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/*
* 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"
/* 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 detector *det)
{
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);
image.det = det;
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));
/* These define the orientation in space */
if ( is_polyhedral(holo) ) {
ERROR("WARNING: Holohedral 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(holo);
if ( has_bisecting_mirror_or_diad(holo) ) omega_max /= 2.0;
phi_max = M_PI;
if ( has_perpendicular_mirror(holo) ) 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",
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;
}
free(cell_rot);
}
progress_bar(omega*1000.0, (omega_max-omega_step)*1000.0,
"Generating templates");
}
priv->n_templates = n_templates;
return (struct _indexingprivate *)priv;
}
void match_templates(struct image *image, IndexingPrivate *ipriv)
{
}
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