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..

3 files changed, 8 insertions, 392 deletions

diff --git a/Makefile.am b/Makefile.am
index bdd3f2be..5a309f76 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -4,7 +4,7 @@ ACLOCAL_AMFLAGS = -I m4
 
 bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \
                src/compare_hkl src/powder_plot src/render_hkl \
-               src/calibrate_detector src/partialator src/reintegrate \
+               src/calibrate_detector src/partialator \
                src/estimate_background src/check_hkl src/sum_stack
 
 noinst_PROGRAMS = tests/list_check
@@ -107,12 +107,6 @@ src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
                      src/symmetry.c src/stream.c src/thread-pool.c
 endif
 
-src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c \
-                          src/utils.c src/detector.c src/peaks.c src/image.c \
-                          src/stream.c src/index.c src/dirax.c src/mosflm.c \
-                          src/geometry.c src/symmetry.c \
-                          src/thread-pool.c src/reflist.c
-
 src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
                                   src/utils.c src/cell.c src/thread-pool.c
 
diff --git a/Makefile.in b/Makefile.in
index f37e4218..b76f0796 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -39,9 +39,9 @@ bin_PROGRAMS = src/pattern_sim$(EXEEXT) src/process_hkl$(EXEEXT) \
 	src/get_hkl$(EXEEXT) src/indexamajig$(EXEEXT) \
 	src/compare_hkl$(EXEEXT) src/powder_plot$(EXEEXT) \
 	src/render_hkl$(EXEEXT) src/calibrate_detector$(EXEEXT) \
-	src/partialator$(EXEEXT) src/reintegrate$(EXEEXT) \
-	src/estimate_background$(EXEEXT) src/check_hkl$(EXEEXT) \
-	src/sum_stack$(EXEEXT) $(am__EXEEXT_1) $(am__EXEEXT_2)
+	src/partialator$(EXEEXT) src/estimate_background$(EXEEXT) \
+	src/check_hkl$(EXEEXT) src/sum_stack$(EXEEXT) $(am__EXEEXT_1) \
+	$(am__EXEEXT_2)
 noinst_PROGRAMS = tests/list_check$(EXEEXT) $(am__EXEEXT_3)
 TESTS = tests/list_check$(EXEEXT) $(am__EXEEXT_3)
 @BUILD_HDFSEE_TRUE@am__append_1 = src/hdfsee
@@ -209,16 +209,6 @@ am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT) \
 src_process_hkl_OBJECTS = $(am_src_process_hkl_OBJECTS)
 src_process_hkl_LDADD = $(LDADD)
 src_process_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
-am_src_reintegrate_OBJECTS = src/reintegrate.$(OBJEXT) \
-	src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
-	src/detector.$(OBJEXT) src/peaks.$(OBJEXT) src/image.$(OBJEXT) \
-	src/stream.$(OBJEXT) src/index.$(OBJEXT) src/dirax.$(OBJEXT) \
-	src/mosflm.$(OBJEXT) src/geometry.$(OBJEXT) \
-	src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
-	src/reflist.$(OBJEXT)
-src_reintegrate_OBJECTS = $(am_src_reintegrate_OBJECTS)
-src_reintegrate_LDADD = $(LDADD)
-src_reintegrate_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
 am_src_render_hkl_OBJECTS = src/render_hkl.$(OBJEXT) \
 	src/cell.$(OBJEXT) src/reflections.$(OBJEXT) \
 	src/utils.$(OBJEXT) src/povray.$(OBJEXT) \
@@ -285,9 +275,8 @@ SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
 	$(src_hdfsee_SOURCES) $(src_indexamajig_SOURCES) \
 	$(src_partialator_SOURCES) $(src_pattern_sim_SOURCES) \
 	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
-	$(src_reintegrate_SOURCES) $(src_render_hkl_SOURCES) \
-	$(src_sum_stack_SOURCES) $(tests_gpu_sim_check_SOURCES) \
-	$(tests_list_check_SOURCES)
+	$(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
+	$(tests_gpu_sim_check_SOURCES) $(tests_list_check_SOURCES)
 DIST_SOURCES = $(src_calibrate_detector_SOURCES) \
 	$(src_check_hkl_SOURCES) $(src_compare_hkl_SOURCES) \
 	$(am__src_cubeit_SOURCES_DIST) \
@@ -295,8 +284,8 @@ DIST_SOURCES = $(src_calibrate_detector_SOURCES) \
 	$(am__src_hdfsee_SOURCES_DIST) \
 	$(am__src_indexamajig_SOURCES_DIST) $(src_partialator_SOURCES) \
 	$(am__src_pattern_sim_SOURCES_DIST) $(src_powder_plot_SOURCES) \
-	$(src_process_hkl_SOURCES) $(src_reintegrate_SOURCES) \
-	$(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
+	$(src_process_hkl_SOURCES) $(src_render_hkl_SOURCES) \
+	$(src_sum_stack_SOURCES) \
 	$(am__tests_gpu_sim_check_SOURCES_DIST) \
 	$(tests_list_check_SOURCES)
 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
@@ -674,12 +663,6 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
 @BUILD_CUBEIT_TRUE@                     src/detector.c src/render.c src/filters.c src/image.c \
 @BUILD_CUBEIT_TRUE@                     src/symmetry.c src/stream.c src/thread-pool.c
 
-src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c \
-                          src/utils.c src/detector.c src/peaks.c src/image.c \
-                          src/stream.c src/index.c src/dirax.c src/mosflm.c \
-                          src/geometry.c src/symmetry.c \
-                          src/thread-pool.c src/reflist.c
-
 src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
                                   src/utils.c src/cell.c src/thread-pool.c
 
@@ -926,11 +909,6 @@ src/process_hkl.$(OBJEXT): src/$(am__dirstamp) \
 src/process_hkl$(EXEEXT): $(src_process_hkl_OBJECTS) $(src_process_hkl_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/process_hkl$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_process_hkl_OBJECTS) $(src_process_hkl_LDADD) $(LIBS)
-src/reintegrate.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/reintegrate$(EXEEXT): $(src_reintegrate_OBJECTS) $(src_reintegrate_DEPENDENCIES) src/$(am__dirstamp)
-	@rm -f src/reintegrate$(EXEEXT)
-	$(AM_V_CCLD)$(LINK) $(src_reintegrate_OBJECTS) $(src_reintegrate_LDADD) $(LIBS)
 src/render_hkl.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/povray.$(OBJEXT): src/$(am__dirstamp) \
@@ -994,7 +972,6 @@ mostlyclean-compile:
 	-rm -f src/process_hkl.$(OBJEXT)
 	-rm -f src/reflections.$(OBJEXT)
 	-rm -f src/reflist.$(OBJEXT)
-	-rm -f src/reintegrate.$(OBJEXT)
 	-rm -f src/render.$(OBJEXT)
 	-rm -f src/render_hkl.$(OBJEXT)
 	-rm -f src/sfac.$(OBJEXT)
@@ -1042,7 +1019,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/process_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflections.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reintegrate.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sfac.Po@am__quote@
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;
-}