From 760cb454d937b1d4cf9fa528e409b00362f380c2 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 26 Mar 2021 15:24:09 +0100 Subject: indexamajig: Add --harvest-file --- src/indexamajig.c | 150 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ src/json-utils.h | 60 ++++++++++++++++++++++ 2 files changed, 210 insertions(+) create mode 100644 src/json-utils.h (limited to 'src') diff --git a/src/indexamajig.c b/src/indexamajig.c index eb39a32c..589fe6ed 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -64,6 +64,7 @@ #include "im-sandbox.h" #include "version.h" +#include "json-utils.h" struct indexamajig_arguments @@ -92,6 +93,7 @@ struct indexamajig_arguments int profile; /* Whether to do wall-clock time profiling */ char **copy_headers; int n_copy_headers; + char *harvest_file; TakeTwoOptions **taketwo_opts_ptr; FelixOptions **felix_opts_ptr; @@ -101,6 +103,141 @@ struct indexamajig_arguments }; +static double nan_if_neg(double n) +{ + if ( n < 0.0 ) { + return NAN; + } else { + return n; + } +} + + +static void write_json_cell(FILE *fh, const char *name, UnitCell *cell) +{ + double a, b, c, al, be, ga; + cell_get_parameters(cell, &a, &b, &c, &al, &be, &ga); + + fprintf(fh, " \"%s\": {\n", name); + fprintf(fh, " \"lattice_type\": \"%s\",\n", + str_lattice(cell_get_lattice_type(cell))); + fprintf(fh, " \"centering\": \"%c\",\n", + cell_get_centering(cell)); + fprintf(fh, " \"unique_axis\": \"%c\",\n", + cell_get_unique_axis(cell)); + fprintf(fh, " \"a_Angstrom\": %f,\n", a*1e10); + fprintf(fh, " \"b_Angstrom\": %f,\n", b*1e10); + fprintf(fh, " \"c_Angstrom\": %f,\n", c*1e10); + fprintf(fh, " \"alpha_deg\": %f,\n", rad2deg(al)); + fprintf(fh, " \"beta_deg\": %f,\n", rad2deg(be)); + fprintf(fh, " \"gamma_deg\": %f\n", rad2deg(ga)); /* NB No comma */ + fprintf(fh, " },\n"); +} + + +static void write_methods(FILE *fh, const char *name, IndexingPrivate *ipriv) +{ + int i, n; + const IndexingMethod *methods; + + fprintf(fh, " \"%s\": [", name); + + methods = indexing_methods(ipriv, &n); + for ( i=0; ihighres); + fprintf(fh, " },\n"); + + fprintf(fh, " \"peaksearch\": {\n"); + write_str(fh, 1, "method", str_peaksearch(args->peaks)); + write_float(fh, 1, "radius_inner_px", args->pk_inn); + write_float(fh, 1, "radius_middle_px", args->pk_mid); + write_float(fh, 1, "radius_outer_px", args->pk_out); + write_bool(fh, 1, "noise_filter", args->noisefilter); + write_int(fh, 1, "median_filter", args->median_filter); + write_float(fh, 1, "threshold_adu", args->threshold); + write_float(fh, 1, "min_squared_gradient_adu2", args->min_sq_gradient); + write_float(fh, 1, "min_snr", args->min_snr); + write_bool(fh, 1, "check_hdf5_snr", args->check_hdf5_snr); + write_bool(fh, 1, "half_pixel_shift", args->half_pixel_shift); + write_int(fh, 1, "min_res_px", args->min_res); + write_int(fh, 1, "max_res_px", args->max_res); + write_int(fh, 1, "max_num_peaks", args->max_n_peaks); + write_int(fh, 1, "max_pixel_count", args->max_pix_count); + write_int(fh, 1, "local_bg_radius_px", args->local_bg_radius); + write_bool(fh, 1, "use_saturated", args->use_saturated); + write_bool(fh, 1, "revalidate_hdf5", 1-args->no_revalidate); + write_float(fh, 1, "min_snr_of_biggest_pixel", args->min_snr_biggest_pix); + write_float(fh, 1, "min_snr_of_peak_pixel", args->min_snr_peak_pix); + write_float(fh, 1, "min_sig_adu", args->min_sig); + write_float(fh, 0, "min_peak_over_neighbour_adu", args->min_peak_over_neighbour); + fprintf(fh, " },\n"); + + fprintf(fh, " \"hitfinding\": {\n"); + write_int(fh, 0, "min_num_peaks", args->min_peaks); + fprintf(fh, " },\n"); + + fprintf(fh, " \"indexing\": {\n"); + write_methods(fh, "methods", args->ipriv); + write_json_cell(fh, "target_cell", args->cell); + write_float(fh, 1, "tolerance_a_percent", 100.0*args->tols[0]); + write_float(fh, 1, "tolerance_b_percent", 100.0*args->tols[1]); + write_float(fh, 1, "tolerance_c_percent", 100.0*args->tols[2]); + write_float(fh, 1, "tolerance_alpha_deg", rad2deg(args->tols[3])); + write_float(fh, 1, "tolerance_beta_deg", rad2deg(args->tols[4])); + write_float(fh, 1, "tolerance_gamma_deg", rad2deg(args->tols[5])); + write_bool(fh, 1, "multi_lattice", if_multi); + write_bool(fh, 1, "refine", if_refine); + write_bool(fh, 1, "retry", if_retry); + write_bool(fh, 1, "check_peaks", if_peaks); + write_bool(fh, 1, "check_cell", if_checkcell); + write_float(fh, 1, "wavelength_estimate_m", args->wavelength_estimate); + write_float(fh, 0, "clen_estimate_m", args->clen_estimate); + fprintf(fh, " },\n"); + + fprintf(fh, " \"integration\": {\n"); + tmp = str_integration_method(args->int_meth); + write_str(fh, 1, "method", tmp); + free(tmp); + write_float(fh, 1, "radius_inner_px", args->ir_inn); + write_float(fh, 1, "radius_middle_px", args->ir_mid); + write_float(fh, 1, "radius_outer_px", args->ir_out); + write_float(fh, 1, "push_res_invm", args->push_res); + write_float(fh, 1, "fix_profile_radius_invm", nan_if_neg(args->fix_profile_r)); + write_float(fh, 1, "fix_divergence_rad", nan_if_neg(args->fix_divergence)); + write_bool(fh, 0, "overpredict", args->overpredict); + fprintf(fh, " }\n"); /* NB No comma */ + + fprintf(fh, "}\n"); + + fclose(fh); +} + + static void show_version(FILE *fh, struct argp_state *state) { printf("CrystFEL: %s\n", crystfel_version_string()); @@ -589,6 +726,10 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) } break; + case 606 : + args->harvest_file = strdup(arg); + break; + default : return ARGP_ERR_UNKNOWN; @@ -636,6 +777,7 @@ int main(int argc, char *argv[]) args.profile = 0; args.copy_headers = NULL; args.n_copy_headers = 0; + args.harvest_file = NULL; args.taketwo_opts_ptr = &taketwo_opts; args.felix_opts_ptr = &felix_opts; args.xgandalf_opts_ptr = &xgandalf_opts; @@ -822,6 +964,8 @@ int main(int argc, char *argv[]) "in stream"}, {"serial-start", 605, "n", OPTION_NO_USAGE, "Start the serial numbers in the stream " "here"}, + {"harvest-file", 606, "filename", OPTION_NO_USAGE, "Write the actual parameters " + "used in JSON format"}, {NULL, 0, 0, OPTION_DOC, "More information:", 99}, @@ -1057,6 +1201,12 @@ int main(int argc, char *argv[]) stream_write_target_cell(st, args.iargs.cell); stream_write_indexing_methods(st, args.indm_str); + if ( args.harvest_file != NULL ) { + write_harvest_file(&args.iargs, args.harvest_file, + args.if_multi, args.if_refine, args.if_retry, + args.if_peaks, args.if_checkcell); + } + free(args.outfile); free(args.indm_str); diff --git a/src/json-utils.h b/src/json-utils.h new file mode 100644 index 00000000..5c03256b --- /dev/null +++ b/src/json-utils.h @@ -0,0 +1,60 @@ +/* + * json-utils.h + * + * JSON writing utilities + * + * Copyright © 2021 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2021 Thomas White + * + * 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 . + * + */ + +static void write_float(FILE *fh, int comma, const char *name, float val) +{ + const char *cs = comma ? "," : ""; + + if ( isnan(val) ) { + fprintf(fh, " \"%s\": null%s\n", name, cs); + } else if ( val > 0.0001 ) { + fprintf(fh, " \"%s\": %f%s\n", name, val, cs); + } else { + fprintf(fh, " \"%s\": %e%s\n", name, val, cs); + } +} + + +static void write_bool(FILE *fh, int comma, const char *name, int val) +{ + fprintf(fh, " \"%s\": %s%s\n", + name, val?"true":"false", comma?",":""); +} + + +static void write_int(FILE *fh, int comma, const char *name, int val) +{ + fprintf(fh, " \"%s\": %i%s\n", name, val, comma?",":""); +} + + +static void write_str(FILE *fh, int comma, const char *name, const char *val) +{ + fprintf(fh, " \"%s\": \"%s\"%s\n", name, val, comma?",":""); +} + -- cgit v1.2.3