Add facetron program for profile fitting and post-refinement

1 files changed, 133 insertions, 0 deletions

diff --git a/src/facetron.c b/src/facetron.c
new file mode 100644
index 00000000..bcaaac48
--- /dev/null
+++ b/src/facetron.c
@@ -0,0 +1,133 @@
+/*
+ * facetron.c
+ *
+ * Profile fitting for coherent nanocrystallography
+ *
+ * (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 "image.h"
+#include "cell.h"
+
+
+static void show_help(const char *s)
+{
+	printf("Syntax: %s [options]\n\n", s);
+	printf(
+"Profile fitting for coherent nanocrystallography.\n"
+"\n"
+"  -h, --help                 Display this help message.\n"
+"\n"
+"  -i, --input=<filename>     Specify the name of the image to work on.\n"
+"  -m, --matrix=<filename>    Specify the file which contains the initial\n"
+"                              orientation matrix.  Can be '-' for stdin,\n"
+"                              which is the default.  Units are nm^-1.\n"
+);
+}
+
+
+static UnitCell *read_orientation_matrix(const char *filename)
+{
+	FILE *mfh;
+	float u, v, w;
+	struct rvec as, bs, cs;
+	UnitCell *cell;
+
+	if ( (filename == NULL) || (strcmp(filename, "-") == 0) ) {
+		mfh = stdin;
+	} else {
+		mfh = fopen(filename, "r");
+	}
+	if ( mfh == NULL ) {
+		ERROR("Failed to open matrix file '%s'\n", filename);
+		return NULL;
+	}
+
+	if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read a-star\n");
+		return NULL;
+	}
+	as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
+	if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read b-star\n");
+		return NULL;
+	}
+	bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
+	if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
+		ERROR("Couldn't read c-star\n");
+		return NULL;
+	}
+	cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
+	cell = cell_new_from_axes(as, bs, cs);
+	fclose(mfh);
+
+	return cell;
+}
+
+
+int main(int argc, char *argv[])
+{
+	int c;
+	char *infile = NULL;
+	char *matrix = NULL;
+	UnitCell *cell;
+
+	/* Long options */
+	const struct option longopts[] = {
+		{"help",               0, NULL,               'h'},
+		{"input",              1, NULL,               'i'},
+		{"matrix",             1, NULL,               'm'},
+		{0, 0, NULL, 0}
+	};
+
+	/* Short options */
+	while ((c = getopt_long(argc, argv, "hi:m:", longopts, NULL)) != -1) {
+
+		switch (c) {
+		case 'h' :
+			show_help(argv[0]);
+			return 0;
+
+		case 'i' :
+			infile = strdup(optarg);
+			break;
+
+		case 'm' :
+			matrix = strdup(optarg);
+			break;
+
+		case 0 :
+			break;
+
+		default :
+			return 1;
+		}
+
+	}
+
+	cell = read_orientation_matrix(matrix);
+	free(matrix);
+	if ( cell == NULL ) {
+		ERROR("Couldn't read initial orientation matrix.\n");
+		return 1;
+	}
+
+	cell_print(cell);
+
+	return 0;
+}