Introduce 'whirligig'

1 files changed, 172 insertions, 0 deletions

diff --git a/src/whirligig.c b/src/whirligig.c
new file mode 100644
index 00000000..e3ad195d
--- /dev/null
+++ b/src/whirligig.c
@@ -0,0 +1,172 @@
+/*
+ * whirligig.c
+ *
+ * Find and combine rotation series
+ *
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2012-2014 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+
+#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 <pthread.h>
+#include <gsl/gsl_errno.h>
+
+#include <image.h>
+#include <utils.h>
+#include <symmetry.h>
+#include <stream.h>
+#include <geometry.h>
+#include <peaks.h>
+#include <thread-pool.h>
+#include <reflist.h>
+#include <reflist-utils.h>
+
+#include "version.h"
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s <input.stream> [options]\n\n", s);
+	printf(
+"Find and combine rotation series.\n"
+"\n"
+"  -h, --help                 Display this help message.\n"
+"      --version              Print CrystFEL version number and exit.\n"
+"      --no-polarisation      Disable polarisation correction.\n");
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	Stream *st;
+	int n_images = 0;
+	int n_crystals = 0;
+	int polarisation = 1;
+
+	/* Long options */
+	const struct option longopts[] = {
+
+		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                3 },
+
+		{"no-polarisation",    0, &polarisation,       0},
+		{"no-polarization",    0, &polarisation,       0},
+		{"polarisation",       0, &polarisation,       1}, /* compat */
+		{"polarization",       0, &polarisation,       1}, /* compat */
+
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "h",
+	                        longopts, NULL)) != -1)
+	{
+
+		switch (c) {
+
+			case 'h' :
+			show_help(argv[0]);
+			return 0;
+
+			case 0 :
+			break;
+
+			case '?' :
+			break;
+
+			default :
+			ERROR("Unhandled option '%c'\n", c);
+			break;
+
+		}
+
+	}
+
+	if ( argc != (optind+1) ) {
+		ERROR("Please provide exactly one stream to process.\n");
+		return 1;
+	}
+
+	st = open_stream_for_read(argv[optind++]);
+	if ( st == NULL ) {
+		ERROR("Failed to open input stream '%s'\n", argv[optind-1]);
+		return 1;
+	}
+
+	do {
+
+		int i;
+		struct image cur;
+
+		cur.div = NAN;
+		cur.bw = NAN;
+		cur.det = NULL;
+		if ( read_chunk_2(st, &cur, STREAM_READ_REFLECTIONS
+		                            | STREAM_READ_UNITCELL) != 0 ) {
+			break;
+		}
+
+		if ( isnan(cur.div) || isnan(cur.bw) ) {
+			ERROR("Chunk doesn't contain beam parameters.\n");
+			return 1;
+		}
+
+		n_images++;
+
+		for ( i=0; i<cur.n_crystals; i++ ) {
+
+			Crystal *cr;
+			RefList *cr_refl;
+
+			cr = cur.crystals[i];
+
+			/* This is the raw list of reflections */
+			cr_refl = crystal_get_reflections(cr);
+
+			if ( polarisation ) {
+				polarisation_correction(cr_refl,
+						        crystal_get_cell(cr),
+						        &cur);
+			}
+
+			n_crystals++;
+
+		}
+
+	} while ( 1 );
+
+	close_stream(st);
+
+	return 0;
+}