Add partial_sim, for generating test streams by geometrical methods

.gitignore

@@ -19,6 +19,7 @@ src/partialator
 src/cubeit
 src/check_hkl
 src/sum_stack
+src/partial_sim
 src/.dirstamp
 *~
 doc/reference/*

Makefile.am

@@ -5,7 +5,7 @@ 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/check_hkl src/sum_stack
+               src/check_hkl src/sum_stack src/partial_sim
 
 noinst_PROGRAMS = tests/list_check tests/integration_check
 
@@ -30,6 +30,12 @@ AM_CFLAGS = -Wall
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
 
+src_partial_sim_SOURCES = src/partial_sim.c src/cell.c src/detector.c \
+                          src/beam-parameters.c src/thread-pool.c src/utils.c \
+                          src/reflist-utils.c src/reflist.c src/symmetry.c \
+                          src/hdf5-file.c src/image.c src/geometry.c \
+                          src/peaks.c src/stream.c
+
 src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
                           src/image.c src/cell.c src/hdf5-file.c \
                           src/detector.c src/peaks.c \
@@ -102,7 +108,7 @@ src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
                                  src/hdf5-file.c src/image.c src/thread-pool.c \
                                  src/detector.c src/stream.c src/cell.c \
                                  src/reflist-utils.c src/reflist.c src/symmetry.c \
-                                 src/peaks.c 
+                                 src/peaks.c
 
 src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
                           src/utils.c src/detector.c src/peaks.c src/image.c \

Makefile.in

@@ -40,7 +40,8 @@ bin_PROGRAMS = src/pattern_sim$(EXEEXT) src/process_hkl$(EXEEXT) \
 	src/compare_hkl$(EXEEXT) src/powder_plot$(EXEEXT) \
 	src/render_hkl$(EXEEXT) src/calibrate_detector$(EXEEXT) \
 	src/partialator$(EXEEXT) src/check_hkl$(EXEEXT) \
-	src/sum_stack$(EXEEXT) $(am__EXEEXT_1) $(am__EXEEXT_2)
+	src/sum_stack$(EXEEXT) src/partial_sim$(EXEEXT) \
+	$(am__EXEEXT_1) $(am__EXEEXT_2)
 noinst_PROGRAMS = tests/list_check$(EXEEXT) \
 	tests/integration_check$(EXEEXT) $(am__EXEEXT_3)
 TESTS = tests/list_check$(EXEEXT) tests/first_merge_check \
@@ -166,6 +167,17 @@ am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
 src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
 src_indexamajig_LDADD = $(LDADD)
 src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am_src_partial_sim_OBJECTS = src/partial_sim.$(OBJEXT) \
+	src/cell.$(OBJEXT) src/detector.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT) src/thread-pool.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/reflist-utils.$(OBJEXT) \
+	src/reflist.$(OBJEXT) src/symmetry.$(OBJEXT) \
+	src/hdf5-file.$(OBJEXT) src/image.$(OBJEXT) \
+	src/geometry.$(OBJEXT) src/peaks.$(OBJEXT) \
+	src/stream.$(OBJEXT)
+src_partial_sim_OBJECTS = $(am_src_partial_sim_OBJECTS)
+src_partial_sim_LDADD = $(LDADD)
+src_partial_sim_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
 am_src_partialator_OBJECTS = src/partialator.$(OBJEXT) \
 	src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
 	src/detector.$(OBJEXT) src/peaks.$(OBJEXT) src/image.$(OBJEXT) \
@@ -283,19 +295,20 @@ am__v_GEN_0 = @echo "  GEN   " $@;
 SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
 	$(src_compare_hkl_SOURCES) $(src_cubeit_SOURCES) \
 	$(src_get_hkl_SOURCES) $(src_hdfsee_SOURCES) \
-	$(src_indexamajig_SOURCES) $(src_partialator_SOURCES) \
-	$(src_pattern_sim_SOURCES) $(src_powder_plot_SOURCES) \
-	$(src_process_hkl_SOURCES) $(src_render_hkl_SOURCES) \
-	$(src_sum_stack_SOURCES) $(tests_gpu_sim_check_SOURCES) \
+	$(src_indexamajig_SOURCES) $(src_partial_sim_SOURCES) \
+	$(src_partialator_SOURCES) $(src_pattern_sim_SOURCES) \
+	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
+	$(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
+	$(tests_gpu_sim_check_SOURCES) \
 	$(tests_integration_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) $(src_get_hkl_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_render_hkl_SOURCES) \
-	$(src_sum_stack_SOURCES) \
+	$(am__src_indexamajig_SOURCES_DIST) $(src_partial_sim_SOURCES) \
+	$(src_partialator_SOURCES) $(am__src_pattern_sim_SOURCES_DIST) \
+	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
+	$(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
 	$(am__tests_gpu_sim_check_SOURCES_DIST) \
 	$(tests_integration_check_SOURCES) $(tests_list_check_SOURCES)
 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
@@ -608,6 +621,12 @@ ACLOCAL_AMFLAGS = -I m4
 AM_CFLAGS = -Wall
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
+src_partial_sim_SOURCES = src/partial_sim.c src/cell.c src/detector.c \
+                          src/beam-parameters.c src/thread-pool.c src/utils.c \
+                          src/reflist-utils.c src/reflist.c src/symmetry.c \
+                          src/hdf5-file.c src/image.c src/geometry.c \
+                          src/peaks.c src/stream.c
+
 src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
 	src/utils.c src/image.c src/cell.c src/hdf5-file.c \
 	src/detector.c src/peaks.c src/reflist-utils.c \
@@ -664,7 +683,7 @@ src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
                                  src/hdf5-file.c src/image.c src/thread-pool.c \
                                  src/detector.c src/stream.c src/cell.c \
                                  src/reflist-utils.c src/reflist.c src/symmetry.c \
-                                 src/peaks.c 
+                                 src/peaks.c
 
 src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
                           src/utils.c src/detector.c src/peaks.c src/image.c \
@@ -889,6 +908,11 @@ src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
 src/indexamajig$(EXEEXT): $(src_indexamajig_OBJECTS) $(src_indexamajig_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/indexamajig$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_indexamajig_OBJECTS) $(src_indexamajig_LDADD) $(LIBS)
+src/partial_sim.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/partial_sim$(EXEEXT): $(src_partial_sim_OBJECTS) $(src_partial_sim_DEPENDENCIES) src/$(am__dirstamp)
+	@rm -f src/partial_sim$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(src_partial_sim_OBJECTS) $(src_partial_sim_LDADD) $(LIBS)
 src/partialator.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/post-refinement.$(OBJEXT): src/$(am__dirstamp) \
@@ -971,6 +995,7 @@ mostlyclean-compile:
 	-rm -f src/index.$(OBJEXT)
 	-rm -f src/indexamajig.$(OBJEXT)
 	-rm -f src/mosflm.$(OBJEXT)
+	-rm -f src/partial_sim.$(OBJEXT)
 	-rm -f src/partialator.$(OBJEXT)
 	-rm -f src/pattern_sim.$(OBJEXT)
 	-rm -f src/peaks.$(OBJEXT)
@@ -1017,6 +1042,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/index.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/indexamajig.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/mosflm.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/partial_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/partialator.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/pattern_sim.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/peaks.Po@am__quote@

src/partial_sim.c

+/*
+ * partial_sim.c
+ *
+ * Generate partials for testing scaling
+ *
+ * (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 "utils.h"
+#include "reflist-utils.h"
+#include "symmetry.h"
+#include "beam-parameters.h"
+#include "detector.h"
+#include "geometry.h"
+#include "stream.h"
+
+
+/* For each reflection in "partial", fill in what the intensity would be
+ * according to "full" */
+static void calculate_partials(RefList *partial, RefList *full, const char *sym)
+{
+	Reflection *refl;
+	RefListIterator *iter;
+
+	for ( refl = first_refl(partial, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) ) {
+
+		signed int h, k, l;
+		Reflection *rfull;
+		double p;
+		double Ip;
+
+		get_indices(refl, &h, &k, &l);
+		get_asymm(h, k, l, &h, &k, &l, sym);
+		p = get_partiality(refl);
+
+		rfull = find_refl(full, h, k, l);
+		if ( rfull == NULL ) {
+			set_redundancy(refl, 0);
+		} else {
+			Ip = p * get_intensity(rfull);
+			set_int(refl, Ip);
+		}
+
+	}
+}
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Generate a stream containing partials from a reflection list.\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"
+" -g. --geometry=<file>   Get detector geometry from file.\n"
+" -b, --beam=<file>       Get beam parameters from file\n"
+" -p, --pdb=<file>        PDB file from which to get the unit cell.\n"
+"\n"
+" -y, --symmetry=<sym>    Symmetry of the input reflection list.\n"
+);
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *input_file = NULL;
+	char *output_file = NULL;
+	char *beamfile = NULL;
+	char *geomfile = NULL;
+	char *cellfile = NULL;
+	struct detector *det = NULL;
+	struct beam_params *beam = NULL;
+	RefList *full;
+	char *sym = NULL;
+	UnitCell *cell = NULL;
+	UnitCell *rcell;
+	struct quaternion orientation;
+	struct image image;
+	FILE *ofh;
+
+	/* Long options */
+	const struct option longopts[] = {
+		{"help",               0, NULL,               'h'},
+		{"output",             1, NULL,               'o'},
+		{"input",              1, NULL,               'i'},
+		{"beam",               1, NULL,               'b'},
+		{"pdb",                1, NULL,               'p'},
+		{"geometry",           1, NULL,               'g'},
+		{"symmetry",           1, NULL,               'y'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:o:b:p:g:y:",
+	                        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 'p' :
+			cellfile = strdup(optarg);
+			break;
+
+		case 'g' :
+			geomfile = strdup(optarg);
+			break;
+
+		case 'y' :
+			sym = strdup(optarg);
+			break;
+
+		case 0 :
+			break;
+
+		default :
+			return 1;
+		}
+
+	}
+
+	/* 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 cell */
+	if ( cellfile == NULL ) {
+		ERROR("You need to give a PDB file with the unit cell.\n");
+		return 1;
+	}
+	cell = load_cell_from_pdb(cellfile);
+	if ( cell == NULL ) {
+		ERROR("Failed to get cell from '%s'\n", cellfile);
+		return 1;
+	}
+	free(cellfile);
+
+	/* Load geometry */
+	if ( geomfile == NULL ) {
+		ERROR("You need to give a geometry file.\n");
+		return 1;
+	}
+	det = get_detector_geometry(geomfile);
+	if ( cell == NULL ) {
+		ERROR("Failed to read geometry from '%s'\n", geomfile);
+		return 1;
+	}
+	free(geomfile);
+
+	/* Load (full) reflections */
+	if ( input_file == NULL ) {
+		ERROR("You must provide a reflection list.\n");
+		return 1;
+	}
+	full = read_reflections(input_file);
+	if ( full == NULL ) {
+		ERROR("Failed to read reflections from '%s'\n", input_file);
+		return 1;
+	}
+	free(input_file);
+	if ( check_list_symmetry(full, sym) ) {
+		ERROR("The input reflection list does not appear to"
+		      " have symmetry %s\n", sym);
+		return 1;
+	}
+
+	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);
+	write_stream_header(ofh, argc, argv);
+
+	/* Set up a random orientation */
+	orientation = random_quaternion();
+	image.indexed_cell = cell_rotate(cell, orientation);
+
+	image.det = det;
+	image.width = det->max_fs;
+	image.height = det->max_ss;
+
+	image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
+	image.div = beam->divergence;
+	image.bw = beam->bandwidth;
+	image.profile_radius = 0.005e9;
+	image.i0_available = 0;
+	image.filename = "(simulated 1)";
+	image.reflections = find_intersections(&image, image.indexed_cell, 0);
+	calculate_partials(image.reflections, full, sym);
+	write_chunk(ofh, &image, STREAM_INTEGRATED);
+	reflist_free(image.reflections);
+
+	/* Rotate the cell by a tiny amount */
+	rcell = rotate_cell(image.indexed_cell,
+	                    deg2rad(0.2), deg2rad(0.0), deg2rad(0.0));
+	cell_free(image.indexed_cell);
+	image.indexed_cell = rcell;
+	image.filename = "(simulated 2)";
+
+	/* Write another chunk */
+	image.reflections = find_intersections(&image, image.indexed_cell, 0);
+	calculate_partials(image.reflections, full, sym);
+	write_chunk(ofh, &image, STREAM_INTEGRATED);
+	reflist_free(image.reflections);
+
+	fclose(ofh);
+	cell_free(cell);
+	free_detector_geometry(det);
+	free(beam);
+	free(sym);
+	reflist_free(full);
+
+	return 0;
+}