From 5c5e2fc2577edf35ee6b7f4ff304181c74b3b0ca Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 5 Jul 2019 12:04:29 +0200 Subject: geoptimiser: Use geometry from stream, if present Simply omit the -g option to use geometry from stream. --- src/geoptimiser.c | 129 +++++++++++++++++++++++++++--------------------------- 1 file changed, 64 insertions(+), 65 deletions(-) (limited to 'src') diff --git a/src/geoptimiser.c b/src/geoptimiser.c index f66ac709..e8aac2c4 100644 --- a/src/geoptimiser.c +++ b/src/geoptimiser.c @@ -3,13 +3,13 @@ * * Refine detector geometry * - * Copyright © 2014-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2014-2019 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2014-2015 Oleksandr Yefanov * 2014-2015 Valerio Mariani - * 2014-2016 Thomas White + * 2014-2019 Thomas White * * This file is part of CrystFEL. * @@ -77,13 +77,11 @@ static void show_help(const char *s) "\n" " --version Print CrystFEL version number and\n" " exit.\n" -" -i, --input= Specify stream file to be used for \n" -" geometry optimization.\n" -" -g. --geometry= Get detector geometry from file.\n" -" -o, --output= Output stream.\n" +" -i, --input= Input stream\n" +" -g. --geometry= Input geometry file (if omitted: from stream).\n" +" -o, --output= Output geometry file.\n" " -q, --quadrants= Rigid group collection for quadrants.\n" -" -c, --connected= Rigid group collection for connected\n" -" ASICs.\n" +" -c, --connected= Rigid group collection for connected ASICs.\n" " --no-error-maps Do not generate error map PNGs.\n" " --stretch-map Generate stretch map PNG (panels distance).\n" " -x, --min-num-peaks-per-pixel= Minimum number of peaks per pixel.\n" @@ -109,9 +107,7 @@ static void show_help(const char *s) struct geoptimiser_params { - char *infile; char *outfile; - char *geometry_filename; int min_num_peaks_per_pix; int max_num_peaks_per_pix; int min_num_pix_per_conn_group; @@ -248,10 +244,9 @@ static double get_average_clen(struct image *image) } -static struct image *read_patterns_from_stream(const char *infile, +static struct image *read_patterns_from_stream(Stream *st, struct detector *det, int *n) { - Stream *st; struct image *images; int n_chunks = 0; int max_images = 1024; @@ -263,13 +258,6 @@ static struct image *read_patterns_from_stream(const char *infile, return NULL; } - st = open_stream_for_read(infile); - if ( st == NULL ) { - ERROR("Failed to open input stream '%s'\n", infile); - free(images); - return NULL; - } - do { images[n_images].det = det; @@ -313,11 +301,10 @@ static struct image *read_patterns_from_stream(const char *infile, } while ( 1 ); - close_stream(st); *n = n_images; - STATUS("Found %i indexed patterns in file %s (from a total of %i).\n", - n_images, infile, n_chunks); + STATUS("Found %i indexed patterns in stream (from a total of %i).\n", + n_images, n_chunks); return images; } @@ -2288,7 +2275,7 @@ void recompute_avg_displ(struct rg_collection *connected, } -int optimize_geometry(struct geoptimiser_params *gparams, +int optimize_geometry(struct geoptimiser_params *gparams, Stream *st, struct detector *det, struct rg_collection *quadrants, struct rg_collection *connected) @@ -2314,6 +2301,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, int n_images = 0; UnitCell *avg_cell; struct gpanel *gpanels; + const char *geometry_data = stream_geometry_file(st); STATUS("Maximum distance between peaks: %0.1f pixels.\n", gparams->max_peak_dist); @@ -2346,10 +2334,9 @@ int optimize_geometry(struct geoptimiser_params *gparams, "Please restart geometry optimization using the " "optimized geometry from this run as input " "geometry file.\n"); - geom_wr = write_detector_geometry_2( - gparams->geometry_filename, - gparams->outfile, det, - gparams->command_line, 1); + geom_wr = write_detector_geometry_3(geometry_data, + gparams->outfile, det, + gparams->command_line, 1); if ( geom_wr != 0 ) { ERROR("Error in writing output geometry file.\n"); return 1; @@ -2391,10 +2378,9 @@ int optimize_geometry(struct geoptimiser_params *gparams, "Please restart geometry optimization using the " "optimized geometry from this run as input " "geometry file.\n"); - geom_wr = write_detector_geometry_2( - gparams->geometry_filename, - gparams->outfile, det, - gparams->command_line, 1); + geom_wr = write_detector_geometry_3(geometry_data, + gparams->outfile, det, + gparams->command_line, 1); if ( geom_wr != 0 ) { ERROR("Error in writing output geometry file.\n"); return 1; @@ -2413,7 +2399,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, } } - images = read_patterns_from_stream(gparams->infile, det, &n_images); + images = read_patterns_from_stream(st, det, &n_images); if ( (n_images < 1) || (images == NULL) ) { ERROR("Error reading stream file\n"); return 1; @@ -2603,7 +2589,7 @@ int optimize_geometry(struct geoptimiser_params *gparams, STATUS("Detector-wide error after correction: RMSD = %0.4f pixels.\n", total_error); - write_ret = write_detector_geometry_2(gparams->geometry_filename, + write_ret = write_detector_geometry_3(geometry_data, gparams->outfile, det, gparams->command_line, 1); if ( write_ret != 0 ) { @@ -2632,21 +2618,20 @@ int main(int argc, char *argv[]) int ret_val; char buffer[256]; char command_line[1024]; - + char *infile = NULL; char *quadrant_coll_name = NULL; char *connected_coll_name = NULL; - + Stream *st; struct geoptimiser_params *gparams; struct detector *det = NULL; struct rg_collection *quadrants; struct rg_collection *connected; struct beam_params beam; + char *geometry_filename = NULL; gparams = malloc(sizeof(struct geoptimiser_params)); gparams->outfile = NULL; - gparams->infile = NULL; - gparams->geometry_filename = NULL; gparams->min_num_peaks_per_pix = 3; gparams->max_num_peaks_per_pix = 0; gparams->min_num_pix_per_conn_group = 100; @@ -2714,18 +2699,11 @@ int main(int argc, char *argv[]) break; case 'i' : - gparams->infile = strdup(optarg); + infile = strdup(optarg); break; case 'g' : - gparams->geometry_filename = strdup(optarg); - det = get_detector_geometry(gparams->geometry_filename, - &beam); - if ( det == NULL ) { - ERROR("Failed to read detector geometry from " - "'%s'\n", optarg); - return 1; - } + geometry_filename = strdup(optarg); break; case 'q' : @@ -2772,12 +2750,7 @@ int main(int argc, char *argv[]) } } - if ( gparams->geometry_filename == NULL ) { - ERROR("You must provide a geometry to optimize.\n"); - return 1; - } - - if ( gparams->infile == NULL ) { + if ( infile == NULL ) { ERROR("You must provide an input stream file.\n"); return 1; } @@ -2799,7 +2772,43 @@ int main(int argc, char *argv[]) return 1; } - strcpy(command_line, "\0"); + command_line[0] = '\0'; + for ( i=0; i 0 ) strcat(command_line, " "); + strcpy(buffer, argv[i]); + strcat(command_line, buffer); + } + +#ifdef CAN_SAVE_TO_PNG +#if !GLIB_CHECK_VERSION(2,36,0) + g_type_init(); +#endif +#endif + + st = open_stream_for_read(infile); + if ( st == NULL ) { + ERROR("Failed to open input stream '%s'\n", infile); + return 1; + } + + if ( geometry_filename == NULL ) { + const char *stgeom = stream_geometry_file(st); + if ( stgeom != NULL ) { + det = get_detector_geometry_from_string(stgeom, &beam, NULL); + } else { + ERROR("No input geometry file given, and no geometry " + "found in stream.\n"); + return 1; + } + } else { + det = get_detector_geometry(geometry_filename, &beam); + free(geometry_filename); + } + + if ( det == NULL ) { + ERROR("Failed to read initial detector geometry.\n"); + return 1; + } quadrants = find_rigid_group_collection_by_name(det, quadrant_coll_name); if ( quadrants == NULL ) { @@ -2816,19 +2825,9 @@ int main(int argc, char *argv[]) return 1; } - for ( i=0; i 0 ) strcat(command_line, " "); - strcpy(buffer, argv[i]); - strcat(command_line, buffer); - } + ret_val = optimize_geometry(gparams, st, det, quadrants, connected); -#ifdef CAN_SAVE_TO_PNG -#if !GLIB_CHECK_VERSION(2,36,0) - g_type_init(); -#endif -#endif - - ret_val = optimize_geometry(gparams, det, quadrants, connected); + close_stream(st); return ret_val; } -- cgit v1.2.3