/* * indexamajig.c * * Find hits, index patterns, output hkl+intensity etc. * * (c) 2006-2010 Thomas White * * Part of CrystFEL - crystallography with a FEL * */ #ifdef HAVE_CONFIG_H #include #endif #include #include #include #include #include #include #include #include "utils.h" #include "hdf5-file.h" #include "index.h" #include "intensities.h" #include "peaks.h" #include "diffraction.h" #include "detector.h" #include "sfac.h" #include "filters.h" static void show_help(const char *s) { printf("Syntax: %s [options]\n\n", s); printf( "Process and index FEL diffraction images.\n" "\n" " -h, --help Display this help message.\n" "\n" " -i, --input= Specify file containing list of images to process.\n" " '-' means stdin, which is the default.\n" " --indexing= Use 'method' for indexing. Choose from:\n" " none : no indexing\n" " dirax : invoke DirAx\n" " --write-drx Write 'xfel.drx' for visualisation of reciprocal\n" " space. Implied by any indexing method other than" " 'none'.\n" " --dump-peaks Write the results of the peak search to stdout.\n" " --near-bragg Output a list of reflection intensities to stdout.\n" " --simulate Simulate the diffraction pattern using the indexed\n" " unit cell.\n" " --clean-image Perform common-mode noise subtraction and\n" " background removal on images before proceeding.\n" " --no-match Don't attempt to match the indexed cell to the\n" " model, just proceed with the one generated by the\n" " auto-indexing procedure.\n" "\n"); } int main(int argc, char *argv[]) { int c; char *filename = NULL; FILE *fh; char *rval; int n_images; int n_hits; int config_noindex = 0; int config_dumpfound = 0; int config_nearbragg = 0; int config_writedrx = 0; int config_simulate = 0; int config_clean = 0; int config_nomatch = 0; IndexingMethod indm; char *indm_str = NULL; /* Long options */ const struct option longopts[] = { {"help", 0, NULL, 'h'}, {"input", 1, NULL, 'i'}, {"no-index", 0, &config_noindex, 1}, {"dump-peaks", 0, &config_dumpfound, 1}, {"near-bragg", 0, &config_nearbragg, 1}, {"write-drx", 0, &config_writedrx, 1}, {"indexing", 1, NULL, 'z'}, {"simulate", 0, &config_simulate, 1}, {"clean-image", 0, &config_clean, 1}, {"no-match", 0, &config_nomatch, 1}, {0, 0, NULL, 0} }; /* Short options */ while ((c = getopt_long(argc, argv, "hi:w", longopts, NULL)) != -1) { switch (c) { case 'h' : { show_help(argv[0]); return 0; } case 'i' : { filename = strdup(optarg); break; } case 'z' : { indm_str = strdup(optarg); break; } case 0 : { break; } default : { return 1; } } } if ( filename == NULL ) { filename = strdup("-"); } if ( strcmp(filename, "-") == 0 ) { fh = stdin; } else { fh = fopen(filename, "r"); } free(filename); if ( fh == NULL ) { ERROR("Failed to open input file\n"); return 1; } if ( indm_str == NULL ) { STATUS("You didn't specify an indexing method, so I won't" " try to index anything. If that isn't what you\n" " wanted, re-run with --indexing=.\n"); indm = INDEXING_NONE; } else if ( strcmp(indm_str, "none") == 0 ) { indm = INDEXING_NONE; } else if ( strcmp(indm_str, "dirax") == 0) { indm = INDEXING_DIRAX; } else { ERROR("Unrecognised indexing method '%s'\n", indm_str); return 1; } n_images = 0; n_hits = 0; do { char line[1024]; struct hdfile *hdfile; struct image image; rval = fgets(line, 1023, fh); if ( rval == NULL ) continue; chomp(line); image.features = NULL; image.molecule = load_molecule(); image.data = NULL; image.indexed_cell = NULL; /* Set up detector configuration */ image.det.n_panels = 2; image.det.panels = malloc(2*sizeof(struct panel)); /* Upper panel */ image.det.panels[0].min_x = 0; image.det.panels[0].max_x = 1023; image.det.panels[0].min_y = 512; image.det.panels[0].max_y = 1023; image.det.panels[0].cx = 491.9; image.det.panels[0].cy = 440.7; image.det.panels[0].clen = 67.0e-3; image.det.panels[0].res = 13333.3; /* 75 micron pixel size */ /* Lower panel */ image.det.panels[1].min_x = 0; image.det.panels[1].max_x = 1023; image.det.panels[1].min_y = 0; image.det.panels[1].max_y = 511; image.det.panels[1].cx = 492.0; image.det.panels[1].cy = 779.7; image.det.panels[1].clen = 75.0e-3; image.det.panels[1].res = 13333.3; /* 75 micron pixel size */ STATUS("Processing '%s'\n", line); n_images++; hdfile = hdfile_open(line); if ( hdfile == NULL ) { continue; } else if ( hdfile_set_first_image(hdfile, "/") ) { ERROR("Couldn't select path\n"); continue; } hdf5_read(hdfile, &image); if ( config_clean ) { clean_image(&image); } /* Perform 'fine' peak search */ search_peaks(&image); if ( image_feature_count(image.features) > 5 ) { if ( config_dumpfound ) dump_peaks(&image); /* Not indexing nor writing xfel.drx? * Then there's nothing left to do. */ if ( (!config_writedrx) && (indm == INDEXING_NONE) ) { goto done; } /* Calculate orientation matrix (by magic) */ if ( config_writedrx || (indm != INDEXING_NONE) ) { index_pattern(&image, indm, config_nomatch); } /* No cell at this point? Then we're done. */ if ( image.indexed_cell == NULL ) goto done; n_hits++; /* Simulation or intensity measurements both require * Ewald sphere vectors */ if ( config_nearbragg || config_simulate ) { /* Simulate a diffraction pattern */ image.sfacs = NULL; image.twotheta = NULL; image.hdr = NULL; /* View head-on (unit cell is tilted) */ image.orientation.w = 1.0; image.orientation.x = 0.0; image.orientation.y = 0.0; image.orientation.z = 0.0; } /* Measure intensities if requested */ if ( config_nearbragg ) { output_intensities(&image, image.indexed_cell); } /* Simulate pattern if requested */ if ( config_simulate ) { image.data = NULL; get_diffraction(&image, 8, 8, 8, 0); if ( image.molecule == NULL ) { ERROR("Couldn't open molecule.pdb\n"); return 1; } record_image(&image, 0, 0, 0); hdf5_write("simulated.h5", image.data, image.width, image.height, H5T_NATIVE_INT16); } } done: free(image.data); image_feature_list_free(image.features); hdfile_close(hdfile); H5close(); } while ( rval != NULL ); fclose(fh); STATUS("There were %i images.\n", n_images); STATUS("%i hits were found.\n", n_hits); return 0; }