @@ struct index_args struct pattern_args { /* "Input" */ - struct filename_plus_event *filename_p_e; + char *filename; + char *event; #ifdef HAVE_MSGPACK msgpack_object *msgpack_obj; #else diff --git a/src/whirligig.c b/src/whirligig.c index 199ad0f3..ee74a25e 100644 --- a/src/whirligig.c +++ b/src/whirligig.c @@ -173,7 +173,7 @@ static void process_series(struct image *images, signed int *ser, Crystal *cr = images[i].crystals[ser[i]]; fprintf(fh, "%4i %5i %s %s %i\n", i, images[i].serial, images[i].filename, - get_event_string(images[i].event), + images[i].ev, ser[i]); p[i] = transform_reflections(crystal_get_reflections(cr), mat[i]); |