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Diffstat (limited to 'libcrystfel/src/integration.c')
| -rw-r--r-- | libcrystfel/src/integration.c | 672 |
1 files changed, 672 insertions, 0 deletions
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c new file mode 100644 index 00000000..d6860fec --- /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; + +} |