Initial integration stuff

1 files changed, 672 insertions, 0 deletions

diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
new file mode 100644
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--- /dev/null
+++ b/libcrystfel/src/integration.c
@@ -0,0 +1,672 @@
+/*
+ * integration.c
+ *
+ * Integration of intensities
+ *
+ * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2010-2013 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <assert.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_eigen.h>
+
+#include "reflist.h"
+#include "cell.h"
+#include "crystal.h"
+#include "cell-utils.h"
+#include "geometry.h"
+#include "image.h"
+#include "peaks.h"
+#include "integration.h"
+
+
+struct integr_ind
+{
+	double res;
+	Reflection *refl;
+};
+
+
+static int compare_resolution(const void *av, const void *bv)
+{
+	const struct integr_ind *a = av;
+	const struct integr_ind *b = bv;
+
+	return a->res > b->res;
+}
+
+
+static struct integr_ind *sort_reflections(RefList *list, UnitCell *cell,
+                                           int *np)
+{
+	struct integr_ind *il;
+	Reflection *refl;
+	RefListIterator *iter;
+	int i, n;
+
+	n = num_reflections(list);
+	*np = 0;  /* For now */
+
+	if ( n == 0 ) return NULL;
+
+	il = calloc(n, sizeof(struct integr_ind));
+	if ( il == NULL ) return NULL;
+
+	i = 0;
+	for ( refl = first_refl(list, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) )
+	{
+		signed int h, k, l;
+		double res;
+
+		if ( get_redundancy(refl) == 0 ) continue;
+
+		get_indices(refl, &h, &k, &l);
+		res = resolution(cell, h, k, l);
+
+		il[i].res = res;
+		il[i].refl = refl;
+
+		i++;
+		assert(i <= n);
+	}
+
+	qsort(il, n, sizeof(struct integr_ind), compare_resolution);
+
+	*np = n;
+	return il;
+}
+
+
+static void check_eigen(gsl_vector *e_val)
+{
+	int i;
+	double vmax, vmin;
+	const int n = e_val->size;
+	const double max_condition = 1e6;
+	const int verbose = 0;
+
+	if ( verbose ) STATUS("Eigenvalues:\n");
+	vmin = +INFINITY;
+	vmax = 0.0;
+	for ( i=0; i<n; i++ ) {
+		double val = gsl_vector_get(e_val, i);
+		if ( verbose ) STATUS("%i: %e\n", i, val);
+		if ( val > vmax ) vmax = val;
+		if ( val < vmin ) vmin = val;
+	}
+
+	for ( i=0; i<n; i++ ) {
+		double val = gsl_vector_get(e_val, i);
+		if ( val < vmax/max_condition ) {
+			gsl_vector_set(e_val, i, 0.0);
+		}
+	}
+
+	vmin = +INFINITY;
+	vmax = 0.0;
+	for ( i=0; i<n; i++ ) {
+		double val = gsl_vector_get(e_val, i);
+		if ( val == 0.0 ) continue;
+		if ( val > vmax ) vmax = val;
+		if ( val < vmin ) vmin = val;
+	}
+	if ( verbose ) {
+		STATUS("Condition number: %e / %e = %5.2f\n",
+		       vmax, vmin, vmax/vmin);
+	}
+}
+
+
+static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M)
+{
+	gsl_matrix *s_vec;
+	gsl_vector *s_val;
+	int err, n;
+	gsl_vector *shifts;
+
+	n = v->size;
+	if ( v->size != M->size1 ) return NULL;
+	if ( v->size != M->size2 ) return NULL;
+
+	s_val = gsl_vector_calloc(n);
+	s_vec = gsl_matrix_calloc(n, n);
+
+	err = gsl_linalg_SV_decomp_jacobi(M, s_vec, s_val);
+	if ( err ) {
+		ERROR("SVD failed: %s\n", gsl_strerror(err));
+		gsl_matrix_free(s_vec);
+		gsl_vector_free(s_val);
+		return NULL;
+	}
+	/* "M" is now "U" */
+
+	check_eigen(s_val);
+
+	shifts = gsl_vector_calloc(n);
+	err = gsl_linalg_SV_solve(M, s_vec, s_val, v, shifts);
+	if ( err ) {
+		ERROR("Matrix solution failed: %s\n", gsl_strerror(err));
+		gsl_matrix_free(s_vec);
+		gsl_vector_free(s_val);
+		gsl_vector_free(shifts);
+		return NULL;
+	}
+
+	gsl_matrix_free(s_vec);
+	gsl_vector_free(s_val);
+
+	return shifts;
+}
+
+
+struct intcontext
+{
+	int halfw;
+	int w;
+	struct image *image;
+	gsl_matrix *bgm;
+};
+
+
+static void addm(gsl_matrix *m, int i, int j, double val)
+{
+	double v = gsl_matrix_get(m, i, j);
+	gsl_matrix_set(m, i, j, v+val);
+}
+
+
+static void addv(gsl_vector *v, int i, double val)
+{
+	double k = gsl_vector_get(v, i);
+	gsl_vector_set(v, i, k+val);
+}
+
+
+static double boxi(struct intcontext *ic,
+                   int fid_fs, int fid_ss, int p, int q)
+{
+	int fs, ss;
+
+	fs = fid_fs + p;
+	ss = fid_ss + q;
+
+	/* FIXME: Wrong panel? */
+	return ic->image->data[fs + ic->image->width*ss];
+}
+
+
+static void fit_bg(struct intcontext *ic,
+                   int fid_fs, int fid_ss,
+                   double *pa, double *pb, double *pc)
+{
+	int p, q;
+	gsl_vector *v;
+	gsl_vector *ans;
+
+	v = gsl_vector_calloc(3);
+
+	for ( p=0; p<ic->w; p++ ) {
+	for ( q=0; q<ic->w; q++ ) {
+		double bi;
+		bi = boxi(ic, fid_fs, fid_ss, p, q);
+
+		addv(v, 0, bi*p);
+		addv(v, 1, bi*q);
+		addv(v, 2, bi);
+	}
+	}
+
+	ans = solve_svd(v, ic->bgm);
+	gsl_vector_free(v);
+
+	*pa = gsl_vector_get(ans, 0);
+	*pb = gsl_vector_get(ans, 1);
+	*pc = gsl_vector_get(ans, 2);
+
+	gsl_vector_free(ans);
+}
+
+
+static void init_intcontext(struct intcontext *ic)
+{
+	int p, q;
+
+	ic->w = 2*ic->halfw + 1;
+
+	ic->bgm = gsl_matrix_calloc(3, 3);
+	if ( ic->bgm == NULL ) {
+		ERROR("Failed to initialise matrix.\n");
+		return;
+	}
+
+	for ( p=0; p<ic->w; p++ ) {
+	for ( q=0; q<ic->w; q++ ) {
+		addm(ic->bgm, 0, 0, p*p);
+		addm(ic->bgm, 0, 1, p*q);
+		addm(ic->bgm, 0, 2, p);
+		addm(ic->bgm, 1, 0, p*q);
+		addm(ic->bgm, 1, 1, q*q);
+		addm(ic->bgm, 1, 2, q);
+		addm(ic->bgm, 2, 0, p);
+		addm(ic->bgm, 2, 1, q);
+		addm(ic->bgm, 2, 2, 1);
+	}
+	}
+}
+
+
+static void measure_all_intensities(RefList *list, struct image *image)
+{
+	Reflection *refl;
+	RefListIterator *iter;
+	struct intcontext ic;
+
+	ic.halfw = 4;
+	ic.image = image;
+	init_intcontext(&ic);
+
+	for ( refl = first_refl(list, &iter);
+		      refl != NULL;
+		      refl = next_refl(refl, iter) )
+	{
+		double pfs, pss;
+		int fid_fs, fid_ss;
+		double a, b, c;
+
+		get_detector_pos(refl, &pfs, &pss);
+		fid_fs = lrint(pfs);
+		fid_ss = lrint(pss);
+		fit_bg(&ic, fid_fs, fid_ss, &a, &b, &c);
+
+		//set_intensity(refl, intensity);
+	}
+}
+
+
+static void estimate_mosaicity(Crystal *cr, struct image *image)
+{
+	int msteps = 50;
+	int i;
+	const double mest = crystal_get_mosaicity(cr);
+	const double mmax = 2.0 * mest;
+	RefList *list;
+
+	STATUS("Initial estimate: m = %f\n", mest);
+
+	crystal_set_mosaicity(cr, mmax);
+	list = find_intersections(image, cr);
+	crystal_set_reflections(cr, list);
+	measure_all_intensities(list, image);
+
+	for ( i=1; i<=msteps; i++ ) {
+
+		/* "m" varies from just over zero up to 2x the given estimate */
+		Reflection *refl;
+		RefListIterator *iter;
+		const double m = mmax*((double)i/msteps);
+		int n_gained = 0;
+		int n_lost = 0;
+		double i_gained = 0.0;
+		double i_lost = 0.0;
+
+		crystal_set_mosaicity(cr, m);
+		update_partialities(cr, PMODEL_SPHERE);
+
+		for ( refl = first_refl(list, &iter);
+		      refl != NULL;
+		      refl = next_refl(refl, iter) )
+		{
+			if ( get_redundancy(refl) == 0 ) {
+				if ( get_temp1(refl) > 0.0 ) {
+					i_lost += get_intensity(refl);
+					n_lost++;
+				}
+				set_temp1(refl, -1.0);
+			} else if ( get_temp1(refl) < 0.0 ) {
+				i_gained += get_intensity(refl);
+				n_gained++;
+				set_temp1(refl, 1.0);
+			}
+		}
+
+		if ( i > 1 ) {
+			STATUS("%.2e %10.2f %4i %10.2f %4i %10.2f\n", m,
+			       i_gained, n_gained, i_lost, n_lost,
+		               i_gained - i_lost);
+		}
+
+	}
+}
+
+
+static void estimate_resolution(RefList *reflections, Crystal *cr,
+                                struct image *image)
+{
+	struct integr_ind *il;
+	int n, i;
+	int score = 1000;  /* FIXME */
+	int cutoff = 0;
+	double limit = 0.0;
+
+	if ( num_reflections(reflections) == 0 ) return;
+
+	il = sort_reflections(reflections, crystal_get_cell(cr), &n);
+	if ( il == NULL ) {
+		ERROR("Couldn't sort reflections\n");
+		return;
+	}
+
+	for ( i=0; i<n; i++ ) {
+
+		double intensity, sigma, snr;
+		Reflection *refl;
+
+		refl = il[i].refl;
+		intensity = get_intensity(refl);
+		sigma = get_esd_intensity(refl);
+
+		/* I/sigma(I) cutoff
+		 * Rejects reflections below --min-integration-snr, or if the
+		 * SNR is clearly silly.  Silly indicates that the intensity
+		 * was zero. */
+		snr = fabs(intensity)/sigma;
+
+		/* Record intensity and set redundancy to 1 on success */
+		if ( !cutoff ) {
+			set_redundancy(refl, 1);
+		} else {
+			set_redundancy(refl, 0);
+		}
+
+		if ( snr > 3.0 ) {
+			score++;
+		} else {
+			score--;
+		}
+
+		//STATUS("%5.2f A, %5.2f, %i\n", 1e10/il[i].res, snr, score);
+		if ( score == 0 ) {
+			limit = il[i].res;
+			cutoff = 1;
+		}
+
+	}
+
+	crystal_set_resolution_limit(cr, limit);
+
+	free(il);
+}
+
+
+static void integrate_refine(Crystal *cr, struct image *image, int use_closer,
+                             double min_snr,
+                             double ir_inn, double ir_mid, double ir_out,
+                             int integrate_saturated, int **bgMasks)
+{
+	RefList *reflections;
+
+	/* Create initial list of reflections with nominal parameters */
+	reflections = find_intersections(image, cr);
+	measure_all_intensities(reflections, image);
+
+	/* Find resolution limit of pattern using this list */
+	estimate_resolution(reflections, cr, image);
+
+	reflist_free(reflections);
+
+	STATUS("Initial resolution estimate = %.2f nm^-1 or %.2f A\n",
+	       crystal_get_resolution_limit(cr)/1e9,
+	       1e9 / crystal_get_resolution_limit(cr));
+
+	/* Estimate the mosaicity of the crystal using this resolution limit */
+	estimate_mosaicity(cr, image);
+
+	/* Create new list of reflections with refined mosaicity */
+	reflections = find_intersections(image, cr);
+	measure_all_intensities(reflections, image);
+
+	estimate_resolution(reflections, cr, image);
+}
+
+
+static void integrate_rings(Crystal *cr, struct image *image, int use_closer,
+                            double min_snr,
+                            double ir_inn, double ir_mid, double ir_out,
+                            int integrate_saturated, int **bgMasks)
+{
+	RefList *list;
+	Reflection *refl;
+	RefListIterator *iter;
+	UnitCell *cell;
+	int n_saturated = 0;
+	double limit = 0.0;
+
+	list = find_intersections(image, cr);
+	if ( list == NULL ) return;
+
+	if ( num_reflections(list) == 0 ) return;
+
+	cell = crystal_get_cell(cr);
+
+	for ( refl = first_refl(list, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) )
+	{
+		double fs, ss, intensity;
+		double d;
+		int idx;
+		double sigma, snr;
+		double pfs, pss;
+		int r;
+		signed int h, k, l;
+		struct panel *p;
+		int pnum, j, found;
+		int saturated;
+		double one_over_d;
+
+		get_detector_pos(refl, &pfs, &pss);
+		get_indices(refl, &h, &k, &l);
+
+		/* Is there a really close feature which was detected? */
+		if ( use_closer ) {
+
+			struct imagefeature *f;
+
+			if ( image->features != NULL ) {
+				f = image_feature_closest(image->features,
+					                  pfs, pss, &d, &idx);
+			} else {
+				f = NULL;
+			}
+
+			/* FIXME: Horrible hardcoded value */
+			if ( (f != NULL) && (d < 10.0) ) {
+
+				double exe;
+
+				exe = get_excitation_error(refl);
+
+				pfs = f->fs;
+				pss = f->ss;
+
+				set_detector_pos(refl, exe, pfs, pss);
+
+			}
+
+		}
+
+		p = find_panel(image->det, pfs, pss);
+		if ( p == NULL ) continue;  /* Next peak */
+		found = 0;
+		for ( j=0; j<image->det->n_panels; j++ ) {
+			if ( &image->det->panels[j] == p ) {
+				pnum = j;
+				found = 1;
+				break;
+			}
+		}
+		if ( !found ) {
+			ERROR("Couldn't find panel %p in list.\n", p);
+			return;
+		}
+
+		r = integrate_peak(image, pfs, pss, &fs, &ss,
+		                   &intensity, &sigma, ir_inn, ir_mid, ir_out,
+		                   bgMasks[pnum], &saturated);
+
+		if ( !r && saturated ) {
+			n_saturated++;
+			if ( !integrate_saturated ) r = 1;
+		}
+
+		/* I/sigma(I) cutoff
+		 * Rejects reflections below --min-integration-snr, or if the
+		 * SNR is clearly silly.  Silly indicates that the intensity
+		 * was zero. */
+		snr = fabs(intensity)/sigma;
+		if ( !r && (isnan(snr) || (snr < min_snr)) ) {
+			r = 1;
+		}
+
+		/* Record intensity and set redundancy to 1 on success */
+		if ( !r ) {
+			set_intensity(refl, intensity);
+			set_esd_intensity(refl, sigma);
+			set_redundancy(refl, 1);
+		} else {
+			set_redundancy(refl, 0);
+		}
+
+		one_over_d = resolution(cell, h, k, l);
+		if ( one_over_d > limit ) limit = one_over_d;
+
+	}
+
+	crystal_set_num_saturated_reflections(cr, n_saturated);
+	crystal_set_resolution_limit(cr, limit);
+	crystal_set_reflections(cr, list);
+}
+
+
+void integrate_all(struct image *image, IntegrationMethod meth,
+                   int use_closer, double min_snr,
+                   double ir_inn, double ir_mid, double ir_out,
+                   int integrate_saturated)
+{
+	int i;
+	int **bgMasks;
+
+	/* Make background masks for all panels */
+	bgMasks = calloc(image->det->n_panels, sizeof(int *));
+	if ( bgMasks == NULL ) {
+		ERROR("Couldn't create list of background masks.\n");
+		return;
+	}
+	for ( i=0; i<image->det->n_panels; i++ ) {
+		int *mask;
+		mask = make_BgMask(image, &image->det->panels[i], ir_inn);
+		if ( mask == NULL ) {
+			ERROR("Couldn't create background mask.\n");
+			return;
+		}
+		bgMasks[i] = mask;
+	}
+
+	for ( i=0; i<image->n_crystals; i++ ) {
+
+		switch ( meth & INTEGRATION_METHOD_MASK ) {
+
+			case INTEGRATION_NONE :
+			return;
+
+			case INTEGRATION_RINGS :
+			integrate_rings(image->crystals[i], image, use_closer,
+			                min_snr, ir_inn, ir_mid, ir_out,
+				        integrate_saturated, bgMasks);
+			return;
+
+			case INTEGRATION_REFINE :
+			integrate_refine(image->crystals[i], image, use_closer,
+			                 min_snr, ir_inn, ir_mid, ir_out,
+				         integrate_saturated, bgMasks);
+			return;
+
+			default :
+			ERROR("Unrecognised integration method %i\n", meth);
+			return;
+
+		}
+
+	}
+
+	for ( i=0; i<image->det->n_panels; i++ ) {
+		free(bgMasks[i]);
+	}
+	free(bgMasks);
+}
+
+
+IntegrationMethod integration_method(const char *str, int *err)
+{
+	int n, i;
+	char **methods;
+	IntegrationMethod meth = INTEGRATION_NONE;
+
+	if ( err != NULL ) *err = 0;
+	n = assplode(str, ",-", &methods, ASSPLODE_NONE);
+
+	for ( i=0; i<n; i++ ) {
+
+		if ( strcmp(methods[i], "rings") == 0) {
+			meth = INTEGRATION_DEFAULTS_RINGS;
+
+		} else if ( strcmp(methods[i], "refine") == 0) {
+			meth = INTEGRATION_DEFAULTS_REFINE;
+
+		} else if ( strcmp(methods[i], "none") == 0) {
+			return INTEGRATION_NONE;
+
+		} else {
+			ERROR("Bad integration method: '%s'\n", str);
+			if ( err != NULL ) *err = 1;
+			return INTEGRATION_NONE;
+		}
+
+		free(methods[i]);
+
+	}
+	free(methods);
+
+	return meth;
+
+}