Add contrib/alter_stream

1 files changed, 215 insertions, 0 deletions

diff --git a/contrib/alter_stream.c b/contrib/alter_stream.c
new file mode 100644
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--- /dev/null
+++ b/contrib/alter_stream.c
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+/*
+ * 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;
+}