From e561d0cd3374f1c126145048ef349335f9f0b143 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Sun, 20 Feb 2011 04:29:21 -0800 Subject: indexamajig: Remove all simulation stuff This was UGLY, and caused maintenance problems. Find a better way to do it if it's really necessary. --- src/indexamajig.c | 217 +----------------------------------------------------- 1 file changed, 1 insertion(+), 216 deletions(-) diff --git a/src/indexamajig.c b/src/indexamajig.c index 7fae3ea6..525fcfc3 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -29,15 +29,12 @@ #include "hdf5-file.h" #include "index.h" #include "peaks.h" -#include "diffraction.h" -#include "diffraction-gpu.h" #include "detector.h" #include "sfac.h" #include "filters.h" #include "reflections.h" #include "thread-pool.h" #include "beam-parameters.h" -#include "symmetry.h" #include "geometry.h" @@ -50,16 +47,12 @@ enum { /* Information about the indexing process which is common to all patterns */ struct static_index_args { - pthread_mutex_t *gpu_mutex; /* Protects "gctx" */ UnitCell *cell; int config_cmfilter; int config_noisefilter; int config_dumpfound; int config_verbose; - int config_alternate; int config_nearbragg; - int config_gpu; - int config_simulate; int config_polar; int config_satcorr; int config_closer; @@ -69,11 +62,6 @@ struct static_index_args struct detector *det; IndexingMethod *indm; IndexingPrivate **ipriv; - const double *intensities; - const unsigned char *flags; - const char *sym; /* Symmetry of "intensities" and "flags" */ - struct gpu_context *gctx; - int gpu_dev; int peaks; int cellr; struct beam_params *beam; @@ -153,11 +141,6 @@ static void show_help(const char *s) " was located by the initial peak search close to\n" " the \"near Bragg\" location, its coordinates will\n" " be taken as the centre instead.\n" -" --simulate Simulate the diffraction pattern using the indexed\n" -" unit cell. The simulated pattern will be saved\n" -" as \"simulated.h5\". You can TRY to combine this\n" -" with \"-j \" with n greater than 1, but it's\n" -" not a good idea.\n" " --dump-peaks Write the results of the peak search to stdout.\n" " The intensities in this list are from the\n" " centroid/integration procedure.\n" @@ -182,16 +165,8 @@ static void show_help(const char *s) " --min-gradient= Minimum gradient for Zaefferer peak search.\n" " Default: 100,000.\n" "\n" -"\nIf you used --simulate, you may also want:\n\n" -" --intensities= Specify file containing reflection intensities\n" -" to use when simulating.\n" -" -y, --symmetry= The symmetry of the intensities file.\n" -"\n" "\nOptions for greater performance or verbosity:\n\n" " --verbose Be verbose about indexing.\n" -" --gpu Use the GPU to speed up the simulation.\n" -" --gpu-dev= Use GPU device . Omit this option to see the\n" -" available devices.\n" " -j Run analyses in parallel. Default 1.\n" "\n" "\nOptions you probably won't need:\n\n" @@ -205,100 +180,11 @@ static void show_help(const char *s) } -static struct image *get_simage(struct image *template, int alternate) -{ - struct image *image; - struct panel panels[2]; - - image = malloc(sizeof(*image)); - - /* Simulate a diffraction pattern */ - image->twotheta = NULL; - image->data = NULL; - image->det = template->det; - image->flags = NULL; - image->f0_available = 0; - image->f0 = 1.0; - - /* Detector geometry for the simulation - * - not necessarily the same as the original. */ - image->width = 1024; - image->height = 1024; - image->det->n_panels = 2; - - if ( alternate ) { - - /* Upper */ - panels[0].min_fs = 0; - panels[0].max_fs = 1023; - panels[0].min_ss = 512; - panels[0].max_ss = 1023; - panels[0].cx = 523.6; - panels[0].cy = 502.5; - panels[0].clen = 56.4e-2; /* 56.4 cm */ - panels[0].res = 13333.3; /* 75 microns/pixel */ - - /* Lower */ - panels[1].min_fs = 0; - panels[1].max_fs = 1023; - panels[1].min_ss = 0; - panels[1].max_ss = 511; - panels[1].cx = 520.8; - panels[1].cy = 525.0; - panels[1].clen = 56.7e-2; /* 56.7 cm */ - panels[1].res = 13333.3; /* 75 microns/pixel */ - - image->det->panels = panels; - - } else { - - /* Copy pointer to old geometry */ - image->det->panels = template->det->panels; - - } - - image->lambda = ph_en_to_lambda(eV_to_J(1.8e3)); - image->features = template->features; - image->filename = template->filename; - image->indexed_cell = template->indexed_cell; - image->f0 = template->f0; - - return image; -} - - -static void simulate_and_write(struct image *simage, struct gpu_context **gctx, - const double *intensities, - const unsigned char *flags, UnitCell *cell, - int gpu_dev, const char *sym) -{ - /* Set up GPU if necessary. - * Unfortunately, setup has to go here since until now we don't know - * enough about the situation. */ - if ( (gctx != NULL) && (*gctx == NULL) ) { - *gctx = setup_gpu(0, simage, intensities, flags, sym, gpu_dev); - } - - if ( (gctx != NULL) && (*gctx != NULL) ) { - get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell); - } else { - get_diffraction(simage, 24, 24, 40, - intensities, NULL, flags, cell, 0, - GRADIENT_MOSAIC, sym); - } - record_image(simage, 0); - - hdf5_write("simulated.h5", simage->data, simage->width, simage->height, - H5T_NATIVE_FLOAT); -} - - static void process_image(void *pp, int cookie) { struct index_args *pargs = pp; struct hdfile *hdfile; struct image image; - struct image *simage; float *data_for_measurement; size_t data_size; char *filename = pargs->filename; @@ -307,16 +193,9 @@ static void process_image(void *pp, int cookie) int config_noisefilter = pargs->static_args.config_noisefilter; int config_dumpfound = pargs->static_args.config_dumpfound; int config_verbose = pargs->static_args.config_verbose; - int config_alternate = pargs->static_args.config_alternate; int config_nearbragg = pargs->static_args.config_nearbragg; - int config_gpu = pargs->static_args.config_gpu; - int config_simulate = pargs->static_args.config_simulate; int config_polar = pargs->static_args.config_polar; IndexingMethod *indm = pargs->static_args.indm; - const double *intensities = pargs->static_args.intensities; - const unsigned char *flags = pargs->static_args.flags; - struct gpu_context *gctx = pargs->static_args.gctx; - const char *sym = pargs->static_args.sym; const struct beam_params *beam = pargs->static_args.beam; image.features = NULL; @@ -417,27 +296,6 @@ static void process_image(void *pp, int cookie) } - simage = get_simage(&image, config_alternate); - - /* Simulate if requested */ - if ( config_simulate ) { - if ( config_gpu ) { - pthread_mutex_lock(pargs->static_args.gpu_mutex); - simulate_and_write(simage, &gctx, intensities, flags, - image.indexed_cell, - pargs->static_args.gpu_dev, sym); - pthread_mutex_unlock(pargs->static_args.gpu_mutex); - } else { - simulate_and_write(simage, NULL, intensities, flags, - image.indexed_cell, 0, sym); - } - } - - /* Finished with alternate image */ - if ( simage->twotheta != NULL ) free(simage->twotheta); - if ( simage->data != NULL ) free(simage->data); - free(simage); - /* Only free cell if found */ cell_free(image.indexed_cell); @@ -504,7 +362,6 @@ static void finalise_image(void *qp, void *pp) int main(int argc, char *argv[]) { int c; - struct gpu_context *gctx = NULL; char *filename = NULL; char *outfile = NULL; FILE *fh; @@ -514,12 +371,9 @@ int main(int argc, char *argv[]) int config_noindex = 0; int config_dumpfound = 0; int config_nearbragg = 0; - int config_simulate = 0; int config_cmfilter = 0; int config_noisefilter = 0; - int config_gpu = 0; int config_verbose = 0; - int config_alternate = 0; int config_polar = 1; int config_satcorr = 1; int config_checkprefix = 1; @@ -535,9 +389,6 @@ int main(int argc, char *argv[]) int reduction_needs_cell; char *indm_str = NULL; UnitCell *cell; - double *intensities = NULL; - unsigned char *flags; - char *intfile = NULL; char *pdb = NULL; char *prefix = NULL; char *speaks = NULL; @@ -547,21 +398,17 @@ int main(int argc, char *argv[]) int nthreads = 1; int i; pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER; - pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER; char prepare_line[1024]; char prepare_filename[1024]; struct queue_args qargs; struct beam_params *beam = NULL; double nominal_photon_energy; - int gpu_dev = -1; - char *sym = NULL; /* Long options */ const struct option longopts[] = { {"help", 0, NULL, 'h'}, {"input", 1, NULL, 'i'}, {"output", 1, NULL, 'o'}, - {"gpu", 0, &config_gpu, 1}, {"no-index", 0, &config_noindex, 1}, {"dump-peaks", 0, &config_dumpfound, 1}, {"peaks", 1, NULL, 2}, @@ -570,13 +417,9 @@ int main(int argc, char *argv[]) {"indexing", 1, NULL, 'z'}, {"geometry", 1, NULL, 'g'}, {"beam", 1, NULL, 'b'}, - {"simulate", 0, &config_simulate, 1}, {"filter-cm", 0, &config_cmfilter, 1}, {"filter-noise", 0, &config_noisefilter, 1}, {"verbose", 0, &config_verbose, 1}, - {"alternate", 0, &config_alternate, 1}, - {"intensities", 1, NULL, 'q'}, - {"symmetry", 1, NULL, 'y'}, {"pdb", 1, NULL, 'p'}, {"prefix", 1, NULL, 'x'}, {"unpolarized", 0, &config_polar, 0}, @@ -586,13 +429,12 @@ int main(int argc, char *argv[]) {"min-gradient", 1, NULL, 4}, {"no-check-prefix", 0, &config_checkprefix, 0}, {"no-closer-peak", 0, &config_closer, 0}, - {"gpu-dev", 1, NULL, 5}, {"insane", 0, &config_insane, 1}, {0, 0, NULL, 0} }; /* Short options */ - while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:y:", + while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:", longopts, NULL)) != -1) { switch (c) { @@ -612,10 +454,6 @@ int main(int argc, char *argv[]) indm_str = strdup(optarg); break; - case 'q' : - intfile = strdup(optarg); - break; - case 'p' : pdb = strdup(optarg); break; @@ -636,10 +474,6 @@ int main(int argc, char *argv[]) threshold = strtof(optarg, NULL); break; - case 'y' : - sym = strdup(optarg); - break; - case 'b' : beam = get_beam_parameters(optarg); if ( beam == NULL ) { @@ -661,10 +495,6 @@ int main(int argc, char *argv[]) min_gradient = strtof(optarg, NULL); break; - case 5 : - gpu_dev = atoi(optarg); - break; - case 0 : break; @@ -702,8 +532,6 @@ int main(int argc, char *argv[]) } free(outfile); - if ( sym == NULL ) sym = strdup("1"); - if ( speaks == NULL ) { speaks = strdup("zaef"); STATUS("You didn't specify a peak detection method.\n"); @@ -719,35 +547,6 @@ int main(int argc, char *argv[]) } free(speaks); - if ( intfile != NULL ) { - - ReflItemList *items; - int i; - - items = read_reflections(intfile, intensities, - NULL, NULL, NULL); - - flags = new_list_flag(); - for ( i=0; ih, it->k, it->l, 1); - } - - if ( check_symmetry(items, sym) ) { - ERROR("The input reflection list does not appear to" - " have symmetry %s\n", sym); - return 1; - } - - delete_items(items); - - } else { - - intensities = NULL; - flags = NULL; - - } - if ( pdb == NULL ) { pdb = strdup("molecule.pdb"); } @@ -869,16 +668,12 @@ int main(int argc, char *argv[]) gsl_set_error_handler_off(); - qargs.static_args.gpu_mutex = &gpu_mutex; qargs.static_args.cell = cell; qargs.static_args.config_cmfilter = config_cmfilter; qargs.static_args.config_noisefilter = config_noisefilter; qargs.static_args.config_dumpfound = config_dumpfound; qargs.static_args.config_verbose = config_verbose; - qargs.static_args.config_alternate = config_alternate; qargs.static_args.config_nearbragg = config_nearbragg; - qargs.static_args.config_gpu = config_gpu; - qargs.static_args.config_simulate = config_simulate; qargs.static_args.config_polar = config_polar; qargs.static_args.config_satcorr = config_satcorr; qargs.static_args.config_closer = config_closer; @@ -889,11 +684,6 @@ int main(int argc, char *argv[]) qargs.static_args.det = det; qargs.static_args.indm = indm; qargs.static_args.ipriv = ipriv; - qargs.static_args.intensities = intensities; - qargs.static_args.flags = flags; - qargs.static_args.sym = sym; - qargs.static_args.gctx = gctx; - qargs.static_args.gpu_dev = gpu_dev; qargs.static_args.peaks = peaks; qargs.static_args.output_mutex = &output_mutex; qargs.static_args.ofh = ofh; @@ -916,14 +706,9 @@ int main(int argc, char *argv[]) cell_free(cell); if ( fh != stdin ) fclose(fh); if ( ofh != stdout ) fclose(ofh); - free(sym); STATUS("There were %i images, of which %i could be indexed.\n", n_images, qargs.n_indexable); - if ( gctx != NULL ) { - cleanup_gpu(gctx); - } - return 0; } -- cgit v1.2.3