diff options
Diffstat (limited to 'contrib')
| -rw-r--r-- | contrib/alter_stream.c | 215 |
1 files changed, 215 insertions, 0 deletions
diff --git a/contrib/alter_stream.c b/contrib/alter_stream.c new file mode 100644 index 00000000..2c5d207b --- /dev/null +++ b/contrib/alter_stream.c @@ -0,0 +1,215 @@ +/* + * alter_stream.c + * + * Do transformations on a stream + * + * (c) 2006-2011 Thomas White <taw@physics.org> + * + * Part of CrystFEL - crystallography with a FEL + * + */ + + +#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 "../src/utils.h" +#include "../src/stream.h" +#include "../src/cell.h" +#include "../src/image.h" +#include "../src/beam-parameters.h" +#include "../src/geometry.h" +#include "../src/peaks.h" + + +static void mess_up_cell(UnitCell *cell) +{ + double ax, ay, az; + double bx, by, bz; + double cx, cy, cz; + + /* Cell noise in percent */ + const double cnoise = 0.5; + + //STATUS("Real:\n"); + //cell_print(cell); + + cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + ax = gaussian_noise(ax, cnoise*fabs(ax)/100.0); + ay = gaussian_noise(ay, cnoise*fabs(ay)/100.0); + az = gaussian_noise(az, cnoise*fabs(az)/100.0); + bx = gaussian_noise(bx, cnoise*fabs(bx)/100.0); + by = gaussian_noise(by, cnoise*fabs(by)/100.0); + bz = gaussian_noise(bz, cnoise*fabs(bz)/100.0); + cx = gaussian_noise(cx, cnoise*fabs(cx)/100.0); + cy = gaussian_noise(cy, cnoise*fabs(cy)/100.0); + cz = gaussian_noise(cz, cnoise*fabs(cz)/100.0); + cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz); + + //STATUS("Changed:\n"); + //cell_print(cell); +} + + +static void show_help(const char *s) +{ + printf("Syntax: %s [options]\n\n", s); + printf( +"Alter a stream.\n" +"\n" +" -h, --help Display this help message.\n" +"\n" +"You need to provide the following basic options:\n" +" -i, --input=<file> Read reflections from <file>.\n" +" -o, --output=<file> Write partials in stream format to <file>.\n" +); +} + + +int main(int argc, char *argv[]) +{ + int c; + char *input_file = NULL; + char *output_file = NULL; + struct image image; + struct detector *det = NULL; + struct beam_params *beam = NULL; + char *beamfile = NULL; + char *geomfile = NULL; + FILE *ifh; + FILE *ofh; + int v; + + /* Long options */ + const struct option longopts[] = { + {"help", 0, NULL, 'h'}, + {"output", 1, NULL, 'o'}, + {"input", 1, NULL, 'i'}, + {"beam", 1, NULL, 'b'}, + {"geometry", 1, NULL, 'g'}, + {0, 0, NULL, 0} + }; + + /* Short options */ + while ((c = getopt_long(argc, argv, "hi:o:b:g:", + longopts, NULL)) != -1) { + + switch (c) { + case 'h' : + show_help(argv[0]); + return 0; + + case 'o' : + output_file = strdup(optarg); + break; + + case 'i' : + input_file = strdup(optarg); + break; + + case 'b' : + beamfile = strdup(optarg); + break; + + case 'g' : + geomfile = strdup(optarg); + break; + + case 0 : + break; + + default : + return 1; + } + + } + + if ( input_file == NULL ) { + ERROR("You must pgive a filename for the output.\n"); + return 1; + } + ifh = fopen(input_file, "r"); + if ( ifh == NULL ) { + ERROR("Couldn't open input file '%s'\n", input_file); + return 1; + } + free(input_file); + + if ( output_file == NULL ) { + ERROR("You must pgive a filename for the output.\n"); + return 1; + } + ofh = fopen(output_file, "w"); + if ( ofh == NULL ) { + ERROR("Couldn't open output file '%s'\n", output_file); + return 1; + } + free(output_file); + + /* Load beam */ + if ( beamfile == NULL ) { + ERROR("You need to provide a beam parameters file.\n"); + return 1; + } + beam = get_beam_parameters(beamfile); + if ( beam == NULL ) { + ERROR("Failed to load beam parameters from '%s'\n", beamfile); + return 1; + } + free(beamfile); + + /* Load geometry */ + if ( geomfile == NULL ) { + ERROR("You need to give a geometry file.\n"); + return 1; + } + det = get_detector_geometry(geomfile); + if ( det == NULL ) { + ERROR("Failed to read geometry from '%s'\n", geomfile); + return 1; + } + free(geomfile); + + write_stream_header(ofh, argc, argv); + + image.det = det; + image.width = det->max_fs; + image.height = det->max_ss; + + image.lambda = 0.0; + image.div = beam->divergence; + image.bw = beam->bandwidth; + image.profile_radius = 0.0001e9; + image.i0_available = 0; + + do { + + image.indexed_cell = NULL; + v = read_chunk(ifh, &image); + if ( (v == 0) && (image.indexed_cell != NULL) ) { + + mess_up_cell(image.indexed_cell); + image.reflections = find_intersections(&image, + image.indexed_cell); + + write_chunk(ofh, &image, STREAM_INTEGRATED); + + } + + } while ( v == 0 ); + + + fclose(ofh); + fclose(ifh); + + return 0; +} |