From c0b01532441407dc97eaa9d44b540f1dd0223990 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 7 Aug 2020 17:43:18 +0200 Subject: Move indexers out of API --- libcrystfel/src/indexers/asdf.c | 1239 +++++++++++++++++ libcrystfel/src/indexers/asdf.h | 56 + libcrystfel/src/indexers/dirax.c | 683 +++++++++ libcrystfel/src/indexers/dirax.h | 52 + libcrystfel/src/indexers/felix.c | 963 +++++++++++++ libcrystfel/src/indexers/felix.h | 52 + libcrystfel/src/indexers/mosflm.c | 945 +++++++++++++ libcrystfel/src/indexers/mosflm.h | 56 + libcrystfel/src/indexers/pinkindexer.c | 646 +++++++++ libcrystfel/src/indexers/pinkindexer.h | 47 + libcrystfel/src/indexers/taketwo.c | 2370 ++++++++++++++++++++++++++++++++ libcrystfel/src/indexers/taketwo.h | 47 + libcrystfel/src/indexers/xds.c | 541 ++++++++ libcrystfel/src/indexers/xds.h | 58 + libcrystfel/src/indexers/xgandalf.c | 497 +++++++ libcrystfel/src/indexers/xgandalf.h | 51 + 16 files changed, 8303 insertions(+) create mode 100644 libcrystfel/src/indexers/asdf.c create mode 100644 libcrystfel/src/indexers/asdf.h create mode 100644 libcrystfel/src/indexers/dirax.c create mode 100644 libcrystfel/src/indexers/dirax.h create mode 100644 libcrystfel/src/indexers/felix.c create mode 100644 libcrystfel/src/indexers/felix.h create mode 100644 libcrystfel/src/indexers/mosflm.c create mode 100644 libcrystfel/src/indexers/mosflm.h create mode 100644 libcrystfel/src/indexers/pinkindexer.c create mode 100644 libcrystfel/src/indexers/pinkindexer.h create mode 100644 libcrystfel/src/indexers/taketwo.c create mode 100644 libcrystfel/src/indexers/taketwo.h create mode 100644 libcrystfel/src/indexers/xds.c create mode 100644 libcrystfel/src/indexers/xds.h create mode 100644 libcrystfel/src/indexers/xgandalf.c create mode 100644 libcrystfel/src/indexers/xgandalf.h (limited to 'libcrystfel/src/indexers') diff --git a/libcrystfel/src/indexers/asdf.c b/libcrystfel/src/indexers/asdf.c new file mode 100644 index 00000000..1536a109 --- /dev/null +++ b/libcrystfel/src/indexers/asdf.c @@ -0,0 +1,1239 @@ +/* + * asdf.c + * + * Alexandra's Superior Direction Finder, or + * Algorithm Similar to DirAx, FFT-based + * + * Copyright © 2014-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2014-2015 Alexandra Tolstikova + * 2015,2017 Thomas White + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "image.h" +#include "utils.h" +#include "peaks.h" +#include "cell-utils.h" +#include "asdf.h" +#include "cell.h" + +/** + * \file asdf.h + */ + +#ifdef HAVE_FFTW + +#define FFTW_NO_Complex /* Please use "double[2]", not C99 "complex", + * despite complex.h possibly already being + * included. For more information, refer to: + * http://www.fftw.org/doc/Complex-numbers.html */ + +#include + +struct fftw_vars { + int N; + fftw_plan p; + double *in; + fftw_complex *out; +}; + + +struct asdf_private { + IndexingMethod indm; + UnitCell *template; + struct fftw_vars fftw; +}; + + +/* Possible direct vector */ +struct tvector { + gsl_vector *t; + int n; // number of fitting reflections + int *fits; +}; + + +struct fftw_vars fftw_vars_new() +{ + int N = 1024; + + struct fftw_vars fftw; + + fftw.N = N; + fftw.in = fftw_malloc(N * sizeof(double)); + fftw.out = fftw_malloc(N * sizeof(fftw_complex)); + fftw.p = fftw_plan_dft_r2c_1d(N, fftw.in, fftw.out, FFTW_MEASURE); + + return fftw; +} + + +static void fftw_vars_free(struct fftw_vars fftw) +{ + fftw_free(fftw.in); + fftw_free(fftw.out); + fftw_destroy_plan(fftw.p); + fftw_cleanup(); +} + + +struct asdf_cell { + gsl_vector *axes[3]; + gsl_vector *reciprocal[3]; + + int n; // number of fitting reflections + double volume; + + int N_refls; // total number of reflections + int *reflections; // reflections[i] = 1 if reflections fits + double **indices; // indices[i] = [h, k, l] for all reflections (not rounded) + + int acl; // minimum number of reflections fitting to one of the axes[] + int n_max; // maximum number of reflections fitting to some t-vector +}; + + +struct tvector tvector_new(int n) +{ + struct tvector t; + + t.t = gsl_vector_alloc(3); + t.n = 0; + t.fits = malloc(sizeof(int) * n); + + return t; +} + + +static int tvector_free(struct tvector t) +{ + gsl_vector_free(t.t); + free(t.fits); + + return 1; +} + + +static int asdf_cell_free(struct asdf_cell *c) +{ + int i; + for ( i = 0; i < 3; i++ ) { + gsl_vector_free(c->axes[i]); + gsl_vector_free(c->reciprocal[i]); + } + + free(c->reflections); + for ( i = 0; i < c->N_refls; i++ ) { + free(c->indices[i]); + } + free(c->indices); + free(c); + + return 1; +} + + +static struct asdf_cell *asdf_cell_new(int n) +{ + struct asdf_cell *c; + c = malloc(sizeof(struct asdf_cell)); + + int i; + for ( i = 0; i < 3; i++ ) { + c->axes[i] = gsl_vector_alloc(3); + c->reciprocal[i] = gsl_vector_alloc(3); + } + + c->N_refls = n; + c->reflections = malloc(sizeof(int) * n); + if (c->reflections == NULL) return NULL; + + c->indices = malloc(sizeof(double *) * n); + if (c->indices == NULL) return NULL; + + for ( i = 0; i < n; i++ ) { + c->indices[i] = malloc(sizeof(double) * 3); + if (c->indices[i] == NULL) return NULL; + } + + c->n = 0; + + c->acl = 0; + c->n_max = 0; + + return c; +} + + +static int asdf_cell_memcpy(struct asdf_cell *dest, struct asdf_cell *src) +{ + int i; + for ( i = 0; i < 3; i++ ) { + gsl_vector_memcpy(dest->axes[i], src->axes[i]); + gsl_vector_memcpy(dest->reciprocal[i], src->reciprocal[i]); + } + + dest->volume = src->volume; + + int n = src->N_refls; + dest->N_refls = n; + + dest->n = src->n; + memcpy(dest->reflections, src->reflections, sizeof(int) * n); + + for (i = 0; i < n; i++ ) { + memcpy(dest->indices[i], src->indices[i], sizeof(double) * 3); + } + + dest->acl = src->acl; + dest->n_max = src->n_max; + return 1; +} + + +/* result = vec1 cross vec2 */ +static int cross_product(gsl_vector *vec1, gsl_vector *vec2, + gsl_vector **result) +{ + double c1[3], c2[3], p[3]; + int i; + for ( i = 0; i < 3; i++ ) { + c1[i] = gsl_vector_get(vec1, i); + c2[i] = gsl_vector_get(vec2, i); + } + + p[0] = c1[1] * c2[2] - c1[2] * c2[1]; + p[1] = - c1[0] * c2[2] + c1[2] * c2[0]; + p[2] = c1[0] * c2[1] - c1[1] * c2[0]; + + for ( i = 0; i < 3; i++ ) { + gsl_vector_set(*result, i, p[i]); + } + + return 1; +} + + +/* Returns triple product of three gsl_vectors */ +static double calc_volume(gsl_vector *vec1, gsl_vector *vec2, gsl_vector *vec3) +{ + double volume; + gsl_vector *cross = gsl_vector_alloc(3); + + cross_product(vec1, vec2, &cross); + gsl_blas_ddot(vec3, cross, &volume); + + gsl_vector_free(cross); + return volume; +} + + +static int calc_reciprocal(gsl_vector **direct, gsl_vector **reciprocal) +{ + double volume; + + cross_product(direct[1], direct[2], &reciprocal[0]); + gsl_blas_ddot(direct[0], reciprocal[0], &volume); + gsl_vector_scale(reciprocal[0], 1/volume); + + cross_product(direct[2], direct[0], &reciprocal[1]); + gsl_vector_scale(reciprocal[1], 1/volume); + + cross_product(direct[0], direct[1], &reciprocal[2]); + gsl_vector_scale(reciprocal[2], 1/volume); + + return 1; +} + + +static int compare_doubles(const void *a, const void *b) +{ + const double *da = (const double *) a; + const double *db = (const double *) b; + + return (*da > *db) - (*da < *db); +} + + +static double max(double a, double b, double c) +{ + double m = a; + if ( m < b ) m = b; + if ( m < c ) m = c; + return m; +} + + +/* Compares tvectors by length */ +static int compare_tvectors(const void *a, const void *b) +{ + struct tvector *ta = (struct tvector *) a; + struct tvector *tb = (struct tvector *) b; + + //~ if (ta->n == tb->n) { + return (gsl_blas_dnrm2(ta->t) > gsl_blas_dnrm2(tb->t)) - + (gsl_blas_dnrm2(ta->t) < gsl_blas_dnrm2(tb->t)); + //~ } + //~ + //~ return (ta->n > tb->n) - (ta->n < tb->n); +} + + +/* Calculates normal to a triplet c1, c2, c3. Returns 0 if reflections are on + * the same line */ +static int calc_normal(gsl_vector *c1, gsl_vector *c2, gsl_vector *c3, + gsl_vector *normal) +{ + gsl_vector *c12 = gsl_vector_alloc(3); + gsl_vector *c23 = gsl_vector_alloc(3); + gsl_vector *c31 = gsl_vector_alloc(3); + gsl_vector *res = gsl_vector_alloc(3); + + cross_product(c1, c2, &c12); + cross_product(c2, c3, &c23); + cross_product(c3, c1, &c31); + + int i; + for ( i = 0; i < 3; i++ ) { + gsl_vector_set(res, i, gsl_vector_get(c12, i) + + gsl_vector_get(c23, i) + + gsl_vector_get(c31, i)); + } + + gsl_vector_free(c12); + gsl_vector_free(c23); + gsl_vector_free(c31); + + double norm = gsl_blas_dnrm2(res); + if ( norm < 0.0001 ) { + gsl_vector_free(res); + return 0; + } else { + gsl_vector_scale(res, 1/norm); + gsl_vector_memcpy(normal, res); + gsl_vector_free(res); + } + + return 1; +} + + +static float find_ds_fft(double *projections, int N_projections, double d_max, + struct fftw_vars fftw) +{ + int n = N_projections; + double projections_sorted[n]; + memcpy(projections_sorted, projections, sizeof(double) * n); + qsort(projections_sorted, n, sizeof(double), compare_doubles); + + int i, k; + + int N = fftw.N; // number of points in fft calculation + double *in = fftw.in; + fftw_complex *out = fftw.out; + fftw_plan p = fftw.p; + + for ( i=0; i=N) || (k<0) ) { + ERROR("Bad k value in find_ds_fft() (k=%i, N=%i)\n", + k, N); + return -1.0; + } + in[k]++; + } + + fftw_execute_dft_r2c(p, in, out); + + int i_max = (int)(d_max * (projections_sorted[n - 1] - + projections_sorted[0])); + + int d = 1; + double max = 0; + double a; + for ( i=1; i<=i_max; i++ ) { + a = sqrt(out[i][0] * out[i][0] + out[i][1] * out[i][1]); + if (a > max) { + max = a; + d = i; + } + } + + double ds = (projections_sorted[n - 1] - projections_sorted[0]) / d; + + return ds; +} + + +/* Returns number of reflections fitting ds. + * A projected reflection fits a one-dimensional lattice with elementary + * lattice vector d* if its absolute distance to the nearest lattice + * point is less than LevelFit. */ +static int check_refl_fitting_ds(double *projections, int N_projections, + double ds, double LevelFit) +{ + if ( ds == 0 ) return 0; + + int i; + int n = 0; + for ( i = 0; i < N_projections; i++ ) { + if ( fabs(projections[i] - + ds * round(projections[i]/ds)) < LevelFit ) + { + n += 1; + } + } + + return n; +} + + +/* Refines d*, writes 1 to fits[i] if the i-th projection fits d* */ +static float refine_ds(double *projections, int N_projections, double ds, + double LevelFit, int *fits) +{ + double fit_refls[N_projections]; + double indices[N_projections]; + + int i; + + int N_fits = 0; + int N_new = N_projections; + + double c1, cov11, sumsq; + double ds_new = ds; + while ( N_fits < N_new ) { + N_fits = 0; + for ( i = 0; i < N_projections; i++ ) { + if ( fabs(projections[i] - ds_new * + round(projections[i] / ds_new)) < LevelFit ) + { + fit_refls[N_fits] = projections[i]; + indices[N_fits] = round(projections[i]/ds_new); + N_fits ++; + fits[i] = 1; + } else { + fits[i] = 0; + } + } + + + gsl_fit_mul(indices, 1, fit_refls, 1, N_fits, &c1, &cov11, + &sumsq); + N_new = check_refl_fitting_ds(projections, N_projections, c1, + LevelFit); + if ( N_new >= N_fits ) { + ds_new = c1; + } + } + + return ds_new; +} + + +static int check_refl_fitting_cell(struct asdf_cell *c, + gsl_vector **reflections, + int N_reflections, double IndexFit) +{ + double dist[3]; + + calc_reciprocal(c->axes, c->reciprocal); + c->n = 0; + int i, j, k; + for( i = 0; i < N_reflections; i += 1 ) { + + for ( j = 0; j < 3; j++ ) dist[j] = 0; + + for ( j = 0; j < 3; j++ ) { + gsl_blas_ddot(reflections[i], c->axes[j], + &c->indices[i][j]); + + for ( k = 0; k < 3; k++ ) { + dist[k] += gsl_vector_get(c->reciprocal[j], k) * + (c->indices[i][j] - round(c->indices[i][j])); + } + } + + /* A reflection fits if the distance (in reciprocal space) + * between the observed and calculated reflection position + * is less than Indexfit */ + + if ( dist[0]*dist[0] + dist[1]*dist[1] + dist[2]*dist[2] < + IndexFit * IndexFit ) { + c->reflections[i] = 1; + c->n++; + } else { + c->reflections[i] = 0; + } + } + + return 1; +} + + +/* Returns 0 when refinement doesn't converge (i.e. all fitting reflections + * lie in the same plane) */ +static int refine_asdf_cell(struct asdf_cell *c, gsl_vector **reflections, + int N_reflections, double IndexFit) +{ + gsl_matrix *X = gsl_matrix_alloc(c->n, 3); + + gsl_vector *r[] = {gsl_vector_alloc(c->n), + gsl_vector_alloc(c->n), + gsl_vector_alloc(c->n)}; + + gsl_vector *res = gsl_vector_alloc(3); + gsl_matrix *cov = gsl_matrix_alloc (3, 3); + double chisq; + + int i, j; + int n = 0; + for ( i = 0; i < N_reflections; i++ ) if ( c->reflections[i] == 1 ) + { + for ( j = 0; j < 3; j++ ) { + gsl_matrix_set(X, n, j, round(c->indices[i][j])); + gsl_vector_set(r[j], n, + gsl_vector_get(reflections[i], j)); + } + n++; + } + + gsl_multifit_linear_workspace *work = gsl_multifit_linear_alloc(c->n, + 3); + + for ( i = 0; i < 3; i++ ) { + gsl_multifit_linear (X, r[i], res, cov, &chisq, work); + + for (j = 0; j < 3; j++ ) { + gsl_vector_set(c->reciprocal[j], i, + gsl_vector_get(res, j)); + } + } + + calc_reciprocal(c->reciprocal, c->axes); + + double a[3]; + for ( i = 0; i < 3; i++ ) { + a[i] = gsl_blas_dnrm2(c->axes[i]); + } + + gsl_multifit_linear_free(work); + gsl_vector_free(res); + gsl_matrix_free(cov); + gsl_matrix_free(X); + for ( i = 0; i < 3; i++ ) { + gsl_vector_free(r[i]); + } + + if ( fabs(a[0]) > 10000 || fabs(a[1]) > 10000 || + fabs(a[2]) > 10000 || isnan(a[0]) ) + { + return 0; + } + + return 1; +} + + +static int reduce_asdf_cell(struct asdf_cell *cl) +{ + double a, b, c, alpha, beta, gamma, ab, bc, ca, bb, cc; + + gsl_vector *va = gsl_vector_alloc(3); + gsl_vector *vb = gsl_vector_alloc(3); + gsl_vector *vc = gsl_vector_alloc(3); + + int changed = 1; + + int n = 0; + while ( changed ) { + n += 1; + changed = 0; + + gsl_vector_memcpy(va, cl->axes[0]); + gsl_vector_memcpy(vb, cl->axes[1]); + gsl_vector_memcpy(vc, cl->axes[2]); + + a = gsl_blas_dnrm2(va); + b = gsl_blas_dnrm2(vb); + c = gsl_blas_dnrm2(vc); + + gsl_blas_ddot(va, vb, &ab); + gsl_blas_ddot(vb, vc, &bc); + gsl_blas_ddot(vc, va, &ca); + + alpha = acos(bc/b/c)/M_PI*180; + beta = acos(ca/a/c)/M_PI*180; + gamma = acos(ab/a/b)/M_PI*180; + + if ( changed == 0 ) { + + if ( gamma < 90 ) { + gsl_vector_scale(vb, -1); + gamma = 180 - gamma; + alpha = 180 - alpha; + } + + gsl_vector_add(vb, va); + bb = gsl_blas_dnrm2(vb); + if ( bb < b ) { + b = bb; + if ( a < b ) { + gsl_vector_memcpy(cl->axes[1], vb); + } else { + gsl_vector_memcpy(cl->axes[1], va); + gsl_vector_memcpy(cl->axes[0], vb); + } + changed = 1; + } + } + + if ( changed == 0 ) { + + if ( beta < 90 ) { + gsl_vector_scale(vc, -1); + beta = 180 - beta; + alpha = 180 - alpha; + } + + gsl_vector_add(vc, va); + cc = gsl_blas_dnrm2(vc); + if ( cc < c ) { + c = cc; + if ( b < c ) { + gsl_vector_memcpy(cl->axes[2], vc); + } else if ( a < c ) { + gsl_vector_memcpy(cl->axes[1], vc); + gsl_vector_memcpy(cl->axes[2], vb); + } else { + gsl_vector_memcpy(cl->axes[0], vc); + gsl_vector_memcpy(cl->axes[1], va); + gsl_vector_memcpy(cl->axes[2], vb); + } + changed = 1; + } + } + + if ( changed == 0 ) { + if ( alpha < 90 ) { + gsl_vector_scale(vc, -1); + beta = 180 - beta; + alpha = 180 - alpha; + } + + gsl_vector_add(vc, vb); + cc = gsl_blas_dnrm2(vc); + if ( cc < c ) { + c = cc; + if ( b < c ) { + gsl_vector_memcpy(cl->axes[2], vc); + } else if ( a < c ) { + gsl_vector_memcpy(cl->axes[1], vc); + gsl_vector_memcpy(cl->axes[2], vb); + } else { + gsl_vector_memcpy(cl->axes[0], vc); + gsl_vector_memcpy(cl->axes[1], va); + gsl_vector_memcpy(cl->axes[2], vb); + } + changed = 1; + } + } + + if (n > 30) changed = 0; + } + + cross_product(cl->axes[0], cl->axes[1], &vc); + gsl_blas_ddot(vc, cl->axes[2], &cl->volume); + if ( cl->volume < 0 ) { + gsl_vector_scale(cl->axes[2], -1); + cl->volume *= -1; + } + + gsl_vector_free(va); + gsl_vector_free(vb); + gsl_vector_free(vc); + + return 1; +} + + +static int check_cell_angles(gsl_vector *va, gsl_vector *vb, gsl_vector *vc, + double max_cos) +{ + double a, b, c, cosa, cosb, cosg, ab, bc, ca; + + a = gsl_blas_dnrm2(va); + b = gsl_blas_dnrm2(vb); + c = gsl_blas_dnrm2(vc); + + gsl_blas_ddot(va, vb, &ab); + gsl_blas_ddot(vb, vc, &bc); + gsl_blas_ddot(vc, va, &ca); + + cosa = bc/b/c; + cosb = ca/a/c; + cosg = ab/a/b; + + if ( fabs(cosa) > max_cos || fabs(cosb) > max_cos || + fabs(cosg) > max_cos ) { + return 0; + } + + return 1; +} + + +/* Returns min(t1.n, t2.n, t3.n) */ +static int find_acl(struct tvector t1, struct tvector t2, struct tvector t3) +{ + int i = t1.n, j = t2.n, k = t3.n; + if ( i <= j && i <= k ) return i; + if ( j <= i && j <= k ) return j; + if ( k <= i && k <= j ) return k; + ERROR("This point never reached!\n"); + abort(); +} + + +static int create_cell(struct tvector tvec1, struct tvector tvec2, + struct tvector tvec3, struct asdf_cell *c, + double IndexFit, double volume_min, double volume_max, + gsl_vector **reflections, int N_reflections) +{ + + double volume = calc_volume(tvec1.t, tvec2.t, tvec3.t); + if ( fabs(volume) < volume_min || fabs(volume) > volume_max ) return 0; + + gsl_vector_memcpy(c->axes[0], tvec1.t); + gsl_vector_memcpy(c->axes[1], tvec2.t); + gsl_vector_memcpy(c->axes[2], tvec3.t); + + c->volume = volume; + check_refl_fitting_cell(c, reflections, N_reflections, IndexFit); + + if ( c->n < 6 ) return 0; + + reduce_asdf_cell(c); + + /* If one of the cell angles > 135 or < 45 return 0 */ + if ( !check_cell_angles(c->axes[0], c->axes[1], + c->axes[2], 0.71) ) return 0; + + /* Index reflections with new cell axes */ + check_refl_fitting_cell(c, reflections, N_reflections, IndexFit); + + /* Refine cell until the number of fitting + * reflections stops increasing */ + int n = 0; + int cell_correct = 1; + while ( c->n - n > 0 && cell_correct ) { + + n = c->n; + cell_correct = refine_asdf_cell(c, reflections, N_reflections, + IndexFit); + check_refl_fitting_cell(c, reflections, N_reflections, + IndexFit); + } + + return cell_correct; +} + + +static int find_cell(struct tvector *tvectors, int N_tvectors, double IndexFit, + double volume_min, double volume_max, int n_max, + gsl_vector **reflections, int N_reflections, + struct asdf_cell *result) +{ + int i, j, k; + + /* Only tvectors with the number of fitting reflections > acl are + * considered */ + int acl = N_reflections < 18 ? 6 : N_reflections/3; + + struct asdf_cell *c = asdf_cell_new(N_reflections); + if (c == NULL) { + ERROR("Failed to allocate asdf_cell in find_cell!\n"); + return 0; + } + + /* Traversing a 3d array in slices perpendicular to the main diagonal */ + int sl; + for ( sl = 0; sl < 3 * N_tvectors - 1; sl++ ) { + + int i_min = sl < 2 * N_tvectors ? 0 : sl - 2 * N_tvectors; + int i_max = sl < N_tvectors ? sl : N_tvectors; + + for ( i = i_min; i < i_max; i++) if (tvectors[i].n > acl ) { + + int j_min = sl - N_tvectors - 2 * i - 1 < 0 ? + i + 1 : sl - N_tvectors - i; + int j_max = sl - N_tvectors - i < 0 ? + sl - i : N_tvectors; + + for ( j = j_min; j < j_max; j++ ) + if ( tvectors[j].n > acl ) { + + k = sl - i - j - 1; + + if ( k > j && tvectors[k].n > acl && + check_cell_angles(tvectors[i].t, + tvectors[j].t, + tvectors[k].t, 0.99) ) + { + + if ( !create_cell(tvectors[i], + tvectors[j], + tvectors[k], + c, IndexFit, + volume_min, + volume_max, + reflections, + N_reflections) ) + { + break; + } + + acl = find_acl(tvectors[i], + tvectors[j], + tvectors[k]); + c->acl = acl; + c->n_max = n_max; + + reduce_asdf_cell(c); + + /* If the new cell has more fitting + * reflections save it to result */ + if ( result->n < c->n ) { + asdf_cell_memcpy(result, c); + } + acl++; + + if ( acl > n_max ) break; + if ( tvectors[j].n <= acl || + tvectors[i].n <= acl ) break; + } + } + if ( acl > n_max ) break; + if ( tvectors[i].n <= acl ) break; + } + if ( acl > n_max ) break; + } + + asdf_cell_free(c); + + if ( result->n ) return 1; + return 0; +} + + +void swap(int *a, int *b) { + int c = *a; + *a = *b; + *b = c; +} + + +/* Generate triplets of integers < N_reflections in random sequence */ +static int **generate_triplets(int N_reflections, int N_triplets_max, int *N) +{ + int i, j, k, l, n; + + /* Number of triplets = c_n^3 if n - number of reflections */ + int N_triplets = N_reflections * (N_reflections - 1) * + (N_reflections - 2) / 6; + + if ( N_triplets > N_triplets_max || N_reflections > 1000 ) { + N_triplets = N_triplets_max; + } + *N = N_triplets; + + int **triplets = malloc(N_triplets * sizeof(int *)); + + if (triplets == NULL) { + ERROR("Failed to allocate triplets in generate_triplets!\n"); + return 0; + } + + int is_in_triplets; + n = 0; + + while ( n < N_triplets ) { + /* Generate three different integer numbers < N_reflections */ + i = rand() % N_reflections; + j = i; + k = i; + while ( j == i ) { + j = rand() % N_reflections; + } + while ( k == i || k == j ) { + k = rand() % N_reflections; + } + + /* Sort (i, j, k) */ + if ( i > k ) swap(&i, &k); + if ( i > j ) swap(&i, &j); + if ( j > k ) swap(&j, &k); + + /* Check if it's already in triplets[] */ + is_in_triplets = 0; + for ( l = 0; l < n; l++ ) { + if ( triplets[l][0] == i && + triplets[l][1] == j && + triplets[l][2] == k ) { + is_in_triplets = 1; + break; + } + } + + if ( is_in_triplets == 0 ) { + triplets[n] = malloc(3 * sizeof(int)); + if (triplets[n] == NULL) { + ERROR("Failed to allocate triplets " + " in generate_triplets!\n"); + return 0; + } + triplets[n][0] = i; + triplets[n][1] = j; + triplets[n][2] = k; + + n++; + } + } + + return triplets; +} + + +static int index_refls(gsl_vector **reflections, int N_reflections, + double d_max, double volume_min, double volume_max, + double LevelFit, double IndexFit, int N_triplets_max, + struct asdf_cell *c, struct fftw_vars fftw) +{ + + int i, k, n; + + int N_triplets; + int **triplets = generate_triplets(N_reflections, N_triplets_max, + &N_triplets); + if ( N_triplets == 0 ) { + return 0; + } + + gsl_vector *normal = gsl_vector_alloc(3); + + double projections[N_reflections]; + double ds; + + int *fits = malloc(N_reflections * sizeof(int)); + if (fits == NULL) { + ERROR("Failed to allocate fits in index_refls!\n"); + return 0; + } + + struct tvector *tvectors = malloc(N_triplets * sizeof(struct tvector)); + if (tvectors == NULL) { + ERROR("Failed to allocate tvectors in index_refls!\n"); + return 0; + } + + int N_tvectors = 0; + + int n_max = 0; // maximum number of reflections fitting one of tvectors + + for ( i = 0; i < N_triplets; i++ ) { + if ( calc_normal(reflections[triplets[i][0]], + reflections[triplets[i][1]], + reflections[triplets[i][2]], + normal) ) + { + + /* Calculate projections of reflections to normal */ + for ( k = 0; k < N_reflections; k++ ) { + gsl_blas_ddot(normal, reflections[k], + &projections[k]); + } + + /* Find ds - period in 1d lattice of projections */ + ds = find_ds_fft(projections, N_reflections, d_max, + fftw); + if ( ds < 0.0 ) { + ERROR("find_ds_fft() failed.\n"); + return 0; + } + + /* Refine ds, write 1 to fits[i] if reflections[i] + * fits ds */ + ds = refine_ds(projections, N_reflections, ds, LevelFit, + fits); + + /* n - number of reflections fitting ds */ + n = check_refl_fitting_ds(projections, N_reflections, + ds, LevelFit); + + /* normal/ds - possible direct vector */ + gsl_vector_scale(normal, 1/ds); + + if ( n > N_reflections/3 && n > 6 ) { + + tvectors[N_tvectors] = tvector_new(N_reflections); + + gsl_vector_memcpy(tvectors[N_tvectors].t, + normal); + memcpy(tvectors[N_tvectors].fits, fits, + N_reflections * sizeof(int)); + + tvectors[N_tvectors].n = n; + + N_tvectors++; + + if (n > n_max) n_max = n; + } + } + + if ( (i != 0 && i % 10000 == 0) || i == N_triplets - 1 ) { + + /* Sort tvectors by length */ + qsort(tvectors, N_tvectors, sizeof(struct tvector), + compare_tvectors); + + /* Three shortest independent tvectors with t.n > acl + * determine the final cell. acl is selected for the + * solution with the maximum number of fitting + * reflections */ + + find_cell(tvectors, N_tvectors, IndexFit, volume_min, + volume_max, n_max, reflections, + N_reflections, c); + + if ( c->n > 4 * n_max / 5 ) { + break; + } + } + } + free(fits); + + for ( i = 0; i < N_tvectors; i++ ) { + tvector_free(tvectors[i]); + } + free(tvectors); + + for ( i = 0; i < N_triplets; i++ ) { + free(triplets[i]); + } + free(triplets); + + gsl_vector_free(normal); + + if ( c->n ) return 1; + + return 0; +} + + +int run_asdf(struct image *image, void *ipriv) +{ + int i, j; + + double LevelFit = 1./1000; + double IndexFit = 1./500; + double d_max = 1000.; // thrice the maximum expected axis length + double volume_min = 100.; + double volume_max = 100000000.; + + int N_triplets_max = 10000; // maximum number of triplets + + struct asdf_private *dp = (struct asdf_private *)ipriv; + + if ( dp->indm & INDEXING_USE_CELL_PARAMETERS ) { + + double a, b, c, gamma, beta, alpha; + cell_get_parameters(dp->template, &a, &b, &c, + &alpha, &beta, &gamma); + + d_max = max(a, b, c) * 3 * 1e10; + + double volume = cell_get_volume(dp->template) / 1e30; + + /* Divide volume constraints by number of lattice points per + * unit cell since asdf always finds primitive cell */ + int latt_points_per_uc = 1; + char centering = cell_get_centering(dp->template); + if ( centering == 'A' || + centering == 'B' || + centering == 'C' || + centering == 'I' ) latt_points_per_uc = 2; + else if ( centering == 'F' ) latt_points_per_uc = 4; + + volume_min = volume * 0.9/latt_points_per_uc; + volume_max = volume * 1.1/latt_points_per_uc; + } + + int n = image_feature_count(image->features); + int N_reflections = 0; + gsl_vector *reflections[n]; + + for ( i=0; ifeatures, i); + if ( f == NULL ) continue; + + reflections[N_reflections] = gsl_vector_alloc(3); + gsl_vector_set(reflections[N_reflections], 0, f->rx/1e10); + gsl_vector_set(reflections[N_reflections], 1, f->ry/1e10); + gsl_vector_set(reflections[N_reflections], 2, f->rz/1e10); + N_reflections++; + } + + struct asdf_cell *c = asdf_cell_new(N_reflections); + if (c == NULL) { + ERROR("Failed to allocate asdf_cell in run_asdf!\n"); + return 0; + } + + if ( N_reflections == 0 ) return 0; + + j = index_refls(reflections, N_reflections, d_max, volume_min, + volume_max, LevelFit, IndexFit, N_triplets_max, c, + dp->fftw); + + for ( i = 0; i < N_reflections; i++ ) { + gsl_vector_free(reflections[i]); + } + + if ( j ) { + + UnitCell *uc; + Crystal *cr; + uc = cell_new(); + + cell_set_cartesian(uc, gsl_vector_get(c->axes[0], 0) * 1e-10, + gsl_vector_get(c->axes[0], 1) * 1e-10, + gsl_vector_get(c->axes[0], 2) * 1e-10, + gsl_vector_get(c->axes[1], 0) * 1e-10, + gsl_vector_get(c->axes[1], 1) * 1e-10, + gsl_vector_get(c->axes[1], 2) * 1e-10, + gsl_vector_get(c->axes[2], 0) * 1e-10, + gsl_vector_get(c->axes[2], 1) * 1e-10, + gsl_vector_get(c->axes[2], 2) * 1e-10); + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + crystal_set_cell(cr, uc); + image_add_crystal(image, cr); + asdf_cell_free(c); + return 1; + + } + + asdf_cell_free(c); + return 0; +} + + +/** + * Prepare the ASDF indexing algorithm + */ +void *asdf_prepare(IndexingMethod *indm, UnitCell *cell) +{ + struct asdf_private *dp; + + /* Flags that asdf knows about */ + *indm &= INDEXING_METHOD_MASK | INDEXING_USE_CELL_PARAMETERS; + + dp = malloc(sizeof(struct asdf_private)); + if ( dp == NULL ) return NULL; + + dp->template = cell; + dp->indm = *indm; + + dp->fftw = fftw_vars_new(); + + return (void *)dp; +} + + +void asdf_cleanup(void *pp) +{ + struct asdf_private *p; + p = (struct asdf_private *)pp; + fftw_vars_free(p->fftw); + free(p); +} + + +const char *asdf_probe(UnitCell *cell) +{ + return "asdf"; +} + +#else /* HAVE_FFTW */ + +int run_asdf(struct image *image, void *ipriv) +{ + ERROR("This copy of CrystFEL was compiled without FFTW support.\n"); + return 0; +} + + +void *asdf_prepare(IndexingMethod *indm, UnitCell *cell) +{ + ERROR("This copy of CrystFEL was compiled without FFTW support.\n"); + ERROR("To use asdf indexing, recompile with FFTW.\n"); + return NULL; +} + + +const char *asdf_probe(UnitCell *cell) +{ + return NULL; +} + + +void asdf_cleanup(void *pp) +{ +} + +#endif /* HAVE_FFTW */ diff --git a/libcrystfel/src/indexers/asdf.h b/libcrystfel/src/indexers/asdf.h new file mode 100644 index 00000000..b3ccffcc --- /dev/null +++ b/libcrystfel/src/indexers/asdf.h @@ -0,0 +1,56 @@ +/* + * asdf.h + * + * Alexandra's Superior Direction Finder, or + * Algorithm Similar to DirAx, FFT-based + * + * Copyright © 2014-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2014-2015 Alexandra Tolstikova + * 2015,2017 Thomas White + * + * 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 . + * + */ + +#ifndef ASDF_H +#define ASDF_H + +#include "index.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/** + * \file asdf.h + * The ASDF indexing algorithm. + */ + +extern int run_asdf(struct image *image, void *ipriv); + +extern void *asdf_prepare(IndexingMethod *indm, UnitCell *cell); +extern const char *asdf_probe(UnitCell *cell); + +extern void asdf_cleanup(void *pp); + +#ifdef __cplusplus +} +#endif + +#endif /* ASDF_H */ diff --git a/libcrystfel/src/indexers/dirax.c b/libcrystfel/src/indexers/dirax.c new file mode 100644 index 00000000..24be87ba --- /dev/null +++ b/libcrystfel/src/indexers/dirax.c @@ -0,0 +1,683 @@ +/* + * dirax.c + * + * Invoke the DirAx auto-indexing program + * + * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2010-2014,2017 Thomas White + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef HAVE_FORKPTY_PTY_H +#include +#endif +#ifdef HAVE_FORKPTY_UTIL_H +#include +#endif + +#include "image.h" +#include "dirax.h" +#include "utils.h" +#include "peaks.h" +#include "cell-utils.h" + + +/** \file dirax.h */ + +#define DIRAX_VERBOSE 0 + +#define MAX_DIRAX_CELL_CANDIDATES (5) + + +typedef enum { + DIRAX_INPUT_NONE, + DIRAX_INPUT_LINE, + DIRAX_INPUT_PROMPT, + DIRAX_INPUT_ACL +} DirAxInputType; + + +struct dirax_private { + IndexingMethod indm; + UnitCell *template; +}; + + +struct dirax_data { + + /* DirAx auto-indexing low-level stuff */ + int pty; + pid_t pid; + char *rbuffer; + int rbufpos; + int rbuflen; + + /* DirAx auto-indexing high-level stuff */ + int step; + int finished_ok; + int read_cell; + int best_acl; + int best_acl_nh; + int acls_tried[MAX_DIRAX_CELL_CANDIDATES]; + int n_acls_tried; + int done; + int success; + + float ax; + float ay; + float az; + float bx; + float by; + float bz; + float cx; + float cy; + float cz; + + struct dirax_private *dp; + +}; + + +static void dirax_parseline(const char *line, struct image *image, + struct dirax_data *dirax) +{ + int rf, i, di, acl, acl_nh; + float d; + + #if DIRAX_VERBOSE + char *copy; + + copy = strdup(line); + for ( i=0; iread_cell = 1; + return; + } + i++; + } + + /* Parse unit cell vectors as appropriate */ + if ( dirax->read_cell == 1 ) { + + /* First row of unit cell values */ + int r; + r = sscanf(line, "%f %f %f %f %f %f", + &d, &d, &d, &dirax->ax, &dirax->ay, &dirax->az); + if ( r != 6 ) { + ERROR("Couldn't understand cell line:\n"); + ERROR("'%s'\n", line); + dirax->read_cell = 0; + return; + } + dirax->ax *= 1e-10; + dirax->ay *= 1e-10; + dirax->az *= 1e-10; + dirax->read_cell++; + return; + + } else if ( dirax->read_cell == 2 ) { + + /* Second row of unit cell values */ + int r; + r = sscanf(line, "%f %f %f %f %f %f", + &d, &d, &d, &dirax->bx, &dirax->by, &dirax->bz); + if ( r != 6 ) { + ERROR("Couldn't understand cell line:\n"); + ERROR("'%s'\n", line); + dirax->read_cell = 0; + return; + } + dirax->bx *= 1e-10; + dirax->by *= 1e-10; + dirax->bz *= 1e-10; + dirax->read_cell++; + return; + + } else if ( dirax->read_cell == 3 ) { + + /* Third row of unit cell values */ + int r; + UnitCell *cell; + Crystal *cr; + + r = sscanf(line, "%f %f %f %f %f %f", + &d, &d, &d, &dirax->cx, &dirax->cy, &dirax->cz); + if ( r != 6 ) { + ERROR("Couldn't understand cell line:\n"); + ERROR("'%s'\n", line); + dirax->read_cell = 0; + return; + } + dirax->cx *= 1e-10; + dirax->cy *= 1e-10; + dirax->cz *= 1e-10; + dirax->read_cell = 0; + + cell = cell_new(); + cell_set_cartesian(cell, dirax->ax, dirax->ay, dirax->az, + dirax->bx, dirax->by, dirax->bz, + dirax->cx, dirax->cy, dirax->cz); + + /* Finished reading a cell. */ + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return; + } + crystal_set_cell(cr, cell); + image_add_crystal(image, cr); + dirax->done = 1; + dirax->success = 1; + + return; + + } + + dirax->read_cell = 0; + + if ( sscanf(line, "%i %i %f %f %f %f %f %f %i", &acl, &acl_nh, + &d, &d, &d, &d, &d, &d, &di) == 9 ) { + if ( acl_nh > dirax->best_acl_nh ) { + + int i, found = 0; + + for ( i=0; in_acls_tried; i++ ) { + if ( dirax->acls_tried[i] == acl ) found = 1; + } + + if ( !found ) { + dirax->best_acl_nh = acl_nh; + dirax->best_acl = acl; + } + + } + } +} + + +static void dirax_sendline(const char *line, struct dirax_data *dirax) +{ + #if DIRAX_VERBOSE + char *copy; + int i; + + copy = strdup(line); + for ( i=0; ipty, line, strlen(line)) == -1 ) { + ERROR("write() To dirax failed: %s\n", strerror(errno)); + } +} + + +static void dirax_send_next(struct image *image, struct dirax_data *dirax) +{ + char tmp[32]; + + switch ( dirax->step ) { + + case 1 : + dirax_sendline("\\echo off\n", dirax); + break; + + case 2 : + snprintf(tmp, 31, "read xfel.drx\n"); + dirax_sendline(tmp, dirax); + break; + + case 3 : + dirax_sendline("dmax 1000\n", dirax); + break; + + case 4 : + dirax_sendline("indexfit 2\n", dirax); + break; + + case 5 : + dirax_sendline("levelfit 1000\n", dirax); + break; + + case 6 : + dirax_sendline("go\n", dirax); + dirax->finished_ok = 1; + break; + + case 7 : + dirax_sendline("acl\n", dirax); + break; + + case 8 : + if ( dirax->best_acl_nh == 0 ) { + /* At this point, DirAx is presenting its ACL prompt + * and waiting for a single number. Use an extra + * newline to choose automatic ACL selection before + * exiting. */ + dirax_sendline("\nexit\n", dirax); + break; + } + snprintf(tmp, 31, "%i\n", dirax->best_acl); + dirax->acls_tried[dirax->n_acls_tried++] = dirax->best_acl; + dirax_sendline(tmp, dirax); + break; + + case 9 : + dirax_sendline("cell\n", dirax); + break; + + case 10 : + if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) { + dirax_sendline("exit\n", dirax); + } else { + /* Go back round for another cell */ + dirax->best_acl_nh = 0; + dirax->step = 7; + dirax_sendline("acl\n", dirax); + } + break; + + default: + dirax_sendline("exit\n", dirax); + return; + + } + + dirax->step++; +} + + +static int dirax_readable(struct image *image, struct dirax_data *dirax) +{ + int rval; + int no_string = 0; + + rval = read(dirax->pty, dirax->rbuffer+dirax->rbufpos, + dirax->rbuflen-dirax->rbufpos); + + if ( (rval == -1) || (rval == 0) ) return 1; + + dirax->rbufpos += rval; + assert(dirax->rbufpos <= dirax->rbuflen); + + while ( (!no_string) && (dirax->rbufpos > 0) ) { + + int i; + int block_ready = 0; + DirAxInputType type = DIRAX_INPUT_NONE; + + /* See if there's a full line in the buffer yet */ + for ( i=0; irbufpos-1; i++ ) { + /* Means the last value looked at is rbufpos-2 */ + + /* Is there a prompt in the buffer? */ + if ( (i+7 <= dirax->rbufpos) + && (!strncmp(dirax->rbuffer+i, "Dirax> ", 7)) ) { + block_ready = 1; + type = DIRAX_INPUT_PROMPT; + break; + } + + /* How about an ACL prompt? */ + if ( (i+10 <= dirax->rbufpos) + && (!strncmp(dirax->rbuffer+i, "acl/auto [", 10)) ) { + block_ready = 1; + type = DIRAX_INPUT_ACL; + break; + } + + if ( (dirax->rbuffer[i] == '\r') + && (dirax->rbuffer[i+1] == '\n') ) { + block_ready = 1; + type = DIRAX_INPUT_LINE; + break; + } + + } + + if ( block_ready ) { + + unsigned int new_rbuflen; + unsigned int endbit_length; + char *block_buffer = NULL; + + switch ( type ) { + + case DIRAX_INPUT_LINE : + /* Make buffer a bit too big to keep Valgrind + * quiet about alignment errors */ + block_buffer = malloc(i+4); + memcpy(block_buffer, dirax->rbuffer, i); + block_buffer[i] = '\0'; + + if ( block_buffer[0] == '\r' ) { + memmove(block_buffer, block_buffer+1, i); + } + + dirax_parseline(block_buffer, image, dirax); + free(block_buffer); + endbit_length = i+2; + break; + + case DIRAX_INPUT_PROMPT : + dirax_send_next(image, dirax); + endbit_length = i+7; + break; + + case DIRAX_INPUT_ACL : + dirax_send_next(image,dirax); + endbit_length = i+10; + break; + + default : + /* Obviously, this never happens :) */ + ERROR("Unrecognised DirAx input mode! " + "I don't know how to understand DirAx\n"); + return 1; + + } + + /* Now the block's been parsed, it should be + * forgotten about */ + memmove(dirax->rbuffer, + dirax->rbuffer + endbit_length, + dirax->rbuflen - endbit_length); + + /* Subtract the number of bytes removed */ + dirax->rbufpos = dirax->rbufpos + - endbit_length; + new_rbuflen = dirax->rbuflen - endbit_length; + if ( new_rbuflen == 0 ) new_rbuflen = 256; + dirax->rbuffer = realloc(dirax->rbuffer, + new_rbuflen); + dirax->rbuflen = new_rbuflen; + + } else { + + if ( dirax->rbufpos==dirax->rbuflen ) { + + /* More buffer space is needed */ + dirax->rbuffer = realloc( + dirax->rbuffer, + dirax->rbuflen + 256); + dirax->rbuflen = dirax->rbuflen + + 256; + /* The new space gets used at the next + * read, shortly... */ + + } + no_string = 1; + + } + + } + + return 0; +} + + +static void write_drx(struct image *image) +{ + FILE *fh; + int i; + char filename[1024]; + + snprintf(filename, 1023, "xfel.drx"); + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + return; + } + fprintf(fh, "%f\n", 0.5); /* Lie about the wavelength. */ + + for ( i=0; ifeatures); i++ ) { + + struct imagefeature *f; + + f = image_get_feature(image->features, i); + if ( f == NULL ) continue; + + fprintf(fh, "%10f %10f %10f %8f\n", + f->rx/1e10, f->ry/1e10, f->rz/1e10, 1.0); + + } + fclose(fh); +} + + +int run_dirax(struct image *image, void *ipriv) +{ + unsigned int opts; + int status; + int rval; + struct dirax_data *dirax; + + write_drx(image); + + dirax = malloc(sizeof(struct dirax_data)); + if ( dirax == NULL ) { + ERROR("Couldn't allocate memory for DirAx data.\n"); + return 0; + } + + dirax->pid = forkpty(&dirax->pty, NULL, NULL, NULL); + if ( dirax->pid == -1 ) { + ERROR("Failed to fork for DirAx: %s\n", strerror(errno)); + return 0; + } + if ( dirax->pid == 0 ) { + + /* Child process: invoke DirAx */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("dirax", "dirax", (char *)NULL); + ERROR("Failed to invoke DirAx.\n"); + _exit(0); + + } + + dirax->rbuffer = malloc(256); + dirax->rbuflen = 256; + dirax->rbufpos = 0; + + /* Set non-blocking */ + opts = fcntl(dirax->pty, F_GETFL); + fcntl(dirax->pty, F_SETFL, opts | O_NONBLOCK); + + dirax->step = 1; /* This starts the "initialisation" procedure */ + dirax->finished_ok = 0; + dirax->read_cell = 0; + dirax->n_acls_tried = 0; + dirax->best_acl_nh = 0; + dirax->done = 0; + dirax->success = 0; + dirax->dp = (struct dirax_private *)ipriv; + + do { + + fd_set fds; + struct timeval tv; + int sval; + + FD_ZERO(&fds); + FD_SET(dirax->pty, &fds); + + tv.tv_sec = 30; + tv.tv_usec = 0; + + sval = select(dirax->pty+1, &fds, NULL, NULL, &tv); + + if ( sval == -1 ) { + + const int err = errno; + + switch ( err ) { + + case EINTR: + STATUS("Restarting select()\n"); + break; + + default: + ERROR("select() failed: %s\n", strerror(err)); + rval = 1; + + } + + } else if ( sval != 0 ) { + rval = dirax_readable(image, dirax); + } else { + ERROR("No response from DirAx..\n"); + rval = 1; + } + + } while ( !rval && !dirax->success ); + + close(dirax->pty); + free(dirax->rbuffer); + waitpid(dirax->pid, &status, 0); + + if ( dirax->finished_ok == 0 ) { + ERROR("DirAx doesn't seem to be working properly.\n"); + } + + rval = dirax->success; + free(dirax); + return rval; +} + + +void *dirax_prepare(IndexingMethod *indm, UnitCell *cell) +{ + struct dirax_private *dp; + + if ( dirax_probe(cell) == NULL ) { + ERROR("DirAx does not appear to run properly.\n"); + ERROR("Please check your DirAx installation.\n"); + return NULL; + } + + /* Flags that DirAx knows about */ + *indm &= INDEXING_METHOD_MASK; + + dp = malloc(sizeof(struct dirax_private)); + if ( dp == NULL ) return NULL; + + dp->template = cell; + dp->indm = *indm; + + return (IndexingPrivate *)dp; +} + + +void dirax_cleanup(void *pp) +{ + struct dirax_private *p; + p = (struct dirax_private *)pp; + free(p); +} + + +const char *dirax_probe(UnitCell *cell) +{ + pid_t pid; + int pty; + int status; + FILE *fh; + char line[1024]; + int ok = 0; + + pid = forkpty(&pty, NULL, NULL, NULL); + if ( pid == -1 ) { + return NULL; + } + if ( pid == 0 ) { + + /* Child process: invoke DirAx */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("dirax", "dirax", (char *)NULL); + _exit(1); + + } + + fh = fdopen(pty, "r"); + if ( fgets(line, 1024, fh) != NULL ) { + if ( strncmp(line, "dirax", 5) == 0 ) { + ok = 1; + } + } + + fclose(fh); + close(pty); + waitpid(pid, &status, 0); + + if ( ok ) return "dirax"; + return NULL; +} diff --git a/libcrystfel/src/indexers/dirax.h b/libcrystfel/src/indexers/dirax.h new file mode 100644 index 00000000..da4ae3d5 --- /dev/null +++ b/libcrystfel/src/indexers/dirax.h @@ -0,0 +1,52 @@ +/* + * dirax.h + * + * Invoke the DirAx auto-indexing program + * + * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2010,2012-2014,2017 Thomas White + * + * 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 . + * + */ + +#ifndef DIRAX_H +#define DIRAX_H + +#include "index.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/** \file dirax.h + * DirAx indexer interface + */ +extern int run_dirax(struct image *image, void *ipriv); + +extern void *dirax_prepare(IndexingMethod *indm, UnitCell *cell); +extern const char *dirax_probe(UnitCell *cell); + +extern void dirax_cleanup(void *pp); + +#ifdef __cplusplus +} +#endif + +#endif /* DIRAX_H */ diff --git a/libcrystfel/src/indexers/felix.c b/libcrystfel/src/indexers/felix.c new file mode 100644 index 00000000..524e68a7 --- /dev/null +++ b/libcrystfel/src/indexers/felix.c @@ -0,0 +1,963 @@ +/* + * felix.c + * + * Invoke Felix for multi-crystal autoindexing. + * + * Copyright © 2015-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2015-2018 Thomas White + * 2015 Kenneth Beyerlein + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + + +/** \file felix.h */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef HAVE_CLOCK_GETTIME +#include +#else +#include +#endif + +#ifdef HAVE_FORKPTY_PTY_H +#include +#endif +#ifdef HAVE_FORKPTY_UTIL_H +#include +#endif + +#include "image.h" +#include "utils.h" +#include "peaks.h" +#include "cell.h" +#include "cell-utils.h" +#include "felix.h" + + +#define FELIX_VERBOSE 0 + + +struct felix_options +{ + double ttmin; /* radians */ + double ttmax; /* radians */ + int min_visits; + double min_completeness; + double max_uniqueness; + int n_voxels; + double fraction_max_visits; + double sigma; + double domega; + double max_internal_angle; +}; + + +/* Global private data, prepared once */ +struct felix_private +{ + IndexingMethod indm; + UnitCell *cell; + + /* Options specific to Felix */ + int spacegroup; + float tthrange_min; + float tthrange_max; + float etarange_min; + float etarange_max; + float domega; + float omegarange_min; + float omegarange_max; + int min_visits; /* related to "cuts" */ + float min_completeness; /* related to "cuts" */ + float max_uniqueness; /* related to "cuts" */ + int n_voxels; /* related to "frustsumsize" */ + float fraction_max_visits; /* related to "frustsumsize" */ + float sigma_tth; /* related to "uncertainties" */ + float sigma_eta; /* related to "uncertainties" */ + float sigma_omega; /* related to "uncertainties" */ + int n_sigmas; + int force4frustums; + float max_internal_angle; + + /*Felix v0.3 options*/ + int orispace_frustum; + int orispace_octa; + char *readhkl_file; + float maxtime; + +}; + + +/* Data needed to call Felix */ +struct felix_data { + + struct felix_private *gp; + + /* Low-level stuff */ + int pty; + pid_t pid; + char *rbuffer; + int rbufpos; + int rbuflen; + +}; + + +static int read_felix(struct felix_private *gp, struct image *image, + char *filename) +{ + FILE *fh; + int d1; + float d2; + float ubi11, ubi12, ubi13; + float ubi21, ubi22, ubi23; + float ubi31, ubi32, ubi33; + float mean_ia; + int ngv; + char line[1024]; + int r; + int n_crystals = 0; + + fh = fopen(filename, "r"); + if ( fh == NULL ) { + ERROR("Can't open '%s'\n", filename); + return 0; + } + + /* Read and discard first line */ + if ( fgets( line, 1024, fh ) == NULL ) { + ERROR("Failed to read *.felix file.\n"); + return 0; + } + + do { + + Crystal *cr; + UnitCell *cell; + + /* One line per grain */ + if ( fgets( line, 1024, fh ) == NULL ) { + break; + } + /* File format of the .felix files + * version 0.1 - 0.2 + * + * r = sscanf(line, "%i %f %i %i %f %f %f %f %f %f %f %f %f" + * "%f %f %f %f %f %f %f %f %f %f %f %f", + * &d1, &mean_ia, &ngv, &ngv_unique, &d2, &d2, &d2, + * &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, &d2, + * &ubi11, &ubi12, &ubi13, + * &ubi21, &ubi22, &ubi23, + * &ubi31, &ubi32, &ubi33); + * + * if ( r != 25 ) { + * ERROR("Only %i parameters in .felix file\n", r); + * return 1; + * } + */ + + /* version 0.3 - present */ + r = sscanf(line, "%i %f %i %f %f %f %f %f %f" + "%f %f %f %f %f %f %f %f %f %f %f %f", + &d1, &mean_ia, &ngv, &d2, &d2, + &d2, &d2, &d2, &d2, &d2, &d2, &d2, + &ubi11, &ubi12, &ubi13, + &ubi21, &ubi22, &ubi23, + &ubi31, &ubi32, &ubi33); + + if ( r != 21 ) { + ERROR("Only %i parameters in .felix file, " + "check version and format.\n", r); + return -1; + } + + cell = cell_new(); + + cell_set_cartesian(cell, ubi12/1e10, ubi13/1e10, ubi11/1e10, + ubi22/1e10, ubi23/1e10, ubi21/1e10, + ubi32/1e10, ubi33/1e10, ubi31/1e10); + cell_set_lattice_type(cell, cell_get_lattice_type(gp->cell)); + cell_set_centering(cell, cell_get_centering(gp->cell)); + cell_set_unique_axis(cell, cell_get_unique_axis(gp->cell)); + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR( "Failed to allocate crystal.\n" ); + return 0; + } + + crystal_set_cell(cr, cell); + + /* Poor indexing criterion for Felix v0.1 + * + * if (mean_ia > MAX_MEAN_IA || ngv < MIN_NGV || + * ngv_unique < MIN_NGV_UNIQUE ){ + * crystal_set_user_flag(cr, 1); + */ + + /* Poor indexing criterion for Felix v0.3 */ + + if ( mean_ia > gp->max_internal_angle ){ + crystal_set_user_flag(cr, 1); + } + + /* All crystals are saved to the image, + * but only good ones will be later written to the stream file. + */ + + image_add_crystal(image, cr); + n_crystals++; + + } while ( !feof(fh) ); + + fclose(fh); + + return n_crystals; +} + + +static void gs_parseline(char *line, struct image *image, + struct felix_data *gs) +{ + #if FELIX_VERBOSE + STATUS("%s\n", line); + #endif +} + + +static int felix_readable(struct image *image, struct felix_data *gs) +{ + int rval; + int no_string = 0; + + rval = read(gs->pty, gs->rbuffer+gs->rbufpos, gs->rbuflen-gs->rbufpos); + + if ( (rval == -1) || (rval == 0) ) return 1; + + gs->rbufpos += rval; + assert(gs->rbufpos <= gs->rbuflen); + + while ( (!no_string) && (gs->rbufpos > 0) ) { + + int i; + int block_ready = 0; + + /* See if there's a full line in the buffer yet */ + for ( i=0; irbufpos-1; i++ ) { + /* Means the last value looked at is rbufpos-2 */ + + if ( (gs->rbuffer[i] == '\r') + && ( gs->rbuffer[i+1] == '\n' ) ) { + block_ready = 1; + break; + } + + } + + if ( block_ready ) { + + unsigned int new_rbuflen; + unsigned int endbit_length; + char *block_buffer = NULL; + + block_buffer = malloc(i+1); + memcpy(block_buffer, gs->rbuffer, i); + block_buffer[i] = '\0'; + + if ( block_buffer[0] == '\r' ) { + memmove(block_buffer, block_buffer+1, i); + } + + gs_parseline(block_buffer, image, gs); + free(block_buffer); + endbit_length = i+2; + + /* Now the block's been parsed, it should be + * forgotten about */ + memmove(gs->rbuffer, + gs->rbuffer + endbit_length, + gs->rbuflen - endbit_length); + + /* Subtract the number of bytes removed */ + gs->rbufpos = gs->rbufpos - endbit_length; + new_rbuflen = gs->rbuflen - endbit_length; + if ( new_rbuflen == 0 ) new_rbuflen = 256; + gs->rbuffer = realloc(gs->rbuffer, new_rbuflen); + gs->rbuflen = new_rbuflen; + + } else { + + if ( gs->rbufpos == gs->rbuflen ) { + + /* More buffer space is needed */ + gs->rbuffer = realloc(gs->rbuffer, + gs->rbuflen + 256); + gs->rbuflen = gs->rbuflen + 256; + /* The new space gets used at the next + * read, shortly... */ + + } + no_string = 1; + + } + + } + + return 0; +} + + +static void write_gve(struct image *image, struct felix_private *gp) +{ + FILE *fh; + int i; + char filename[1024]; + double a, b, c, al, be, ga; + snprintf(filename, 1023, "xfel.gve"); + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + return; + } + + cell_get_parameters(gp->cell, &a, &b, &c, &al, &be, &ga); + fprintf(fh, "%.6f %.6f %.6f %.6f %.6f %.6f P\n", a*1e10, b*1e10, c*1e10, + rad2deg(al), rad2deg(be), rad2deg(ga)); + fprintf(fh, "# wavelength = %.6f\n", image->lambda*1e10); + fprintf(fh, "# wedge = 0.000000\n"); + fprintf(fh, "# ds h k l\n"); + fprintf(fh, "# xr yr zr xc yc ds eta omega\n"); + + for ( i=0; ifeatures); i++ ) { + + struct imagefeature *f; + + f = image_get_feature(image->features, i); + if ( f == NULL ) continue; + + fprintf(fh, "%.6f %.6f %.6f 0 0 %.6f %.6f %.6f 0\n", + f->rz/1e10, f->rx/1e10, f->ry/1e10, + modulus(f->rx, f->ry, f->rz)/1e10, /* dstar */ + rad2deg(atan2(f->ry, f->rx)), 0.0); /* eta, omega */ + + } + fclose(fh); +} + + +static char *write_ini(struct image *image, struct felix_private *gp) +{ + FILE *fh; + char *filename; + char gveFilename[1024]; + char logFilename[1024]; + + filename = malloc(1024); + if ( filename == NULL ) return NULL; + + snprintf(filename, 1023, "xfel.ini"); + snprintf(gveFilename, 1023, "xfel.gve"); + snprintf(logFilename, 1023, "xfel.log"); + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + free(filename); + return NULL; + } + + fprintf(fh, "spacegroup %i\n", gp->spacegroup); + fprintf(fh, "tthrange %f %f\n", rad2deg(gp->tthrange_min), + rad2deg(gp->tthrange_max)); + fprintf(fh, "etarange %f %f\n", gp->etarange_min, gp->etarange_max); + fprintf(fh, "domega %f\n", gp->domega); + fprintf(fh, "omegarange %f %f\n", gp->omegarange_min, gp->omegarange_max); + fprintf(fh, "filespecs %s %s\n", gveFilename, logFilename); + fprintf(fh, "cuts %i %f %f\n", gp->min_visits, gp->min_completeness, + gp->max_uniqueness); + fprintf(fh, "frustumsize %i %f\n", gp->n_voxels, + gp->fraction_max_visits); + fprintf(fh, "uncertainties %f %f %f\n", gp->sigma_tth, + gp->sigma_eta, gp->sigma_omega); + fprintf(fh, "nsigmas %i\n", gp->n_sigmas); + + if ( gp->force4frustums == 1 ){ + fprintf(fh, "force4frustums\n"); + } + + if ( gp->orispace_frustum == 1 ){ + fprintf(fh, "orispace frustum\n"); + } else if ( gp->orispace_octa ==1 ){ + fprintf(fh, "orispace octa\n"); + } else{ + ERROR("No felix supported orispace specified.\n"); + free(filename); + filename = NULL; + } + + /* If an hkl file is not specified, generate the peak list. */ + if ( gp->readhkl_file != NULL ){ + fprintf(fh, "readhkl %s\n", gp->readhkl_file); + } else{ + fprintf(fh, "genhkl\n"); + } + + fprintf(fh, "maxtime %f\n", gp->maxtime); + + fclose(fh); + + return filename; +} + + +int felix_index(struct image *image, IndexingPrivate *ipriv) +{ + unsigned int opts; + int status; + int rval; + struct felix_data *felix; + struct felix_private *gp = (struct felix_private *) ipriv; + char *ini_filename; + char gff_filename[1024]; + + write_gve (image, gp); + ini_filename = write_ini (image, gp); + + if ( ini_filename == NULL ) { + ERROR("Failed to write ini file for Felix.\n"); + return 0; + } + + felix = malloc(sizeof(struct felix_data)); + if ( felix == NULL ) { + ERROR("Couldn't allocate memory for Felix data.\n"); + return 0; + } + + felix->gp = gp; + + snprintf(gff_filename, 1023, "xfel.felix"); + remove(gff_filename); + + felix->pid = forkpty(&felix->pty, NULL, NULL, NULL); + if ( felix->pid == -1 ) { + ERROR("Failed to fork for Felix: %s\n", strerror(errno)); + return 0; + } + if ( felix->pid == 0 ) { + + /* Child process: invoke Felix */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + STATUS("Running Felix '%s'\n", ini_filename); + execlp("Felix", "Felix", ini_filename, (char *)NULL); + ERROR("Failed to invoke Felix.\n"); + _exit(0); + + } + + free(ini_filename); + + felix->rbuffer = malloc(256); + felix->rbuflen = 256; + felix->rbufpos = 0; + + /* Set non-blocking */ + opts = fcntl(felix->pty, F_GETFL); + fcntl(felix->pty, F_SETFL, opts | O_NONBLOCK); + + do { + + fd_set fds; + struct timeval tv; + int sval; + + FD_ZERO(&fds); + FD_SET(felix->pty, &fds); + + tv.tv_sec = gp->maxtime + 1.0; + tv.tv_usec = 0; + + sval = select(felix->pty+1, &fds, NULL, NULL, &tv); + + if ( sval == -1 ) { + + const int err = errno; + + switch ( err ) { + + case EINTR: + STATUS("Restarting select()\n"); + rval = 0; + break; + + default: + ERROR("select() failed: %s\n", strerror(err)); + rval = 1; + + } + + } else if ( sval != 0 ) { + rval = felix_readable(image, felix); + } else { + ERROR("No response from Felix..\n"); + rval = 1; + } + + } while ( !rval ); + + close(felix->pty); + free(felix->rbuffer); + waitpid(felix->pid, &status, 0); + + if ( status != 0 ) { + ERROR("Felix either timed out, or is not working properly.\n"); + free(felix); + return 0; + } + + rval = read_felix(gp, image, gff_filename); + + free(felix); + return rval; + +} + + +static int sg_number_for_cell(UnitCell *cell) +{ + LatticeType lattice = cell_get_lattice_type(cell); + char cen = cell_get_centering(cell); + + switch (lattice) + { + case L_TRICLINIC: + return 1; /* P1 */ + + case L_MONOCLINIC: + switch ( cen ) { + case 'P' : return 3; /* P2 */ + case 'C' : return 5; /* C2 */ + default : return 0; + } + + case L_ORTHORHOMBIC: + switch ( cen ) { + case 'P' : return 16; /* P222 */ + case 'C' : return 21; /* C222 */ + case 'F' : return 22; /* F222 */ + case 'I' : return 23; /* I222 */ + case 'A' : return 38; /* Amm2 */ + default : return 0; + } + + case L_TETRAGONAL: + switch ( cen ) { + case 'P' : return 89; /* P422 */ + case 'I' : return 97; /* I422 */ + default : return 0; + } + + case L_RHOMBOHEDRAL: + return 155; /* R32 */ + + case L_HEXAGONAL: + switch ( cen ) { + case 'P' : return 177; /* P622 */ + case 'H' : return 143; /* P3 */ + default : return 0; + } + + case L_CUBIC: + switch ( cen ) { + case 'P' : return 207; /* P432 */ + case 'F' : return 209; /* F432 */ + case 'I' : return 211; /* I432 */ + default : return 0; + } + + default: + return 0; + } +} + + +void *felix_prepare(IndexingMethod *indm, UnitCell *cell, + struct felix_options *opts) +{ + struct felix_private *gp; + + if ( !cell_has_parameters(cell) ) { + ERROR("Felix needs a unit cell.\n"); + return NULL; + } + + if ( felix_probe(cell) == NULL ) { + ERROR("Felix does not appear to run properly.\n"); + ERROR("Please check your Felix installation.\n"); + return NULL; + } + + gp = calloc(1, sizeof(*gp)); + if ( gp == NULL ) return NULL; + + /* Flags that Felix knows about */ + *indm &= INDEXING_METHOD_MASK + | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS; + + gp->cell = cell; + gp->indm = *indm; + + /* Default values of felix options */ + gp->spacegroup = sg_number_for_cell(cell); + if ( gp->spacegroup == 0 ) { + ERROR("Couldn't determine representative space group for your cell.\n"); + ERROR("Try again with a more conventional cell.\n"); + return NULL; + } + + /* Default parameters */ + gp->n_voxels = 100; + gp->etarange_min = 0; + gp->etarange_max = 360; + gp->domega = 2; + gp->omegarange_min = -1.0; + gp->omegarange_max = 1.0; + gp->min_visits = 15; + gp->min_completeness = 0.001; + gp->max_uniqueness = 0.5; + gp->fraction_max_visits = 0.75; + gp->sigma_tth = 0.2; + gp->sigma_eta = 0.2; + gp->sigma_omega = 0.2; + gp->n_sigmas = 1; + gp->force4frustums = 0; + gp->orispace_frustum = 1; + gp->orispace_octa = 0; + gp->readhkl_file = NULL; + gp->maxtime = 120.0; + gp->tthrange_min = deg2rad(0.0); + gp->tthrange_max = deg2rad(30.0); + gp->max_internal_angle = 0.25; + + if ( opts->ttmin > 0.0 ) { + gp->tthrange_min = opts->ttmin; + } + if ( opts->ttmax > 0.0 ) { + gp->tthrange_max = opts->ttmax; + } + if ( opts->min_visits > 0 ) { + gp->min_visits = opts->min_visits; + } + if ( opts->min_completeness > 0.0 ) { + gp->min_completeness = opts->min_completeness; + } + if ( opts->max_uniqueness > 0.0 ) { + gp->max_uniqueness = opts->max_uniqueness; + } + if ( opts->n_voxels > 0 ) { + gp->n_voxels = opts->n_voxels; + } + if ( opts->fraction_max_visits > 0.0 ) { + gp->fraction_max_visits = opts->fraction_max_visits; + } + if ( opts->sigma > 0.0 ) { + gp->sigma_tth = opts->sigma; + gp->sigma_eta = opts->sigma; + gp->sigma_omega = opts->sigma; + } + if ( opts->domega > 0.0 ) { + gp->domega = opts->domega; + } + if ( opts->max_internal_angle > 0 ) { + gp->max_internal_angle = opts->max_internal_angle; + } + + return (IndexingPrivate *)gp; +} + + +void felix_cleanup(IndexingPrivate *pp) +{ + struct felix_private *p; + + p = (struct felix_private *) pp; + free(p->readhkl_file); + free(p); +} + + +static int file_exists(const char *filename) +{ + struct stat s; + + if ( stat(filename, &s) != 0 ) { + if ( errno == ENOENT ) return 0; + ERROR("Failed to check for %s.\n", filename); + exit(1); + } + + return 1; +} + + +const char *felix_probe(UnitCell *cell) +{ + pid_t pid; + int pty; + int status; + FILE *fh; + char line[1024]; + int ok = 0; + + if ( !cell_has_parameters(cell) ) { + return NULL; + } + + /* Felix will write gmon.out when we test it, which we are + * are going to delete afterwards. Better check the file doesn't exist + * first, in case it was important. */ + if ( file_exists("gmon.out") ) { + ERROR("Please move or delete gmon.out from the working " + "directory first.\n"); + exit(1); + } + + pid = forkpty(&pty, NULL, NULL, NULL); + if ( pid == -1 ) { + return NULL; + } + if ( pid == 0 ) { + + /* Child process: invoke DirAx */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("Felix", "Felix", (char *)NULL); + _exit(1); + + } + + fh = fdopen(pty, "r"); + if ( fgets(line, 1024, fh) == NULL ) { + ok = 0; + } else { + if ( strncmp(line, "Felix", 5) == 0 ) { + ok = 1; + } + } + + fclose(fh); + close(pty); + waitpid(pid, &status, 0); + + unlink("gmon.out"); + + if ( ok ) return "felix"; + return NULL; +} + + +static void felix_show_help() +{ + printf("Parameters for the Felix indexing algorithm:\n" +" --felix-domega Degree range of omega (moscaicity) to consider.\n" +" Default: 2\n" +" --felix-fraction-max-visits\n" +" Cutoff for minimum fraction of the max visits.\n" +" Default: 0.75\n" +" --felix-max-internal-angle\n" +" Cutoff for maximum internal angle between observed\n" +" spots and predicted spots. Default: 0.25\n" +" --felix-max-uniqueness\n" +" Cutoff for maximum fraction of found spots which\n" +" can belong to other crystallites. Default: 0.5\n" +" --felix-min-completeness\n" +" Cutoff for minimum fraction of projected spots\n" +" found in the pattern. Default: 0.001\n" +" --felix-min-visits\n" +" Cutoff for minimum number of voxel visits.\n" +" Default: 15\n" +" --felix-num-voxels Number of voxels for Rodrigues space search\n" +" Default: 100\n" +" --felix-sigma The sigma of the 2theta, eta and omega angles.\n" +" Default: 0.2\n" +" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n" +" Default: 30\n" +" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n" +" Default: 0\n" +); +} + + +static error_t felix_parse_arg(int key, char *arg, + struct argp_state *state) +{ + struct felix_options **opts_ptr = state->input; + float tmp; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct felix_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->ttmin = -1.0; + (*opts_ptr)->ttmax = -1.0; + (*opts_ptr)->min_visits = 0; + (*opts_ptr)->min_completeness = -1.0; + (*opts_ptr)->max_uniqueness = -1.0; + (*opts_ptr)->n_voxels = 0; + (*opts_ptr)->fraction_max_visits = -1.0; + (*opts_ptr)->sigma = -1.0; + (*opts_ptr)->domega = -1.0; + (*opts_ptr)->max_internal_angle = -1.0; + break; + + case 1 : + felix_show_help(); + return EINVAL; + + case 2 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-min\n"); + return EINVAL; + } + (*opts_ptr)->ttmin = deg2rad(tmp); + break; + + case 3 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-max\n"); + return EINVAL; + } + (*opts_ptr)->ttmax = deg2rad(tmp); + break; + + case 4 : + if ( sscanf(arg, "%d", &(*opts_ptr)->min_visits) != 1 ) { + ERROR("Invalid value for --felix-min-visits\n"); + return EINVAL; + } + break; + + case 5 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->min_completeness) != 1 ) { + ERROR("Invalid value for --felix-min-completeness\n"); + return EINVAL; + } + break; + + case 6 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_uniqueness) != 1 ) { + ERROR("Invalid value for --felix-max-uniqueness\n"); + return EINVAL; + } + break; + + case 7 : + if ( sscanf(arg, "%d", &(*opts_ptr)->n_voxels) != 1 ) { + ERROR("Invalid value for --felix-num-voxels\n"); + return EINVAL; + } + break; + + case 8 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->fraction_max_visits) != 1 ) { + ERROR("Invalid value for --felix-fraction-max-visits\n"); + return EINVAL; + } + break; + + case 9 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->sigma) != 1 ) { + ERROR("Invalid value for --felix-sigma\n"); + return EINVAL; + } + break; + + case 10 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->domega) != 1 ) { + ERROR("Invalid value for --felix-domega\n"); + return EINVAL; + } + break; + + case 11 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_internal_angle) != 1 ) { + ERROR("Invalid value for --felix-max-internal-angle\n"); + return EINVAL; + } + break; + + default : + return ARGP_ERR_UNKNOWN; + + } + + return 0; +} + + +static struct argp_option felix_options[] = { + + {"help-felix", 1, NULL, OPTION_NO_USAGE, + "Show options for Felix indexing algorithm", 99}, + {"felix-tthrange-min", 2, "2theta", OPTION_HIDDEN, NULL}, + {"felix-tthrange-max", 3, "2theta", OPTION_HIDDEN, NULL}, + {"felix-min-visits", 4, "n", OPTION_HIDDEN, NULL}, + {"felix-min-completeness", 5, "frac", OPTION_HIDDEN, NULL}, + {"felix-max-uniqueness", 6, "n", OPTION_HIDDEN, NULL}, + {"felix-num-voxels", 7, "n", OPTION_HIDDEN, NULL}, + {"felix-fraction-max-visits", 8, "n", OPTION_HIDDEN, NULL}, + {"felix-sigma", 9, "n", OPTION_HIDDEN, NULL}, + {"felix-domega", 10, "n", OPTION_HIDDEN, NULL}, + {"felix-max-internal-angle", 11, "ang", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp felix_argp = { felix_options, felix_parse_arg, + NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/indexers/felix.h b/libcrystfel/src/indexers/felix.h new file mode 100644 index 00000000..3c9d4a94 --- /dev/null +++ b/libcrystfel/src/indexers/felix.h @@ -0,0 +1,52 @@ +/* + * felix.h + * + * Invoke Felix for multi-crystal autoindexing + * + * Copyright © 2013-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2010-2013,2017 Thomas White + * 2013-2014 Kenneth Beyerlein + * + * 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 . + * + */ + +#ifndef FELIX_H +#define FELIX_H + +#include + +#include "cell.h" + +/** + * \file felix.h + * Felix indexer interface + */ + +extern void *felix_prepare(IndexingMethod *indm, UnitCell *cell, + struct felix_options *opts); + +extern const char *felix_probe(UnitCell *cell); + +extern void felix_cleanup(IndexingPrivate *pp); + +extern int felix_index(struct image *image, IndexingPrivate *p); + + +#endif /* FELIX_H */ diff --git a/libcrystfel/src/indexers/mosflm.c b/libcrystfel/src/indexers/mosflm.c new file mode 100644 index 00000000..bacd345f --- /dev/null +++ b/libcrystfel/src/indexers/mosflm.c @@ -0,0 +1,945 @@ +/* + * mosflm.c + * + * Invoke the DPS auto-indexing algorithm through MOSFLM + * + * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * Copyright © 2012 Richard Kirian + * + * Authors: + * 2010 Richard Kirian + * 2010-2018 Thomas White + * 2014 Takanori Nakane + * + * 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 . + * + */ + +/* TODO: + * + * Properly read the newmat file (don't use fscanf-- spaces between numers + * are not guaranteed) + * + * "Success" is indicated by existence of NEWMAT file written by mosflm. + * Better to interact with mosflm directly in order to somehow verify success. + * + * Investigate how these keywords affect mosflms behavior: + * + * MOSAICITY + * DISPERSION + * DIVERGENCE + * POLARISATION + * POSTREF BEAM + * POSTREF USEBEAM OFF + * PREREFINE ON + * EXTRA ON + * POSTREF ON + * + * These did not seem to affect the results by my (Rick's) experience, probably + * because they are only used conjunction with image intensity data, but it's + * worth another look at the documentation. + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef HAVE_FORKPTY_PTY_H +#include +#endif +#ifdef HAVE_FORKPTY_UTIL_H +#include +#endif + +#ifdef HAVE_CLOCK_GETTIME +#include +#else +#include +#endif + +#include "image.h" +#include "mosflm.h" +#include "utils.h" +#include "peaks.h" +#include "cell-utils.h" + +/** \file mosflm.h */ + +#define MOSFLM_VERBOSE 0 +#define FAKE_CLEN (0.1) + + +typedef enum { + MOSFLM_INPUT_NONE, + MOSFLM_INPUT_LINE, + MOSFLM_INPUT_PROMPT +} MOSFLMInputType; + + + +struct mosflm_private { + IndexingMethod indm; + UnitCell *template; +}; + + +struct mosflm_data { + + /* MOSFLM auto-indexing low-level stuff */ + int pty; + pid_t pid; + char *rbuffer; + int rbufpos; + int rbuflen; + + /* MOSFLM high-level stuff */ + char newmatfile[128]; + char imagefile[128]; + char sptfile[128]; + int step; + int finished_ok; + int done; + int success; + + struct mosflm_private *mp; + +}; + +static int check_mosflm_cell(struct mosflm_private *mp, struct image *image, + UnitCell *cell) +{ + Crystal *cr; + + /* If we sent lattice information, make sure that we got back what we + * asked for, not (e.g.) some "H" version of a rhombohedral R cell */ + if ( mp->indm & INDEXING_USE_LATTICE_TYPE ) { + + LatticeType latt_m, latt_r; + char cen_m, cen_r; + + /* What we asked for */ + latt_r = cell_get_lattice_type(mp->template); + cen_r = cell_get_centering(mp->template); + + /* What we got back */ + latt_m = cell_get_lattice_type(cell); + cen_m = cell_get_centering(cell); + + if ( latt_r != latt_m ) { + ERROR("Lattice type produced by MOSFLM (%i) does not " + "match what was requested (%i). " + "Please report this.\n", latt_m, latt_r); + return 0; + } + + if ( (latt_m != L_MONOCLINIC) && (cen_r != cen_m) ) { + ERROR("Centering produced by MOSFLM (%c) does not " + "match what was requested (%c). " + "Please report this.\n", cen_m, cen_r); + return 0; + } + /* If it's monoclinic, see the warning in mosflm_prepare() */ + + } + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + + crystal_set_cell(cr, cell); + + image_add_crystal(image, cr); + + return 1; +} + + +static void mosflm_parseline(const char *line, struct image *image, + struct mosflm_data *dirax) +{ + if ( MOSFLM_VERBOSE || (strncmp(line, "Invocation:", 11) == 0) ) { + char *copy; + int i; + + copy = strdup(line); + for ( i=0; ilambda; + + cell = cell_new(); + + /* The relationship between the coordinates in the spot file and the + * resulting matrix is diabolically complicated. This transformation + * seems to work, but is not derived by working through all the + * transformations. */ + cell_set_reciprocal(cell, + -asy*c, -asz*c, asx*c, + -bsy*c, -bsz*c, bsx*c, + -csy*c, -csz*c, csx*c); + cell_set_centering(cell, cen); + cell_set_lattice_type(cell, latt); + cell_set_unique_axis(cell, ua); + //STATUS("My cell:\n"); + //cell_print(cell); + + if ( check_mosflm_cell(mosflm->mp, image, cell) ) { + mosflm->success = 1; + mosflm->done = 1; + } + + return 0; +} + + +/* Write .spt file for mosflm */ +static void write_spt(struct image *image, const char *filename) +{ + FILE *fh; + int i; + int n; + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + return; + } + + /* Number of pixels in x, number of pixels in y, pixel size (mm), + * YSCALE, OMEGA */ + fputs("1 1 0.0 1.0 0.0\n", fh); + + /* INVERTX, ISWUNG */ + fputs("0 1\n", fh); + + /* XBEAM, YBEAM */ + fputs("0.0 0.0\n", fh); + + n = image_feature_count(image->features); + for ( i=0; ifeatures, i); + if ( f == NULL ) continue; + + ttx = angle_between_2d(0.0, 1.0, + f->rx, 1.0/image->lambda + f->rz); + tty = angle_between_2d(0.0, 1.0, + f->ry, 1.0/image->lambda + f->rz); + if ( f->rx < 0.0 ) ttx *= -1.0; + if ( f->ry < 0.0 ) tty *= -1.0; + x = -tan(ttx)*FAKE_CLEN; + y = tan(tty)*FAKE_CLEN; + + fprintf(fh, "%10.2f %10.2f 0.0 0.0 1000.0 10.0\n", + x*1e3, y*1e3); + + } + + fputs("-999.0 -999.0 -999.0 -999.0 -999.0 -999.0\n", fh); + + fclose(fh); +} + + +/* Write a dummy 1x1 pixel image file for MOSFLM. Without post refinement, + * MOSFLM will ignore this, but it must be present. */ +static void write_img(struct image *image, const char *filename) +{ + FILE *fh; + unsigned short int *intimage; + + intimage = malloc(sizeof(unsigned short int)); + intimage[0] = 1; + + fh = fopen(filename, "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", filename); + return; + } + + /* Write header */ + fprintf(fh, "{\nHEADER_BYTES=512;\n"); + fprintf(fh, "BYTE_ORDER=little_endian;\n"); + fprintf(fh, "TYPE=unsigned_short;\n"); + fprintf(fh, "DIM=2;\n"); + fprintf(fh, "SIZE1=1;\n"); + fprintf(fh, "SIZE2=1;\n"); + fprintf(fh, "}\n"); + + /* Header padding */ + while ( ftell(fh) < 512 ) fprintf(fh," "); + + fwrite(intimage, sizeof(unsigned short int), 1, fh); + free(intimage); + fclose(fh); +} + + +static void mosflm_sendline(const char *line, struct mosflm_data *mosflm) +{ + #if MOSFLM_VERBOSE + char *copy; + int i; + + copy = strdup(line); + for ( i=0; ipty, line, strlen(line)) == -1 ) { + ERROR("write() to MOSFLM failed: %s\n", strerror(errno)); + } +} + + +/* Turn what we know about the unit cell into something which we can give to + * MOSFLM to make it give us only indexing results compatible with the cell. */ +static char *mosflm_spacegroup_for_lattice(UnitCell *cell) +{ + LatticeType latt; + char centering; + char *g = NULL; + char *result; + char ua; + + latt = cell_get_lattice_type(cell); + centering = cell_get_centering(cell); + ua = cell_get_unique_axis(cell); + + switch ( latt ) + { + case L_TRICLINIC : + g = "1"; + break; + + case L_MONOCLINIC : + switch ( ua ) { + case 'a' : g = "211"; break; + case 'b' : g = "121"; break; + case 'c' : g = "112"; break; + } + break; + + case L_ORTHORHOMBIC : + g = "222"; + break; + + case L_TETRAGONAL : + g = "4"; + break; + + case L_RHOMBOHEDRAL : + g = "3"; + break; + + case L_HEXAGONAL : + if ( centering != 'H' ) { + g = "6"; + } else { + g = "3"; + } + break; + + case L_CUBIC : + g = "23"; + break; + } + assert(g != NULL); + + result = malloc(32); + if ( result == NULL ) return NULL; + + snprintf(result, 31, "%c%s", centering, g); + + return result; +} + + +static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm) +{ + char tmp[256]; + char cen; + double wavelength; + double a = 0, b = 0, c = 0, alpha = 0, beta = 0, gamma = 0; + + switch ( mosflm->step ) + { + case 1 : + /* Backwards-compatible workaround for different Mosflm behaviour + * in version 7.2.2 */ + mosflm_sendline("DETECTOR ADSC\n", mosflm); + break; + + case 2 : + mosflm_sendline("DETECTOR ROTATION HORIZONTAL" + " ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL" + " RECTANGULAR\n", mosflm); + break; + + case 3 : + if ( (mosflm->mp->indm & INDEXING_USE_LATTICE_TYPE) + && (mosflm->mp->template != NULL) ) + { + char *symm; + + if ( cell_get_lattice_type(mosflm->mp->template) + == L_RHOMBOHEDRAL ) { + mosflm_sendline("CRYSTAL R\n", mosflm); + } + + symm = mosflm_spacegroup_for_lattice(mosflm->mp->template); + snprintf(tmp, 255, "SYMM %s\n", symm); + //STATUS("Asking MOSFLM for '%s'\n", symm); + free(symm); + mosflm_sendline(tmp, mosflm); + + } else { + mosflm_sendline("\n", mosflm); + } + break; + + case 4 : + snprintf(tmp, 255, "DISTANCE %f\n", FAKE_CLEN*1e3); + mosflm_sendline(tmp, mosflm); + break; + + case 5 : + mosflm_sendline("BEAM 0.0 0.0\n", mosflm); + break; + + case 6 : + wavelength = image->lambda*1e10; + snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength); + mosflm_sendline(tmp, mosflm); + break; + + case 7 : + snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile); + mosflm_sendline(tmp, mosflm); + break; + + case 8 : + snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile); + mosflm_sendline(tmp, mosflm); + break; + + case 9 : + if ( mosflm->mp->indm & INDEXING_USE_CELL_PARAMETERS ) { + cell_get_parameters(mosflm->mp->template, + &a, &b, &c, &alpha, &beta, &gamma); + cen = cell_get_centering(mosflm->mp->template); + /* Old MOSFLM simply ignores CELL and CENTERING subkeywords. + * So this doesn't do any harm. + * TODO: but still better to show WARNING if MOSFLM is old. */ + snprintf(tmp, 255, "AUTOINDEX DPS FILE %s IMAGE 1 " + "MAXCELL 1000 REFINE " + "CELL %.1f %.1f %.1f %.1f %.1f %.1f " + "CENTERING %c\n", + mosflm->sptfile, a*1e10, b*1e10, c*1e10, + rad2deg(alpha), rad2deg(beta), rad2deg(gamma), + cen); + } else { + snprintf(tmp, 255, "AUTOINDEX DPS FILE %s IMAGE 1 " + "MAXCELL 1000 REFINE\n", mosflm->sptfile); + } + mosflm_sendline(tmp, mosflm); + break; + + case 10 : + mosflm_sendline("GO\n", mosflm); + mosflm->finished_ok = 1; + break; + + default: + mosflm_sendline("exit\n", mosflm); + return; + } + + mosflm->step++; +} + + +static int mosflm_readable(struct image *image, struct mosflm_data *mosflm) +{ + int rval; + int no_string = 0; + + rval = read(mosflm->pty, mosflm->rbuffer+mosflm->rbufpos, + mosflm->rbuflen-mosflm->rbufpos); + if ( (rval == -1) || (rval == 0) ) return 1; + + mosflm->rbufpos += rval; + assert(mosflm->rbufpos <= mosflm->rbuflen); + + while ( (!no_string) && (mosflm->rbufpos > 0) ) { + + int i; + int block_ready = 0; + MOSFLMInputType type = MOSFLM_INPUT_NONE; + + /* See if there's a full line in the buffer yet */ + for ( i=0; irbufpos-1; i++ ) { + /* Means the last value looked at is rbufpos-2 */ + + /* Is there a prompt in the buffer? */ + if ( (i+10 <= mosflm->rbufpos) + && (!strncmp(mosflm->rbuffer+i, "MOSFLM => ", 10)) ) { + block_ready = 1; + type = MOSFLM_INPUT_PROMPT; + break; + } + + if ( (mosflm->rbuffer[i] == '\r') + && (mosflm->rbuffer[i+1] == '\n') ) { + block_ready = 1; + type = MOSFLM_INPUT_LINE; + break; + } + + } + + if ( block_ready ) { + + unsigned int new_rbuflen; + unsigned int endbit_length; + char *block_buffer = NULL; + + switch ( type ) { + + case MOSFLM_INPUT_LINE : + block_buffer = malloc(i+1); + memcpy(block_buffer, mosflm->rbuffer, i); + block_buffer[i] = '\0'; + + if ( block_buffer[0] == '\r' ) { + memmove(block_buffer, block_buffer+1, i); + } + + mosflm_parseline(block_buffer, image, mosflm); + free(block_buffer); + endbit_length = i+2; + break; + + case MOSFLM_INPUT_PROMPT : + mosflm_send_next(image, mosflm); + endbit_length = i+7; + break; + + default : + + /* Obviously, this never happens :) */ + ERROR("Unrecognised MOSFLM input mode! " + "I don't know how to understand MOSFLM\n"); + return 1; + + } + + /* Now the block's been parsed, it should be + * forgotten about */ + memmove(mosflm->rbuffer, + mosflm->rbuffer + endbit_length, + mosflm->rbuflen - endbit_length); + + /* Subtract the number of bytes removed */ + mosflm->rbufpos = mosflm->rbufpos + - endbit_length; + new_rbuflen = mosflm->rbuflen - endbit_length; + if ( new_rbuflen == 0 ) new_rbuflen = 256; + mosflm->rbuffer = realloc(mosflm->rbuffer, + new_rbuflen); + mosflm->rbuflen = new_rbuflen; + + } else { + + if ( mosflm->rbufpos==mosflm->rbuflen ) { + + /* More buffer space is needed */ + mosflm->rbuffer = realloc( + mosflm->rbuffer, + mosflm->rbuflen + 256); + mosflm->rbuflen = mosflm->rbuflen + 256; + /* The new space gets used at the next + * read, shortly... */ + + } + no_string = 1; + + } + + } + + return 0; +} + + +int run_mosflm(struct image *image, void *ipriv) +{ + struct mosflm_data *mosflm; + unsigned int opts; + int status; + int rval; + + mosflm = malloc(sizeof(struct mosflm_data)); + if ( mosflm == NULL ) { + ERROR("Couldn't allocate memory for MOSFLM data.\n"); + return 0; + } + + snprintf(mosflm->imagefile, 127, "xfel_001.img"); + write_img(image, mosflm->imagefile); /* Dummy image */ + + snprintf(mosflm->sptfile, 127, "xfel_001.spt"); + write_spt(image, mosflm->sptfile); + + snprintf(mosflm->newmatfile, 127, "xfel.newmat"); + remove(mosflm->newmatfile); + + mosflm->pid = forkpty(&mosflm->pty, NULL, NULL, NULL); + + if ( mosflm->pid == -1 ) { + ERROR("Failed to fork for MOSFLM: %s\n", strerror(errno)); + free(mosflm); + return 0; + } + if ( mosflm->pid == 0 ) { + + /* Child process: invoke MOSFLM */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("mosflm", "mosflm", (char *)NULL); + execlp("ipmosflm", "ipmosflm", (char *)NULL); + ERROR("Invocation: Failed to invoke MOSFLM: %s\n", + strerror(errno)); + _exit(0); + + } + + mosflm->rbuffer = malloc(256); + mosflm->rbuflen = 256; + mosflm->rbufpos = 0; + + /* Set non-blocking */ + opts = fcntl(mosflm->pty, F_GETFL); + fcntl(mosflm->pty, F_SETFL, opts | O_NONBLOCK); + + mosflm->step = 1; /* This starts the "initialisation" procedure */ + mosflm->finished_ok = 0; + mosflm->mp = (struct mosflm_private *)ipriv; + mosflm->done = 0; + mosflm->success = 0; + + rval = 0; + do { + + fd_set fds; + struct timeval tv; + int sval; + + FD_ZERO(&fds); + FD_SET(mosflm->pty, &fds); + + tv.tv_sec = 30; + tv.tv_usec = 0; + + sval = select(mosflm->pty+1, &fds, NULL, NULL, &tv); + + if ( sval == -1 ) { + + const int err = errno; + + switch ( err ) { + + case EINTR: + STATUS("Restarting select()\n"); + break; + + default: + ERROR("select() failed: %s\n", strerror(err)); + rval = 1; + + } + + } else if ( sval != 0 ) { + rval = mosflm_readable(image, mosflm); + } else { + ERROR("No response from MOSFLM..\n"); + rval = 1; + } + + } while ( !rval ); + + close(mosflm->pty); + free(mosflm->rbuffer); + waitpid(mosflm->pid, &status, 0); + + if ( mosflm->finished_ok == 0 ) { + ERROR("MOSFLM doesn't seem to be working properly.\n"); + } else { + /* Read the mosflm NEWMAT file and get cell if found */ + read_newmat(mosflm, mosflm->newmatfile, image); + } + + rval = mosflm->success; + free(mosflm); + return rval; +} + + +void *mosflm_prepare(IndexingMethod *indm, UnitCell *cell) +{ + struct mosflm_private *mp; + + if ( mosflm_probe(cell) == NULL ) { + ERROR("Mosflm does not appear to run properly.\n"); + ERROR("Please check your Mosflm installation.\n"); + return NULL; + } + + /* Flags that MOSFLM knows about */ + *indm &= INDEXING_METHOD_MASK + | INDEXING_USE_LATTICE_TYPE | INDEXING_USE_CELL_PARAMETERS; + + if ( (cell != NULL) && (cell_get_centering(cell) == 'I') + && (cell_get_lattice_type(cell) == L_MONOCLINIC) ) + { + ERROR("WARNING: Mosflm always gives the monoclinic C cell in " + "preference to the monoclinic I cell choice.\n"); + ERROR("To get a higher indexing rate, convert your cell to the " + "monoclinic C cell choice.\n"); + } + + mp = malloc(sizeof(struct mosflm_private)); + if ( mp == NULL ) return NULL; + + mp->template = cell; + mp->indm = *indm; + + return (IndexingPrivate *)mp; +} + + +void mosflm_cleanup(void *pp) +{ + struct mosflm_private *p; + p = (struct mosflm_private *)pp; + free(p); +} + + +static void chop_word(char *s) +{ + int i; + size_t l = strlen(s); + for ( i=0; i + * 2012-2014,2017 Thomas White + * + * 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 . + * + */ + +#ifndef MOSFLM_H +#define MOSFLM_H + +#include "index.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/** + * \file mosflm.h + * MOSFLM indexer interface + */ + +extern int run_mosflm(struct image *image, void *ipriv); + +extern void *mosflm_prepare(IndexingMethod *indm, UnitCell *cell); +extern const char *mosflm_probe(UnitCell *cell); + +extern void mosflm_cleanup(void *pp); + +#ifdef __cplusplus +} +#endif + +#endif /* MOSFLM_H */ diff --git a/libcrystfel/src/indexers/pinkindexer.c b/libcrystfel/src/indexers/pinkindexer.c new file mode 100644 index 00000000..67bd48f5 --- /dev/null +++ b/libcrystfel/src/indexers/pinkindexer.c @@ -0,0 +1,646 @@ +/* + * pinkindexer.c + * + * Interface to PinkIndexer + * + * Copyright © 2017-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2019 Yaroslav Gevorkov + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "pinkindexer.h" + + +#include +#include +#include + +#include "utils.h" +#include "cell-utils.h" +#include "peaks.h" + +struct pinkIndexer_options { + unsigned int considered_peaks_count; + unsigned int angle_resolution; + unsigned int refinement_type; + float maxResolutionForIndexing_1_per_A; + float tolerance; + int multi; + int thread_count; + int min_peaks; + int no_check_indexed; + float reflectionRadius; /* In m^-1 */ + float customPhotonEnergy; + float customBandwidth; + float maxRefinementDisbalance; +}; + +#ifdef HAVE_PINKINDEXER + +#include +#include +#include + +#define MAX_MULTI_LATTICE_COUNT 8 + +struct pinkIndexer_private_data { + PinkIndexer *pinkIndexer; + reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A; + float *intensities; + + IndexingMethod indm; + UnitCell *cellTemplate; + int threadCount; + int multi; + int min_peaks; + + int no_check_indexed; + + float maxRefinementDisbalance; + + IntegerMatrix *centeringTransformation; + LatticeTransform_t latticeReductionTransform; +}; + +//static void reduceCell(UnitCell* cell, LatticeTransform_t* appliedReductionTransform); +//static void restoreCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform); +static void reduceReciprocalCell(UnitCell* cell, LatticeTransform_t* appliedReductionTransform); +static void restoreReciprocalCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform); +static void makeRightHanded(UnitCell* cell); +static void update_detector(struct detector *det, double xoffs, double yoffs); + +int run_pinkIndexer(struct image *image, void *ipriv) +{ + struct pinkIndexer_private_data* pinkIndexer_private_data = (struct pinkIndexer_private_data*) ipriv; + reciprocalPeaks_1_per_A_t* reciprocalPeaks_1_per_A = &(pinkIndexer_private_data->reciprocalPeaks_1_per_A); + float *intensities = pinkIndexer_private_data->intensities; + + int peakCountMax = image_feature_count(image->features); + if (peakCountMax < 5) { + int goodLatticesCount = 0; + return goodLatticesCount; + } + reciprocalPeaks_1_per_A->peakCount = 0; + for (int i = 0; i < peakCountMax && i < MAX_PEAK_COUNT_FOR_INDEXER; i++) { + struct imagefeature *f; + f = image_get_feature(image->features, i); + if (f == NULL) { + continue; + } + + reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = f->rz * 1e-10; + reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = f->rx * 1e-10; + reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = f->ry * 1e-10; + intensities[reciprocalPeaks_1_per_A->peakCount] = (float) (f->intensity); + reciprocalPeaks_1_per_A->peakCount++; + } + int indexed = 0; + Lattice_t indexedLattice[MAX_MULTI_LATTICE_COUNT]; + float center_shift[MAX_MULTI_LATTICE_COUNT][2]; + + + + do { + int peakCount = reciprocalPeaks_1_per_A->peakCount; + int matchedPeaksCount = PinkIndexer_indexPattern(pinkIndexer_private_data->pinkIndexer, + &(indexedLattice[indexed]), center_shift[indexed], reciprocalPeaks_1_per_A, intensities, + pinkIndexer_private_data->maxRefinementDisbalance, + pinkIndexer_private_data->threadCount); + + if(matchedPeaksCount == -1){ + STATUS("WARNING: Indexing solution was rejected due to too large disbalance of the refinement." + "If you see this message often, check the documentation for the parameter " + "--pinkIndexer-max-refinement-disbalance\n"); + + matchedPeaksCount = 0; + } + + printf("matchedPeaksCount %d from %d\n",matchedPeaksCount,peakCount); + if ((matchedPeaksCount >= 25 && matchedPeaksCount >= peakCount * 0.30) + || matchedPeaksCount >= peakCount * 0.4 + || matchedPeaksCount >= 70 + || pinkIndexer_private_data->no_check_indexed == 1) + { + UnitCell *uc; + uc = cell_new(); + + Lattice_t *l = &(indexedLattice[indexed]); + + cell_set_reciprocal(uc, l->ay * 1e10, l->az * 1e10, l->ax * 1e10, + l->by * 1e10, l->bz * 1e10, l->bx * 1e10, + l->cy * 1e10, l->cz * 1e10, l->cx * 1e10); + + restoreReciprocalCell(uc, &pinkIndexer_private_data->latticeReductionTransform); + + UnitCell *new_cell_trans = cell_transform_intmat(uc, pinkIndexer_private_data->centeringTransformation); + cell_free(uc); + uc = new_cell_trans; + + cell_set_lattice_type(new_cell_trans, cell_get_lattice_type(pinkIndexer_private_data->cellTemplate)); + cell_set_centering(new_cell_trans, cell_get_centering(pinkIndexer_private_data->cellTemplate)); + cell_set_unique_axis(new_cell_trans, cell_get_unique_axis(pinkIndexer_private_data->cellTemplate)); + + if (validate_cell(uc)) { + ERROR("pinkIndexer: problem with returned cell!\n"); + } + + Crystal * cr = crystal_new(); + if (cr == NULL) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + crystal_set_cell(cr, uc); + crystal_set_det_shift(cr, center_shift[indexed][0], center_shift[indexed][1]); + update_detector(image->det, center_shift[indexed][0], center_shift[indexed][1]); + image_add_crystal(image, cr); + indexed++; + + } else { + break; + } + } while (pinkIndexer_private_data->multi + && indexed <= MAX_MULTI_LATTICE_COUNT + && reciprocalPeaks_1_per_A->peakCount >= pinkIndexer_private_data->min_peaks); + + return indexed; +} + +void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, + struct pinkIndexer_options *pinkIndexer_opts, + const DataTemplate *dtempl) +{ + if ( beam->photon_energy_from != NULL && pinkIndexer_opts->customPhotonEnergy <= 0) { + ERROR("For pinkIndexer, the photon_energy must be defined as a " + "constant in the geometry file or as a parameter (see --pinkIndexer-override-photon-energy)\n"); + return NULL; + } + if ( (det->panels[0].clen_from != NULL) && pinkIndexer_opts->refinement_type == + REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed) { + ERROR("Using center refinement makes it necessary to have the detector distance fixed in the geometry file!"); + return NULL; + } + if(cell == NULL){ + ERROR("Pink indexer needs a unit cell file to be specified!"); + return NULL; + } + + struct pinkIndexer_private_data* pinkIndexer_private_data = malloc(sizeof(struct pinkIndexer_private_data)); + allocReciprocalPeaks(&(pinkIndexer_private_data->reciprocalPeaks_1_per_A)); + pinkIndexer_private_data->intensities = malloc(MAX_PEAK_COUNT_FOR_INDEXER * sizeof(float)); + pinkIndexer_private_data->indm = *indm; + pinkIndexer_private_data->cellTemplate = cell; + pinkIndexer_private_data->threadCount = pinkIndexer_opts->thread_count; + pinkIndexer_private_data->multi = pinkIndexer_opts->multi; + pinkIndexer_private_data->min_peaks = pinkIndexer_opts->min_peaks; + pinkIndexer_private_data->no_check_indexed = pinkIndexer_opts->no_check_indexed; + pinkIndexer_private_data->maxRefinementDisbalance = pinkIndexer_opts->maxRefinementDisbalance; + + UnitCell* primitiveCell = uncenter_cell(cell, &pinkIndexer_private_data->centeringTransformation, NULL); + + //reduceCell(primitiveCell, &pinkIndexer_private_data->latticeReductionTransform); + reduceReciprocalCell(primitiveCell, &pinkIndexer_private_data->latticeReductionTransform); + + double asx, asy, asz, bsx, bsy, bsz, csx, csy, csz; + int ret = cell_get_reciprocal(primitiveCell, &asx, &asy, &asz, &bsx, &bsy, &bsz, &csx, &csy, &csz); + if (ret != 0) { + ERROR("cell_get_reciprocal did not finish properly!"); + } + + Lattice_t lattice = { .ax = asz * 1e-10, .ay = asx * 1e-10, .az = asy * 1e-10, + .bx = bsz * 1e-10, .by = bsx * 1e-10, .bz = bsy * 1e-10, + .cx = csz * 1e-10, .cy = csx * 1e-10, .cz = csy * 1e-10 }; + + float detectorDistance_m; + if ( det->panels[0].clen_from != NULL ) { + detectorDistance_m = 0.25; /* fake value */ + } else { + detectorDistance_m = det->panels[0].clen + det->panels[0].coffset; + } + + float beamEenergy_eV = beam->photon_energy; + float nonMonochromaticity = beam->bandwidth*5; + if(pinkIndexer_opts->customPhotonEnergy > 0){ + beamEenergy_eV = pinkIndexer_opts->customPhotonEnergy; + } + if(pinkIndexer_opts->customBandwidth >= 0){ + nonMonochromaticity = pinkIndexer_opts->customBandwidth; + } + + float reflectionRadius_1_per_A; + if (pinkIndexer_opts->reflectionRadius < 0) { + reflectionRadius_1_per_A = 0.02 + * sqrt(lattice.ax * lattice.ax + lattice.ay * lattice.ay + lattice.az * lattice.az); + } + else { + reflectionRadius_1_per_A = pinkIndexer_opts->reflectionRadius * 1e10; /* m^-1 to A^-1*/ + } + + if(beamEenergy_eV > 75000 && nonMonochromaticity < 0.02 && reflectionRadius_1_per_A < 0.0005){ + STATUS("Trying to index electron diffraction? It might be helpful to set a higher reflection radius (see documentation for --pinkIndexer-reflection-radius)") + } + + float divergenceAngle_deg = 0.01; //fake + + float tolerance = pinkIndexer_opts->tolerance; + Lattice_t sampleReciprocalLattice_1_per_A = lattice; + float detectorRadius_m = 0.03; //fake, only for prediction + ExperimentSettings* experimentSettings = ExperimentSettings_new(beamEenergy_eV, detectorDistance_m, + detectorRadius_m, divergenceAngle_deg, nonMonochromaticity, sampleReciprocalLattice_1_per_A, tolerance, + reflectionRadius_1_per_A); + + consideredPeaksCount_t consideredPeaksCount = pinkIndexer_opts->considered_peaks_count; + angleResolution_t angleResolution = pinkIndexer_opts->angle_resolution; + refinementType_t refinementType = pinkIndexer_opts->refinement_type; + float maxResolutionForIndexing_1_per_A = pinkIndexer_opts->maxResolutionForIndexing_1_per_A; + pinkIndexer_private_data->pinkIndexer = PinkIndexer_new(experimentSettings, consideredPeaksCount, angleResolution, + refinementType, + maxResolutionForIndexing_1_per_A); + + ExperimentSettings_delete(experimentSettings); + cell_free(primitiveCell); + + /* Flags that pinkIndexer knows about */ + *indm &= INDEXING_METHOD_MASK + | INDEXING_USE_CELL_PARAMETERS; + + return pinkIndexer_private_data; +} + +//static void reduceCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +//{ +// double ax, ay, az, bx, by, bz, cx, cy, cz; +// cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); +// +// Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; +// +// reduceLattice(&l, appliedReductionTransform); +// +// cell_set_cartesian(cell, l.ax, l.ay, l.az, +// l.bx, l.by, l.bz, +// l.cx, l.cy, l.cz); +// +// makeRightHanded(cell); +//} +// +//static void restoreCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +//{ +// +// double ax, ay, az, bx, by, bz, cx, cy, cz; +// cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); +// +// Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; +// +// restoreLattice(&l, appliedReductionTransform); +// +// cell_set_cartesian(cell, l.ax, l.ay, l.az, +// l.bx, l.by, l.bz, +// l.cx, l.cy, l.cz); +// +// makeRightHanded(cell); +//} + +static void reduceReciprocalCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +{ + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; + + reduceLattice(&l, appliedReductionTransform); + + cell_set_reciprocal(cell, l.ax, l.ay, l.az, + l.bx, l.by, l.bz, + l.cx, l.cy, l.cz); + + makeRightHanded(cell); +} + +static void restoreReciprocalCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +{ + + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; + + restoreLattice(&l, appliedReductionTransform); + + cell_set_reciprocal(cell, l.ax, l.ay, l.az, + l.bx, l.by, l.bz, + l.cx, l.cy, l.cz); + + makeRightHanded(cell); +} + +static void makeRightHanded(UnitCell *cell) +{ + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + if (!right_handed(cell)) { + cell_set_cartesian(cell, -ax, -ay, -az, -bx, -by, -bz, -cx, -cy, -cz); + } +} + +//hack for electron crystallography while crystal_set_det_shift is not working approprietly +static void update_detector(struct detector *det, double xoffs, double yoffs) +{ + int i; + + for (i = 0; i < det->n_panels; i++) { + struct panel *p = &det->panels[i]; + p->cnx += xoffs * p->res; + p->cny += yoffs * p->res; + } +} + +void pinkIndexer_cleanup(void *pp) +{ + struct pinkIndexer_private_data* pinkIndexer_private_data = (struct pinkIndexer_private_data*) pp; + + freeReciprocalPeaks(pinkIndexer_private_data->reciprocalPeaks_1_per_A); + free(pinkIndexer_private_data->intensities); + intmat_free(pinkIndexer_private_data->centeringTransformation); + PinkIndexer_delete(pinkIndexer_private_data->pinkIndexer); +} + +const char *pinkIndexer_probe(UnitCell *cell) +{ + return "pinkIndexer"; +} + +#else /* HAVE_PINKINDEXER */ + +int run_pinkIndexer(struct image *image, void *ipriv) +{ + ERROR("This copy of CrystFEL was compiled without PINKINDEXER support.\n"); + return 0; +} + +extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, + struct pinkIndexer_options *pinkIndexer_opts, + const DataTemplate *dtempl) +{ + ERROR("This copy of CrystFEL was compiled without PINKINDEXER support.\n"); + ERROR("To use PINKINDEXER indexing, recompile with PINKINDEXER.\n"); + return NULL; +} + +void pinkIndexer_cleanup(void *pp) +{ +} + +const char *pinkIndexer_probe(UnitCell *cell) +{ + return NULL; +} + +#endif /* HAVE_PINKINDEXER */ + +static void pinkIndexer_show_help() +{ + printf( +"Parameters for the PinkIndexer indexing algorithm:\n" +" --pinkIndexer-considered-peaks-count=n\n" +" Considered peaks count, 0 (fewest) to 4 (most)\n" +" Default: 4\n" +" --pinkIndexer-angle-resolution=n\n" +" Angle resolution, 0 (loosest) to 4 (most dense)\n" +" Default: 2\n" +" --pinkIndexer-refinement-type=n\n" +" Refinement type, 0 (none) to 5 (most accurate)\n" +" Default: 1\n" +" --pinkIndexer-tolerance=n\n" +" Relative tolerance of the lattice vectors.\n" +" Default 0.06\n" +" --pinkIndexer-reflection-radius=n\n" +" Radius of the reflections in reciprocal space.\n" +" Specified in 1/A. Default is 2%% of a*.\n" +" --pinkIndexer-max-resolution-for-indexing=n\n" +" Measured in 1/A\n" +" --pinkIndexer-multi Use pinkIndexers own multi indexing.\n" +" --pinkIndexer-thread-count=n\n" +" Thread count for internal parallelization \n" +" Default: 1\n" +" --pinkIndexer-no-check-indexed\n" +" Disable internal check for correct indexing\n" +" solutions\n" +" --pinkIndexer-max-refinement-disbalance=n\n" +" Maximum disbalance after refinement:\n" +" 0 (no disbalance) to 2 (extreme disbalance), default 0.4\n" +" --pinkIndexer-override-photon-energy=ev\n" +" Mean energy in eV to use for indexing.\n" +" --pinkIndexer-override-bandwidth=n\n" +" Bandwidth in (delta energy)/(mean energy) to use for indexing.\n" +" --pinkIndexer-override-visible-energy-range=min-max\n" +" Overrides photon energy and bandwidth according to a range of \n" +" energies that have high enough intensity to produce \"visible\" \n" +" Bragg spots on the detector.\n" +" Min and max range borders are separated by a minus sign (no whitespace).\n" + ); +} + + +static error_t pinkindexer_parse_arg(int key, char *arg, + struct argp_state *state) +{ + float tmp, tmp2; + struct pinkIndexer_options **opts_ptr = state->input; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct pinkIndexer_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->considered_peaks_count = 4; + (*opts_ptr)->angle_resolution = 2; + (*opts_ptr)->refinement_type = 1; + (*opts_ptr)->tolerance = 0.06; + (*opts_ptr)->maxResolutionForIndexing_1_per_A = +INFINITY; + (*opts_ptr)->thread_count = 1; + (*opts_ptr)->multi = 0; + (*opts_ptr)->no_check_indexed = 0; + (*opts_ptr)->min_peaks = 2; + (*opts_ptr)->reflectionRadius = -1; + (*opts_ptr)->customPhotonEnergy = -1; + (*opts_ptr)->customBandwidth = -1; + (*opts_ptr)->maxRefinementDisbalance = 0.4; + break; + + case 1 : + pinkIndexer_show_help(); + return EINVAL; + + case 2 : + if (sscanf(arg, "%u", &(*opts_ptr)->considered_peaks_count) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-considered-peaks-count\n"); + return EINVAL; + } + break; + + case 3 : + if (sscanf(arg, "%u", &(*opts_ptr)->angle_resolution) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-angle_resolution\n"); + return EINVAL; + } + break; + + case 4 : + if (sscanf(arg, "%u", &(*opts_ptr)->refinement_type) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-refinement-type\n"); + return EINVAL; + } + break; + + case 5 : + if (sscanf(arg, "%d", &(*opts_ptr)->thread_count) != 1) + { + ERROR("Invalid value for --pinkIndexer-thread-count\n"); + return EINVAL; + } + break; + + case 6 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxResolutionForIndexing_1_per_A) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-max-resolution-for-indexing\n"); + return EINVAL; + } + break; + + case 7 : + if (sscanf(arg, "%f", &(*opts_ptr)->tolerance) != 1) + { + ERROR("Invalid value for --pinkIndexer-tolerance\n"); + return EINVAL; + } + break; + + case 8 : + (*opts_ptr)->multi = 1; + break; + + case 9 : + (*opts_ptr)->no_check_indexed = 1; + break; + + case 10 : + if (sscanf(arg, "%f", &tmp) != 1) { + ERROR("Invalid value for --pinkIndexer-reflection-radius\n"); + return EINVAL; + } + (*opts_ptr)->reflectionRadius = tmp / 1e10; /* A^-1 to m^-1 */ + break; + + case 11 : + if (sscanf(arg, "%f", &(*opts_ptr)->customPhotonEnergy) != 1) + { + ERROR("Invalid value for --pinkIndexer-override-photon-energy\n"); + return EINVAL; + } + break; + + case 12 : + if (sscanf(arg, "%f", &(*opts_ptr)->customBandwidth) != 1) + { + ERROR("Invalid value for --pinkIndexer-override-bandwidth\n"); + return EINVAL; + } + break; + case 13 : + if (sscanf(arg, "%f-%f", &tmp, &tmp2) != 2) + { + ERROR("Invalid value for --pinkIndexer-override-visible-energy-range\n"); + return EINVAL; + } + (*opts_ptr)->customPhotonEnergy = (tmp + tmp2)/2; + (*opts_ptr)->customBandwidth = (tmp2 - tmp)/(*opts_ptr)->customPhotonEnergy; + if((*opts_ptr)->customBandwidth < 0){ + (*opts_ptr)->customBandwidth *= -1; + } + break; + case 14 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxRefinementDisbalance) != 1) + { + ERROR("Invalid value for --pinkIndexer-max-refinement-disbalance\n"); + return EINVAL; + } + } + + return 0; +} + + +static struct argp_option pinkindexer_options[] = { + + {"help-pinkindexer", 1, NULL, OPTION_NO_USAGE, + "Show options for PinkIndexer indexing algorithm", 99}, + + {"pinkIndexer-considered-peaks-count", 2, "n", OPTION_HIDDEN, NULL}, + {"pinkIndexer-cpc", 2, "n", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-angle-resolution", 3, "ang", OPTION_HIDDEN, NULL}, + {"pinkIndexer-ar", 3, "ang", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-refinement-type", 4, "t", OPTION_HIDDEN, NULL}, + {"pinkIndexer-rt", 4, "t", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-thread-count", 5, "n", OPTION_HIDDEN, NULL}, + {"pinkIndexer-tc", 5, "n", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-max-resolution-for-indexing", 6, "res", OPTION_HIDDEN, NULL}, + {"pinkIndexer-mrfi", 6, "res", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-tolerance", 7, "tol", OPTION_HIDDEN, NULL}, + {"pinkIndexer-tol", 7, "tol", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-multi", 8, NULL, OPTION_HIDDEN, NULL}, + + {"pinkIndexer-no-check-indexed", 9, NULL, OPTION_HIDDEN, NULL}, + + {"pinkIndexer-reflection-radius", 10, "r", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-override-photon-energy", 11, "ev", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-override-bandwidth", 12, "bw", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-override-visible-energy-range", 13, "overridenVisibleEnergyRange", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-max-refinement-disbalance", 14, "maxDisbalance", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp pinkIndexer_argp = { pinkindexer_options, + pinkindexer_parse_arg, + NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/indexers/pinkindexer.h b/libcrystfel/src/indexers/pinkindexer.h new file mode 100644 index 00000000..cab88a75 --- /dev/null +++ b/libcrystfel/src/indexers/pinkindexer.h @@ -0,0 +1,47 @@ +/* + * pinkindexer.h + * + * Interface to PinkIndexer + * + * Copyright © 2017-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2019 Yaroslav Gevorkov + * + * 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 . + * + */ + +#ifndef LIBCRYSTFEL_SRC_PINKINDEXER_H_ +#define LIBCRYSTFEL_SRC_PINKINDEXER_H_ + +#include + +#include "index.h" +#include "datatemplate.h" + +extern int run_pinkIndexer(struct image *image, void *ipriv); + +extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, + struct pinkIndexer_options *pinkIndexer_opts, + const DataTemplate *dtempl); + +extern void pinkIndexer_cleanup(void *pp); + +extern const char *pinkIndexer_probe(UnitCell *cell); + +#endif /* LIBCRYSTFEL_SRC_PINKINDEXER_H_ */ diff --git a/libcrystfel/src/indexers/taketwo.c b/libcrystfel/src/indexers/taketwo.c new file mode 100644 index 00000000..65265b0e --- /dev/null +++ b/libcrystfel/src/indexers/taketwo.c @@ -0,0 +1,2370 @@ +/* + * taketwo.c + * + * Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL + * + * Copyright © 2016-2017 Helen Ginn + * Copyright © 2016-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2016-2017 Helen Ginn + * 2016-2017 Thomas White + * + * 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 . + * + */ + +/** + * \file taketwo.h + + * ## Code outline + + * ### Get ready for calculation + * * Pre-calculate symmetry operations (generate_rotation_symops()) + * * Pre-calculate theoretical vectors from unit cell dimensions + * (gen_theoretical_vecs()) + * * Generate observed vectors from data (gen_observed_vecs()) + * * Match observed vectors to theoretical vectors (match_obs_to_cell_vecs()) + * + * ### Business bit + * + * ... n.b. rearranging to find all seeds in advance. + * + * * Find starting seeds (find_seeds()): + * - Loop through pairs of observed vectors + * - If they share a spot, find matching pairs of theoretical vectors + * - Remove all duplicate matches due to symmetry operations + * - For the remainder, loop through the matches and extend the seeds + * (start_seed()). + * - If it returns a membership greater than the highest member threshold, + * return the matrix to CrystFEL. + * + * * Extending a seed (start_seed()): + * - Generate a rotation matrix which matches the chosen start seed. + * - Loop through all observed vectors starting from 0. + * - Find another vector to add to the network, if available + * (find_next_index()). + * - If the index is not available, then give up if there were too many dead + * ends. Otherwise, remove the last member and pretend like that didn't + * happen, so it won't happen again. + * - Add the vector to increment the membership list. + * - If the membership number exceeds the maximum, tidy up the solution and + * return a success. + * - If the membership does not, then resume the loop and search for the + * next vector. + * + * * Finding the next member (find_next_index()): + * - Go through the observed vectors, starting from the last index + 1 to + * explore only the "new" vectors. + * - If the vector does not share a spot with the current array of vectors, + * then skip it. + * - We must loop through all the current vectors in the network, and see if + * they match the newcomer for a given matching theoretical vector. + * - We only accept a match if the rotation matrix matches the seed matrix + * for a single matching theoretical vector. + * - If it does match, we can return a success. + * + * * Tidying the solution (finish_solution()): + * - This chooses the most common rotation matrix of the bunch to choose to + * send to CrystFEL. But this should probably take the average instead, + * which is very possible. + * + * * Clean up the mess (cleanup_taketwo_obs_vecs()) + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include +#include +#include +#include +#include +#include + +#include "cell.h" +#include "cell-utils.h" +#include "index.h" +#include "taketwo.h" +#include "peaks.h" +#include "symmetry.h" + +struct taketwo_options +{ + int member_thresh; + double len_tol; + double angle_tol; + double trace_tol; +}; + +/** + * \param obsvec an observed vector between two spots + * \param matches array of matching theoretical vectors from unit cell + * \param match_num number of matches + * \param distance length of obsvec (do I need this?) + * \param her_rlp pointer to first rlp position for difference vec + * \param his_rlp pointer to second rlp position for difference vec + * + * Structure representing 3D vector between two potential Bragg peaks + * in reciprocal space, and an array of potential matching theoretical + * vectors from unit cell/centering considerations. + **/ +struct SpotVec +{ + struct rvec obsvec; + struct TheoryVec *matches; + int match_num; + int assignment; + int in_network; + double distance; + struct rvec *her_rlp; + struct rvec *his_rlp; +}; + +/** + * theoryvec + */ + +struct TheoryVec +{ + struct rvec vec; + int asym; +}; + + +/** + * seed + */ + +struct Seed +{ + int obs1; + int obs2; + int idx1; + int idx2; + double score; +}; + +struct taketwo_private +{ + IndexingMethod indm; + struct taketwo_options *opts; + UnitCell *cell; + int serial_num; /**< Serial of last image, -1 if unassigned */ + unsigned int xtal_num; /**< last number of crystals recorded */ + + struct TheoryVec *theory_vecs; /**< Theoretical vectors for given unit cell */ + unsigned int vec_count; /**< Number of theoretical vectors */ + + gsl_matrix **prevSols; /**< Previous solutions to be ignored */ + unsigned int numPrevs; /**< Previous solution count */ + double *prevScores; /**< previous solution scores */ + unsigned int *membership; /**< previous solution was success or failure */ + +}; + +/** + * Internal structure which gets passed the various functions looking after + * the indexing bits and bobs. */ +struct TakeTwoCell +{ + UnitCell *cell; /**< Contains unit cell dimensions */ + gsl_matrix **rotSymOps; + unsigned int numOps; + + struct SpotVec *obs_vecs; + struct Seed *seeds; + int seed_count; + int obs_vec_count; + + /* Options */ + int member_thresh; + double len_tol; /**< In reciprocal metres */ + double angle_tol; /**< In radians */ + double trace_tol; /**< Contains sqrt(4*(1-cos(angle))) */ + + /** A given solution to refine */ + gsl_matrix *solution; + + double x_ang; /**< Rotations in radians to apply to x axis of solution */ + double y_ang; /**< Rotations in radians to apply to y axis of solution */ + double z_ang; /**< Rotations in radians to apply to z axis of solution */ + + /**< Temporary memory always allocated for calculations */ + gsl_matrix *twiz1Tmp; + /**< Temporary memory always allocated for calculations */ + gsl_matrix *twiz2Tmp; + /**< Temporary memory always allocated for calculations */ + gsl_vector *vec1Tmp; + /**< Temporary memory always allocated for calculations */ + gsl_vector *vec2Tmp; +}; + + +/* Maximum distance between two rlp sizes to consider info for indexing */ +#define MAX_RECIP_DISTANCE (0.15*1e10) + +/* Tolerance for two lengths in reciprocal space to be considered the same */ +#define RECIP_TOLERANCE (0.0010*1e10) + +/* Threshold for network members to consider a potential solution */ +#define NETWORK_MEMBER_THRESHOLD (20) + +/* Minimum for network members to consider a potential solution */ +#define MINIMUM_MEMBER_THRESHOLD (5) + +/* Maximum dead ends for a single branch extension during indexing */ +#define MAX_DEAD_ENDS (10) + +/* Maximum observed vectors before TakeTwo gives up and deals with + * what is already there. */ +#define MAX_OBS_VECTORS 100000 + +/* Tolerance for two angles to be considered the same */ +#define ANGLE_TOLERANCE (deg2rad(0.6)) + +/* Tolerance for rot_mats_are_similar */ +#define TRACE_TOLERANCE (deg2rad(3.0)) + +/* Initial step size for refinement of solutions */ +#define ANGLE_STEP_SIZE (deg2rad(0.5)) + +/* Final required step size for refinement of solutions */ +#define ANGLE_CONVERGE_SIZE (deg2rad(0.01)) + +/* TODO: Multiple lattices */ + + +/* ------------------------------------------------------------------------ + * apologetic function + * ------------------------------------------------------------------------*/ + +void apologise() +{ + printf("Error - could not allocate memory for indexing.\n"); +} + +/* ------------------------------------------------------------------------ + * functions concerning aspects of rvec which are very likely to be + * incorporated somewhere else in CrystFEL and therefore may need to be + * deleted and references connected to a pre-existing function. (Lowest level) + * ------------------------------------------------------------------------*/ + +static struct rvec new_rvec(double new_u, double new_v, double new_w) +{ + struct rvec new_rvector; + new_rvector.u = new_u; + new_rvector.v = new_v; + new_rvector.w = new_w; + + return new_rvector; +} + +static struct rvec rvec_add_rvec(struct rvec first, struct rvec second) +{ + struct rvec diff = new_rvec(second.u + first.u, + second.v + first.v, + second.w + first.w); + + return diff; +} + + +static struct rvec diff_vec(struct rvec from, struct rvec to) +{ + struct rvec diff = new_rvec(to.u - from.u, + to.v - from.v, + to.w - from.w); + + return diff; +} + +static double sq_length(struct rvec vec) +{ + double sqlength = (vec.u * vec.u + vec.v * vec.v + vec.w * vec.w); + + return sqlength; +} + + +static double rvec_length(struct rvec vec) +{ + return sqrt(sq_length(vec)); +} + + +static void normalise_rvec(struct rvec *vec) +{ + double length = rvec_length(*vec); + vec->u /= length; + vec->v /= length; + vec->w /= length; +} + + +static double rvec_cosine(struct rvec v1, struct rvec v2) +{ + double dot_prod = v1.u * v2.u + v1.v * v2.v + v1.w * v2.w; + double v1_length = rvec_length(v1); + double v2_length = rvec_length(v2); + + double cos_theta = dot_prod / (v1_length * v2_length); + + return cos_theta; +} + + +static double rvec_angle(struct rvec v1, struct rvec v2) +{ + double cos_theta = rvec_cosine(v1, v2); + double angle = acos(cos_theta); + + return angle; +} + + +static struct rvec rvec_cross(struct rvec a, struct rvec b) +{ + struct rvec c; + + c.u = a.v*b.w - a.w*b.v; + c.v = -(a.u*b.w - a.w*b.u); + c.w = a.u*b.v - a.v*b.u; + + return c; +} + +/* +static void show_rvec(struct rvec r2) +{ + struct rvec r = r2; + normalise_rvec(&r); + STATUS("[ %.3f %.3f %.3f ]\n", r.u, r.v, r.w); +} +*/ + + +/* ------------------------------------------------------------------------ + * functions called under the core functions, still specialised (Level 3) + * ------------------------------------------------------------------------*/ + +/* cell_transform_gsl_direct() doesn't do quite what we want here. + * The matrix m should be post-multiplied by a matrix of real or reciprocal + * basis vectors (it doesn't matter which because it's just a rotation). + * M contains the basis vectors written in columns: M' = mM */ +static UnitCell *cell_post_smiley_face(UnitCell *in, gsl_matrix *m) +{ + gsl_matrix *c; + double asx, asy, asz; + double bsx, bsy, bsz; + double csx, csy, csz; + gsl_matrix *res; + UnitCell *out; + + cell_get_cartesian(in, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + + c = gsl_matrix_alloc(3, 3); + gsl_matrix_set(c, 0, 0, asx); + gsl_matrix_set(c, 1, 0, asy); + gsl_matrix_set(c, 2, 0, asz); + gsl_matrix_set(c, 0, 1, bsx); + gsl_matrix_set(c, 1, 1, bsy); + gsl_matrix_set(c, 2, 1, bsz); + gsl_matrix_set(c, 0, 2, csx); + gsl_matrix_set(c, 1, 2, csy); + gsl_matrix_set(c, 2, 2, csz); + + res = gsl_matrix_calloc(3, 3); + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, m, c, 0.0, res); + + out = cell_new_from_cell(in); + cell_set_cartesian(out, gsl_matrix_get(res, 0, 0), + gsl_matrix_get(res, 1, 0), + gsl_matrix_get(res, 2, 0), + gsl_matrix_get(res, 0, 1), + gsl_matrix_get(res, 1, 1), + gsl_matrix_get(res, 2, 1), + gsl_matrix_get(res, 0, 2), + gsl_matrix_get(res, 1, 2), + gsl_matrix_get(res, 2, 2)); + + gsl_matrix_free(res); + gsl_matrix_free(c); + return out; +} + + +static void rotation_around_axis(struct rvec c, double th, + gsl_matrix *res) +{ + double omc = 1.0 - cos(th); + double s = sin(th); + gsl_matrix_set(res, 0, 0, cos(th) + c.u*c.u*omc); + gsl_matrix_set(res, 0, 1, c.u*c.v*omc - c.w*s); + gsl_matrix_set(res, 0, 2, c.u*c.w*omc + c.v*s); + gsl_matrix_set(res, 1, 0, c.u*c.v*omc + c.w*s); + gsl_matrix_set(res, 1, 1, cos(th) + c.v*c.v*omc); + gsl_matrix_set(res, 1, 2, c.v*c.w*omc - c.u*s); + gsl_matrix_set(res, 2, 0, c.w*c.u*omc - c.v*s); + gsl_matrix_set(res, 2, 1, c.w*c.v*omc + c.u*s); + gsl_matrix_set(res, 2, 2, cos(th) + c.w*c.w*omc); +} + +/** Rotate GSL matrix by three angles along x, y and z axes */ +static void rotate_gsl_by_angles(gsl_matrix *sol, double x, double y, + double z, gsl_matrix *result) +{ + gsl_matrix *x_rot = gsl_matrix_alloc(3, 3); + gsl_matrix *y_rot = gsl_matrix_alloc(3, 3); + gsl_matrix *z_rot = gsl_matrix_alloc(3, 3); + gsl_matrix *xy_rot = gsl_matrix_alloc(3, 3); + gsl_matrix *xyz_rot = gsl_matrix_alloc(3, 3); + + struct rvec x_axis = new_rvec(1, 0, 0); + struct rvec y_axis = new_rvec(1, 0, 0); + struct rvec z_axis = new_rvec(1, 0, 0); + + rotation_around_axis(x_axis, x, x_rot); + rotation_around_axis(y_axis, y, y_rot); + rotation_around_axis(z_axis, z, z_rot); + + /* Collapse the rotations in x and y onto z */ + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, x_rot, + y_rot, 0.0, xy_rot); + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, xy_rot, + z_rot, 0.0, xyz_rot); + + /* Apply the whole rotation offset to the solution */ + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, xyz_rot, + sol, 0.0, result); + + gsl_matrix_free(x_rot); + gsl_matrix_free(y_rot); + gsl_matrix_free(z_rot); + gsl_matrix_free(xy_rot); + gsl_matrix_free(xyz_rot); +} + + +/* Rotate vector (vec1) around axis (axis) by angle theta. Find value of + * theta for which the angle between (vec1) and (vec2) is minimised. */ +static void closest_rot_mat(struct rvec vec1, struct rvec vec2, + struct rvec axis, gsl_matrix *twizzle) +{ + /* Let's have unit vectors */ + normalise_rvec(&vec1); + normalise_rvec(&vec2); + normalise_rvec(&axis); + + /* Redeclaring these to try and maintain readability and + * check-ability against the maths I wrote down */ + double a = vec2.u; double b = vec2.v; double c = vec2.w; + double p = vec1.u; double q = vec1.v; double r = vec1.w; + double x = axis.u; double y = axis.v; double z = axis.w; + + /* Components in handwritten maths online when I upload it */ + double A = a*(p*x*x - p + x*y*q + x*z*r) + + b*(p*x*y + q*y*y - q + r*y*z) + + c*(p*x*z + q*y*z + r*z*z - r); + + double B = a*(y*r - z*q) + b*(p*z - r*x) + c*(q*x - p*y); + + double tan_theta = - B / A; + double theta = atan(tan_theta); + + /* Now we have two possible solutions, theta or theta+pi + * and we need to work out which one. This could potentially be + * simplified - do we really need so many cos/sins? maybe check + * the 2nd derivative instead? */ + double cc = cos(theta); + double C = 1 - cc; + double s = sin(theta); + double occ = -cc; + double oC = 1 - occ; + double os = -s; + + double pPrime = (x*x*C+cc)*p + (x*y*C-z*s)*q + (x*z*C+y*s)*r; + double qPrime = (y*x*C+z*s)*p + (y*y*C+cc)*q + (y*z*C-x*s)*r; + double rPrime = (z*x*C-y*s)*p + (z*y*C+x*s)*q + (z*z*C+cc)*r; + + double pDbPrime = (x*x*oC+occ)*p + (x*y*oC-z*os)*q + (x*z*oC+y*os)*r; + double qDbPrime = (y*x*oC+z*os)*p + (y*y*oC+occ)*q + (y*z*oC-x*os)*r; + double rDbPrime = (z*x*oC-y*os)*p + (z*y*oC+x*os)*q + (z*z*oC+occ)*r; + + double cosAlpha = pPrime * a + qPrime * b + rPrime * c; + double cosAlphaOther = pDbPrime * a + qDbPrime * b + rDbPrime * c; + + int addPi = (cosAlphaOther > cosAlpha); + double bestAngle = theta + addPi * M_PI; + + /* Don't return an identity matrix which has been rotated by + * theta around "axis", but do assign it to twizzle. */ + rotation_around_axis(axis, bestAngle, twizzle); +} + +static double matrix_trace(gsl_matrix *a) +{ + int i; + double tr = 0.0; + + assert(a->size1 == a->size2); + for ( i=0; isize1; i++ ) { + tr += gsl_matrix_get(a, i, i); + } + return tr; +} + +static char *add_ua(const char *inp, char ua) +{ + char *pg = malloc(64); + if ( pg == NULL ) return NULL; + snprintf(pg, 63, "%s_ua%c", inp, ua); + return pg; +} + + +static char *get_chiral_holohedry(UnitCell *cell) +{ + LatticeType lattice = cell_get_lattice_type(cell); + char *pg; + char *pgout = 0; + + switch (lattice) + { + case L_TRICLINIC: + pg = "1"; + break; + + case L_MONOCLINIC: + pg = "2"; + break; + + case L_ORTHORHOMBIC: + pg = "222"; + break; + + case L_TETRAGONAL: + pg = "422"; + break; + + case L_RHOMBOHEDRAL: + pg = "3_R"; + break; + + case L_HEXAGONAL: + if ( cell_get_centering(cell) == 'H' ) { + pg = "3_H"; + } else { + pg = "622"; + } + break; + + case L_CUBIC: + pg = "432"; + break; + + default: + pg = "error"; + break; + } + + switch (lattice) + { + case L_TRICLINIC: + case L_ORTHORHOMBIC: + case L_RHOMBOHEDRAL: + case L_CUBIC: + pgout = strdup(pg); + break; + + case L_MONOCLINIC: + case L_TETRAGONAL: + case L_HEXAGONAL: + pgout = add_ua(pg, cell_get_unique_axis(cell)); + break; + + default: + break; + } + + return pgout; +} + + +static SymOpList *sym_ops_for_cell(UnitCell *cell) +{ + SymOpList *rawList; + + char *pg = get_chiral_holohedry(cell); + rawList = get_pointgroup(pg); + free(pg); + + return rawList; +} + +static int rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2, + gsl_matrix *sub, gsl_matrix *mul, + double *score, struct TakeTwoCell *cell) +{ + double tr; + + gsl_matrix_memcpy(sub, rot1); + gsl_matrix_sub(sub, rot2); /* sub = rot1 - rot2 */ + + gsl_blas_dgemm(CblasNoTrans, CblasTrans, 1.0, sub, sub, 0.0, mul); + + tr = matrix_trace(mul); + if (score != NULL) *score = tr; + + return (tr < cell->trace_tol); +} + +static int symm_rot_mats_are_similar(gsl_matrix *rot1, gsl_matrix *rot2, + struct TakeTwoCell *cell) +{ + int i; + + gsl_matrix *sub = gsl_matrix_calloc(3, 3); + gsl_matrix *mul = gsl_matrix_calloc(3, 3); + + for (i = 0; i < cell->numOps; i++) { + gsl_matrix *testRot = gsl_matrix_alloc(3, 3); + gsl_matrix *symOp = cell->rotSymOps[i]; + + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, rot1, symOp, + 0.0, testRot); + + if (rot_mats_are_similar(testRot, rot2, sub, mul, NULL, cell)) { + gsl_matrix_free(testRot); + gsl_matrix_free(sub); + gsl_matrix_free(mul); + return 1; + } + + gsl_matrix_free(testRot); + } + + gsl_matrix_free(sub); + gsl_matrix_free(mul); + + return 0; +} + +static void rotation_between_vectors(struct rvec a, struct rvec b, + gsl_matrix *twizzle) +{ + double th = rvec_angle(a, b); + struct rvec c = rvec_cross(a, b); + normalise_rvec(&c); + rotation_around_axis(c, th, twizzle); +} + + +static void rvec_to_gsl(gsl_vector *newVec, struct rvec v) +{ + gsl_vector_set(newVec, 0, v.u); + gsl_vector_set(newVec, 1, v.v); + gsl_vector_set(newVec, 2, v.w); +} + + +struct rvec gsl_to_rvec(gsl_vector *a) +{ + struct rvec v; + v.u = gsl_vector_get(a, 0); + v.v = gsl_vector_get(a, 1); + v.w = gsl_vector_get(a, 2); + return v; +} + + +/* Code me in gsl_matrix language to copy the contents of the function + * in cppxfel (IndexingSolution::createSolution). This function is quite + * intensive on the number crunching side so simple angle checks are used + * to 'pre-scan' vectors beforehand. */ +static gsl_matrix *generate_rot_mat(struct rvec obs1, struct rvec obs2, + struct rvec cell1, struct rvec cell2, + struct TakeTwoCell *cell) +{ + gsl_matrix *fullMat; + rvec_to_gsl(cell->vec1Tmp, cell2); + + normalise_rvec(&obs1); + normalise_rvec(&obs2); + normalise_rvec(&cell1); + normalise_rvec(&cell2); + + /* Rotate reciprocal space so that the first simulated vector lines up + * with the observed vector. */ + rotation_between_vectors(cell1, obs1, cell->twiz1Tmp); + + normalise_rvec(&obs1); + + /* Multiply cell2 by rotateSpotDiffMatrix --> cell2vr */ + gsl_blas_dgemv(CblasNoTrans, 1.0, cell->twiz1Tmp, cell->vec1Tmp, + 0.0, cell->vec2Tmp); + + /* Now we twirl around the firstAxisUnit until the rotated simulated + * vector matches the second observed vector as closely as possible. */ + + closest_rot_mat(gsl_to_rvec(cell->vec2Tmp), obs2, obs1, cell->twiz2Tmp); + + /* We want to apply the first matrix and then the second matrix, + * so we multiply these. */ + fullMat = gsl_matrix_calloc(3, 3); + gsl_blas_dgemm(CblasTrans, CblasTrans, 1.0, + cell->twiz1Tmp, cell->twiz2Tmp, 0.0, fullMat); + gsl_matrix_transpose(fullMat); + + return fullMat; +} + + +static int obs_vecs_share_spot(struct SpotVec *her_obs, struct SpotVec *his_obs) +{ + if ( (her_obs->her_rlp == his_obs->her_rlp) || + (her_obs->her_rlp == his_obs->his_rlp) || + (her_obs->his_rlp == his_obs->her_rlp) || + (her_obs->his_rlp == his_obs->his_rlp) ) { + return 1; + } + + return 0; +} + + +static int obs_shares_spot_w_array(struct SpotVec *obs_vecs, int test_idx, + int *members, int num) +{ + int i; + + struct SpotVec *her_obs = &obs_vecs[test_idx]; + + for ( i=0; iobs_vecs; + struct SpotVec *her_obs = &obs_vecs[her]; + struct SpotVec *his_obs = &obs_vecs[his]; + + *match_count = 0; + + double min_angle = deg2rad(2.5); + double max_angle = deg2rad(187.5); + + /* calculate angle between observed vectors */ + double obs_angle = rvec_angle(her_obs->obsvec, his_obs->obsvec); + + /* calculate angle between all potential theoretical vectors */ + + int i, j; + for ( i=0; imatch_num; i++ ) { + for ( j=0; jmatch_num; j++ ) { + double score = 0; + + struct rvec *her_match = &her_obs->matches[i].vec; + struct rvec *his_match = &his_obs->matches[j].vec; + + double her_dist = rvec_length(*her_match); + double his_dist = rvec_length(*his_match); + + double theory_angle = rvec_angle(*her_match, + *his_match); + + /* is this angle a match? */ + + double angle_diff = fabs(theory_angle - obs_angle); + + /* within basic tolerance? */ + if ( angle_diff != angle_diff || + angle_diff > cell->angle_tol ) { + continue; + } + + double add = angle_diff; + if (add == add) { + score += add * her_dist * his_dist; + } + + /* If the angles are too close to 0 + or 180, one axis ill-determined */ + if (theory_angle < min_angle || + theory_angle > max_angle) { + continue; + } + + /* check that third vector adequately completes + * triangle */ + + struct rvec theory_diff = diff_vec(*his_match, *her_match); + struct rvec obs_diff = diff_vec(his_obs->obsvec, + her_obs->obsvec); + + theory_angle = rvec_angle(*her_match, + theory_diff); + obs_angle = rvec_angle(her_obs->obsvec, obs_diff); + angle_diff = fabs(obs_angle - theory_angle); + + double diff_dist = rvec_length(obs_diff); + + if (angle_diff > ANGLE_TOLERANCE) { + continue; + } + + add = angle_diff; + if (add == add) { + score += add * her_dist * diff_dist; + } + + theory_angle = rvec_angle(*his_match, + theory_diff); + obs_angle = rvec_angle(his_obs->obsvec, obs_diff); + + if (fabs(obs_angle - theory_angle) > ANGLE_TOLERANCE) { + continue; + } + + add = angle_diff; + if (add == add) { + score += add * his_dist * diff_dist; + } + + /* we add a new seed to the array */ + size_t new_size = (*match_count + 1); + new_size *= sizeof(struct Seed); + + /* Reallocate the array to fit in another match */ + struct Seed *tmp_seeds = realloc(*seeds, new_size); + + if ( tmp_seeds == NULL ) { + apologise(); + } + + (*seeds) = tmp_seeds; + + (*seeds)[*match_count].obs1 = her; + (*seeds)[*match_count].obs2 = his; + (*seeds)[*match_count].idx1 = i; + (*seeds)[*match_count].idx2 = j; + (*seeds)[*match_count].score = score * 1000; + + (*match_count)++; + } + } + + return (*match_count > 0); +} + +/* ------------------------------------------------------------------------ + * core functions regarding the meat of the TakeTwo algorithm (Level 2) + * ------------------------------------------------------------------------*/ + +static signed int finish_solution(gsl_matrix *rot, struct SpotVec *obs_vecs, + int *obs_members, int *match_members, + int member_num, struct TakeTwoCell *cell) +{ + gsl_matrix *sub = gsl_matrix_calloc(3, 3); + gsl_matrix *mul = gsl_matrix_calloc(3, 3); + + gsl_matrix **rotations = malloc(sizeof(*rotations)* pow(member_num, 2) + - member_num); + + int i, j, count; + + count = 0; + for ( i=0; i<1; i++ ) { + for ( j=0; jobs_vecs; + struct SpotVec *her_obs = &obs_vecs[her]; + struct SpotVec *his_obs = &obs_vecs[his]; + struct rvec i_obsvec = her_obs->obsvec; + struct rvec j_obsvec = his_obs->obsvec; + struct rvec i_cellvec = her_obs->matches[her_match].vec; + struct rvec j_cellvec = his_obs->matches[his_match].vec; + + gsl_matrix *mat = generate_rot_mat(i_obsvec, j_obsvec, + i_cellvec, j_cellvec, cell); + + return mat; +} + +static int weed_duplicate_matches(struct Seed **seeds, + int *match_count, struct TakeTwoCell *cell) +{ + int num_occupied = 0; + gsl_matrix **old_mats = calloc(*match_count, sizeof(gsl_matrix *)); + + if (old_mats == NULL) + { + apologise(); + return 0; + } + + signed int i, j; + + int duplicates = 0; + + /* Now we weed out the self-duplicates from the remaining batch */ + + for (i = *match_count - 1; i >= 0; i--) { + int her_match = (*seeds)[i].idx1; + int his_match = (*seeds)[i].idx2; + + gsl_matrix *mat; + mat = rot_mat_from_indices((*seeds)[i].obs1, (*seeds)[i].obs2, + her_match, his_match, cell); + + int found = 0; + + for (j = 0; j < num_occupied; j++) { + if (old_mats[j] && mat && + symm_rot_mats_are_similar(old_mats[j], mat, cell)) + { + // we have found a duplicate, so flag as bad. + (*seeds)[i].idx1 = -1; + (*seeds)[i].idx2 = -1; + found = 1; + + duplicates++; + + gsl_matrix_free(mat); + break; + } + } + + if (!found) { + // we have not found a duplicate, add to list. + old_mats[num_occupied] = mat; + num_occupied++; + } + } + + for (i = 0; i < num_occupied; i++) { + if (old_mats[i]) { + gsl_matrix_free(old_mats[i]); + } + } + + free(old_mats); + + return 1; +} + +static signed int find_next_index(gsl_matrix *rot, int *obs_members, + int *match_members, int start, int member_num, + int *match_found, struct TakeTwoCell *cell) +{ + struct SpotVec *obs_vecs = cell->obs_vecs; + int obs_vec_count = cell->obs_vec_count; + gsl_matrix *sub = gsl_matrix_calloc(3, 3); + gsl_matrix *mul = gsl_matrix_calloc(3, 3); + + int i, j, k; + + for ( i=start; imatches[match_members[j]].vec; + + struct rvec me_obs = me->obsvec; + struct rvec you_obs = you->obsvec; + + int one_is_okay = 0; + + /* Loop through all possible theoretical vector + * matches for the newcomer.. */ + + for ( k=0; kmatch_num; k++ ) { + + gsl_matrix *test_rot; + + struct rvec me_cell = me->matches[k].vec; + + test_rot = generate_rot_mat(me_obs, + you_obs, me_cell, you_cell, + cell); + + double trace = 0; + int ok = rot_mats_are_similar(rot, test_rot, + sub, mul, &trace, cell); + + gsl_matrix_free(test_rot); + + if (ok) { + one_is_okay = 1; + + /* We are only happy if the vector + * matches for only one kind of + * theoretical vector. We don't want to + * accept mixtures of theoretical vector + * matches. */ + if (matched >= 0 && k == matched) { + *match_found = k; + } else if (matched < 0) { + matched = k; + } else { + one_is_okay = 0; + break; + } + } + } + + if (!one_is_okay) { + all_ok = 0; + break; + } + } + + + if (all_ok) { + gsl_matrix_free(sub); + gsl_matrix_free(mul); + return i; + } + } + + /* give up. */ + gsl_matrix_free(sub); + gsl_matrix_free(mul); + return -1; +} + +/** + * Reward target function for refining solution to all vectors in a + * given image. Sum of exponentials of the negative distances, which + * means that the reward decays as the distance from the nearest + * theoretical vector reduces. */ +static double obs_to_sol_score(struct TakeTwoCell *ttCell) +{ + double total = 0; + int count = 0; + int i; + gsl_matrix *solution = ttCell->solution; + gsl_matrix *full_rot = gsl_matrix_alloc(3, 3); + rotate_gsl_by_angles(solution, ttCell->x_ang, ttCell->y_ang, + ttCell->z_ang, full_rot); + + for (i = 0; i < ttCell->obs_vec_count; i++) + { + struct rvec *obs = &ttCell->obs_vecs[i].obsvec; + rvec_to_gsl(ttCell->vec1Tmp, *obs); + + /* Rotate all the observed vectors by the modified soln */ + /* ttCell->vec2Tmp = 1.0 * full_rot * ttCell->vec1Tmp */ + gsl_blas_dgemv(CblasTrans, 1.0, full_rot, ttCell->vec1Tmp, + 0.0, ttCell->vec2Tmp); + struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp); + + int j = ttCell->obs_vecs[i].assignment; + + if (j < 0) continue; + + struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec; + struct rvec diff = diff_vec(rotated, *match); + + double length = rvec_length(diff); + + double addition = exp(-(1 / RECIP_TOLERANCE) * length); + total += addition; + count++; + } + + total /= (double)-count; + + gsl_matrix_free(full_rot); + + return total; +} + +/** + * Matches every observed vector in the image to its closest theoretical + * neighbour after applying the rotation matrix, in preparation for + * refining the rotation matrix to match these. */ +static void match_all_obs_to_sol(struct TakeTwoCell *ttCell) +{ + int i, j; + double total = 0; + int count = 0; + gsl_matrix *solution = ttCell->solution; + + for (i = 0; i < ttCell->obs_vec_count; i++) + { + struct rvec *obs = &ttCell->obs_vecs[i].obsvec; + rvec_to_gsl(ttCell->vec1Tmp, *obs); + + /* ttCell->vec2Tmp = 1.0 * solution * ttCell->vec1Tmp */ + gsl_blas_dgemv(CblasTrans, 1.0, solution, ttCell->vec1Tmp, + 0.0, ttCell->vec2Tmp); + struct rvec rotated = gsl_to_rvec(ttCell->vec2Tmp); + + double smallest = FLT_MAX; + int assigned = -1; + + for (j = 0; j < ttCell->obs_vecs[i].match_num; j++) + { + struct rvec *match = &ttCell->obs_vecs[i].matches[j].vec; + struct rvec diff = diff_vec(rotated, *match); + + double length = rvec_length(diff); + if (length < smallest) + { + smallest = length; + assigned = j; + } + } + + ttCell->obs_vecs[i].assignment = assigned; + + if (smallest != FLT_MAX) + { + double addition = exp(-(1 / RECIP_TOLERANCE) * smallest); + total += addition; + count++; + + } + } + + total /= (double)count; +} + +/** + * Refines a matrix against all of the observed vectors against their + * closest theoretical neighbour, by perturbing the matrix along the principle + * axes until it maximises a reward function consisting of the sum of + * the distances of individual observed vectors to their closest + * theoretical neighbour. Reward function means that noise and alternative + * lattices do not dominate the equation! + **/ +static void refine_solution(struct TakeTwoCell *ttCell) +{ + match_all_obs_to_sol(ttCell); + + int i, j, k; + const int total = 3 * 3 * 3; + const int middle = (total - 1) / 2; + + struct rvec steps[total]; + double start = obs_to_sol_score(ttCell); + const int max_tries = 100; + + int count = 0; + double size = ANGLE_STEP_SIZE; + + /* First we create our combinations of steps */ + for (i = -1; i <= 1; i++) { + for (j = -1; j <= 1; j++) { + for (k = -1; k <= 1; k++) { + struct rvec vec = new_rvec(i, j, k); + steps[count] = vec; + count++; + } + } + } + + struct rvec current = new_rvec(ttCell->x_ang, ttCell->y_ang, + ttCell->z_ang); + + double best = start; + count = 0; + + while (size > ANGLE_CONVERGE_SIZE && count < max_tries) + { + struct rvec sized[total]; + + int best_num = middle; + for (i = 0; i < total; i++) + { + struct rvec sized_step = steps[i]; + sized_step.u *= size; + sized_step.v *= size; + sized_step.w *= size; + + struct rvec new_angles = rvec_add_rvec(current, + sized_step); + + sized[i] = new_angles; + + ttCell->x_ang = sized[i].u; + ttCell->y_ang = sized[i].v; + ttCell->z_ang = sized[i].w; + + double score = obs_to_sol_score(ttCell); + + if (score < best) + { + best = score; + best_num = i; + } + } + + if (best_num == middle) + { + size /= 2; + } + + current = sized[best_num]; + count++; + } + + ttCell->x_ang = 0; + ttCell->y_ang = 0; + ttCell->z_ang = 0; + + gsl_matrix *tmp = gsl_matrix_alloc(3, 3); + rotate_gsl_by_angles(ttCell->solution, current.u, + current.v, current.w, tmp); + gsl_matrix_free(ttCell->solution); + ttCell->solution = tmp; +} + + +static unsigned int grow_network(gsl_matrix *rot, int obs_idx1, int obs_idx2, + int match_idx1, int match_idx2, + struct TakeTwoCell *cell) +{ + + struct SpotVec *obs_vecs = cell->obs_vecs; + int obs_vec_count = cell->obs_vec_count; + int *obs_members; + int *match_members; + + /* Clear the in_network status of all vectors to start */ + int i; + for (i = 0; i < obs_vec_count; i++) + { + obs_vecs[i].in_network = 0; + } + + /* indices of members of the self-consistent network of vectors */ + obs_members = malloc((cell->member_thresh+3)*sizeof(int)); + match_members = malloc((cell->member_thresh+3)*sizeof(int)); + if ( (obs_members == NULL) || (match_members == NULL) ) { + apologise(); + return 0; + } + + /* initialise the ones we know already */ + obs_members[0] = obs_idx1; + obs_members[1] = obs_idx2; + match_members[0] = match_idx1; + match_members[1] = match_idx2; + int member_num = 2; + + /* counter for dead ends which must not exceed MAX_DEAD_ENDS + * before it is reset in an additional branch */ + int dead_ends = 0; + + /* we start from 0 */ + int start = 0; + + while ( 1 ) { + + if (start > obs_vec_count) { + free(obs_members); + free(match_members); + return 0; + } + + int match_found = -1; + + signed int next_index = find_next_index(rot, obs_members, + match_members, + 0, member_num, + &match_found, cell); + + if ( member_num < 2 ) { + free(obs_members); + free(match_members); + return 0; + } + + if ( next_index < 0 ) { + /* If there have been too many dead ends, give up + * on indexing altogether. + **/ + if ( dead_ends > MAX_DEAD_ENDS ) { + break; + } + + /* We have not had too many dead ends. Try removing + the last member and continue. */ + member_num--; + dead_ends++; + + continue; + } + + /* Elongation of the network was successful */ + obs_vecs[next_index].in_network = 1; + obs_members[member_num] = next_index; + match_members[member_num] = match_found; + + member_num++; + + /* If member_num is high enough, we want to return a yes */ + if ( member_num > cell->member_thresh ) break; + + } + + finish_solution(rot, obs_vecs, obs_members, + match_members, member_num, cell); + + free(obs_members); + free(match_members); + + return ( member_num ); +} + + +static unsigned int start_seed(int i, int j, int i_match, int j_match, + gsl_matrix **rotation, struct TakeTwoCell *cell) +{ + struct SpotVec *obs_vecs = cell->obs_vecs; + + gsl_matrix *rot_mat; + + rot_mat = generate_rot_mat(obs_vecs[i].obsvec, + obs_vecs[j].obsvec, + obs_vecs[i].matches[i_match].vec, + obs_vecs[j].matches[j_match].vec, + cell); + + /* Try to expand this rotation matrix to a larger network */ + + int member_num = grow_network(rot_mat, i, j, i_match, j_match, + cell); + + /* return this matrix and if it was immediately successful */ + *rotation = rot_mat; + + return member_num; +} + +static int sort_seed_by_score(const void *av, const void *bv) +{ + struct Seed *a = (struct Seed *)av; + struct Seed *b = (struct Seed *)bv; + return a->score > b->score; +} + +static void remove_old_solutions(struct TakeTwoCell *cell, + struct taketwo_private *tp) +{ + int duplicates = 0; + struct Seed *seeds = cell->seeds; + unsigned int total = cell->seed_count; + + /* First we remove duplicates with previous solutions */ + + int i, j; + for (i = total - 1; i >= 0; i--) { + int her_match = seeds[i].idx1; + int his_match = seeds[i].idx2; + + gsl_matrix *mat; + mat = rot_mat_from_indices(seeds[i].obs1, seeds[i].obs2, + her_match, his_match, cell); + + if (mat == NULL) + { + continue; + } + + for (j = 0; j < tp->numPrevs; j++) + { + int sim = symm_rot_mats_are_similar(tp->prevSols[j], + mat, cell); + + /* Found a duplicate with a previous solution */ + if (sim) + { + seeds[i].idx1 = -1; + seeds[i].idx2 = -1; + duplicates++; + break; + } + } + + gsl_matrix_free(mat); + } + +// STATUS("Removing %i duplicates due to prev solutions.\n", duplicates); +} + +static int find_seeds(struct TakeTwoCell *cell, struct taketwo_private *tp) +{ + struct SpotVec *obs_vecs = cell->obs_vecs; + int obs_vec_count = cell->obs_vec_count; + + /* loop round pairs of vectors to try and find a suitable + * seed to start building a self-consistent network of vectors + */ + int i, j; + + for ( i=1; i + MAX_RECIP_DISTANCE && cell->seed_count > 100) { + continue; + } + + /** Check to see if there is a shared spot - opportunity + * for optimisation by generating a look-up table + * by spot instead of by vector. + */ + int shared = obs_vecs_share_spot(&obs_vecs[i], + &obs_vecs[j]); + if ( !shared ) continue; + + /* cell vector index matches stored in i, j and total + * number stored in int matches. + */ + int seed_num = 0; + struct Seed *seeds = NULL; + + /* Check to see if any angles match from the cell + * vectors */ + obs_vecs_match_angles(i, j, &seeds, &seed_num, cell); + + if (seed_num == 0) + { + /* Nothing to clean up here */ + continue; + } + + /* Weed out the duplicate seeds (from symmetric + * reflection pairs) */ + weed_duplicate_matches(&seeds, &seed_num, cell); + + /* Add all the new seeds to the full list */ + + size_t new_size = cell->seed_count + seed_num; + new_size *= sizeof(struct Seed); + + struct Seed *tmp = realloc(cell->seeds, new_size); + + if (tmp == NULL) { + apologise(); + } + + cell->seeds = tmp; + + for (int i = 0; i < seed_num; i++) + { + if (seeds[i].idx1 < 0 || seeds[i].idx2 < 0) + { + continue; + } + + cell->seeds[cell->seed_count] = seeds[i]; + cell->seed_count++; + } + + free(seeds); + } + } + + qsort(cell->seeds, cell->seed_count, sizeof(struct Seed), + sort_seed_by_score); + + + return 1; +} + +static unsigned int start_seeds(gsl_matrix **rotation, struct TakeTwoCell *cell) +{ + struct Seed *seeds = cell->seeds; + int seed_num = cell->seed_count; + int member_num = 0; + int max_members = 0; + gsl_matrix *rot = NULL; + + /* We have seeds! Pass each of them through the seed-starter */ + /* If a seed has the highest achieved membership, make note...*/ + int k; + for ( k=0; k max_members) + { + if ( *rotation != NULL ) { + /* Free previous best */ + gsl_matrix_free(*rotation); + } + *rotation = rot; + max_members = member_num; + } else { + gsl_matrix_free(rot); + } + + if (member_num >= NETWORK_MEMBER_THRESHOLD) { + free(seeds); + return max_members; + } + } + + free(seeds); + + return max_members; +} + + +static void set_gsl_matrix(gsl_matrix *mat, + double asx, double asy, double asz, + double bsx, double bsy, double bsz, + double csx, double csy, double csz) +{ + gsl_matrix_set(mat, 0, 0, asx); + gsl_matrix_set(mat, 0, 1, asy); + gsl_matrix_set(mat, 0, 2, asz); + gsl_matrix_set(mat, 1, 0, bsx); + gsl_matrix_set(mat, 1, 1, bsy); + gsl_matrix_set(mat, 1, 2, bsz); + gsl_matrix_set(mat, 2, 0, csx); + gsl_matrix_set(mat, 2, 1, csy); + gsl_matrix_set(mat, 2, 2, csz); +} + +static int generate_rotation_sym_ops(struct TakeTwoCell *ttCell) +{ + SymOpList *rawList = sym_ops_for_cell(ttCell->cell); + + /* Now we must convert these into rotation matrices rather than hkl + * transformations (affects triclinic, monoclinic, rhombohedral and + * hexagonal space groups only) */ + + double asx, asy, asz; + double bsx, bsy, bsz; + double csx, csy, csz; + + gsl_matrix *recip = gsl_matrix_alloc(3, 3); + gsl_matrix *cart = gsl_matrix_alloc(3, 3); + + cell_get_reciprocal(ttCell->cell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + + set_gsl_matrix(recip, asx, asy, asz, + asx, bsy, bsz, + csx, csy, csz); + + cell_get_cartesian(ttCell->cell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + + set_gsl_matrix(cart, asx, bsx, csx, + asy, bsy, csy, + asz, bsz, csz); + + + int i, j, k; + int numOps = num_equivs(rawList, NULL); + + ttCell->rotSymOps = malloc(numOps * sizeof(gsl_matrix *)); + ttCell->numOps = numOps; + + if (ttCell->rotSymOps == NULL) { + apologise(); + return 0; + } + + for (i = 0; i < numOps; i++) + { + gsl_matrix *symOp = gsl_matrix_alloc(3, 3); + IntegerMatrix *op = get_symop(rawList, NULL, i); + + for (j = 0; j < 3; j++) { + for (k = 0; k < 3; k++) { + gsl_matrix_set(symOp, j, k, intmat_get(op, j, k)); + } + } + + gsl_matrix *first = gsl_matrix_calloc(3, 3); + gsl_matrix *second = gsl_matrix_calloc(3, 3); + + /* Each equivalence is of the form: + cartesian * symOp * reciprocal. + First multiplication: symOp * reciprocal */ + + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, + 1.0, symOp, recip, + 0.0, first); + + /* Second multiplication: cartesian * first */ + + gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, + 1.0, cart, first, + 0.0, second); + + ttCell->rotSymOps[i] = second; + + gsl_matrix_free(symOp); + gsl_matrix_free(first); + } + + gsl_matrix_free(cart); + gsl_matrix_free(recip); + + free_symoplist(rawList); + + return 1; +} + +struct sortme +{ + struct TheoryVec v; + double dist; +}; + +static int sort_theory_distances(const void *av, const void *bv) +{ + struct sortme *a = (struct sortme *)av; + struct sortme *b = (struct sortme *)bv; + return a->dist > b->dist; +} + +static int match_obs_to_cell_vecs(struct TheoryVec *cell_vecs, int cell_vec_count, + struct TakeTwoCell *cell) +{ + struct SpotVec *obs_vecs = cell->obs_vecs; + int obs_vec_count = cell->obs_vec_count; + int i, j; + + for ( i=0; i cell->len_tol ) continue; + + /* we have a match, add to array! */ + + size_t new_size = (count+1)*sizeof(struct sortme); + for_sort = realloc(for_sort, new_size); + + if ( for_sort == NULL ) return 0; + + for_sort[count].v = cell_vecs[j]; + for_sort[count].dist = dist_diff; + count++; + + } + + /* Pointers to relevant things */ + + struct TheoryVec **match_array; + int *match_count; + + match_array = &(obs_vecs[i].matches); + match_count = &(obs_vecs[i].match_num); + + /* Sort in order to get most agreeable matches first */ + qsort(for_sort, count, sizeof(struct sortme), sort_theory_distances); + *match_array = malloc(count*sizeof(struct TheoryVec)); + *match_count = count; + for ( j=0; jdistance > b->distance; +} + +static int gen_observed_vecs(struct rvec *rlps, int rlp_count, + struct TakeTwoCell *cell) +{ + int i, j; + int count = 0; + + /* maximum distance squared for comparisons */ + double max_sq_length = pow(MAX_RECIP_DISTANCE, 2); + + for ( i=0; i max_sq_length ) continue; + + count++; + + struct SpotVec *temp_obs_vecs; + temp_obs_vecs = realloc(cell->obs_vecs, + count*sizeof(struct SpotVec)); + + if ( temp_obs_vecs == NULL ) { + return 0; + } else { + cell->obs_vecs = temp_obs_vecs; + + /* initialise all SpotVec struct members */ + + struct SpotVec spot_vec; + spot_vec.obsvec = diff; + spot_vec.distance = sqrt(sqlength); + spot_vec.matches = NULL; + spot_vec.assignment = -1; + spot_vec.match_num = 0; + spot_vec.her_rlp = &rlps[i]; + spot_vec.his_rlp = &rlps[j]; + + cell->obs_vecs[count - 1] = spot_vec; + } + } + } + + /* Sort such that the shortest distances are searched first. */ + qsort(cell->obs_vecs, count, sizeof(struct SpotVec), compare_spot_vecs); + + cell->obs_vec_count = count; + + return 1; +} + + +static int gen_theoretical_vecs(UnitCell *cell, struct TheoryVec **cell_vecs, + unsigned int *vec_count) +{ + double a, b, c, alpha, beta, gamma; + int h_max, k_max, l_max; + double asx, asy, asz; + double bsx, bsy, bsz; + double csx, csy, csz; + + cell_get_reciprocal(cell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + + SymOpList *rawList = sym_ops_for_cell(cell); + + cell_get_parameters(cell, &a, &b, &c, &alpha, &beta, &gamma); + + /* find maximum Miller (h, k, l) indices for a given resolution */ + h_max = MAX_RECIP_DISTANCE * a; + k_max = MAX_RECIP_DISTANCE * b; + l_max = MAX_RECIP_DISTANCE * c; + + int h, k, l; + int _h, _k, _l; + int count = 0; + + for ( h=-h_max; h<=+h_max; h++ ) { + for ( k=-k_max; k<=+k_max; k++ ) { + for ( l=-l_max; l<=+l_max; l++ ) { + + struct rvec cell_vec; + + /* Exclude systematic absences from centering concerns */ + if ( forbidden_reflection(cell, h, k, l) ) continue; + + int asymmetric = 0; + get_asymm(rawList, h, k, l, &_h, &_k, &_l); + + if (h == _h && k == _k && l == _l) { + asymmetric = 1; + } + + cell_vec.u = h*asx + k*bsx + l*csx; + cell_vec.v = h*asy + k*bsy + l*csy; + cell_vec.w = h*asz + k*bsz + l*csz; + + struct TheoryVec theory; + theory.vec = cell_vec; + theory.asym = asymmetric; + + /* add this to our array - which may require expanding */ + count++; + + struct TheoryVec *temp_cell_vecs; + temp_cell_vecs = realloc(*cell_vecs, + count*sizeof(struct TheoryVec)); + + if ( temp_cell_vecs == NULL ) { + return 0; + } else { + *cell_vecs = temp_cell_vecs; + (*cell_vecs)[count - 1] = theory; + } + } + } + } + + *vec_count = count; + + free_symoplist(rawList); + + return 1; +} + + +/* ------------------------------------------------------------------------ + * cleanup functions - called from run_taketwo(). + * ------------------------------------------------------------------------*/ + +static void cleanup_taketwo_obs_vecs(struct SpotVec *obs_vecs, + int obs_vec_count) +{ + int i; + for ( i=0; inumOps; i++ ) { + gsl_matrix_free(ttCell->rotSymOps[i]); + } + free(ttCell->rotSymOps); + + cleanup_taketwo_obs_vecs(ttCell->obs_vecs, + ttCell->obs_vec_count); + + gsl_vector_free(ttCell->vec1Tmp); + gsl_vector_free(ttCell->vec2Tmp); + gsl_matrix_free(ttCell->twiz1Tmp); + gsl_matrix_free(ttCell->twiz2Tmp); +} + + +/* ------------------------------------------------------------------------ + * external functions - top level functions (Level 1) + * ------------------------------------------------------------------------*/ + +/** + * @cell: target unit cell + * @rlps: spot positions on detector back-projected into recripocal + * space depending on detector geometry etc. + * @rlp_count: number of rlps in rlps array. + * @rot: pointer to be given an assignment (hopefully) if indexing is + * successful. + **/ +static UnitCell *run_taketwo(UnitCell *cell, const struct taketwo_options *opts, + struct rvec *rlps, int rlp_count, + struct taketwo_private *tp) +{ + UnitCell *result; + int success = 0; + gsl_matrix *solution = NULL; + + /* Initialise TakeTwoCell */ + struct TakeTwoCell ttCell; + ttCell.cell = cell; + ttCell.seeds = NULL; + ttCell.seed_count = 0; + ttCell.rotSymOps = NULL; + ttCell.obs_vecs = NULL; + ttCell.twiz1Tmp = gsl_matrix_calloc(3, 3); + ttCell.twiz2Tmp = gsl_matrix_calloc(3, 3); + ttCell.vec1Tmp = gsl_vector_calloc(3); + ttCell.vec2Tmp = gsl_vector_calloc(3); + ttCell.numOps = 0; + ttCell.obs_vec_count = 0; + ttCell.solution = NULL; + ttCell.x_ang = 0; + ttCell.y_ang = 0; + ttCell.z_ang = 0; + + success = generate_rotation_sym_ops(&ttCell); + if ( !success ) { + cleanup_taketwo_cell(&ttCell); + return NULL; + } + + success = gen_observed_vecs(rlps, rlp_count, &ttCell); + if ( !success ) { + cleanup_taketwo_cell(&ttCell); + return NULL; + } + + if ( opts->member_thresh < 0 ) { + ttCell.member_thresh = NETWORK_MEMBER_THRESHOLD; + } else { + ttCell.member_thresh = opts->member_thresh; + } + + if ( opts->len_tol < 0.0 ) { + ttCell.len_tol = RECIP_TOLERANCE; + } else { + ttCell.len_tol = opts->len_tol; /* Already in m^-1 */ + } + + if ( opts->angle_tol < 0.0 ) { + ttCell.angle_tol = ANGLE_TOLERANCE; + } else { + ttCell.angle_tol = opts->angle_tol; /* Already in radians */ + } + + if ( opts->trace_tol < 0.0 ) { + ttCell.trace_tol = sqrt(4.0*(1.0-cos(TRACE_TOLERANCE))); + } else { + ttCell.trace_tol = sqrt(4.0*(1.0-cos(opts->trace_tol))); + } + + success = match_obs_to_cell_vecs(tp->theory_vecs, tp->vec_count, + &ttCell); + + if ( !success ) { + cleanup_taketwo_cell(&ttCell); + return NULL; + } + + /* Find all the seeds, then take each one and extend them, returning + * a solution if it exceeds the NETWORK_MEMBER_THRESHOLD. */ + find_seeds(&ttCell, tp); + remove_old_solutions(&ttCell, tp); + unsigned int members = start_seeds(&solution, &ttCell); + + if ( solution == NULL ) { + cleanup_taketwo_cell(&ttCell); + return NULL; + } + + /* If we have a solution, refine against vectors in the entire image */ + ttCell.solution = solution; + refine_solution(&ttCell); + solution = ttCell.solution; + double score = obs_to_sol_score(&ttCell); + + /* Add the current solution to the previous solutions list */ + int new_size = (tp->numPrevs + 1) * sizeof(gsl_matrix *); + gsl_matrix **tmp = realloc(tp->prevSols, new_size); + double *tmpScores = realloc(tp->prevScores, + (tp->numPrevs + 1) * sizeof(double)); + unsigned int *tmpSuccesses; + tmpSuccesses = realloc(tp->membership, + (tp->numPrevs + 1) * sizeof(unsigned int)); + + if (!tmp) { + apologise(); + } + + tp->prevSols = tmp; + tp->prevScores = tmpScores; + tp->membership = tmpSuccesses; + + tp->prevSols[tp->numPrevs] = solution; + tp->prevScores[tp->numPrevs] = score; + tp->membership[tp->numPrevs] = members; + tp->numPrevs++; + + /* Prepare the solution for CrystFEL friendliness */ + result = cell_post_smiley_face(cell, solution); + cleanup_taketwo_cell(&ttCell); + + return result; +} + +/* Cleans up the per-image information for taketwo */ + +static void partial_taketwo_cleanup(struct taketwo_private *tp) +{ + if (tp->prevSols != NULL) + { + for (int i = 0; i < tp->numPrevs; i++) + { + gsl_matrix_free(tp->prevSols[i]); + } + + free(tp->prevSols); + } + + free(tp->prevScores); + free(tp->membership); + tp->prevScores = NULL; + tp->membership = NULL; + tp->xtal_num = 0; + tp->numPrevs = 0; + tp->prevSols = NULL; + +} + +/* CrystFEL interface hooks */ + +int taketwo_index(struct image *image, void *priv) +{ + Crystal *cr; + UnitCell *cell; + struct rvec *rlps; + int n_rlps = 0; + int i; + struct taketwo_private *tp = (struct taketwo_private *)priv; + + /* Check serial number against previous for solution tracking */ + int this_serial = image->serial; + + if (tp->serial_num == this_serial) + { + tp->xtal_num = image->n_crystals; + } + else + { + /* + for (i = 0; i < tp->numPrevs; i++) + { + STATUS("score, %i, %.5f, %i\n", + this_serial, tp->prevScores[i], + tp->membership[i]); + } + */ + + partial_taketwo_cleanup(tp); + tp->serial_num = this_serial; + tp->xtal_num = image->n_crystals; + } + + /* + STATUS("Indexing %i with %i attempts, %i crystals\n", this_serial, tp->attempts, + image->n_crystals); + */ + + rlps = malloc((image_feature_count(image->features)+1)*sizeof(struct rvec)); + for ( i=0; ifeatures); i++ ) { + struct imagefeature *pk = image_get_feature(image->features, i); + if ( pk == NULL ) continue; + rlps[n_rlps].u = pk->rx; + rlps[n_rlps].v = pk->ry; + rlps[n_rlps].w = pk->rz; + n_rlps++; + } + rlps[n_rlps].u = 0.0; + rlps[n_rlps].v = 0.0; + rlps[n_rlps++].w = 0.0; + + cell = run_taketwo(tp->cell, tp->opts, rlps, n_rlps, tp); + free(rlps); + if ( cell == NULL ) return 0; + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + + crystal_set_cell(cr, cell); + + image_add_crystal(image, cr); + + return 1; +} + + +void *taketwo_prepare(IndexingMethod *indm, struct taketwo_options *opts, + UnitCell *cell) +{ + struct taketwo_private *tp; + + /* Flags that TakeTwo knows about */ + *indm &= INDEXING_METHOD_MASK | INDEXING_USE_LATTICE_TYPE + | INDEXING_USE_CELL_PARAMETERS; + + if ( !( (*indm & INDEXING_USE_LATTICE_TYPE) + && (*indm & INDEXING_USE_CELL_PARAMETERS)) ) + { + ERROR("TakeTwo indexing requires cell and lattice type " + "information.\n"); + return NULL; + } + + if ( cell == NULL ) { + ERROR("TakeTwo indexing requires a unit cell.\n"); + return NULL; + } + + STATUS("*******************************************************************\n"); + STATUS("***** Welcome to TakeTwo *****\n"); + STATUS("*******************************************************************\n"); + STATUS(" If you use these indexing results, please keep a roof\n"); + STATUS(" over the author's head by citing this paper.\n\n"); + + STATUS("o o o o o o o o o o o o\n"); + STATUS(" o o o o o o o o o o o \n"); + STATUS("o o\n"); + STATUS(" o The citation is: o \n"); + STATUS("o Ginn et al., Acta Cryst. (2016). D72, 956-965 o\n"); + STATUS(" o Thank you! o \n"); + STATUS("o o\n"); + STATUS(" o o o o o o o o o o o \n"); + STATUS("o o o o o o o o o o o o\n"); + + + STATUS("\n"); + + tp = malloc(sizeof(struct taketwo_private)); + if ( tp == NULL ) return NULL; + + tp->cell = cell; + tp->indm = *indm; + tp->serial_num = -1; + tp->xtal_num = 0; + tp->prevSols = NULL; + tp->numPrevs = 0; + tp->prevScores = NULL; + tp->membership = NULL; + tp->vec_count = 0; + tp->theory_vecs = NULL; + + gen_theoretical_vecs(cell, &tp->theory_vecs, &tp->vec_count); + + return tp; +} + + +void taketwo_cleanup(IndexingPrivate *pp) +{ + struct taketwo_private *tp = (struct taketwo_private *)pp; + + partial_taketwo_cleanup(tp); + free(tp->theory_vecs); + + free(tp); +} + + +const char *taketwo_probe(UnitCell *cell) +{ + if ( cell_has_parameters(cell) ) return "taketwo"; + return NULL; +} + + +static void taketwo_show_help() +{ + printf("Parameters for the TakeTwo indexing algorithm:\n" +" --taketwo-member-threshold\n" +" Minimum number of members in network\n" +" --taketwo-len-tolerance\n" +" Reciprocal space length tolerance (1/A)\n" +" --taketwo-angle-tolerance\n" +" Reciprocal space angle tolerance (in degrees)\n" +" --taketwo-trace-tolerance\n" +" Rotation matrix equivalence tolerance (in degrees)\n" +); +} + + +static error_t taketwo_parse_arg(int key, char *arg, + struct argp_state *state) +{ + struct taketwo_options **opts_ptr = state->input; + float tmp; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct taketwo_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->member_thresh = -1.0; + (*opts_ptr)->len_tol = -1.0; + (*opts_ptr)->angle_tol = -1.0; + (*opts_ptr)->trace_tol = -1.0; + break; + + case 1 : + taketwo_show_help(); + return EINVAL; + + case 2 : + if ( sscanf(arg, "%i", &(*opts_ptr)->member_thresh) != 1 ) + { + ERROR("Invalid value for --taketwo-member-threshold\n"); + return EINVAL; + } + break; + + case 3 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-len-tol\n"); + return EINVAL; + } + (*opts_ptr)->len_tol = tmp * 1e10; /* Convert to m^-1 */ + break; + + case 4 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-angle-tol\n"); + return EINVAL; + } + (*opts_ptr)->angle_tol = deg2rad(tmp); + break; + + case 5 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-trace-tol\n"); + return EINVAL; + } + (*opts_ptr)->trace_tol = deg2rad(tmp); + break; + + default : + return ARGP_ERR_UNKNOWN; + + } + + return 0; +} + + +static struct argp_option taketwo_options[] = { + + {"help-taketwo", 1, NULL, OPTION_NO_USAGE, + "Show options for TakeTwo indexing algorithm", 99}, + + {"taketwo-member-threshold", 2, "n", OPTION_HIDDEN, NULL}, + {"taketwo-len-tolerance", 3, "one_over_A", OPTION_HIDDEN, NULL}, + {"taketwo-angle-tolerance", 4, "deg", OPTION_HIDDEN, NULL}, + {"taketwo-trace-tolerance", 5, "deg", OPTION_HIDDEN, NULL}, + {0} +}; + + +struct argp taketwo_argp = { taketwo_options, taketwo_parse_arg, + NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/indexers/taketwo.h b/libcrystfel/src/indexers/taketwo.h new file mode 100644 index 00000000..50fa221d --- /dev/null +++ b/libcrystfel/src/indexers/taketwo.h @@ -0,0 +1,47 @@ +/* + * taketwo.h + * + * Rewrite of TakeTwo algorithm (Acta D72 (8) 956-965) for CrystFEL + * + * Copyright © 2016-2017 Helen Ginn + * Copyright © 2016-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2016 Helen Ginn + * 2016-2017 Thomas White + * + * 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 . + * + */ + +#ifndef TAKETWO_H +#define TAKETWO_H + +#include + +#include "cell.h" +#include "index.h" + +/** \file taketwo.h */ + +extern void *taketwo_prepare(IndexingMethod *indm, struct taketwo_options *opts, + UnitCell *cell); +extern const char *taketwo_probe(UnitCell *cell); +extern int taketwo_index(struct image *image, void *priv); +extern void taketwo_cleanup(IndexingPrivate *pp); + +#endif /* TAKETWO_H */ diff --git a/libcrystfel/src/indexers/xds.c b/libcrystfel/src/indexers/xds.c new file mode 100644 index 00000000..02610d5e --- /dev/null +++ b/libcrystfel/src/indexers/xds.c @@ -0,0 +1,541 @@ +/* + * xds.c + * + * Invoke xds for crystal autoindexing + * + * Copyright © 2013-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * Copyright © 2013 Cornelius Gati + * + * Authors: + * 2010-2018 Thomas White + * 2013 Cornelius Gati + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef HAVE_FORKPTY_PTY_H +#include +#endif +#ifdef HAVE_FORKPTY_UTIL_H +#include +#endif + +#include "xds.h" +#include "cell.h" +#include "image.h" +#include "utils.h" +#include "peaks.h" +#include "cell-utils.h" + +/** \file xds.h */ + +/* Fake pixel size and camera length, both in metres */ +#define FAKE_PIXEL_SIZE (70e-6) +#define FAKE_CLEN (0.1) + + +/* Global private data, prepared once */ +struct xds_private +{ + IndexingMethod indm; + UnitCell *cell; +}; + + +/* Essentially the reverse of xds_spacegroup_for_lattice(), below */ +static int convert_spacegroup_number(int spg, LatticeType *lt, char *cen, + char *ua) +{ + switch ( spg ) { + + case 1: *lt = L_TRICLINIC; *cen = 'P'; *ua = '*'; return 0; + case 3: *lt = L_MONOCLINIC; *cen = 'P'; *ua = 'b'; return 0; + case 5: *lt = L_MONOCLINIC; *cen = 'C'; *ua = 'b'; return 0; + case 16: *lt = L_ORTHORHOMBIC; *cen = 'P'; *ua = '*'; return 0; + case 21: *lt = L_ORTHORHOMBIC; *cen = 'C'; *ua = '*'; return 0; + case 22: *lt = L_ORTHORHOMBIC; *cen = 'F'; *ua = '*'; return 0; + case 23: *lt = L_ORTHORHOMBIC; *cen = 'I'; *ua = '*'; return 0; + case 75: *lt = L_TETRAGONAL; *cen = 'P'; *ua = 'c'; return 0; + case 79: *lt = L_TETRAGONAL; *cen = 'I'; *ua = 'c'; return 0; + case 143: *lt = L_HEXAGONAL; *cen = 'P'; *ua = 'c'; return 0; + case 146: *lt = L_HEXAGONAL; *cen = 'H'; *ua = 'c'; return 0; + case 195: *lt = L_CUBIC; *cen = 'P'; *ua = '*'; return 0; + case 196: *lt = L_CUBIC; *cen = 'F'; *ua = '*'; return 0; + case 197: *lt = L_CUBIC; *cen = 'I'; *ua = '*'; return 0; + default: return 1; + + } +} + + +static int read_cell(struct image *image) +{ + FILE * fh; + float ax, ay, az; + float bx, by, bz; + float cx, cy, cz; + int spg; + char *rval, line[1024]; + UnitCell *cell; + LatticeType latticetype; + char centering, ua; + Crystal *cr; + + fh = fopen("IDXREF.LP", "r"); + if ( fh == NULL ) return 0; /* Not indexable */ + + do { + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + + } while ( strcmp(line, " ***** DIFFRACTION PARAMETERS USED AT START OF " + "INTEGRATION *****\n") != 0 ); + + /* Find and read space group number */ + do { + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + } while ( strncmp(line, " SPACE GROUP NUMBER ", 20) != 0 ); + sscanf(line+20, "%i\n", &spg); + + /* Find and read a */ + do { + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + } while ( strncmp(line, " COORDINATES OF UNIT CELL A-AXIS ", 33) != 0 ); + if ( sscanf(line+33, "%f %f %f\n", &ax, &ay, &az) < 3 ) { + fclose(fh); + return 0; + } + + /* Read b */ + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + if ( sscanf(line+33, "%f %f %f\n", &bx, &by, &bz) < 3 ) { + fclose(fh); + return 0; + } + + /* Read c */ + rval = fgets(line, 1023, fh); + if ( rval == NULL ) { + fclose(fh); + return 0; + } + if ( sscanf(line+33, "%f %f %f\n", &cx, &cy, &cz) < 3 ) { + fclose(fh); + return 0; + } + + cell = cell_new(); + cell_set_cartesian(cell, + -ax*1e-10, -ay*1e-10, -az*1e-10, + -bx*1e-10, -by*1e-10, -bz*1e-10, + cx*1e-10, cy*1e-10, cz*1e-10); + if ( convert_spacegroup_number(spg, &latticetype, ¢ering, &ua) ) { + ERROR("Failed to convert XDS space group number (%i)\n", spg); + return 0; + } + cell_set_lattice_type(cell, latticetype); + cell_set_centering(cell, centering); + cell_set_unique_axis(cell, ua); + + cr = crystal_new(); + if ( cr == NULL ) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + crystal_set_cell(cr, cell); + image_add_crystal(image, cr); + + return 1; +} + + +static void write_spot(struct image *image) +{ + FILE *fh; + int i; + int n; + + fh = fopen("SPOT.XDS", "w"); + if ( !fh ) { + ERROR("Couldn't open temporary file '%s'\n", "SPOT.XDS"); + return; + } + + n = image_feature_count(image->features); + for ( i=0; ifeatures, i); + if ( f == NULL ) continue; + if ( f->intensity <= 0 ) continue; + + ttx = angle_between_2d(0.0, 1.0, + f->rx, 1.0/image->lambda + f->rz); + tty = angle_between_2d(0.0, 1.0, + f->ry, 1.0/image->lambda + f->rz); + if ( f->rx < 0.0 ) ttx *= -1.0; + if ( f->ry < 0.0 ) tty *= -1.0; + x = tan(ttx)*FAKE_CLEN; + y = tan(tty)*FAKE_CLEN; + + x = (x / FAKE_PIXEL_SIZE) + 1500; + y = (y / FAKE_PIXEL_SIZE) + 1500; + + fprintf(fh, "%10.2f %10.2f %10.2f %10.0f.\n", + x, y, 0.5, f->intensity); + + } + fclose(fh); +} + + +/* Turn what we know about the unit cell into something which we can give to + * XDS to make it give us only indexing results compatible with the cell. */ +static const char *xds_spacegroup_for_lattice(UnitCell *cell) +{ + LatticeType latt; + char centering; + char *g = NULL; + + latt = cell_get_lattice_type(cell); + centering = cell_get_centering(cell); + + switch ( latt ) + { + case L_TRICLINIC : + if ( centering == 'P' ) { + g = "1"; + } + break; + + case L_MONOCLINIC : + if ( centering == 'P' ) { + g = "3"; + } else if ( centering == 'C' ) { + g = "5"; + } + break; + + case L_ORTHORHOMBIC : + if ( centering == 'P' ) { + g = "16"; + } else if ( centering == 'C' ) { + g = "21"; + } else if ( centering == 'F' ) { + g = "22"; + } else if ( centering == 'I' ) { + g = "23"; + } + break; + + case L_TETRAGONAL : + if ( centering == 'P' ) { + g = "75"; + } else if ( centering == 'I' ) { + g = "79"; + } + break; + + /* Unfortunately, XDS only does "hexagonal H" */ + case L_RHOMBOHEDRAL : + return NULL; + + case L_HEXAGONAL : + if ( centering == 'P' ) { + g = "143"; + } + if ( centering == 'H' ) { + g = "146"; + } + break; + + case L_CUBIC : + if ( centering == 'P' ) { + g = "195"; + } else if ( centering == 'F' ) { + g = "196"; + } else if ( centering == 'I' ) { + g = "197"; + } + break; + } + + return g; +} + + +static int write_inp(struct image *image, struct xds_private *xp) +{ + FILE *fh; + + fh = fopen("XDS.INP", "w"); + if ( !fh ) { + ERROR("Couldn't open XDS.INP\n"); + return 1; + } + + fprintf(fh, "JOB= IDXREF\n"); + fprintf(fh, "ORGX= 1500\n"); + fprintf(fh, "ORGY= 1500\n"); + fprintf(fh, "DETECTOR_DISTANCE= %f\n", FAKE_CLEN*1e3); + fprintf(fh, "OSCILLATION_RANGE= 0.300\n"); + fprintf(fh, "X-RAY_WAVELENGTH= %.6f\n", image->lambda*1e10); + fprintf(fh, "NAME_TEMPLATE_OF_DATA_FRAMES=???.img \n"); + fprintf(fh, "DATA_RANGE=1 1\n"); + fprintf(fh, "SPOT_RANGE=1 1\n"); + + if ( xp->indm & INDEXING_USE_LATTICE_TYPE ) { + fprintf(fh, "SPACE_GROUP_NUMBER= %s\n", + xds_spacegroup_for_lattice(xp->cell)); + } else { + fprintf(fh, "SPACE_GROUP_NUMBER= 0\n"); + } + + if ( xp->indm & INDEXING_USE_CELL_PARAMETERS ) { + + double a, b, c, al, be, ga; + + cell_get_parameters(xp->cell, &a, &b, &c, &al, &be, &ga); + + fprintf(fh, "UNIT_CELL_CONSTANTS= " + "%.2f %.2f %.2f %.2f %.2f %.2f\n", + a*1e10, b*1e10, c*1e10, + rad2deg(al), rad2deg(be), rad2deg(ga)); + + } else { + fprintf(fh, "UNIT_CELL_CONSTANTS= 0 0 0 0 0 0\n"); + } + + fprintf(fh, "NX= 3000\n"); + fprintf(fh, "NY= 3000\n"); + fprintf(fh, "QX= %f\n", FAKE_PIXEL_SIZE*1e3); /* Pixel size in mm */ + fprintf(fh, "QY= %f\n", FAKE_PIXEL_SIZE*1e3); /* Pixel size in mm */ + fprintf(fh, "INDEX_ORIGIN=0 0 0\n"); + fprintf(fh, "DIRECTION_OF_DETECTOR_X-AXIS=1 0 0\n"); + fprintf(fh, "DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0\n"); + fprintf(fh, "INCIDENT_BEAM_DIRECTION=0 0 1\n"); + fprintf(fh, "ROTATION_AXIS=0 1 0\n"); + fprintf(fh, "DETECTOR= CSPAD\n"); + fprintf(fh, "MINIMUM_VALID_PIXEL_VALUE= 1\n"); + fprintf(fh, "OVERLOAD= 200000000\n"); + fprintf(fh, "REFINE(IDXREF)= CELL ORIENTATION\n"); + fprintf(fh, "INDEX_ERROR= 0.3\n"); + fprintf(fh, "INDEX_MAGNITUDE= 15\n"); + fprintf(fh, "INDEX_QUALITY= 0.2\n"); + fprintf(fh, "MAXIMUM_ERROR_OF_SPOT_POSITION= 5.0\n"); + + fclose(fh); + + return 0; +} + + +int run_xds(struct image *image, void *priv) +{ + int status; + int rval; + int n; + pid_t pid; + int pty; + struct xds_private *xp = (struct xds_private *)priv; + + if ( write_inp(image, xp) ) { + ERROR("Failed to write XDS.INP file for XDS.\n"); + return 0; + } + + n = image_feature_count(image->features); + if ( n < 25 ) return 0; + + write_spot(image); + + /* Delete any old indexing result which may exist */ + remove("IDXREF.LP"); + + pid = forkpty(&pty, NULL, NULL, NULL); + + if ( pid == -1 ) { + ERROR("Failed to fork for XDS\n"); + return 0; + } + if ( pid == 0 ) { + + /* Child process: invoke XDS */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("xds", "xds", (char *)NULL); + ERROR("Failed to invoke XDS.\n"); + _exit(0); + + } + waitpid(pid, &status, 0); + + close(pty); + rval = read_cell(image); + + return rval; +} + + +void *xds_prepare(IndexingMethod *indm, UnitCell *cell) +{ + struct xds_private *xp; + + if ( xds_probe(cell) == NULL ) { + ERROR("XDS does not appear to run properly.\n"); + ERROR("Please check your XDS installation.\n"); + return NULL; + } + + /* Either cell,latt and cell provided, or nocell-nolatt and no cell + * - complain about anything else. Could figure this out automatically, + * but we'd have to decide whether the user just forgot the cell, or + * forgot "-nolatt", or whatever. */ + if ( (*indm & INDEXING_USE_LATTICE_TYPE) + && !(*indm & INDEXING_USE_CELL_PARAMETERS) ) + { + ERROR("Invalid XDS options (-latt-nocell): " + "try xds-nolatt-nocell.\n"); + return NULL; + } + + if ( (*indm & INDEXING_USE_CELL_PARAMETERS) + && !(*indm & INDEXING_USE_LATTICE_TYPE) ) + { + ERROR("Invalid XDS options (-cell-nolatt): " + "try xds-nolatt-nocell.\n"); + return NULL; + } + + if ( (cell != NULL) && (xds_spacegroup_for_lattice(cell) == NULL) ) { + ERROR("Don't know how to ask XDS for your cell.\n"); + return NULL; + } + + xp = calloc(1, sizeof(*xp)); + if ( xp == NULL ) return NULL; + + /* Flags that XDS knows about */ + *indm &= INDEXING_METHOD_MASK | INDEXING_USE_LATTICE_TYPE + | INDEXING_USE_CELL_PARAMETERS; + + xp->cell = cell; + xp->indm = *indm; + + return xp; +} + + +void xds_cleanup(void *pp) +{ + struct xds_private *xp; + + xp = (struct xds_private *)pp; + free(xp); +} + + +const char *xds_probe(UnitCell *cell) +{ + pid_t pid; + int pty; + int status; + FILE *fh; + char line[1024]; + int ok = 0; + int l; + + pid = forkpty(&pty, NULL, NULL, NULL); + if ( pid == -1 ) { + return NULL; + } + if ( pid == 0 ) { + + /* Child process */ + struct termios t; + + /* Turn echo off */ + tcgetattr(STDIN_FILENO, &t); + t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL); + tcsetattr(STDIN_FILENO, TCSANOW, &t); + + execlp("xds", "xds", (char *)NULL); + _exit(1); + + } + + fh = fdopen(pty, "r"); + + for ( l=0; l<10; l++ ) { + char *pos; + if ( fgets(line, 1024, fh) != NULL ) { + pos = strstr(line, "** XDS **"); + if ( pos != NULL ) { + ok = 1; + } + } + } + + fclose(fh); + close(pty); + waitpid(pid, &status, 0); + + if ( !ok ) return NULL; + + if ( cell_has_parameters(cell) ) return "xds-cell-latt"; + return "xds-nocell-nolatt"; +} diff --git a/libcrystfel/src/indexers/xds.h b/libcrystfel/src/indexers/xds.h new file mode 100644 index 00000000..8c4dc6d0 --- /dev/null +++ b/libcrystfel/src/indexers/xds.h @@ -0,0 +1,58 @@ +/* + * xds.h + * + * Invoke xds for crystal autoindexing + * + * Copyright © 2013-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * Copyright © 2013 Cornelius Gati + * + * Authors: + * 2010-2013,2017 Thomas White + * 2013 Cornelius Gati + * + * 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 . + * + */ + +#ifndef XDS_H +#define XDS_H + +#include "cell.h" +#include "index.h" + +#ifdef __cplusplus +extern "C" { +#endif + +/** + * \file xds.h + * XDS indexer interface + */ + +extern int run_xds(struct image *image, void *ipriv); + +extern void *xds_prepare(IndexingMethod *indm, UnitCell *cell); + +extern const char *xds_probe(UnitCell *cell); + +extern void xds_cleanup(void *pp); + +#ifdef __cplusplus +} +#endif + +#endif /* XDS_H */ diff --git a/libcrystfel/src/indexers/xgandalf.c b/libcrystfel/src/indexers/xgandalf.c new file mode 100644 index 00000000..2d2dca48 --- /dev/null +++ b/libcrystfel/src/indexers/xgandalf.c @@ -0,0 +1,497 @@ +/* + * xgandalf.c + * + * Interface to XGANDALF indexer + * + * Copyright © 2017-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2018 Yaroslav Gevorkov + * + * 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 . + * + */ + +#ifdef HAVE_CONFIG_H +#include +#endif + +#include "xgandalf.h" + +#include + +#include "utils.h" +#include "cell-utils.h" +#include "peaks.h" + +#ifdef HAVE_XGANDALF +#include "xgandalf/adaptions/crystfel/Lattice.h" +#include "xgandalf/adaptions/crystfel/ExperimentSettings.h" +#include "xgandalf/adaptions/crystfel/IndexerPlain.h" +#endif + +/** \file xgandalf.h */ + +struct xgandalf_options { + unsigned int sampling_pitch; + unsigned int grad_desc_iterations; + float tolerance; + unsigned int no_deviation_from_provided_cell; + float minLatticeVectorLength_A; + float maxLatticeVectorLength_A; + int maxPeaksForIndexing; +}; + +#ifdef HAVE_XGANDALF + +struct xgandalf_private_data { + IndexerPlain *indexer; + reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A; + + IndexingMethod indm; + UnitCell *cellTemplate; + Lattice_t sampleRealLattice_A; //same as cellTemplate + IntegerMatrix *centeringTransformation; + LatticeTransform_t latticeReductionTransform; +}; + +#define FAKE_DETECTOR_DISTANCE (0.1) +#define FAKE_DETECTOR_RADIUS (0.1) +#define FAKE_BEAM_ENERGY (1) +#define FAKE_DIVERGENCE_ANGLE_DEG (0.05) +#define FAKE_NON_MONOCHROMATICITY (0.005) +#define FAKE_REFLECTION_RADIUS (0.0001) + +#define MAX_ASSEMBLED_LATTICES_COUNT (10) + +static void reduceCell(UnitCell* cell, LatticeTransform_t* appliedReductionTransform); +static void restoreCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform); +static void makeRightHanded(UnitCell* cell); + +int run_xgandalf(struct image *image, void *ipriv) +{ + struct xgandalf_private_data *xgandalf_private_data = (struct xgandalf_private_data*) ipriv; + reciprocalPeaks_1_per_A_t *reciprocalPeaks_1_per_A = &(xgandalf_private_data->reciprocalPeaks_1_per_A); + + int peakCountMax = image_feature_count(image->features); + reciprocalPeaks_1_per_A->peakCount = 0; + for (int i = 0; i < peakCountMax && i < MAX_PEAK_COUNT_FOR_INDEXER; i++) { + struct imagefeature *f; + f = image_get_feature(image->features, i); + if (f == NULL) { + continue; + } + + reciprocalPeaks_1_per_A->coordinates_x[reciprocalPeaks_1_per_A->peakCount] = f->rx * 1e-10; + reciprocalPeaks_1_per_A->coordinates_y[reciprocalPeaks_1_per_A->peakCount] = f->ry * 1e-10; + reciprocalPeaks_1_per_A->coordinates_z[reciprocalPeaks_1_per_A->peakCount] = f->rz * 1e-10; + reciprocalPeaks_1_per_A->peakCount++; + } + + Lattice_t assembledLattices[MAX_ASSEMBLED_LATTICES_COUNT]; + int assembledLatticesCount; + IndexerPlain_index(xgandalf_private_data->indexer, + assembledLattices, + &assembledLatticesCount, + MAX_ASSEMBLED_LATTICES_COUNT, + *reciprocalPeaks_1_per_A, + NULL); + + if (assembledLatticesCount > 0) { //no multi-lattice at the moment + assembledLatticesCount = 1; + } + + int goodLatticesCount = assembledLatticesCount; + for (int i = 0; i < assembledLatticesCount && i < 1; i++) { + reorderLattice(&(xgandalf_private_data->sampleRealLattice_A), + &assembledLattices[i]); + + UnitCell *uc; + uc = cell_new(); + + Lattice_t *l = &assembledLattices[i]; + + cell_set_cartesian(uc, l->ax * 1e-10, l->ay * 1e-10, l->az * 1e-10, + l->bx * 1e-10, l->by * 1e-10, l->bz * 1e-10, + l->cx * 1e-10, l->cy * 1e-10, l->cz * 1e-10); + makeRightHanded(uc); + + if(xgandalf_private_data->cellTemplate != NULL){ + restoreCell(uc, &xgandalf_private_data->latticeReductionTransform); + + UnitCell *new_cell_trans = cell_transform_intmat(uc, xgandalf_private_data->centeringTransformation); + cell_free(uc); + uc = new_cell_trans; + + cell_set_lattice_type(new_cell_trans, cell_get_lattice_type(xgandalf_private_data->cellTemplate)); + cell_set_centering(new_cell_trans, cell_get_centering(xgandalf_private_data->cellTemplate)); + cell_set_unique_axis(new_cell_trans, cell_get_unique_axis(xgandalf_private_data->cellTemplate)); + } + + if (validate_cell(uc)) { + STATUS("Problem with returned cell!\n"); + } + + Crystal *cr = crystal_new(); + if (cr == NULL) { + ERROR("Failed to allocate crystal.\n"); + return 0; + } + crystal_set_cell(cr, uc); + image_add_crystal(image, cr); + + } + + return goodLatticesCount; +} + +void *xgandalf_prepare(IndexingMethod *indm, UnitCell *cell, + struct xgandalf_options *xgandalf_opts) +{ + struct xgandalf_private_data *xgandalf_private_data = malloc(sizeof(struct xgandalf_private_data)); + allocReciprocalPeaks(&(xgandalf_private_data->reciprocalPeaks_1_per_A)); + xgandalf_private_data->indm = *indm; + xgandalf_private_data->cellTemplate = NULL; + xgandalf_private_data->centeringTransformation = NULL; + + float tolerance = xgandalf_opts->tolerance; + samplingPitch_t samplingPitch = xgandalf_opts->sampling_pitch; + gradientDescentIterationsCount_t gradientDescentIterationsCount = xgandalf_opts->grad_desc_iterations; + + if (*indm & INDEXING_USE_CELL_PARAMETERS) { + + xgandalf_private_data->cellTemplate = cell; + + UnitCell* primitiveCell = uncenter_cell(cell, &xgandalf_private_data->centeringTransformation, NULL); + + reduceCell(primitiveCell, &xgandalf_private_data->latticeReductionTransform); + + double asx, asy, asz, bsx, bsy, bsz, csx, csy, csz; + int ret = cell_get_reciprocal(primitiveCell, &asx, &asy, &asz, + &bsx, &bsy, &bsz, + &csx, &csy, &csz); + if (ret != 0) { + ERROR("cell_get_reciprocal did not finish properly!"); + } + + Lattice_t sampleReciprocalLattice_1_per_A = { + .ax = asx * 1e-10, .ay = asy * 1e-10, .az = asz * 1e-10, + .bx = bsx * 1e-10, .by = bsy * 1e-10, .bz = bsz * 1e-10, + .cx = csx * 1e-10, .cy = csy * 1e-10, .cz = csz * 1e-10 }; + + double ax, ay, az, bx, by, bz, cx, cy, cz; + ret = cell_get_cartesian(primitiveCell, &ax, &ay, &az, + &bx, &by, &bz, + &cx, &cy, &cz); + if (ret != 0) { + ERROR("cell_get_cartesian did not finish properly!"); + } + Lattice_t sampleRealLattice_A = { + .ax = ax * 1e10, .ay = ay * 1e10, .az = az * 1e10, + .bx = bx * 1e10, .by = by * 1e10, .bz = bz * 1e10, + .cx = cx * 1e10, .cy = cy * 1e10, .cz = cz * 1e10 }; + xgandalf_private_data->sampleRealLattice_A = sampleRealLattice_A; + + ExperimentSettings *experimentSettings = + ExperimentSettings_new(FAKE_BEAM_ENERGY, + FAKE_DETECTOR_DISTANCE, + FAKE_DETECTOR_RADIUS, + FAKE_DIVERGENCE_ANGLE_DEG, + FAKE_NON_MONOCHROMATICITY, + sampleReciprocalLattice_1_per_A, + tolerance, + FAKE_REFLECTION_RADIUS); + + xgandalf_private_data->indexer = IndexerPlain_new(experimentSettings); + + if (xgandalf_opts->no_deviation_from_provided_cell) { + IndexerPlain_setRefineWithExactLattice(xgandalf_private_data->indexer, 1); + } + + ExperimentSettings_delete(experimentSettings); + cell_free(primitiveCell); + + } else { + + Lattice_t sampleRealLattice_A = { 0, 0, 0, 0, 0, 0, 0, 0, 0 }; + xgandalf_private_data->sampleRealLattice_A = sampleRealLattice_A; + + ExperimentSettings *experimentSettings = + ExperimentSettings_new_nolatt(FAKE_BEAM_ENERGY, + FAKE_DETECTOR_DISTANCE, + FAKE_DETECTOR_RADIUS, + FAKE_DIVERGENCE_ANGLE_DEG, + FAKE_NON_MONOCHROMATICITY, + xgandalf_opts->minLatticeVectorLength_A, + xgandalf_opts->maxLatticeVectorLength_A, + FAKE_REFLECTION_RADIUS); + + xgandalf_private_data->indexer = IndexerPlain_new(experimentSettings); + + ExperimentSettings_delete(experimentSettings); + } + + IndexerPlain_setSamplingPitch(xgandalf_private_data->indexer, + samplingPitch); + IndexerPlain_setGradientDescentIterationsCount(xgandalf_private_data->indexer, + gradientDescentIterationsCount); + IndexerPlain_setMaxPeaksToUseForIndexing(xgandalf_private_data->indexer, + xgandalf_opts->maxPeaksForIndexing); + + /* Flags that XGANDALF knows about */ + *indm &= INDEXING_METHOD_MASK | INDEXING_USE_CELL_PARAMETERS; + + return xgandalf_private_data; +} + + +void xgandalf_cleanup(void *pp) +{ + struct xgandalf_private_data *xgandalf_private_data = pp; + + freeReciprocalPeaks(xgandalf_private_data->reciprocalPeaks_1_per_A); + IndexerPlain_delete(xgandalf_private_data->indexer); + if(xgandalf_private_data->centeringTransformation != NULL){ + intmat_free(xgandalf_private_data->centeringTransformation); + } + free(xgandalf_private_data); +} + +static void reduceCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +{ + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; + + reduceLattice(&l, appliedReductionTransform); + + cell_set_cartesian(cell, l.ax, l.ay, l.az, + l.bx, l.by, l.bz, + l.cx, l.cy, l.cz); + + makeRightHanded(cell); +} + +static void restoreCell(UnitCell *cell, LatticeTransform_t* appliedReductionTransform) +{ + + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + Lattice_t l = { ax, ay, az, bx, by, bz, cx, cy, cz }; + + restoreLattice(&l, appliedReductionTransform); + + cell_set_cartesian(cell, l.ax, l.ay, l.az, + l.bx, l.by, l.bz, + l.cx, l.cy, l.cz); + + makeRightHanded(cell); +} + +static void makeRightHanded(UnitCell *cell) +{ + double ax, ay, az, bx, by, bz, cx, cy, cz; + cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); + + if ( !right_handed(cell) ) { + cell_set_cartesian(cell, -ax, -ay, -az, -bx, -by, -bz, -cx, -cy, -cz); + } +} + + +const char *xgandalf_probe(UnitCell *cell) +{ + return "xgandalf"; +} + +#else + +int run_xgandalf(struct image *image, void *ipriv) +{ + ERROR("This copy of CrystFEL was compiled without XGANDALF support.\n"); + return 0; +} + + +void *xgandalf_prepare(IndexingMethod *indm, UnitCell *cell, + struct xgandalf_options *xgandalf_opts) +{ + ERROR("This copy of CrystFEL was compiled without XGANDALF support.\n"); + ERROR("To use XGANDALF indexing, recompile with XGANDALF.\n"); + return NULL; +} + + +void xgandalf_cleanup(void *pp) +{ +} + + +const char *xgandalf_probe(UnitCell *cell) +{ + return NULL; +} + +#endif // HAVE_XGANDALF + +static void xgandalf_show_help() +{ + printf("Parameters for the TakeTwo indexing algorithm:\n" +" --xgandalf-sampling-pitch\n" +" Sampling pitch: 0 (loosest) to 4 (most dense)\n" +" or with secondary Miller indices: 5 (loosest) to\n" +" 7 (most dense). Default: 6\n" +" --xgandalf-grad-desc-iterations\n" +" Gradient descent iterations: 0 (few) to 5 (many)\n" +" Default: 4\n" +" --xgandalf-fast-execution Shortcut to set\n" +" --xgandalf-sampling-pitch=2\n" +" --xgandalf-grad-desc-iterations=3\n" +" --xgandalf-tolerance Relative tolerance of the lattice vectors.\n" +" Default is 0.02\n" +" --xgandalf-no-deviation-from-provided-cell\n" +" Force the fitted cell to have the same lattice\n" +" parameters as the provided one\n" +" --xgandalf-min-lattice-vector-length\n" +" Minimum possible lattice vector length in A.\n" +" Default: 30 A\n" +" --xgandalf-max-lattice-vector-length\n" +" Maximum possible lattice vector length in A.\n" +" Default: 250 A\n" +" --xgandalf-max-peaks\n" +" Maximum number of peaks used for indexing.\n" +" All peaks are used for refinement.\n" +" Default: 250\n" +); +} + + +static error_t xgandalf_parse_arg(int key, char *arg, + struct argp_state *state) +{ + struct xgandalf_options **opts_ptr = state->input; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct xgandalf_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->sampling_pitch = 6; + (*opts_ptr)->grad_desc_iterations = 4; + (*opts_ptr)->tolerance = 0.02; + (*opts_ptr)->no_deviation_from_provided_cell = 0; + (*opts_ptr)->minLatticeVectorLength_A = 30; + (*opts_ptr)->maxLatticeVectorLength_A = 250; + (*opts_ptr)->maxPeaksForIndexing = 250; + break; + + case 1 : + xgandalf_show_help(); + return EINVAL; + + case 2 : + if (sscanf(arg, "%u", &(*opts_ptr)->sampling_pitch) != 1) { + ERROR("Invalid value for --xgandalf-sampling-pitch\n"); + return EINVAL; + } + break; + + case 3 : + if (sscanf(arg, "%u", &(*opts_ptr)->grad_desc_iterations) != 1) { + ERROR("Invalid value for --xgandalf-grad-desc-iterations\n"); + return EINVAL; + } + break; + + case 4 : + if (sscanf(arg, "%f", &(*opts_ptr)->tolerance) != 1) { + ERROR("Invalid value for --xgandalf-tolerance\n"); + return EINVAL; + } + break; + + case 5 : + (*opts_ptr)->no_deviation_from_provided_cell = 1; + break; + + case 6 : + if (sscanf(arg, "%f", &(*opts_ptr)->minLatticeVectorLength_A) != 1) { + ERROR("Invalid value for --xgandalf-min-lattice-vector-length\n"); + return EINVAL; + } + break; + + case 7 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxLatticeVectorLength_A) != 1) { + ERROR("Invalid value for --xgandalf-max-lattice-vector-length\n"); + return EINVAL; + } + break; + + case 8 : + (*opts_ptr)->sampling_pitch = 2; + (*opts_ptr)->grad_desc_iterations = 3; + break; + + case 9 : + if (sscanf(arg, "%i", &(*opts_ptr)->maxPeaksForIndexing) != 1) { + ERROR("Invalid value for --xgandalf-max-peaks\n"); + return EINVAL; + } + break; + + } + + return 0; +} + + +static struct argp_option xgandalf_options[] = { + + {"help-xgandalf", 1, NULL, OPTION_NO_USAGE, + "Show options for XGANDALF indexing algorithm", 99}, + + {"xgandalf-sampling-pitch", 2, "pitch", OPTION_HIDDEN, NULL}, + {"xgandalf-sps", 2, "pitch", OPTION_HIDDEN, NULL}, + + {"xgandalf-grad-desc-iterations", 3, "n", OPTION_HIDDEN, NULL}, + {"xgandalf-gdis", 3, "n", OPTION_HIDDEN, NULL}, + + {"xgandalf-tolerance", 4, "t", OPTION_HIDDEN, NULL}, + {"xgandalf-tol", 4, "t", OPTION_HIDDEN, NULL}, + + {"xgandalf-no-deviation-from-provided-cell", 5, NULL, OPTION_HIDDEN, NULL}, + {"xgandalf-ndfpc", 5, NULL, OPTION_HIDDEN, NULL}, + + {"xgandalf-min-lattice-vector-length", 6, "len", OPTION_HIDDEN, NULL}, + {"xgandalf-min-lvl", 6, "len", OPTION_HIDDEN, NULL}, + + {"xgandalf-max-lattice-vector-length", 7, "len", OPTION_HIDDEN, NULL}, + {"xgandalf-max-lvl", 7, "len", OPTION_HIDDEN, NULL}, + + {"xgandalf-fast-execution", 8, NULL, OPTION_HIDDEN, NULL}, + + {"xgandalf-max-peaks", 9, "n", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp xgandalf_argp = { xgandalf_options, xgandalf_parse_arg, + NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/indexers/xgandalf.h b/libcrystfel/src/indexers/xgandalf.h new file mode 100644 index 00000000..288d141a --- /dev/null +++ b/libcrystfel/src/indexers/xgandalf.h @@ -0,0 +1,51 @@ +/* + * xgandalf.h + * + * Interface to XGANDALF indexer + * + * Copyright © 2017-2020 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2018 Yaroslav Gevorkov + * + * 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 . + * + */ + +#ifndef LIBCRYSTFEL_SRC_XGANDALF_H +#define LIBCRYSTFEL_SRC_XGANDALF_H + +#include +#include + +/** + * \file xgandalf.h + * XGANDALF indexer interface + */ + +#include "index.h" + +extern int run_xgandalf(struct image *image, void *ipriv); + +extern void *xgandalf_prepare(IndexingMethod *indm, UnitCell *cell, + struct xgandalf_options *xgandalf_opts); + +extern void xgandalf_cleanup(void *pp); +extern const char *xgandalf_probe(UnitCell *cell); + + +#endif /* LIBCRYSTFEL_SRC_XGANDALF_H */ -- cgit v1.2.3