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-rw-r--r--src/reintegrate.c354
1 files changed, 0 insertions, 354 deletions
diff --git a/src/reintegrate.c b/src/reintegrate.c
deleted file mode 100644
index fcffd499..00000000
--- a/src/reintegrate.c
+++ /dev/null
@@ -1,354 +0,0 @@
-/*
- * reintegrate.c
- *
- * Like "indexamajig", but skip the indexing step
- *
- * (c) 2006-2010 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 <pthread.h>
-#include <sys/time.h>
-#include <assert.h>
-
-#include "utils.h"
-#include "hdf5-file.h"
-#include "symmetry.h"
-#include "peaks.h"
-#include "stream.h"
-#include "index.h"
-#include "thread-pool.h"
-
-
-struct static_integration_args
-{
- struct detector *det;
- pthread_mutex_t *output_mutex; /* Protects the output stream */
- int config_cmfilter;
- int config_polar;
- int config_satcorr;
- int config_sa;
- int config_closer;
- int config_sanity;
- FILE *ofh;
-};
-
-
-struct integration_args
-{
- char *filename;
- UnitCell *cell;
-
- struct static_integration_args static_args;
-};
-
-
-struct queue_args
-{
- FILE *fh;
- const char *prefix;
- int config_basename;
-
- struct static_integration_args static_args;
-};
-
-
-static void show_help(const char *s)
-{
- printf("Syntax: %s [options]\n\n", s);
- printf(
-"Like 'indexamajig', but skip the indexing step.\n"
-"\n"
-" -h, --help Display this help message.\n"
-"\n"
-" -i, --input=<filename> Specify the name of the input 'stream'.\n"
-" (must be a file, not e.g. stdin)\n"
-" -o, --output=<filename> Write out stream to this file. '-' for stdout.\n"
-" -g. --geometry=<file> Get detector geometry from file.\n"
-" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
-" --basename Remove the directory parts of the filenames.\n"
-" --no-check-prefix Don't attempt to correct the --prefix.\n"
-" --check-sanity Check that indexed locations approximately correspond\n"
-" with detected peaks.\n"
-" --filter-cm Perform common-mode noise subtraction on images\n"
-" before proceeding. Intensities will be extracted\n"
-" from the image as it is after this processing.\n"
-" --unpolarized Don't correct for the polarisation of the X-rays.\n"
-" --no-sat-corr Don't correct values of saturated peaks using a\n"
-" table included in the HDF5 file.\n"
-" --no-sa Don't correct for the differing solid angles of\n"
-" the pixels.\n"
-" --no-closer-peak Don't integrate from the location of a nearby peak\n"
-" instead of the position closest to the reciprocal\n"
-" lattice point.\n"
-" -j <n> Run <n> analyses in parallel.\n");
-}
-
-
-static void process_image(void *pg, int cookie)
-{
- struct integration_args *apargs = pg;
- struct static_integration_args *pargs = &apargs->static_args;
- struct hdfile *hdfile;
- struct image image;
-
- image.features = NULL;
- image.data = NULL;
- image.flags = NULL;
- image.indexed_cell = NULL;
- image.filename = apargs->filename;
- image.det = pargs->det;
-
- STATUS("Processing '%s'\n", apargs->filename);
-
- hdfile = hdfile_open(apargs->filename);
- if ( hdfile == NULL ) {
- return;
- } else if ( hdfile_set_first_image(hdfile, "/") ) {
- ERROR("Couldn't select path\n");
- hdfile_close(hdfile);
- return;
- }
-
- hdf5_read(hdfile, &image, pargs->config_satcorr);
-
- map_all_peaks(&image);
-
- /* Sanity check */
- if ( pargs->config_sanity
- && !peak_sanity_check(&image, image.indexed_cell, 1, 0.006e9) ) {
-
- STATUS("Failed peak sanity check.\n");
-
- } else {
-
- RefList *reflections;
-
- reflections = find_projected_peaks(&image, image.indexed_cell,
- 0, 0.1);
-
- reflist_free(reflections);
- }
-
- pthread_mutex_lock(pargs->output_mutex);
- write_chunk(pargs->ofh, &image, pargs->stream_flags);
- pthread_mutex_unlock(pargs->output_mutex);
-
-
- free(image.data);
- if ( image.flags != NULL ) free(image.flags);
- hdfile_close(hdfile);
-
- free(apargs->filename);
- cell_free(apargs->cell);
- free(apargs);
-}
-
-
-static void *get_image(void *qp)
-{
- struct integration_args *pargs;
- struct queue_args *qargs = qp;
- UnitCell *cell;
- char *filename;
- double ph_ev;
-
- /* Get the next filename */
- if ( find_chunk(qargs->fh, &cell, &filename, &ph_ev) ) {
- return NULL;
- }
-
- pargs = malloc(sizeof(struct integration_args));
-
- if ( qargs->config_basename ) {
- char *tmp;
- tmp = safe_basename(filename);
- free(filename);
- filename = tmp;
- }
-
- memcpy(&pargs->static_args, &qargs->static_args,
- sizeof(struct static_integration_args));
-
- pargs->cell = cell;
- pargs->filename = malloc(1024);
- snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, filename);
- free(filename);
-
- return pargs;
-}
-
-
-static void integrate_all(int nthreads, struct detector *det, FILE *fh,
- int config_basename, const char *prefix,
- int config_cmfilter, int config_polar,
- int config_satcorr, int config_sa, int config_closer,
- int config_sanity, FILE *ofh)
-{
- struct queue_args qargs;
- pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
-
- /* Information required to choose the next image */
- qargs.fh = fh;
- qargs.prefix = prefix;
- qargs.config_basename = config_basename;
-
- /* Information for the task which does not vary */
- qargs.static_args.det = det;
- qargs.static_args.config_cmfilter = config_cmfilter;
- qargs.static_args.config_polar = config_polar;
- qargs.static_args.config_satcorr = config_satcorr;
- qargs.static_args.config_sa = config_sa;
- qargs.static_args.config_closer = config_closer;
- qargs.static_args.config_sanity = qargs.static_args.config_sanity;
- qargs.static_args.output_mutex = &output_mutex;
- qargs.static_args.ofh = ofh;
-
- run_threads(nthreads, process_image, get_image, NULL, &qargs, 0);
-}
-
-
-int main(int argc, char *argv[])
-{
- int c;
- char *infile = NULL;
- char *outfile = NULL;
- char *geomfile = NULL;
- FILE *fh;
- FILE *ofh;
- char *prefix = NULL;
- int nthreads = 1;
- int config_basename = 0;
- int config_checkprefix = 1;
- int config_closer = 1;
- int config_polar = 1;
- int config_sanity = 0;
- int config_satcorr = 1;
- int config_sa = 1;
- int config_cmfilter = 0;
- struct detector *det;
-
- /* Long options */
- const struct option longopts[] = {
- {"help", 0, NULL, 'h'},
- {"input", 1, NULL, 'i'},
- {"output", 1, NULL, 'o'},
- {"geometry", 1, NULL, 'g'},
- {"prefix", 1, NULL, 'x'},
- {"basename", 0, &config_basename, 1},
- {"no-check-prefix", 0, &config_checkprefix, 0},
- {"no-closer-peak", 0, &config_closer, 0},
- {"unpolarized", 0, &config_polar, 0},
- {"check-sanity", 0, &config_sanity, 1},
- {"sat-corr", 0, &config_satcorr, 1},
- {"no-sat-corr", 0, &config_satcorr, 0},
- {"no-sa", 0, &config_sa, 0},
- {"filter-cm", 0, &config_cmfilter, 1},
- {0, 0, NULL, 0}
- };
-
- /* Short options */
- while ((c = getopt_long(argc, argv, "hi:g:x:j:o:",
- longopts, NULL)) != -1)
- {
-
- switch (c) {
- case 'h' :
- show_help(argv[0]);
- return 0;
-
- case 'i' :
- infile = strdup(optarg);
- break;
-
- case 'o' :
- outfile = strdup(optarg);
- break;
-
- case 'g' :
- geomfile = strdup(optarg);
- break;
-
- case 'x' :
- prefix = strdup(optarg);
- break;
-
- case 'j' :
- nthreads = atoi(optarg);
- break;
-
- case 0 :
- break;
-
- default :
- return 1;
- }
-
- }
-
- if ( infile == NULL ) {
- infile = strdup("-");
- }
- if ( strcmp(infile, "-") == 0 ) {
- fh = stdin;
- } else {
- fh = fopen(infile, "r");
- }
- if ( fh == NULL ) {
- ERROR("Failed to open input file '%s'\n", infile);
- return 1;
- }
- free(infile);
-
- if ( outfile == NULL ) {
- outfile = strdup("-");
- }
- if ( strcmp(outfile, "-") == 0 ) {
- ofh = stdout;
- } else {
- ofh = fopen(outfile, "w");
- }
- if ( ofh == NULL ) {
- ERROR("Failed to open output file '%s'\n", outfile);
- return 1;
- }
- free(outfile);
-
- if ( prefix == NULL ) {
- prefix = strdup("");
- } else {
- if ( config_checkprefix ) {
- prefix = check_prefix(prefix);
- }
- }
-
- det = get_detector_geometry(geomfile);
- if ( det == NULL ) {
- ERROR("Failed to read detector geometry from '%s'\n", geomfile);
- return 1;
- }
- free(geomfile);
-
- rewind(fh);
- integrate_all(nthreads, det, fh, config_basename, prefix,
- config_cmfilter, config_polar, config_satcorr, config_sa,
- config_closer, config_sanity, ofh);
-
- fclose(fh);
- free(prefix);
-
- return 0;
-}
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