indexamajig: Prepare for other indexing methods which need initial setup

10 files changed, 180 insertions, 15 deletions

diff --git a/Makefile.am b/Makefile.am
index b3905371..e8cc6ffd 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -6,5 +6,5 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h \
              data/defs.h src/parameters-lcls.tmp \
              data/diffraction.cl data/sfac src/likelihood.h src/symmetry.h \
-             src/povray.h
+             src/povray.h src/index-priv.h
 SUBDIRS = src data
diff --git a/Makefile.in b/Makefile.in
index 6d42920d..55a85578 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -203,7 +203,7 @@ EXTRA_DIST = configure src/cell.h src/hdf5-file.h src/image.h \
              src/filters.h src/diffraction-gpu.h src/cl-utils.h \
              data/defs.h src/parameters-lcls.tmp \
              data/diffraction.cl data/sfac src/likelihood.h src/symmetry.h \
-             src/povray.h
+             src/povray.h src/index-priv.h
 
 SUBDIRS = src data
 all: config.h
diff --git a/src/Makefile.am b/src/Makefile.am
index 34f8a9a0..81089265 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -22,7 +22,7 @@ process_hkl_LDADD = @LIBS@
 
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
                       peaks.c index.c filters.c diffraction.c detector.c \
-                      sfac.c dirax.c reflections.c
+                      sfac.c dirax.c reflections.c templates.c
 indexamajig_LDADD = @LIBS@
 if HAVE_OPENCL
 indexamajig_SOURCES += diffraction-gpu.c cl-utils.c
diff --git a/src/Makefile.in b/src/Makefile.in
index 4716d60e..23079835 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -88,15 +88,15 @@ hdfsee_OBJECTS = $(am_hdfsee_OBJECTS)
 hdfsee_DEPENDENCIES =
 am__indexamajig_SOURCES_DIST = indexamajig.c hdf5-file.c utils.c \
 	cell.c image.c peaks.c index.c filters.c diffraction.c \
-	detector.c sfac.c dirax.c reflections.c diffraction-gpu.c \
-	cl-utils.c
+	detector.c sfac.c dirax.c reflections.c templates.c \
+	diffraction-gpu.c cl-utils.c
 @HAVE_OPENCL_TRUE@am__objects_1 = diffraction-gpu.$(OBJEXT) \
 @HAVE_OPENCL_TRUE@	cl-utils.$(OBJEXT)
 am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
 	utils.$(OBJEXT) cell.$(OBJEXT) image.$(OBJEXT) peaks.$(OBJEXT) \
 	index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \
 	detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \
-	reflections.$(OBJEXT) $(am__objects_1)
+	reflections.$(OBJEXT) templates.$(OBJEXT) $(am__objects_1)
 indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
 indexamajig_DEPENDENCIES =
 am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \
@@ -259,7 +259,7 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
 process_hkl_LDADD = @LIBS@
 indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c cell.c image.c \
 	peaks.c index.c filters.c diffraction.c detector.c sfac.c \
-	dirax.c reflections.c $(am__append_3)
+	dirax.c reflections.c templates.c $(am__append_3)
 indexamajig_LDADD = @LIBS@
 @HAVE_GTK_TRUE@hdfsee_SOURCES = hdfsee.c displaywindow.c render.c hdf5-file.c utils.c image.c \
 @HAVE_GTK_TRUE@                 filters.c
@@ -432,6 +432,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sfac.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/statistics.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/symmetry.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/templates.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@
 
 .c.o:
diff --git a/src/index-priv.h b/src/index-priv.h
new file mode 100644
index 00000000..3d8c8a22
--- /dev/null
+++ b/src/index-priv.h
@@ -0,0 +1,29 @@
+/*
+ * index-priv.h
+ *
+ * Indexing private data
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifndef INDEXPRIV_H
+#define INDEXPRIV_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "index.h"
+
+struct _indexingprivate
+{
+	IndexingMethod indm;
+};
+
+
+#endif	/* INDEXPRIV_H */
diff --git a/src/index.c b/src/index.c
index 70b23640..7273d64b 100644
--- a/src/index.c
+++ b/src/index.c
@@ -27,6 +27,33 @@
 #include "sfac.h"
 #include "detector.h"
 #include "index.h"
+#include "index-priv.h"
+#include "templates.h"
+
+
+/* Base class constructor for unspecialised indexing private data */
+static IndexingPrivate *indexing_private(IndexingMethod indm)
+{
+	struct _indexingprivate *priv;
+	priv = calloc(1, sizeof(struct _indexingprivate));
+	priv->indm = indm;
+	return priv;
+}
+
+
+IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
+                                  const char *filename)
+{
+	switch ( indm ) {
+	case INDEXING_NONE :
+		return indexing_private(indm);
+	case INDEXING_DIRAX :
+		return indexing_private(indm);
+	case INDEXING_TEMPLATE :
+		return generate_templates(cell, filename);
+	}
+	return 0;
+}
 
 
 static void write_drx(struct image *image)
@@ -60,7 +87,7 @@ static void write_drx(struct image *image)
 
 
 void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
-                   int no_match, int verbose)
+                   int no_match, int verbose, IndexingPrivate *ipriv)
 {
 	int i;
 	int nc = 0;
@@ -87,8 +114,16 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod indm,
 	image->ncells = 0;
 
 	/* Index (or not) as appropriate */
-	if ( indm == INDEXING_NONE ) return;
-	if ( indm == INDEXING_DIRAX ) run_dirax(image);
+	switch ( indm ) {
+	case INDEXING_NONE :
+		return;
+	case INDEXING_DIRAX :
+		run_dirax(image);
+		break;
+	case INDEXING_TEMPLATE :
+		match_templates(image, ipriv);
+		break;
+	}
 
 	if ( image->ncells == 0 ) {
 		STATUS("No candidate cells found.\n");
diff --git a/src/index.h b/src/index.h
index b30db837..1c637f47 100644
--- a/src/index.h
+++ b/src/index.h
@@ -19,16 +19,22 @@
 
 
 #include "cell.h"
-
+#include "image.h"
 
 typedef enum {
 	INDEXING_NONE,
 	INDEXING_DIRAX,
-	INDEXING_MATCH
+	INDEXING_TEMPLATE
 } IndexingMethod;
 
 
+typedef struct _indexingprivate IndexingPrivate;
+
+extern IndexingPrivate *prepare_indexing(IndexingMethod indm, UnitCell *cell,
+                                         const char *filename);
+
 extern void index_pattern(struct image *image, UnitCell *cell,
-                          IndexingMethod indm, int no_match, int verbose);
+                          IndexingMethod indm, int no_match, int verbose,
+                          IndexingPrivate *priv);
 
 #endif	/* INDEX_H */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f7eef166..ec4e18c4 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -64,6 +64,7 @@ struct process_args
 	int config_sa;
 	struct detector *det;
 	IndexingMethod indm;
+	IndexingPrivate *ipriv;
 	const double *intensities;
 	struct gpu_context *gctx;
 
@@ -98,6 +99,7 @@ static void show_help(const char *s)
 "      --indexing=<method> Use 'method' for indexing.  Choose from:\n"
 "                           none     : no indexing\n"
 "                           dirax    : invoke DirAx\n"
+"                           template : index by template matching\n"
 "  -g. --geometry=<file>   Get detector geometry from file.\n"
 "\n\nWith just the above options, this program does not do much of practical "
 "use.\nYou should also enable some of the following:\n\n"
@@ -339,7 +341,7 @@ static struct process_result process_image(struct process_args *pargs)
 	/* Calculate orientation matrix (by magic) */
 	if ( config_writedrx || (indm != INDEXING_NONE) ) {
 		index_pattern(&image, cell, indm, config_nomatch,
-		              config_verbose);
+		              config_verbose, pargs->ipriv);
 	}
 
 	/* No cell at this point?  Then we're done. */
@@ -478,6 +480,9 @@ int main(int argc, char *argv[])
 	int i;
 	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
 	pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
+	char prepare_line[1024];
+	char prepare_filename[1024];
+	IndexingPrivate *ipriv;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -597,6 +602,8 @@ int main(int argc, char *argv[])
 		indm = INDEXING_NONE;
 	} else if ( strcmp(indm_str, "dirax") == 0) {
 		indm = INDEXING_DIRAX;
+	} else if ( strcmp(indm_str, "template") == 0) {
+		indm = INDEXING_TEMPLATE;
 	} else {
 		ERROR("Unrecognised indexing method '%s'\n", indm_str);
 		return 1;
@@ -615,7 +622,7 @@ int main(int argc, char *argv[])
 	}
 	free(geometry);
 
-	if ( !config_nomatch ) {
+	if ( (!config_nomatch) || (indm == INDEXING_TEMPLATE) ) {
 		cell = load_cell_from_pdb(pdb);
 		if ( cell == NULL ) {
 			ERROR("Couldn't read unit cell (from %s)\n", pdb);
@@ -627,6 +634,21 @@ int main(int argc, char *argv[])
 	}
 	free(pdb);
 
+	/* Get first filename and use it to set up the indexing */
+	rval = fgets(prepare_line, 1023, fh);
+	if ( rval == NULL ) {
+		ERROR("Failed to get filename to prepare indexing.\n");
+		return 1;
+	}
+	chomp(prepare_line);
+	snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
+	ipriv = prepare_indexing(indm, cell, prepare_filename);
+	if ( ipriv == NULL ) {
+		ERROR("Failed to prepare indexing.\n");
+		return 1;
+	}
+	rewind(fh);
+
 	gsl_set_error_handler_off();
 	n_images = 0;
 	n_hits = 0;
@@ -673,6 +695,7 @@ int main(int argc, char *argv[])
 		pargs->config_sa = config_sa;
 		pargs->cell = cell;
 		pargs->det = det;
+		pargs->ipriv = ipriv;
 		pargs->indm = indm;
 		pargs->intensities = intensities;
 		pargs->gctx = gctx;
diff --git a/src/templates.c b/src/templates.c
new file mode 100644
index 00000000..db28b9b9
--- /dev/null
+++ b/src/templates.c
@@ -0,0 +1,41 @@
+/*
+ * templates.c
+ *
+ * Indexing by template matching
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "index.h"
+#include "index-priv.h"
+
+
+/* Private data for template indexing */
+struct _indexingprivate_template
+{
+	struct _indexingprivate base;
+};
+
+
+IndexingPrivate *generate_templates(UnitCell *cell, const char *filename)
+{
+	struct _indexingprivate_template *priv;
+
+	priv = calloc(1, sizeof(struct _indexingprivate_template));
+	priv->base.indm = INDEXING_TEMPLATE;
+
+	return (struct _indexingprivate *)priv;
+}
+
+
+void match_templates(struct image *image, IndexingPrivate *ipriv)
+{
+}
diff --git a/src/templates.h b/src/templates.h
new file mode 100644
index 00000000..dad46843
--- /dev/null
+++ b/src/templates.h
@@ -0,0 +1,30 @@
+/*
+ * templates.h
+ *
+ * Indexing by template matching
+ *
+ * (c) 2006-2010 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+#ifndef TEMPLATES_H
+#define TEMPLATES_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include "index.h"
+#include "image.h"
+#include "cell.h"
+
+extern IndexingPrivate *generate_templates(UnitCell *cell,
+                                           const char *filename);
+
+
+extern void match_templates(struct image *image, IndexingPrivate *ipriv);
+
+#endif	/* TEMPLATES_H */