/* * indexamajig.c * * Index patterns, output hkl+intensity etc. * * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * Copyright © 2012 Lorenzo Galli * * Authors: * 2010-2017 Thomas White * 2011 Richard Kirian * 2012 Lorenzo Galli * 2012 Chunhong Yoon * 2017 Valerio Mariani * * 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 . * */ #ifdef HAVE_CONFIG_H #include #endif #include #include #include #include #include #include #include #include #include #include #include #include "version.h" #include "utils.h" #include "hdf5-file.h" #include "index.h" #include "peaks.h" #include "detector.h" #include "filters.h" #include "thread-pool.h" #include "geometry.h" #include "stream.h" #include "reflist-utils.h" #include "cell-utils.h" #include "integration.h" #include "taketwo.h" #include "im-sandbox.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" " --version Print CrystFEL version number and exit.\n" "\n" " -i, --input= Filename of list of images to process.\n" " -o, --output= Output stream filename.\n" "\n" " --indexing= Use 'methods' for indexing. Provide one or more\n" " methods separated by commas.\n" " See 'man indexamajig' for details.\n" " -g. --geometry= Get detector geometry from file.\n" " -p, --pdb= File (PDB or CrystFEL unit cell format) from which\n" " to get the unit cell. Default: 'molecule.pdb'.\n" " --basename Remove the directory parts of the filenames.\n" " -x, --prefix=

Prefix filenames from input file with

.\n" " --peaks= Use 'method' for finding peaks. Choose from:\n" " zaef : Use Zaefferer (2000) gradient detection.\n" " This is the default method.\n" " peakfinder8: Use Peakfinder8 algorithm.\n" " hdf5 : Get from a table in HDF5 file.\n" " cxi : Get from CXI format HDF5 file.\n" " --hdf5-peaks=

Find peaks table in HDF5 file here.\n" " Default: /processing/hitfinder/peakinfo\n" " --integration= Perform final pattern integration using .\n" "\n\n" "For more control over the process, you might need:\n\n" " --tolerance= Set the tolerances for cell comparison.\n" " Default: 5,5,5,1.5.\n" " --filter-noise Apply an aggressive noise filter which sets all\n" " pixels in each 3x3 region to zero if any of them\n" " have negative values. Intensity measurement will\n" " be performed on the image as it was before this.\n" " --median-filter= Apply a median filter to the image data. Intensity\n" " measurement will be performed on the image as it\n" " was before this. The side length of the median\n" " filter box will be 2+1.\n" " Default: 0 (no filter).\n" " --no-sat-corr Don't correct values of saturated peaks using a\n" " table included in the HDF5 file.\n" " --threshold= Only accept peaks above ADU in both the\n" " Zaefferer and Peakfinder8 algorithms.\n" " Default: 800.\n" " --min-gradient= Minimum squared gradient for Zaefferer peak\n" " search. Default: 100,000.\n" " --min-snr= Minimum signal-to-noise ratio for peaks, with both\n" " Zaefferer and Peakfinder8 algorithms.\n" " Default: 5.\n" " --min-pix-count= Only accept peaks if they include more than \n" " pixels, in the Peakfinder8 algorithm.\n" " Default: 2.\n" " --max-pix-count= Only accept peaks if they include less than \n" " pixels, in the Peakfinder8 algorithm.\n" " Default: 200.\n" " --min-peaks= Minimum number of peaks for indexing.\n" " --local-bg-radius= Radius (in pixels) to use for the estimation of\n" " local background in the Peakfinder8 algorithm.\n" " Default: 3.\n" " --min-res= Only accept peaks if they lay at more than \n" " pixels from the center of the detector, in the\n" " peakfinder8 algorithm. Default: 0.\n" " --max-res= Only accept peaks if they lay at less than \n" " pixels from the center of the detector, in the\n" " peakfinder8 algorithm. Default: 1200.\n" " --check-hdf5-snr Check SNR for peaks from --peaks=hdf5.\n" " --peak-radius= Integration radii for peak search.\n" " --int-radius= Set the integration radii. Default: 4,5,7.\n" " --push-res= Integrate higher than apparent resolution cutoff.\n" " --highres= Absolute resolution cutoff in Angstroms.\n" " --fix-profile-radius Fix the reciprocal space profile radius for spot\n" " prediction (default: automatically determine.\n" " --fix-bandwidth Set the bandwidth for spot prediction.\n" " --fix-divergence Set the divergence (full angle) for spot prediction.\n" "\n" "\nFor time-resolved stuff, you might want to use:\n\n" " --copy-hdf5-field Copy the value of field into the stream. You\n" " can use this option as many times as you need.\n" "\n" "\nOverall control of the indexing process:\n\n" " --no-check-cell Don't check lattice parameters against input cell.\n" " --no-cell-combinations Don't use axis combinations when checking cell.\n" " --no-multi Don't repeat indexing to index multiple hits.\n" " --no-retry Don't repeat indexing to increase indexing rate.\n" " --no-refine Skip the prediction refinement step.\n" "\n" "\nOptions for greater performance:\n\n" " -j Run analyses in parallel. Default 1.\n" " --temp-dir= Put the temporary folder under .\n" "\n" "\nOptions you probably won't need:\n\n" " --no-check-prefix Don't attempt to correct the --prefix.\n" " --no-use-saturated During the initial peak search, reject\n" " peaks which contain pixels above max_adu.\n" " --no-revalidate Don't re-integrate and check HDF5 peaks for\n" " validity.\n" " --no-peaks-in-stream Do not record peak search results in the stream.\n" " --no-refls-in-stream Do not record integrated reflections in the stream.\n" " --no-non-hits-in-stream Do not include non-hit frames in the stream.\n" " (see --min-peaks)\n" " --int-diag= Show debugging information about reflections.\n" " --profile Show timing data for performance monitoring.\n" " --no-half-pixel-shift Don't offset the HDF5 peak locations by 0.5 px.\n" "\nLow-level options for the felix indexer:\n\n" " --felix-options Change the default arguments passed to the indexer.\n" " Given as a list of comma separated list of \n" " indexer specific, key word arguments.\n" " Example: \"arg1=10,arg2=500\" \n" "\nLow-level options for the TakeTwo indexer:\n\n" " --taketwo-member-threshold Minimum number of members in network\n" " --taketwo-len-tolerance Reciprocal space length tolerance (1/A)\n" " --taketwo-angle-tolerance Reciprocal space angle tolerance (in degrees)\n" " --taketwo-trace-tolerance Rotation matrix equivalence tolerance (in degrees)\n" ); } 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; in_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); } } int main(int argc, char *argv[]) { int c; char *filename = NULL; char *outfile = NULL; FILE *fh; Stream *st; int config_checkprefix = 1; int config_basename = 0; int integrate_saturated = 0; char *indm_str = NULL; char *cellfile = NULL; char *prefix = NULL; char *speaks = NULL; char *toler = NULL; int n_proc = 1; struct index_args iargs; char *intrad = NULL; char *pkrad = NULL; char *int_str = NULL; char *tempdir = NULL; char *int_diag = NULL; char *geom_filename = NULL; struct beam_params beam; int have_push_res = 0; int len; char *command_line_peak_path = NULL; int if_refine = 1; int if_nocomb = 0; int if_nocheck = 0; int if_peaks = 0; int if_multi = 1; int if_retry = 1; /* Defaults */ iargs.cell = NULL; iargs.noisefilter = 0; iargs.median_filter = 0; iargs.satcorr = 1; iargs.tols[0] = 5.0; iargs.tols[1] = 5.0; iargs.tols[2] = 5.0; iargs.tols[3] = 1.5; iargs.threshold = 800.0; iargs.min_gradient = 100000.0; iargs.min_snr = 5.0; iargs.min_pix_count = 2; iargs.max_pix_count = 200; iargs.min_res = 0; iargs.max_res = 1200; iargs.local_bg_radius = 3; iargs.check_hdf5_snr = 0; iargs.det = NULL; iargs.peaks = PEAK_ZAEF; iargs.beam = &beam; iargs.hdf5_peak_path = NULL; iargs.half_pixel_shift = 1; iargs.copyme = NULL; iargs.pk_inn = -1.0; iargs.pk_mid = -1.0; iargs.pk_out = -1.0; iargs.ir_inn = 4.0; iargs.ir_mid = 5.0; iargs.ir_out = 7.0; iargs.use_saturated = 1; iargs.no_revalidate = 0; iargs.stream_peaks = 1; iargs.stream_refls = 1; iargs.stream_nonhits = 1; iargs.int_diag = INTDIAG_NONE; iargs.copyme = new_imagefile_field_list(); iargs.min_peaks = 0; if ( iargs.copyme == NULL ) { ERROR("Couldn't allocate HDF5 field list.\n"); return 1; } iargs.ipriv = NULL; /* No default */ iargs.int_meth = integration_method("rings-nocen-nosat-nograd", NULL); iargs.push_res = 0.0; iargs.highres = +INFINITY; iargs.fix_profile_r = -1.0; iargs.fix_bandwidth = -1.0; iargs.fix_divergence = -1.0; iargs.felix_options = NULL; iargs.profile = 0; iargs.taketwo_opts.member_thresh = -1; iargs.taketwo_opts.len_tol = -1.0; iargs.taketwo_opts.angle_tol = -1.0; iargs.taketwo_opts.trace_tol = -1.0; /* Long options */ const struct option longopts[] = { /* Options with long and short versions */ {"help", 0, NULL, 'h'}, {"version", 0, NULL, 'v'}, {"input", 1, NULL, 'i'}, {"output", 1, NULL, 'o'}, {"indexing", 1, NULL, 'z'}, {"geometry", 1, NULL, 'g'}, {"pdb", 1, NULL, 'p'}, {"prefix", 1, NULL, 'x'}, {"threshold", 1, NULL, 't'}, {"beam", 1, NULL, 'b'}, /* Long-only options with no arguments */ {"filter-noise", 0, &iargs.noisefilter, 1}, {"no-check-prefix", 0, &config_checkprefix, 0}, {"basename", 0, &config_basename, 1}, {"no-peaks-in-stream", 0, &iargs.stream_peaks, 0}, {"no-refls-in-stream", 0, &iargs.stream_refls, 0}, {"no-non-hits-in-stream", 0, &iargs.stream_nonhits, 0}, {"integrate-saturated",0, &integrate_saturated, 1}, {"no-use-saturated", 0, &iargs.use_saturated, 0}, {"no-revalidate", 0, &iargs.no_revalidate, 1}, {"check-hdf5-snr", 0, &iargs.check_hdf5_snr, 1}, {"profile", 0, &iargs.profile, 1}, {"no-half-pixel-shift",0, &iargs.half_pixel_shift, 0}, {"no-refine", 0, &if_refine, 0}, {"no-cell-combinations",0,&if_nocomb, 1}, {"no-check-cell", 0, &if_nocheck, 1}, {"no-cell-check", 0, &if_nocheck, 1}, {"check-peaks", 0, &if_peaks, 1}, {"no-retry", 0, &if_retry, 0}, {"no-multi", 0, &if_multi, 0}, /* Long-only options which don't actually do anything */ {"no-sat-corr", 0, &iargs.satcorr, 0}, {"sat-corr", 0, &iargs.satcorr, 1}, {"no-check-hdf5-snr", 0, &iargs.check_hdf5_snr, 0}, {"use-saturated", 0, &iargs.use_saturated, 1}, /* Long-only options with arguments */ {"peaks", 1, NULL, 2}, {"cell-reduction", 1, NULL, 3}, {"min-gradient", 1, NULL, 4}, {"record", 1, NULL, 5}, {"cpus", 1, NULL, 6}, {"cpugroup", 1, NULL, 7}, {"cpuoffset", 1, NULL, 8}, {"hdf5-peaks", 1, NULL, 9}, {"copy-hdf5-field", 1, NULL, 10}, {"min-snr", 1, NULL, 11}, {"tolerance", 1, NULL, 13}, {"int-radius", 1, NULL, 14}, {"median-filter", 1, NULL, 15}, {"integration", 1, NULL, 16}, {"temp-dir", 1, NULL, 17}, {"int-diag", 1, NULL, 18}, {"push-res", 1, NULL, 19}, {"res-push", 1, NULL, 19}, /* compat */ {"peak-radius", 1, NULL, 20}, {"highres", 1, NULL, 21}, {"fix-profile-radius", 1, NULL, 22}, {"fix-bandwidth", 1, NULL, 23}, {"fix-divergence", 1, NULL, 24}, {"felix-options", 1, NULL, 25}, {"min-pix-count", 1, NULL, 26}, {"max-pix-count", 1, NULL, 27}, {"local-bg-radius", 1, NULL, 28}, {"min-res", 1, NULL, 29}, {"max-res", 1, NULL, 30}, {"min-peaks", 1, NULL, 31}, {"taketwo-member-threshold", 1, NULL, 32}, {"taketwo-member-thresh", 1, NULL, 32}, {"taketwo-len-tolerance", 1, NULL, 33}, {"taketwo-len-tol", 1, NULL, 33}, {"taketwo-angle-tolerance", 1, NULL, 34}, {"taketwo-angle-tol", 1, NULL, 34}, {"taketwo-trace-tolerance", 1, NULL, 35}, {"taketwo-trace-tol", 1, NULL, 35}, {0, 0, NULL, 0} }; /* Short options */ while ((c = getopt_long(argc, argv, "hi:o:z:p:x:j:g:t:vb:", longopts, NULL)) != -1) { switch (c) { case 'h' : show_help(argv[0]); return 0; case 'v' : printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n"); printf(CRYSTFEL_BOILERPLATE"\n"); return 0; case 'b' : ERROR("WARNING: This version of CrystFEL no longer " "uses beam files. Please remove the beam file " "from your indexamajig command line.\n"); return 1; case 'i' : filename = strdup(optarg); break; case 'o' : outfile = strdup(optarg); break; case 'z' : indm_str = strdup(optarg); break; case 'p' : cellfile = strdup(optarg); break; case 'x' : prefix = strdup(optarg); break; case 'j' : n_proc = atoi(optarg); break; case 'g' : geom_filename = optarg; break; case 't' : iargs.threshold = strtof(optarg, NULL); break; case 2 : speaks = strdup(optarg); break; case 3 : ERROR("The option '--cell-reduction' is no longer " "used.\n" "The complete indexing behaviour is now " "controlled using '--indexing'.\n" "See 'man indexamajig' for details of the " "available methods.\n"); return 1; case 4 : iargs.min_gradient = strtof(optarg, NULL); break; case 5 : ERROR("The option '--record' is no longer used.\n" "Use '--no-peaks-in-stream' and" "'--no-refls-in-stream' if you need to control" "the contents of the stream.\n"); return 1; case 6 : case 7 : case 8 : ERROR("The options --cpus, --cpugroup and --cpuoffset" " are no longer used by indexamajig.\n"); break; case 9 : free(command_line_peak_path); command_line_peak_path = strdup(optarg); break; case 10 : add_imagefile_field(iargs.copyme, optarg); break; case 11 : iargs.min_snr = strtof(optarg, NULL); break; case 13 : toler = strdup(optarg); break; case 14 : intrad = strdup(optarg); break; case 15 : iargs.median_filter = atoi(optarg); break; case 16 : int_str = strdup(optarg); break; case 17 : tempdir = strdup(optarg); break; case 18 : int_diag = strdup(optarg); break; case 19 : if ( sscanf(optarg, "%f", &iargs.push_res) != 1 ) { ERROR("Invalid value for --push-res\n"); return 1; } iargs.push_res *= 1e9; /* nm^-1 -> m^-1 */ have_push_res = 1; break; case 20 : pkrad = strdup(optarg); break; case 21 : if ( sscanf(optarg, "%f", &iargs.highres) != 1 ) { ERROR("Invalid value for --highres\n"); return 1; } /* A -> m^-1 */ iargs.highres = 1.0 / (iargs.highres/1e10); break; case 22 : if ( sscanf(optarg, "%f", &iargs.fix_profile_r) != 1 ) { ERROR("Invalid value for " "--fix-profile-radius\n"); return 1; } break; case 23 : if ( sscanf(optarg, "%f", &iargs.fix_bandwidth) != 1 ) { ERROR("Invalid value for --fix-bandwidth\n"); return 1; } break; case 24 : if ( sscanf(optarg, "%f", &iargs.fix_divergence) != 1 ) { ERROR("Invalid value for --fix-divergence\n"); return 1; } break; case 25 : /* Remove leading and trailing quotes */ len = strlen(optarg); if ( optarg[len-1] == '\'' || optarg[len-1] == '\"' ){ optarg[len-1] = 0; } if ( optarg[0] == '\'' || optarg[0] == '\"' ){ iargs.felix_options = strdup( optarg+1 ); } else { iargs.felix_options = strdup( optarg ); } break; case 26: iargs.min_pix_count = atoi(optarg); break; case 27: iargs.max_pix_count = atoi(optarg); break; case 28: iargs.local_bg_radius = atoi(optarg); break; case 29: iargs.min_res = atoi(optarg); break; case 30: iargs.max_res = atoi(optarg); break; case 31: iargs.min_peaks = atoi(optarg); break; case 32: if ( sscanf(optarg, "%i", &iargs.taketwo_opts.member_thresh) != 1 ) { ERROR("Invalid value for --taketwo-member-threshold\n"); return 1; } break; case 33: if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.len_tol) != 1 ) { ERROR("Invalid value for --taketwo-len-tolerance\n"); return 1; } /* Convert to m^-1 */ iargs.taketwo_opts.len_tol *= 1e10; break; case 34: if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.angle_tol) != 1 ) { ERROR("Invalid value for --taketwo-angle-tolerance\n"); return 1; } /* Convert to radians */ iargs.taketwo_opts.angle_tol = deg2rad(iargs.taketwo_opts.angle_tol); break; case 35: if ( sscanf(optarg, "%lf", &iargs.taketwo_opts.trace_tol) != 1 ) { ERROR("Invalid value for --taketwo-trace-tolerance\n"); return 1; } /* Convert to radians */ iargs.taketwo_opts.trace_tol = deg2rad(iargs.taketwo_opts.trace_tol); break; case 0 : break; case '?' : break; default : ERROR("Unhandled option '%c'\n", c); break; } } /* Check for minimal information */ if ( filename == NULL ) { ERROR("You need to provide the input filename (use -i)\n"); return 1; } if ( geom_filename == NULL ) { ERROR("You need to specify the geometry filename (use -g)\n"); return 1; } if ( outfile == NULL ) { ERROR("You need to specify the output filename (use -o)\n"); return 1; } if ( tempdir == NULL ) { tempdir = strdup("."); } /* Open input */ if ( strcmp(filename, "-") == 0 ) { fh = stdin; } else { fh = fopen(filename, "r"); } if ( fh == NULL ) { ERROR("Failed to open input file '%s'\n", filename); return 1; } free(filename); /* Parse peak detection method */ if ( speaks == NULL ) { speaks = strdup("zaef"); STATUS("You didn't specify a peak detection method.\n"); STATUS("I'm using 'zaef' for you.\n"); } if ( strcmp(speaks, "zaef") == 0 ) { iargs.peaks = PEAK_ZAEF; } else if ( strcmp(speaks, "peakfinder8") == 0 ) { iargs.peaks = PEAK_PEAKFINDER8; } else if ( strcmp(speaks, "hdf5") == 0 ) { iargs.peaks = PEAK_HDF5; } else if ( strcmp(speaks, "cxi") == 0 ) { iargs.peaks = PEAK_CXI; } else { ERROR("Unrecognised peak detection method '%s'\n", speaks); return 1; } free(speaks); /* Check prefix (if given) */ if ( prefix == NULL ) { prefix = strdup(""); } else { if ( config_checkprefix ) { prefix = check_prefix(prefix); } } /* Check number of processes */ if ( n_proc == 0 ) { ERROR("Invalid number of processes.\n"); return 1; } /* Load detector geometry */ iargs.det = get_detector_geometry_2(geom_filename, iargs.beam, &iargs.hdf5_peak_path); if ( iargs.det == NULL ) { ERROR("Failed to read detector geometry from '%s'\n", geom_filename); return 1; } add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam); /* If no peak path from geometry file, use these (but see later) */ if ( iargs.hdf5_peak_path == NULL ) { if ( iargs.peaks == PEAK_HDF5 ) { iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo"); } else if ( iargs.peaks == PEAK_CXI ) { iargs.hdf5_peak_path = strdup("/entry_1/result_1"); } } /* If an HDF5 peak path was given on the command line, use it */ if ( command_line_peak_path != NULL ) { free(iargs.hdf5_peak_path); iargs.hdf5_peak_path = command_line_peak_path; } /* Parse integration method */ if ( int_str != NULL ) { int err; iargs.int_meth = integration_method(int_str, &err); if ( err ) { ERROR("Invalid integration method '%s'\n", int_str); return 1; } free(int_str); } if ( integrate_saturated ) { /* Option provided for backwards compatibility */ iargs.int_meth |= INTEGRATION_SATURATED; } if ( have_push_res && !(iargs.int_meth & INTEGRATION_RESCUT) ) { ERROR("WARNING: You used --push-res, but not -rescut, " "therefore --push-res will have no effect.\n"); } /* Parse unit cell tolerance */ if ( toler != NULL ) { int ttt; ttt = sscanf(toler, "%f,%f,%f,%f", &iargs.tols[0], &iargs.tols[1], &iargs.tols[2], &iargs.tols[3]); if ( ttt != 4 ) { ERROR("Invalid parameters for '--tolerance'\n"); return 1; } free(toler); } /* Parse integration radii */ if ( intrad != NULL ) { int r; r = sscanf(intrad, "%f,%f,%f", &iargs.ir_inn, &iargs.ir_mid, &iargs.ir_out); if ( r != 3 ) { ERROR("Invalid parameters for '--int-radius'\n"); return 1; } free(intrad); } else { STATUS("WARNING: You did not specify --int-radius.\n"); STATUS("WARNING: I will use the default values, which are" " probably not appropriate for your patterns.\n"); } /* Parse peak radii (used for peak detection) */ if ( pkrad != NULL ) { int r; r = sscanf(pkrad, "%f,%f,%f", &iargs.pk_inn, &iargs.pk_mid, &iargs.pk_out); if ( r != 3 ) { ERROR("Invalid parameters for '--peak-radius'\n"); return 1; } free(pkrad); } if ( iargs.pk_inn < 0.0 ) { iargs.pk_inn = iargs.ir_inn; iargs.pk_mid = iargs.ir_mid; iargs.pk_out = iargs.ir_out; } /* Load unit cell (if given) */ if ( cellfile != NULL ) { iargs.cell = load_cell_from_file(cellfile); if ( iargs.cell == NULL ) { ERROR("Couldn't read unit cell (from %s)\n", cellfile); return 1; } free(cellfile); } else { iargs.cell = NULL; } /* Parse integration diagnostic */ if ( int_diag != NULL ) { int r; signed int h, k, l; if ( strcmp(int_diag, "random") == 0 ) { iargs.int_diag = INTDIAG_RANDOM; } if ( strcmp(int_diag, "all") == 0 ) { iargs.int_diag = INTDIAG_ALL; } if ( strcmp(int_diag, "negative") == 0 ) { iargs.int_diag = INTDIAG_NEGATIVE; } if ( strcmp(int_diag, "implausible") == 0 ) { iargs.int_diag = INTDIAG_IMPLAUSIBLE; } if ( strcmp(int_diag, "strong") == 0 ) { iargs.int_diag = INTDIAG_STRONG; } r = sscanf(int_diag, "%i,%i,%i", &h, &k, &l); if ( r == 3 ) { iargs.int_diag = INTDIAG_INDICES; iargs.int_diag_h = h; iargs.int_diag_k = k; iargs.int_diag_l = l; } if ( (iargs.int_diag == INTDIAG_NONE) && (strcmp(int_diag, "none") != 0) ) { ERROR("Invalid value for --int-diag.\n"); return 1; } free(int_diag); } /* Open output stream */ st = open_stream_for_write_3(outfile, geom_filename, iargs.cell, argc, argv); if ( st == NULL ) { ERROR("Failed to open stream '%s'\n", outfile); return 1; } free(outfile); /* Prepare the indexing system */ if ( indm_str == NULL ) { STATUS("You didn't specify an indexing method, so I won't try " " to index anything.\n" "If that isn't what you wanted, re-run with" " --indexing=.\n"); if ( iargs.cell != NULL ) { STATUS("Ignoring your unit cell.\n"); } iargs.ipriv = NULL; } else if ( strcmp(indm_str, "none") == 0 ) { STATUS("Indexing/integration disabled.\n"); if ( iargs.cell != NULL ) { STATUS("Ignoring your unit cell.\n"); } iargs.ipriv = NULL; } else { IndexingFlags flags = 0; if ( iargs.cell != NULL ) { STATUS("This is what I understood your unit cell to be:\n"); cell_print(iargs.cell); } else { STATUS("No reference unit cell provided.\n"); } if ( if_nocomb ) { flags |= INDEXING_CHECK_CELL_AXES; } else { flags |= INDEXING_CHECK_CELL_COMBINATIONS; } if ( if_nocheck ) { flags &= ~INDEXING_CHECK_CELL_AXES; flags &= ~INDEXING_CHECK_CELL_COMBINATIONS; } if ( if_refine ) { flags |= INDEXING_REFINE; } if ( if_peaks ) { flags |= INDEXING_CHECK_PEAKS; } if ( if_multi ) { flags |= INDEXING_MULTI; } if ( if_retry ) { flags |= INDEXING_RETRY; } iargs.ipriv = setup_indexing(indm_str, iargs.cell, iargs.det, iargs.tols, flags, iargs.felix_options, &iargs.taketwo_opts); if ( iargs.ipriv == NULL ) { ERROR("Failed to set up indexing system\n"); return 1; } free(indm_str); } gsl_set_error_handler_off(); create_sandbox(&iargs, n_proc, prefix, config_basename, fh, st, tempdir); free_imagefile_field_list(iargs.copyme); cell_free(iargs.cell); free(iargs.beam->photon_energy_from); free(prefix); free(tempdir); free_detector_geometry(iargs.det); free(iargs.hdf5_peak_path); close_stream(st); cleanup_indexing(iargs.ipriv); return 0; }