Remove template indexing

1 files changed, 0 insertions, 326 deletions

diff --git a/src/templates.c b/src/templates.c
deleted file mode 100644
index ed557afa..00000000
--- a/src/templates.c
+++ /dev/null
@@ -1,326 +0,0 @@
-/*
- * 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"
-#include "symmetry.h"
-#include "utils.h"
-#include "geometry.h"
-#include "hdf5-file.h"
-#include "peaks.h"
-#include "reflist.h"
-
-#include <assert.h>
-
-
-#define INTEGRATION_SQUARE_SIDE (10)
-#define THRESHOLD (500)
-
-
-/* Private data for template indexing */
-struct _indexingprivate_template
-{
-	struct _indexingprivate base;
-	UnitCell *cell;
-	int n_templates;
-	struct template *templates;
-};
-
-
-struct template {
-	double omega;
-	double phi;
-	RefList *spots;
-};
-
-
-/* Generate templates for the given cell using a representative image */
-IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
-                                    struct detector *det,
-                                    double nominal_photon_energy)
-{
-	struct _indexingprivate_template *priv;
-	const char *sym;
-	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;
-	int i;
-
-	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);
-	image.det = det;
-	if ( image.lambda < 0.0 ) image.lambda = nominal_photon_energy;
-
-	priv = calloc(1, sizeof(struct _indexingprivate_template));
-	priv->base.indm = INDEXING_TEMPLATE;
-
-	sym = cell_get_pointgroup(cell);
-
-	/* These define the orientation in space */
-	if ( is_polyhedral(sym) ) {
-		ERROR("WARNING: Point group is polyhedral.\n");
-		ERROR("This means I can't properly determine the orientation");
-		ERROR(" ranges for template matching.  Expect trouble.\n");
-	}
-	omega_max = 2.0*M_PI / rotational_order(sym);
-	if ( has_bisecting_mirror_or_diad(sym) ) omega_max /= 2.0;
-	phi_max = M_PI;
-	if ( has_perpendicular_mirror(sym) ) phi_max /= 2.0;
-
-	/* One more axis would define the rotation in the plane of the image */
-
-	STATUS("Orientation ranges in %s: %.0f-%.0f, %.0f-%.0f deg.\n",
-	       sym, 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);
-
-	priv->templates = malloc(n_templates * sizeof(struct template));
-
-	i = 0;
-	for ( omega = 0.0; omega < omega_max-omega_step; omega += omega_step ) {
-	for ( phi = 0.0; phi < phi_max-phi_step; phi += phi_step ) {
-
-		RefList *reflections;
-		UnitCell *cell_rot;
-
-		assert(i < n_templates);
-
-		cell_rot = rotate_cell(cell, omega, phi, 0.0);
-
-		reflections = find_intersections(&image, cell_rot, 0);
-		if ( reflections == NULL ) {
-			ERROR("Template calculation failed.\n");
-			return NULL;
-		}
-
-		priv->templates[i].omega = omega;
-		priv->templates[i].phi = phi;
-		priv->templates[i].spots = reflections;
-		i++;
-
-		free(cell_rot);
-
-	}
-	progress_bar(omega*1000.0, (omega_max-2.0*omega_step)*1000.0,
-	             "Generating templates");
-	}
-
-	priv->n_templates = n_templates;
-	priv->cell = cell_new_from_cell(cell);
-
-	free(image.data);
-	free(image.flags);
-
-	return (struct _indexingprivate *)priv;
-}
-
-
-static int fast_integrate_peak(struct image *image, int xp, int yp)
-{
-	int x, y;
-	double total = 0;
-	int r = INTEGRATION_SQUARE_SIDE;
-
-	for ( x=xp-r; x<=xp+r; x++ ) {
-	for ( y=yp-r; y<=yp+r; y++ ) {
-
-		int val;
-
-		if ( (x>=image->width) || (x<0) ) continue;
-		if ( (y>=image->height) || (y<0) ) continue;
-
-		val = image->data[x+image->width*y];
-
-		if ( val < THRESHOLD ) continue;
-		total += val;
-
-	}
-	}
-
-	return total;
-}
-
-
-static double integrate_all_rot(struct image *image, RefList *reflections,
-                                double rot)
-{
-	double itot = 0.0;
-	double cosr, sinr;
-	int num_int = 0;
-	Reflection *refl;
-	RefListIterator *iter;
-
-	cosr = cos(rot);
-	sinr = sin(rot);
-
-	for ( refl = first_refl(reflections, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) ) {
-
-		float xp, yp;
-		double x, y;
-
-		get_detector_pos(refl, &x, &y);
-
-		xp =  cosr*x + sinr*y;
-		yp = -sinr*x + cosr*y;
-
-		itot += fast_integrate_peak(image, rint(xp), rint(yp));
-		num_int++;
-
-	}
-
-	return itot / num_int;
-}
-
-
-/* Return the mean of the distances between peaks in the image and peaks from
- * the given template. */
-static double mean_distance(struct image *image, RefList *reflections,
-                            double rot)
-{
-	double dtot = 0.0;
-	double cosr, sinr;
-	int num_dist = 0;
-	Reflection *refl;
-	RefListIterator *iter;
-
-	cosr = cos(rot);
-	sinr = sin(rot);
-
-	/* For each template peak */
-	for ( refl = first_refl(reflections, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) ) {
-
-		float xp, yp;
-		int j;
-		double min_dsq;
-		double x, y;
-
-		get_detector_pos(refl, &x, &y);
-
-		xp =  cosr*x + sinr*y;
-		yp = -sinr*x + cosr*y;
-
-		/* Compare to every real peak */
-		min_dsq = +INFINITY;
-		for ( j=0; j<image_feature_count(image->features); j++ ) {
-
-			struct imagefeature *f;
-			double this_dsq;
-
-			f = image_get_feature(image->features, j);
-
-			this_dsq = pow(f->x - xp, 2.0) + pow(f->y - yp, 2.0);
-			if ( this_dsq < min_dsq ) min_dsq = this_dsq;
-
-		}
-
-		if ( min_dsq < pow(50.0, 2.0) ) {
-			dtot += sqrt(min_dsq);
-			num_dist++;
-		}
-
-	}
-
-	return dtot / num_dist;
-}
-
-
-void match_templates(struct image *image, IndexingPrivate *ipriv)
-{
-	struct _indexingprivate_template *priv
-	        = (struct _indexingprivate_template *)ipriv;
-	int i, max_i;
-	double max, rot, rot_max, rot_step, rot_best;
-	const int peaks = 0;
-
-	if ( peaks ) {
-		max = INFINITY;
-	} else {
-		max = 0.0;
-	}
-	max_i = 0;
-	rot_max = 2.0*M_PI;
-	rot_step = 2.0*M_PI / 360.0;  /* 1 deg steps */
-	rot_best = 0.0;
-
-	for ( i=0; i<priv->n_templates; i++ ) {
-	for ( rot=0.0; rot<rot_max; rot+=rot_step ) {
-
-		double val;
-		int best;
-
-		if ( !peaks ) {
-			val = integrate_all_rot(image, priv->templates[i].spots,
-			                        rot);
-			best = val > max;
-		} else {
-			val = mean_distance(image, priv->templates[i].spots,
-			                    rot);
-			best = val < max;
-		}
-
-		if ( best ) {
-			max = val;
-			max_i = i;
-			rot_best = rot;
-		}
-
-	}
-	progress_bar(i, priv->n_templates-1, "Indexing");
-	}
-
-	STATUS("%i (%.2f, %.2f, %.2f): %.2f\n", max_i,
-	                                  rad2deg(priv->templates[max_i].omega),
-	                                  rad2deg(priv->templates[max_i].phi),
-	                                  rad2deg(rot_best), max);
-
-	image->ncells = 1;
-	image->candidate_cells[0] = rotate_cell(priv->cell,
-	                                        priv->templates[max_i].omega,
-	                                        priv->templates[max_i].phi,
-	                                        rot_best);
-}
-
-
-void free_templates(IndexingPrivate *priv)
-{
-	int i;
-	struct _indexingprivate_template *tpriv
-	        = (struct _indexingprivate_template *)priv;
-
-	for ( i=0; i<tpriv->n_templates; i++ ) {
-		free(tpriv->templates[i].spots);
-	}
-
-	free(tpriv->templates);
-	cell_free(tpriv->cell);
-	free(tpriv);
-}