diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | Makefile.am | 4 | ||||
| -rw-r--r-- | src/whirligig.c | 172 |
3 files changed, 176 insertions, 1 deletions
@@ -35,6 +35,7 @@ src/check_hkl src/partial_sim src/cell_explorer src/ambigator +src/whirligig src/.dirstamp *~ doc/reference/libcrystfel/* diff --git a/Makefile.am b/Makefile.am index 83e736ce..3aca82ed 100644 --- a/Makefile.am +++ b/Makefile.am @@ -5,7 +5,7 @@ ACLOCAL_AMFLAGS = -I m4 bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \ src/compare_hkl src/partialator src/check_hkl src/partial_sim \ - src/ambigator src/geoptimiser + src/ambigator src/geoptimiser src/whirligig noinst_PROGRAMS = tests/list_check tests/integration_check \ tests/pr_p_gradient_check tests/symmetry_check \ @@ -95,6 +95,8 @@ src_ambigator_SOURCES = src/ambigator.c src_geoptimiser_SOURCES = src/geoptimiser.c +src_whirligig_SOURCES = src/whirligig.c + if HAVE_CAIRO if HAVE_PANGO if HAVE_PANGOCAIRO diff --git a/src/whirligig.c b/src/whirligig.c new file mode 100644 index 00000000..e3ad195d --- /dev/null +++ b/src/whirligig.c @@ -0,0 +1,172 @@ +/* + * whirligig.c + * + * Find and combine rotation series + * + * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2012-2014 Thomas White <taw@physics.org> + * + * 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 <http://www.gnu.org/licenses/>. + * + */ + + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +#include <stdarg.h> +#include <stdlib.h> +#include <stdio.h> +#include <string.h> +#include <unistd.h> +#include <getopt.h> +#include <assert.h> +#include <pthread.h> +#include <gsl/gsl_errno.h> + +#include <image.h> +#include <utils.h> +#include <symmetry.h> +#include <stream.h> +#include <geometry.h> +#include <peaks.h> +#include <thread-pool.h> +#include <reflist.h> +#include <reflist-utils.h> + +#include "version.h" + + +static void show_help(const char *s) +{ + printf("Syntax: %s <input.stream> [options]\n\n", s); + printf( +"Find and combine rotation series.\n" +"\n" +" -h, --help Display this help message.\n" +" --version Print CrystFEL version number and exit.\n" +" --no-polarisation Disable polarisation correction.\n"); +} + + +int main(int argc, char *argv[]) +{ + int c; + Stream *st; + int n_images = 0; + int n_crystals = 0; + int polarisation = 1; + + /* Long options */ + const struct option longopts[] = { + + {"help", 0, NULL, 'h'}, + {"version", 0, NULL, 3 }, + + {"no-polarisation", 0, &polarisation, 0}, + {"no-polarization", 0, &polarisation, 0}, + {"polarisation", 0, &polarisation, 1}, /* compat */ + {"polarization", 0, &polarisation, 1}, /* compat */ + + {0, 0, NULL, 0} + }; + + /* Short options */ + while ((c = getopt_long(argc, argv, "h", + longopts, NULL)) != -1) + { + + switch (c) { + + case 'h' : + show_help(argv[0]); + return 0; + + case 0 : + break; + + case '?' : + break; + + default : + ERROR("Unhandled option '%c'\n", c); + break; + + } + + } + + if ( argc != (optind+1) ) { + ERROR("Please provide exactly one stream to process.\n"); + return 1; + } + + st = open_stream_for_read(argv[optind++]); + if ( st == NULL ) { + ERROR("Failed to open input stream '%s'\n", argv[optind-1]); + return 1; + } + + do { + + int i; + struct image cur; + + cur.div = NAN; + cur.bw = NAN; + cur.det = NULL; + if ( read_chunk_2(st, &cur, STREAM_READ_REFLECTIONS + | STREAM_READ_UNITCELL) != 0 ) { + break; + } + + if ( isnan(cur.div) || isnan(cur.bw) ) { + ERROR("Chunk doesn't contain beam parameters.\n"); + return 1; + } + + n_images++; + + for ( i=0; i<cur.n_crystals; i++ ) { + + Crystal *cr; + RefList *cr_refl; + + cr = cur.crystals[i]; + + /* This is the raw list of reflections */ + cr_refl = crystal_get_reflections(cr); + + if ( polarisation ) { + polarisation_correction(cr_refl, + crystal_get_cell(cr), + &cur); + } + + n_crystals++; + + } + + } while ( 1 ); + + close_stream(st); + + return 0; +} |