Add contrib/alter_stream

4 files changed, 278 insertions, 19 deletions

diff --git a/.gitignore b/.gitignore
index a29b27ee..d60f8cdc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,3 +29,7 @@ src/partial_sim
 src/.dirstamp
 *~
 doc/reference/*
+contrib/.deps
+contrib/*.o
+contrib/.dirstamp
+contrib/alter_stream
diff --git a/Makefile.am b/Makefile.am
index 2c4672ce..489a5dd2 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -5,7 +5,8 @@ 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/partial_sim
+               src/check_hkl src/sum_stack src/partial_sim \
+               contrib/alter_stream
 
 noinst_PROGRAMS = tests/list_check tests/integration_check \
                   tests/pr_gradient_check
@@ -127,6 +128,12 @@ src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
                      src/reflist.c src/reflist-utils.c
 endif
 
+contrib_alter_stream_SOURCES = contrib/alter_stream.c src/stream.c src/image.c \
+                               src/thread-pool.c src/detector.c src/utils.c \
+                               src/cell.c src/reflist-utils.c src/reflist.c \
+                               src/symmetry.c src/hdf5-file.c \
+                               src/beam-parameters.c src/geometry.c src/peaks.c
+
 tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
                            src/utils.c
 
diff --git a/Makefile.in b/Makefile.in
index 1413d922..2ca908cd 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -41,7 +41,7 @@ bin_PROGRAMS = src/pattern_sim$(EXEEXT) src/process_hkl$(EXEEXT) \
 	src/render_hkl$(EXEEXT) src/calibrate_detector$(EXEEXT) \
 	src/partialator$(EXEEXT) src/check_hkl$(EXEEXT) \
 	src/sum_stack$(EXEEXT) src/partial_sim$(EXEEXT) \
-	$(am__EXEEXT_1) $(am__EXEEXT_2)
+	contrib/alter_stream$(EXEEXT) $(am__EXEEXT_1) $(am__EXEEXT_2)
 noinst_PROGRAMS = tests/list_check$(EXEEXT) \
 	tests/integration_check$(EXEEXT) \
 	tests/pr_gradient_check$(EXEEXT) $(am__EXEEXT_3)
@@ -89,6 +89,17 @@ am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" \
 @HAVE_OPENCL_TRUE@am__EXEEXT_3 = tests/gpu_sim_check$(EXEEXT)
 PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
 am__dirstamp = $(am__leading_dot)dirstamp
+am_contrib_alter_stream_OBJECTS = contrib/alter_stream.$(OBJEXT) \
+	src/stream.$(OBJEXT) src/image.$(OBJEXT) \
+	src/thread-pool.$(OBJEXT) src/detector.$(OBJEXT) \
+	src/utils.$(OBJEXT) src/cell.$(OBJEXT) \
+	src/reflist-utils.$(OBJEXT) src/reflist.$(OBJEXT) \
+	src/symmetry.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
+	src/beam-parameters.$(OBJEXT) src/geometry.$(OBJEXT) \
+	src/peaks.$(OBJEXT)
+contrib_alter_stream_OBJECTS = $(am_contrib_alter_stream_OBJECTS)
+contrib_alter_stream_LDADD = $(LDADD)
+contrib_alter_stream_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
 am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
 	src/utils.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
 	src/image.$(OBJEXT) src/thread-pool.$(OBJEXT) \
@@ -307,7 +318,8 @@ am__v_CCLD_0 = @echo "  CCLD  " $@;
 AM_V_GEN = $(am__v_GEN_$(V))
 am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
 am__v_GEN_0 = @echo "  GEN   " $@;
-SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
+SOURCES = $(contrib_alter_stream_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_partial_sim_SOURCES) \
@@ -317,10 +329,10 @@ SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
 	$(tests_gpu_sim_check_SOURCES) \
 	$(tests_integration_check_SOURCES) $(tests_list_check_SOURCES) \
 	$(tests_pr_gradient_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) \
+DIST_SOURCES = $(contrib_alter_stream_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_partial_sim_SOURCES) \
 	$(src_partialator_SOURCES) $(am__src_pattern_sim_SOURCES_DIST) \
 	$(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
@@ -717,6 +729,12 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
 @BUILD_CUBEIT_TRUE@                     src/symmetry.c src/stream.c src/thread-pool.c \
 @BUILD_CUBEIT_TRUE@                     src/reflist.c src/reflist-utils.c
 
+contrib_alter_stream_SOURCES = contrib/alter_stream.c src/stream.c src/image.c \
+                               src/thread-pool.c src/detector.c src/utils.c \
+                               src/cell.c src/reflist-utils.c src/reflist.c \
+                               src/symmetry.c src/hdf5-file.c \
+                               src/beam-parameters.c src/geometry.c src/peaks.c
+
 tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
                            src/utils.c
 
@@ -853,24 +871,28 @@ clean-binPROGRAMS:
 
 clean-noinstPROGRAMS:
 	-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)
+contrib/$(am__dirstamp):
+	@$(MKDIR_P) contrib
+	@: > contrib/$(am__dirstamp)
+contrib/$(DEPDIR)/$(am__dirstamp):
+	@$(MKDIR_P) contrib/$(DEPDIR)
+	@: > contrib/$(DEPDIR)/$(am__dirstamp)
+contrib/alter_stream.$(OBJEXT): contrib/$(am__dirstamp) \
+	contrib/$(DEPDIR)/$(am__dirstamp)
 src/$(am__dirstamp):
 	@$(MKDIR_P) src
 	@: > src/$(am__dirstamp)
 src/$(DEPDIR)/$(am__dirstamp):
 	@$(MKDIR_P) src/$(DEPDIR)
 	@: > src/$(DEPDIR)/$(am__dirstamp)
-src/calibrate_detector.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
-src/utils.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
-src/hdf5-file.$(OBJEXT): src/$(am__dirstamp) \
+src/stream.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/image.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/thread-pool.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/detector.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/stream.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
+src/utils.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/cell.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/reflist-utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
@@ -878,7 +900,18 @@ src/reflist.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/symmetry.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/hdf5-file.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/beam-parameters.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/geometry.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 src/peaks.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+contrib/alter_stream$(EXEEXT): $(contrib_alter_stream_OBJECTS) $(contrib_alter_stream_DEPENDENCIES) contrib/$(am__dirstamp)
+	@rm -f contrib/alter_stream$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(contrib_alter_stream_OBJECTS) $(contrib_alter_stream_LDADD) $(LIBS)
+src/calibrate_detector.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 src/calibrate_detector$(EXEEXT): $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/calibrate_detector$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_LDADD) $(LIBS)
@@ -905,8 +938,6 @@ src/cubeit$(EXEEXT): $(src_cubeit_OBJECTS) $(src_cubeit_DEPENDENCIES) src/$(am__
 	$(AM_V_CCLD)$(LINK) $(src_cubeit_OBJECTS) $(src_cubeit_LDADD) $(LIBS)
 src/get_hkl.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/beam-parameters.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/get_hkl$(EXEEXT): $(src_get_hkl_OBJECTS) $(src_get_hkl_DEPENDENCIES) src/$(am__dirstamp)
 	@rm -f src/get_hkl$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(src_get_hkl_OBJECTS) $(src_get_hkl_LDADD) $(LIBS)
@@ -925,8 +956,6 @@ src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
 src/dirax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
 src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
-src/geometry.$(OBJEXT): src/$(am__dirstamp) \
-	src/$(DEPDIR)/$(am__dirstamp)
 src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1004,6 +1033,7 @@ tests/pr_gradient_check$(EXEEXT): $(tests_pr_gradient_check_OBJECTS) $(tests_pr_
 
 mostlyclean-compile:
 	-rm -f *.$(OBJEXT)
+	-rm -f contrib/alter_stream.$(OBJEXT)
 	-rm -f src/beam-parameters.$(OBJEXT)
 	-rm -f src/calibrate_detector.$(OBJEXT)
 	-rm -f src/cell.$(OBJEXT)
@@ -1052,6 +1082,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@contrib/$(DEPDIR)/alter_stream.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/beam-parameters.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/calibrate_detector.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/cell.Po@am__quote@
@@ -1658,6 +1689,8 @@ clean-generic:
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
 	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f contrib/$(DEPDIR)/$(am__dirstamp)
+	-rm -f contrib/$(am__dirstamp)
 	-rm -f src/$(DEPDIR)/$(am__dirstamp)
 	-rm -f src/$(am__dirstamp)
 	-rm -f tests/$(DEPDIR)/$(am__dirstamp)
@@ -1673,7 +1706,7 @@ clean-am: clean-binPROGRAMS clean-generic clean-noinstPROGRAMS \
 
 distclean: distclean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
-	-rm -rf src/$(DEPDIR) tests/$(DEPDIR)
+	-rm -rf contrib/$(DEPDIR) src/$(DEPDIR) tests/$(DEPDIR)
 	-rm -f Makefile
 distclean-am: clean-am distclean-compile distclean-generic \
 	distclean-hdr distclean-tags
@@ -1722,7 +1755,7 @@ installcheck-am:
 maintainer-clean: maintainer-clean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
 	-rm -rf $(top_srcdir)/autom4te.cache
-	-rm -rf src/$(DEPDIR) tests/$(DEPDIR)
+	-rm -rf contrib/$(DEPDIR) src/$(DEPDIR) tests/$(DEPDIR)
 	-rm -f Makefile
 maintainer-clean-am: distclean-am maintainer-clean-generic
 
diff --git a/contrib/alter_stream.c b/contrib/alter_stream.c
new file mode 100644
index 00000000..2c5d207b
--- /dev/null
+++ b/contrib/alter_stream.c
@@ -0,0 +1,215 @@
+/*
+ * alter_stream.c
+ *
+ * Do transformations on a stream
+ *
+ * (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 "../src/utils.h"
+#include "../src/stream.h"
+#include "../src/cell.h"
+#include "../src/image.h"
+#include "../src/beam-parameters.h"
+#include "../src/geometry.h"
+#include "../src/peaks.h"
+
+
+static void mess_up_cell(UnitCell *cell)
+{
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+
+	/* Cell noise in percent */
+	const double cnoise = 0.5;
+
+	//STATUS("Real:\n");
+	//cell_print(cell);
+
+	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
+	ax = gaussian_noise(ax, cnoise*fabs(ax)/100.0);
+	ay = gaussian_noise(ay, cnoise*fabs(ay)/100.0);
+	az = gaussian_noise(az, cnoise*fabs(az)/100.0);
+	bx = gaussian_noise(bx, cnoise*fabs(bx)/100.0);
+	by = gaussian_noise(by, cnoise*fabs(by)/100.0);
+	bz = gaussian_noise(bz, cnoise*fabs(bz)/100.0);
+	cx = gaussian_noise(cx, cnoise*fabs(cx)/100.0);
+	cy = gaussian_noise(cy, cnoise*fabs(cy)/100.0);
+	cz = gaussian_noise(cz, cnoise*fabs(cz)/100.0);
+	cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
+
+	//STATUS("Changed:\n");
+	//cell_print(cell);
+}
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Alter a stream.\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"
+);
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *input_file = NULL;
+	char *output_file = NULL;
+	struct image image;
+	struct detector *det = NULL;
+	struct beam_params *beam = NULL;
+	char *beamfile = NULL;
+	char *geomfile = NULL;
+	FILE *ifh;
+	FILE *ofh;
+	int v;
+
+	/* Long options */
+	const struct option longopts[] = {
+		{"help",               0, NULL,               'h'},
+		{"output",             1, NULL,               'o'},
+		{"input",              1, NULL,               'i'},
+		{"beam",               1, NULL,               'b'},
+		{"geometry",           1, NULL,               'g'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:o:b:g:",
+	                        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 'g' :
+			geomfile = strdup(optarg);
+			break;
+
+		case 0 :
+			break;
+
+		default :
+			return 1;
+		}
+
+	}
+
+	if ( input_file == NULL ) {
+		ERROR("You must pgive a filename for the output.\n");
+		return 1;
+	}
+	ifh = fopen(input_file, "r");
+	if ( ifh == NULL ) {
+		ERROR("Couldn't open input file '%s'\n", input_file);
+		return 1;
+	}
+	free(input_file);
+
+	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);
+
+	/* 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 geometry */
+	if ( geomfile == NULL ) {
+		ERROR("You need to give a geometry file.\n");
+		return 1;
+	}
+	det = get_detector_geometry(geomfile);
+	if ( det == NULL ) {
+		ERROR("Failed to read geometry from '%s'\n", geomfile);
+		return 1;
+	}
+	free(geomfile);
+
+	write_stream_header(ofh, argc, argv);
+
+	image.det = det;
+	image.width = det->max_fs;
+	image.height = det->max_ss;
+
+	image.lambda = 0.0;
+	image.div = beam->divergence;
+	image.bw = beam->bandwidth;
+	image.profile_radius = 0.0001e9;
+	image.i0_available = 0;
+
+	do {
+
+		image.indexed_cell = NULL;
+		v = read_chunk(ifh, &image);
+		if ( (v == 0) && (image.indexed_cell != NULL) ) {
+
+			mess_up_cell(image.indexed_cell);
+			image.reflections = find_intersections(&image,
+			                               image.indexed_cell);
+
+			write_chunk(ofh, &image, STREAM_INTEGRATED);
+
+		}
+
+	} while ( v == 0 );
+
+
+	fclose(ofh);
+	fclose(ifh);
+
+	return 0;
+}