Add facetron program for profile fitting and post-refinement

8 files changed, 174 insertions, 18 deletions

diff --git a/.gitignore b/.gitignore
index c0e36603..0bd94740 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,4 +15,5 @@ src/compare_hkl
 src/powder_plot
 src/render_hkl
 src/calibrate_detector
+src/facetron
 *~
diff --git a/scripts/test-facetron b/scripts/test-facetron
new file mode 100755
index 00000000..e10132d7
--- /dev/null
+++ b/scripts/test-facetron
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+echo $1 | indexamajig --indexing=dirax -i - \
+                      -g ~/crystfel/examples/lcls-dec.geom \
+                      -p ~/lcls/1JB0.pdb \
+                      --near-bragg --filter-cm \
+        2>/dev/null | grep 'star' | cut -d"=" -f 2 | cut -d" " -f 1-4 \
+        | ~/crystfel/src/facetron
diff --git a/src/Makefile.am b/src/Makefile.am
index a61ebb6b..8f88ead7 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,5 +1,5 @@
 bin_PROGRAMS = pattern_sim process_hkl get_hkl indexamajig compare_hkl \
-               powder_plot render_hkl calibrate_detector
+               powder_plot render_hkl calibrate_detector facetron
 
 if HAVE_GTK
 bin_PROGRAMS += hdfsee
@@ -55,4 +55,7 @@ calibrate_detector_SOURCES = calibrate_detector.c utils.c hdf5-file.c image.c \
                              sfac.c
 calibrate_detector_LDADD = @LIBS@
 
+facetron_SOURCES = facetron.c cell.c
+facetron_LDADD = @LIBS@
+
 INCLUDES = "-I$(top_srcdir)/data"
diff --git a/src/Makefile.in b/src/Makefile.in
index 7cd5226c..85dc14ee 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -35,7 +35,7 @@ POST_UNINSTALL = :
 bin_PROGRAMS = pattern_sim$(EXEEXT) process_hkl$(EXEEXT) \
 	get_hkl$(EXEEXT) indexamajig$(EXEEXT) compare_hkl$(EXEEXT) \
 	powder_plot$(EXEEXT) render_hkl$(EXEEXT) \
-	calibrate_detector$(EXEEXT) $(am__EXEEXT_1)
+	calibrate_detector$(EXEEXT) facetron$(EXEEXT) $(am__EXEEXT_1)
 @HAVE_GTK_TRUE@am__append_1 = hdfsee
 @HAVE_OPENCL_TRUE@am__append_2 = diffraction-gpu.c cl-utils.c
 @HAVE_OPENCL_TRUE@am__append_3 = diffraction-gpu.c cl-utils.c
@@ -63,6 +63,9 @@ am_compare_hkl_OBJECTS = compare_hkl.$(OBJEXT) sfac.$(OBJEXT) \
 	statistics.$(OBJEXT) symmetry.$(OBJEXT)
 compare_hkl_OBJECTS = $(am_compare_hkl_OBJECTS)
 compare_hkl_DEPENDENCIES =
+am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT)
+facetron_OBJECTS = $(am_facetron_OBJECTS)
+facetron_DEPENDENCIES =
 am_get_hkl_OBJECTS = get_hkl.$(OBJEXT) sfac.$(OBJEXT) cell.$(OBJEXT) \
 	utils.$(OBJEXT) reflections.$(OBJEXT) symmetry.$(OBJEXT)
 get_hkl_OBJECTS = $(am_get_hkl_OBJECTS)
@@ -134,12 +137,13 @@ AM_V_GEN = $(am__v_GEN_$(V))
 am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
 am__v_GEN_0 = @echo "  GEN   " $@;
 SOURCES = $(calibrate_detector_SOURCES) $(compare_hkl_SOURCES) \
-	$(get_hkl_SOURCES) $(hdfsee_SOURCES) $(indexamajig_SOURCES) \
-	$(pattern_sim_SOURCES) $(powder_plot_SOURCES) \
-	$(process_hkl_SOURCES) $(render_hkl_SOURCES)
+	$(facetron_SOURCES) $(get_hkl_SOURCES) $(hdfsee_SOURCES) \
+	$(indexamajig_SOURCES) $(pattern_sim_SOURCES) \
+	$(powder_plot_SOURCES) $(process_hkl_SOURCES) \
+	$(render_hkl_SOURCES)
 DIST_SOURCES = $(calibrate_detector_SOURCES) $(compare_hkl_SOURCES) \
-	$(get_hkl_SOURCES) $(am__hdfsee_SOURCES_DIST) \
-	$(am__indexamajig_SOURCES_DIST) \
+	$(facetron_SOURCES) $(get_hkl_SOURCES) \
+	$(am__hdfsee_SOURCES_DIST) $(am__indexamajig_SOURCES_DIST) \
 	$(am__pattern_sim_SOURCES_DIST) $(powder_plot_SOURCES) \
 	$(process_hkl_SOURCES) $(render_hkl_SOURCES)
 ETAGS = etags
@@ -272,6 +276,8 @@ calibrate_detector_SOURCES = calibrate_detector.c utils.c hdf5-file.c image.c \
                              sfac.c
 
 calibrate_detector_LDADD = @LIBS@
+facetron_SOURCES = facetron.c cell.c
+facetron_LDADD = @LIBS@
 INCLUDES = "-I$(top_srcdir)/data"
 all: all-am
 
@@ -350,6 +356,9 @@ calibrate_detector$(EXEEXT): $(calibrate_detector_OBJECTS) $(calibrate_detector_
 compare_hkl$(EXEEXT): $(compare_hkl_OBJECTS) $(compare_hkl_DEPENDENCIES) 
 	@rm -f compare_hkl$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(compare_hkl_OBJECTS) $(compare_hkl_LDADD) $(LIBS)
+facetron$(EXEEXT): $(facetron_OBJECTS) $(facetron_DEPENDENCIES) 
+	@rm -f facetron$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(facetron_OBJECTS) $(facetron_LDADD) $(LIBS)
 get_hkl$(EXEEXT): $(get_hkl_OBJECTS) $(get_hkl_DEPENDENCIES) 
 	@rm -f get_hkl$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(get_hkl_OBJECTS) $(get_hkl_LDADD) $(LIBS)
@@ -387,6 +396,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/diffraction.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dirax.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/displaywindow.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/facetron.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/filters.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/get_hkl.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hdf5-file.Po@am__quote@
diff --git a/src/cell.c b/src/cell.c
index 3edcc8ef..79261249 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -150,8 +150,7 @@ UnitCell *cell_new_from_parameters(double a, double b, double c,
 }
 
 
-static UnitCell *cell_new_from_axes(struct rvec as, struct rvec bs,
-                                    struct rvec cs)
+UnitCell *cell_new_from_axes(struct rvec as, struct rvec bs, struct rvec cs)
 {
 	UnitCell *cell;
 
diff --git a/src/cell.h b/src/cell.h
index ab67a594..113e6512 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -16,6 +16,14 @@
 #include <config.h>
 #endif
 
+/* A 3D vector in reciprocal space */
+struct rvec
+{
+	double   u;
+	double   v;
+	double   w;
+};
+
 typedef struct _unitcell UnitCell;
 
 extern UnitCell *cell_new(void);
@@ -25,6 +33,9 @@ extern UnitCell *cell_new_from_cell(UnitCell *orig);
 extern UnitCell *cell_new_from_parameters(double a, double b, double c,
 				double alpha, double beta, double gamma);
 
+extern UnitCell *cell_new_from_axes(struct rvec as, struct rvec bs,
+                                    struct rvec cs);
+
 extern void cell_set_cartesian(UnitCell *cell,
 			double ax, double ay, double az,
 			double bx, double by, double bz,
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;
+}
diff --git a/src/image.h b/src/image.h
index 3b31b2fa..613b0989 100644
--- a/src/image.h
+++ b/src/image.h
@@ -58,15 +58,6 @@ struct imagefeature {
 typedef struct _imagefeaturelist ImageFeatureList;
 
 
-/* A 3D vector in reciprocal space */
-struct rvec
-{
-	double   u;
-	double   v;
-	double   w;
-};
-
-
 struct reflhit {
 	signed int h;
 	signed int k;