Generation of templates (needs debugging)

6 files changed, 122 insertions, 145 deletions

diff --git a/src/Makefile.am b/src/Makefile.am
index b7108918..7fdf6dc9 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -22,7 +22,8 @@ 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 templates.c symmetry.c
+                      sfac.c dirax.c reflections.c templates.c symmetry.c \
+                      geometry.c
 indexamajig_LDADD = @LIBS@
 if HAVE_OPENCL
 indexamajig_SOURCES += diffraction-gpu.c cl-utils.c
@@ -56,7 +57,7 @@ calibrate_detector_SOURCES = calibrate_detector.c utils.c hdf5-file.c image.c \
 calibrate_detector_LDADD = @LIBS@
 
 facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
-                   image.c diffraction.c sfac.c
+                   image.c diffraction.c sfac.c geometry.c
 facetron_LDADD = @LIBS@
 
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c
diff --git a/src/Makefile.in b/src/Makefile.in
index 9355ef39..4b4da1f7 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -71,7 +71,7 @@ cubeit_DEPENDENCIES =
 am_facetron_OBJECTS = facetron.$(OBJEXT) cell.$(OBJEXT) \
 	hdf5-file.$(OBJEXT) utils.$(OBJEXT) detector.$(OBJEXT) \
 	peaks.$(OBJEXT) image.$(OBJEXT) diffraction.$(OBJEXT) \
-	sfac.$(OBJEXT)
+	sfac.$(OBJEXT) geometry.$(OBJEXT)
 facetron_OBJECTS = $(am_facetron_OBJECTS)
 facetron_DEPENDENCIES =
 am_get_hkl_OBJECTS = get_hkl.$(OBJEXT) sfac.$(OBJEXT) cell.$(OBJEXT) \
@@ -89,7 +89,7 @@ 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 templates.c symmetry.c \
-	diffraction-gpu.c cl-utils.c
+	geometry.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) \
@@ -97,7 +97,7 @@ am_indexamajig_OBJECTS = indexamajig.$(OBJEXT) hdf5-file.$(OBJEXT) \
 	index.$(OBJEXT) filters.$(OBJEXT) diffraction.$(OBJEXT) \
 	detector.$(OBJEXT) sfac.$(OBJEXT) dirax.$(OBJEXT) \
 	reflections.$(OBJEXT) templates.$(OBJEXT) symmetry.$(OBJEXT) \
-	$(am__objects_1)
+	geometry.$(OBJEXT) $(am__objects_1)
 indexamajig_OBJECTS = $(am_indexamajig_OBJECTS)
 indexamajig_DEPENDENCIES =
 am__pattern_sim_SOURCES_DIST = pattern_sim.c diffraction.c utils.c \
@@ -260,7 +260,8 @@ 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 templates.c symmetry.c $(am__append_3)
+	dirax.c reflections.c templates.c symmetry.c geometry.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
@@ -286,7 +287,7 @@ calibrate_detector_SOURCES = calibrate_detector.c utils.c hdf5-file.c image.c \
 
 calibrate_detector_LDADD = @LIBS@
 facetron_SOURCES = facetron.c cell.c hdf5-file.c utils.c detector.c peaks.c \
-                   image.c diffraction.c sfac.c
+                   image.c diffraction.c sfac.c geometry.c
 
 facetron_LDADD = @LIBS@
 cubeit_SOURCES = cubeit.c cell.c hdf5-file.c utils.c
@@ -415,6 +416,7 @@ distclean-compile:
 @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)/geometry.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@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/hdfsee.Po@am__quote@
diff --git a/src/cell.c b/src/cell.c
index d6464a71..d6d101cc 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -207,6 +207,9 @@ static int cell_crystallographic_to_cartesian(UnitCell *cell,
 {
 	double tmp, V, cosalphastar, cstar;
 
+	/* Note: Please consider and possibly change the ranges for template
+	 * matching (in templates.c) if the calculations below are altered. */
+
 	/* Firstly: Get a in terms of x, y and z
 	 * +a (cryst) is defined to lie along +x (cart) */
 	*ax = cell->a;
diff --git a/src/facetron.c b/src/facetron.c
index 0fa6b643..0c2b4d56 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -26,10 +26,7 @@
 #include "cell.h"
 #include "hdf5-file.h"
 #include "detector.h"
-#include "peaks.h"
-
-
-#define MAX_HITS (1024)
+#include "geometry.h"
 
 
 static void show_help(const char *s)
@@ -116,136 +113,6 @@ static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
 }
 
 
-static struct reflhit *find_intersections(struct image *image, UnitCell *cell,
-                                          double divergence, double bandwidth,
-                                          int *n, int output)
-{
-	double asx, asy, asz;
-	double bsx, bsy, bsz;
-	double csx, csy, csz;
-	struct reflhit *hits;
-	int np = 0;
-	int hmax, kmax, lmax;
-	double mres;
-	signed int h, k, l;
-
-	hits = malloc(sizeof(struct reflhit)*MAX_HITS);
-	if ( hits == NULL ) {
-		*n = 0;
-		return NULL;
-	}
-
-	cell_get_reciprocal(cell, &asx, &asy, &asz,
-	                          &bsx, &bsy, &bsz,
-	                          &csx, &csy, &csz);
-
-	mres = 1.0 / 8.0e-10;  /* 8 Angstroms */
-	hmax = mres / modulus(asx, asy, asz);
-	kmax = mres / modulus(bsx, bsy, bsz);
-	lmax = mres / modulus(csx, csy, csz);
-
-	for ( h=-hmax; h<hmax; h++ ) {
-	for ( k=-kmax; k<kmax; k++ ) {
-	for ( l=-lmax; l<lmax; l++ ) {
-
-		double xl, yl, zl;
-		double ds_sq, dps_sq;
-		double delta, divfact;
-		double llow, lhigh;
-		double xd, yd, cl;
-		double xda, yda;
-		int p;
-		int found = 0;
-
-		if ( (h==0) && (k==0) && (l==0) ) continue;
-
-		llow = image->lambda - image->lambda*bandwidth/2.0;
-		lhigh = image->lambda + image->lambda*bandwidth/2.0;
-
-		/* Get the coordinates of the reciprocal lattice point */
-		zl = h*asz + k*bsz + l*csz;
-		if ( zl < 0.0 ) continue;  /* Do this check very early */
-		xl = h*asx + k*bsx + l*csx;
-		yl = h*asy + k*bsy + l*csy;
-
-		ds_sq = modulus_squared(xl, yl, zl);  /* d*^2 */
-		delta = divergence/image->lambda;
-		dps_sq = ds_sq + pow(delta, 2.0);  /* d'*^2 */
-
-		/* In range? */
-		divfact = 2.0 * delta * sqrt(xl*xl + yl*yl);
-		if ( ds_sq - 2.0*zl/llow > 0.0 ) continue;
-		if ( ds_sq - 2.0*zl/lhigh < 0.0 ) continue;
-
-		/* Work out which panel this peak would fall on */
-		for ( p=0; p<image->det->n_panels; p++ ) {
-
-			/* Camera length for this panel */
-			cl = image->det->panels[p].clen;
-
-			/* Coordinates of peak relative to central beam, in m */
-			xd = cl*xl / (ds_sq/(2.0*zl) - zl);
-			yd = cl*yl / (ds_sq/(2.0*zl) - zl);
-
-			/* Convert to pixels */
-			xd *= image->det->panels[p].res;
-			yd *= image->det->panels[p].res;
-
-			/* Add the coordinates of the central beam */
-			xda = xd + image->det->panels[p].cx;
-			yda = yd + image->det->panels[p].cy;
-
-			/* Now, is this on this panel? */
-			if ( xda < image->det->panels[p].min_x ) continue;
-			if ( xda > image->det->panels[p].max_x ) continue;
-			if ( yda < image->det->panels[p].min_y ) continue;
-			if ( yda > image->det->panels[p].max_y ) continue;
-
-			/* Woohoo! */
-			found = 1;
-			break;
-
-		}
-
-		if ( !found ) continue;
-
-		hits[np].h = h;
-		hits[np].k = k;
-		hits[np].l = l;
-		np++;
-
-		if ( output ) {
-			printf("%i %i %i 0.0 (at %f,%f)\n", h, k, l, xda, yda);
-		}
-
-	}
-	}
-	}
-
-	*n = np;
-	return hits;
-}
-
-
-static double integrate_all(struct image *image, struct reflhit *hits, int n)
-{
-	double itot = 0.0;
-	int i;
-
-	for ( i=0; i<n; i++ ) {
-
-		float x, y, intensity;
-
-		if ( integrate_peak(image, hits[i].x, hits[i].y, &x, &y,
-                                    &intensity, 0, 0) ) continue;
-
-		itot += intensity;
-	}
-
-	return itot;
-}
-
-
 static void get_trial_cell(UnitCell *out, UnitCell *in, int i, double step)
 {
 	double asx, asy, asz;
diff --git a/src/symmetry.c b/src/symmetry.c
index 6611e617..6511d173 100644
--- a/src/symmetry.c
+++ b/src/symmetry.c
@@ -456,7 +456,8 @@ int is_polyhedral(const char *sym)
 }
 
 
-/* Returns the order of the highest axis of proper or improper rotation */
+/* Returns the order of the characteristic axis of proper or improper rotation
+ * for the point group.  This should be the rotation about the c axis. */
 int rotational_order(const char *sym)
 {
 	/* Triclinic */
diff --git a/src/templates.c b/src/templates.c
index 98182bbe..fd4616b2 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -18,28 +18,101 @@
 #include "index-priv.h"
 #include "symmetry.h"
 #include "utils.h"
+#include "geometry.h"
+#include "hdf5-file.h"
 
 
 /* Private data for template indexing */
 struct _indexingprivate_template
 {
 	struct _indexingprivate base;
+	int n_templates;
+	struct template *templates;
 };
 
 
+struct template {
+	double omega;
+	double phi;
+	int n;
+	struct reflhit spots;  /* Made into an array by Magic */
+};
+
+
+UnitCell *rotate_cell(UnitCell *in, double omega, double phi)
+{
+	UnitCell *out;
+	double asx, asy, asz;
+	double bsx, bsy, bsz;
+	double csx, csy, csz;
+	double xnew, ynew, znew;
+
+	cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy,
+	                        &bsz, &csx, &csy, &csz);
+
+	/* Rotate by "omega" about +z (parallel to c* and c unless triclinic) */
+	xnew = asx*cos(omega) + asy*sin(omega);
+	ynew = -asx*sin(omega) + asy*cos(omega);
+	znew = asz;
+	asx = xnew;  asy = ynew;  asz = znew;
+	xnew = bsx*cos(omega) + bsy*sin(omega);
+	ynew = -bsx*sin(omega) + bsy*cos(omega);
+	znew = bsz;
+	bsx = xnew;  bsy = ynew;  bsz = znew;
+	xnew = csx*cos(omega) + csy*sin(omega);
+	ynew = -csx*sin(omega) + csy*cos(omega);
+	znew = csz;
+	csx = xnew;  csy = ynew;  csz = znew;
+
+	/* Rotate by "phi" about +x (not parallel to anything specific) */
+	xnew = asx;
+	ynew = asy*cos(phi) + asz*sin(phi);
+	znew = -asy*sin(phi) + asz*cos(phi);
+	asx = xnew;  asy = ynew;  asz = znew;
+	xnew = bsx;
+	ynew = bsy*cos(phi) + bsz*sin(phi);
+	znew = -bsy*sin(phi) + bsz*cos(phi);
+	bsx = xnew;  bsy = ynew;  bsz = znew;
+	xnew = csx;
+	ynew = csy*cos(phi) + csz*sin(phi);
+	znew = -csy*sin(phi) + csz*cos(phi);
+	csx = xnew;  csy = ynew;  csz = znew;
+
+	out = cell_new_from_cell(in);
+	cell_set_reciprocal(out, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+	return out;
+}
+
+
 /* Generate templates for the given cell using a representative image */
 IndexingPrivate *generate_templates(UnitCell *cell, const char *filename)
 {
 	struct _indexingprivate_template *priv;
 	const char *holo;
 	double omega_max, phi_max;
+	int n_templates;
+	const double omega_step = deg2rad(0.5);
+	const double phi_step = deg2rad(0.5);
+	double omega, phi;
+	struct image image;
+	struct hdfile *hdfile;
+
+	hdfile = hdfile_open(filename);
+	if ( hdfile == NULL ) {
+		return NULL;
+	} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
+		ERROR("Couldn't select path\n");
+		return NULL;
+	}
+	hdf5_read(hdfile, &image, 0);
+	hdfile_close(hdfile);
 
 	priv = calloc(1, sizeof(struct _indexingprivate_template));
 	priv->base.indm = INDEXING_TEMPLATE;
 
 	/* We can only distinguish orientations within the holohedral cell */
 	holo = get_holohedral(cell_get_pointgroup(cell));
-	STATUS("%s\n", holo);
 
 	/* These define the orientation in space */
 	if ( is_polyhedral(holo) ) {
@@ -54,8 +127,38 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename)
 
 	/* One more axis would define the rotation in the plane of the image */
 
-	STATUS("Orientation ranges: %5.0f -> %5.0f, %5.0f -> %5.0f deg.\n",
-	       0.0, rad2deg(omega_max), 0.0, rad2deg(phi_max));
+	STATUS("Orientation ranges in %s: %.0f-%.0f, %.0f-%.0f deg.\n",
+	       holo, 0.0, rad2deg(omega_max), 0.0, rad2deg(phi_max));
+
+	n_templates = (omega_max * phi_max)/(omega_step * phi_step);
+	STATUS("%i templates to be calculated.\n", n_templates);
+
+	for ( omega = 0.0; omega < omega_max; omega += omega_step ) {
+	for ( phi = 0.0; phi < phi_max; phi += phi_step ) {
+
+		int n;
+		struct reflhit *hits;
+		UnitCell *cell_rot;
+
+		cell_rot = rotate_cell(cell, omega, phi);
+
+		hits = find_intersections(&image, cell_rot, 5.0e-3,
+		                          3.0/100.0, &n, 0);
+		if ( hits == NULL ) {
+			ERROR("Template calculation failed.\n");
+			return NULL;
+		}
+
+		STATUS("%.2f, %.2f : %i features\n",
+		       rad2deg(omega), rad2deg(phi), n);
+
+		free(cell_rot);
+
+	}
+	STATUS("Finished omega=%.2f\n", rad2deg(omega));
+	}
+
+	priv->n_templates = n_templates;
 
 	return (struct _indexingprivate *)priv;
 }