Remove 'reintegrate'

What it really does isn't that well defined, and it'd be a lot of work
to define it usefully.  Removing it for now..

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;
-}