diff options
Diffstat (limited to 'libcrystfel/src')
| -rw-r--r-- | libcrystfel/src/detector.c | 14 | ||||
| -rw-r--r-- | libcrystfel/src/geometry.c | 2 | ||||
| -rw-r--r-- | libcrystfel/src/image.h | 2 | ||||
| -rw-r--r-- | libcrystfel/src/index.c | 71 | ||||
| -rw-r--r-- | libcrystfel/src/index.h | 11 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.c | 535 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.h | 65 |
7 files changed, 693 insertions, 7 deletions
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c index 201b9041..4d008e65 100644 --- a/libcrystfel/src/detector.c +++ b/libcrystfel/src/detector.c @@ -1070,6 +1070,19 @@ static void parse_toplevel(struct detector *det, struct beam_params *beam, } } + } else if ( strcmp(key, "photon_energy_bandwidth") == 0 ) { + if ( beam != NULL ) { + double v; + char *end; + v = strtod(val, &end); + if ( (val[0] != '\0') && (end[0] == '\0') ) { + beam->bandwidth = v; + } else { + ERROR("Invalid value for " + "photon_energy_bandwidth\n"); + } + } + } else if ( strcmp(key, "photon_energy_scale") == 0 ) { if ( beam != NULL ) { beam->photon_energy_scale = atof(val); @@ -1202,6 +1215,7 @@ struct detector *get_detector_geometry_from_string(const char *string, beam->photon_energy = 0.0; beam->photon_energy_from = NULL; beam->photon_energy_scale = 1.0; + beam->bandwidth = 0.00000001; } det->n_panels = 0; diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c index 5b2107d1..fc42a8de 100644 --- a/libcrystfel/src/geometry.c +++ b/libcrystfel/src/geometry.c @@ -332,7 +332,7 @@ static Reflection *check_reflection(struct image *image, Crystal *cryst, /* Closest point on Ewald sphere. * Project zl to 0, bit of a hack... */ - const double zlp0 = zl>0?zl:0; + const double zlp0 = zl<0?zl:0; exerr2 = (x-xl)*(x-xl) + (y-yl)*(y-yl) + (z-zl)*(z-zl); /* Weighted average between projected lattice point diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h index 706b06b1..04fb18a0 100644 --- a/libcrystfel/src/image.h +++ b/libcrystfel/src/image.h @@ -110,6 +110,8 @@ struct beam_params char *photon_energy_from; /**< HDF5 dataset name */ double photon_energy_scale; /**< Scale factor for photon energy, if it * comes from an image header */ + double bandwidth; /**< FWHM bandwidth as a fraction of + * wavelength */ }; diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index f6e81109..049c3ba0 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -58,6 +58,7 @@ #include "predict-refine.h" #include "taketwo.h" #include "xgandalf.h" +#include "pinkindexer.h" /** \file index.h */ @@ -71,6 +72,7 @@ struct _indexingprivate struct taketwo_options *ttopts; struct xgandalf_options *xgandalf_opts; + struct pinkIndexer_options *pinkIndexer_opts; int n_methods; IndexingMethod *methods; @@ -195,6 +197,10 @@ static char *base_indexer_str(IndexingMethod indm) strcpy(str, "xgandalf"); break; + case INDEXING_PINKINDEXER: + strcpy(str, "pinkIndexer"); + break; + case INDEXING_SIMULATION : strcpy(str, "simulation"); break; @@ -232,7 +238,9 @@ static char *friendly_indexer_name(IndexingMethod m) static void *prepare_method(IndexingMethod *m, UnitCell *cell, + struct detector *det, struct beam_params *beam, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options* pinkIndexer_opts, struct felix_options *felix_opts) { char *str; @@ -277,6 +285,11 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell, priv = xgandalf_prepare(m, cell, xgandalf_opts); break; + case INDEXING_PINKINDEXER : + priv = pinkIndexer_prepare(m, cell, pinkIndexer_opts, + det, beam); + break; + default : ERROR("Don't know how to prepare indexing method %i\n", *m); break; @@ -305,10 +318,11 @@ static void *prepare_method(IndexingMethod *m, UnitCell *cell, IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, - struct detector *det, float *tols, - IndexingFlags flags, + struct detector *det, struct beam_params *beam, + float *tols, IndexingFlags flags, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options *pinkIndexer_opts, struct felix_options *felix_opts) { int i, n; @@ -333,7 +347,6 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, ERROR("The indexing method should contain only the method itself and "); ERROR("prior information modifiers ('cell' or 'latt')\n"); ERROR("To disable prediction refinement ('norefine'), use --no-refine.\n"); - ERROR("To check cell axes only ('axes'), use --no-cell-combinations.\n"); ERROR("To disable all unit cell checks ('raw'), use --no-check-cell.\n"); ERROR("To disable peak alignment check ('bad'), use --no-check-peaks.\n"); ERROR("To disable indexing retry ('noretry'), use --no-retry.\n"); @@ -403,11 +416,36 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, int j; ipriv->engine_private[i] = prepare_method(&methods[i], cell, + det, beam, xgandalf_opts, + pinkIndexer_opts, felix_opts); if ( ipriv->engine_private[i] == NULL ) return NULL; + if ( (methods[i] & INDEXING_METHOD_MASK) == INDEXING_PINKINDEXER ) { + if ( n > 1 ) { + ERROR("WARNING: Using PinkIndexer at the same " + "time as other indexers is not " + "recommended.\n"); + } + + if ( flags & INDEXING_CHECK_PEAKS ) { + ERROR("WARNING: Setting --no-check-peaks " + "because PinkIndexer is in use.\n"); + } + flags |= INDEXING_CHECK_PEAKS; + flags ^= INDEXING_CHECK_PEAKS; + + if ( flags & INDEXING_REFINE ) { + ERROR("WARNING: Setting --no-refine because " + "PinkIndexer is in use.\n"); + } + flags |= INDEXING_REFINE; + flags ^= INDEXING_REFINE; + } + + for ( j=0; j<i; j++ ) { if ( methods[i] == methods[j] ) { ERROR("Duplicate indexing method.\n"); @@ -430,6 +468,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, ipriv->ttopts = ttopts; ipriv->xgandalf_opts = xgandalf_opts; + ipriv->pinkIndexer_opts = pinkIndexer_opts; STATUS("List of indexing methods:\n"); for ( i=0; i<n; i++ ) { @@ -445,6 +484,13 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, } +const IndexingMethod *indexing_methods(IndexingPrivate *p, int *n) +{ + *n = p->n_methods; + return p->methods; +} + + void cleanup_indexing(IndexingPrivate *ipriv) { int n; @@ -490,6 +536,10 @@ void cleanup_indexing(IndexingPrivate *ipriv) xgandalf_cleanup(ipriv->engine_private[n]); break; + case INDEXING_PINKINDEXER : + pinkIndexer_cleanup(ipriv->engine_private[n]); + break; + default : ERROR("Don't know how to clean up indexing method %i\n", ipriv->methods[n]); @@ -602,6 +652,11 @@ static int try_indexer(struct image *image, IndexingMethod indm, r = taketwo_index(image, ipriv->ttopts, mpriv); break; + case INDEXING_PINKINDEXER : + set_last_task(last_task, "indexing:pinkindexer"); + r = run_pinkIndexer(image, mpriv); + break; + case INDEXING_XGANDALF : set_last_task(last_task, "indexing:xgandalf"); r = run_xgandalf(image, mpriv); @@ -1000,6 +1055,13 @@ IndexingMethod get_indm_from_string_2(const char *str, int *err) method = INDEXING_DEFAULTS_XGANDALF; have_method = 1; + } else if ( (strcmp(bits[i], "pinkIndexer") == 0) + || (strcmp(bits[i], "pinkindexer") == 0) ) + { + if ( have_method ) return warn_method(str); + method = INDEXING_DEFAULTS_PINKINDEXER; + have_method = 1; + } else if ( strcmp(bits[i], "none") == 0) { if ( have_method ) return warn_method(str); method = INDEXING_NONE; @@ -1098,9 +1160,10 @@ char *detect_indexing_methods(UnitCell *cell) do_probe(asdf_probe, cell, methods); do_probe(xds_probe, cell, methods); do_probe(xgandalf_probe, cell, methods); - /* Don't automatically use TakeTwo or Felix (yet) */ + /* Don't automatically use TakeTwo, Felix or PinkIndexer (yet) */ //do_probe(taketwo_probe, cell, methods); //do_probe(felix_probe, cell, methods); + //do_probe(pinkIndexer_probe, cell, methods); if ( strlen(methods) == 0 ) { free(methods); diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index eb5cf7e4..5e9e40ad 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -63,6 +63,8 @@ #define INDEXING_DEFAULTS_XGANDALF (INDEXING_XGANDALF | INDEXING_USE_CELL_PARAMETERS) +#define INDEXING_DEFAULTS_PINKINDEXER (INDEXING_PINKINDEXER | INDEXING_USE_CELL_PARAMETERS) + /** * An enumeration of all the available indexing methods. **/ @@ -79,6 +81,7 @@ typedef enum { INDEXING_ASDF = 8, /**< Use built-in ASDF algorithm */ INDEXING_TAKETWO = 9, /**< Use built-in TakeTwo algorithm */ INDEXING_XGANDALF = 10, /**< Use XGANDALF (via optional library) */ + INDEXING_PINKINDEXER = 11,/**< Use PinkIndexer (via optional library) */ INDEXING_ERROR = 255, /**< Special value for unrecognised indexing * engine */ @@ -146,16 +149,20 @@ extern IndexingMethod get_indm_from_string_2(const char *method, int *err); #include "image.h" #include "taketwo.h" #include "xgandalf.h" +#include "pinkindexer.h" #include "felix.h" - extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell, - struct detector *det, float *ltl, + struct detector *det, + struct beam_params *beam, float *ltl, IndexingFlags flags, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options *pinkIndexer_opts, struct felix_options *felix_opts); +extern const IndexingMethod *indexing_methods(IndexingPrivate *p, int *n); + extern char *detect_indexing_methods(UnitCell *cell); extern void index_pattern(struct image *image, IndexingPrivate *ipriv); diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c new file mode 100644 index 00000000..811aa3c8 --- /dev/null +++ b/libcrystfel/src/pinkindexer.c @@ -0,0 +1,535 @@ +/* + * pinkindexer.c + * + * Interface to PinkIndexer + * + * Copyright © 2017-2019 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2019 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + * + */ + +#include "pinkindexer.h" + +#ifdef HAVE_PINKINDEXER + +#include <stdlib.h> + +#include "utils.h" +#include "cell-utils.h" +#include "peaks.h" + +#include "pinkIndexer/adaptions/crystfel/Lattice.h" +#include "pinkIndexer/adaptions/crystfel/ExperimentSettings.h" +#include "pinkIndexer/adaptions/crystfel/PinkIndexer.h" + +#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; + + 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]; + + float maxRefinementDisbalance = 0.4; + + 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, + maxRefinementDisbalance, + pinkIndexer_private_data->threadCount); + + 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, + struct detector *det, struct beam_params *beam) +{ + if ( beam->photon_energy_from != NULL ) { + ERROR("For pinkIndexer, the photon_energy must be defined as a " + "constant in the geometry file\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!"); + } + + 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; + + 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; + 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; + } + + 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, + struct detector *det, struct beam_params *beam) +{ + 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 show_help() +{ + printf("Parameters for the PinkIndexer indexing algorithm:\n" +" --pinkIndexer-considered-peaks-count\n" +" Considered peaks count, 0 (fewest) to 4 (most)\n" +" Default: 4\n" +" --pinkIndexer-angle-resolution\n" +" Angle resolution, 0 (loosest) to 4 (most dense)\n" +" Default: 2\n" +" --pinkIndexer-refinement-type\n" +" Refinement type, 0 (none) to 5 (most accurate)\n" +" Default: 1\n" +" --pinkIndexer-tolerance\n" +" Relative tolerance of the lattice vectors.\n" +" Default 0.06\n" +" --pinkIndexer-reflection-radius\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" +" Measured in 1/A\n" +" --pinkIndexer-multi Use pinkIndexers own multi indexing.\n" +" --pinkIndexer-thread-count\n" +" Thread count for internal parallelization \n" +" Default: 1\n" +" --pinkIndexer-no-check-indexed\n" +" Disable internal check for correct indexing\n" +" solutions\n" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + float tmp; + 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; + break; + + case 1 : + 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; + + } + + return 0; +} + + +static struct argp_option 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}, + + {0} +}; + + +struct argp pinkIndexer_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h new file mode 100644 index 00000000..0169d028 --- /dev/null +++ b/libcrystfel/src/pinkindexer.h @@ -0,0 +1,65 @@ +/* + * pinkindexer.h + * + * Interface to PinkIndexer + * + * Copyright © 2017-2019 Deutsches Elektronen-Synchrotron DESY, + * a research centre of the Helmholtz Association. + * + * Authors: + * 2017-2019 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> + * + * This file is part of CrystFEL. + * + * CrystFEL is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * CrystFEL is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + * + */ + +#ifndef LIBCRYSTFEL_SRC_PINKINDEXER_H_ +#define LIBCRYSTFEL_SRC_PINKINDEXER_H_ + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +typedef struct pinkIndexer_options PinkIndexerOptions; +extern struct argp pinkIndexer_argp; + +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 */ +}; + +#include <stddef.h> +#include "index.h" + +extern int run_pinkIndexer(struct image *image, void *ipriv); + +extern void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, + struct pinkIndexer_options *pinkIndexer_opts, + struct detector *det, struct beam_params *beam); + +extern void pinkIndexer_cleanup(void *pp); + +extern const char *pinkIndexer_probe(UnitCell *cell); + +#endif /* LIBCRYSTFEL_SRC_PINKINDEXER_H_ */ |