diff options
Diffstat (limited to 'libcrystfel')
| -rw-r--r-- | libcrystfel/CMakeLists.txt | 3 | ||||
| -rw-r--r-- | libcrystfel/config.h.cmake.in | 2 | ||||
| -rw-r--r-- | libcrystfel/src/index.c | 31 | ||||
| -rw-r--r-- | libcrystfel/src/index.h | 6 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.c | 361 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.h | 46 |
6 files changed, 446 insertions, 3 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt index 67a20ee5..fdba725e 100644 --- a/libcrystfel/CMakeLists.txt +++ b/libcrystfel/CMakeLists.txt @@ -14,6 +14,7 @@ pkg_search_module(FFTW fftw3) set(HAVE_CURSES ${CURSES_FOUND}) set(HAVE_FFTW ${FFTW_FOUND}) set(HAVE_XGANDALF ${XGANDALF_FOUND}) +set(HAVE_PINKINDEXER ${PINKINDEXER_FOUND}) set(HAVE_FDIP ${FDIP_FOUND}) # Find out where forkpty() is declared @@ -67,6 +68,7 @@ set(LIBCRYSTFEL_SOURCES src/peakfinder8.c src/taketwo.c src/xgandalf.c + src/pinkindexer.c src/rational.c src/spectrum.c ${BISON_symopp_OUTPUTS} @@ -108,6 +110,7 @@ set(LIBCRYSTFEL_HEADERS src/peakfinder8.h src/taketwo.h src/xgandalf.h + src/pinkindexer.h src/rational.h src/spectrum.h ) diff --git a/libcrystfel/config.h.cmake.in b/libcrystfel/config.h.cmake.in index ea26c1a2..b7ad4c7a 100644 --- a/libcrystfel/config.h.cmake.in +++ b/libcrystfel/config.h.cmake.in @@ -4,6 +4,8 @@ #cmakedefine HAVE_CPU_AFFINITY #cmakedefine HAVE_FFTW #cmakedefine HAVE_XGANDALF +#cmakedefine HAVE_NBP +#cmakedefine HAVE_PINKINDEXER #cmakedefine HAVE_FDIP #cmakedefine HAVE_CURSES diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 4c82e868..cc004d9a 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; @@ -233,6 +239,7 @@ static char *friendly_indexer_name(IndexingMethod m) static void *prepare_method(IndexingMethod *m, UnitCell *cell, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options* pinkIndexer_opts, struct felix_options *felix_opts) { char *str; @@ -277,6 +284,10 @@ 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); + break; + default : ERROR("Don't know how to prepare indexing method %i\n", *m); break; @@ -309,6 +320,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, IndexingFlags flags, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options *pinkIndexer_opts, struct felix_options *felix_opts) { int i, n; @@ -403,7 +415,7 @@ IndexingPrivate *setup_indexing(const char *method_list, UnitCell *cell, int j; ipriv->engine_private[i] = prepare_method(&methods[i], cell, - xgandalf_opts, + xgandalf_opts, pinkIndexer_opts, felix_opts); if ( ipriv->engine_private[i] == NULL ) return NULL; @@ -430,6 +442,7 @@ 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++ ) { @@ -490,6 +503,10 @@ 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]); @@ -601,6 +618,10 @@ static int try_indexer(struct image *image, IndexingMethod indm, r = taketwo_index(image, ipriv->ttopts, mpriv); break; + case INDEXING_PINKINDEXER : + r = run_pinkIndexer(image, mpriv); + break; + case INDEXING_XGANDALF : set_last_task(last_task, "indexing:xgandalf"); r = run_xgandalf(image, mpriv); @@ -999,6 +1020,11 @@ 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) { + 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; @@ -1097,9 +1123,10 @@ 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 ec7ed61b..ab38016f 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 */ @@ -146,14 +149,15 @@ 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, IndexingFlags flags, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, + struct pinkIndexer_options *pinkIndexer_opts, struct felix_options *felix_opts); extern char *detect_indexing_methods(UnitCell *cell); diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c new file mode 100644 index 00000000..2002533f --- /dev/null +++ b/libcrystfel/src/pinkindexer.c @@ -0,0 +1,361 @@ +/* + * pinkIndexer.c + * + * Created on: Nov 27, 2017 + * Author: gevorkov + */ + +#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; + printf("\ntotal peaks count %i\n", peakCount); + int matchedPeaksCount = PinkIndexer_indexPattern(pinkIndexer_private_data->pinkIndexer, + &(indexedLattice[indexed]), center_shift[indexed], reciprocalPeaks_1_per_A, intensities, + maxRefinementDisbalance, + pinkIndexer_private_data->threadCount); + + printf("center shift = %f %f", center_shift[indexed][0], center_shift[indexed][1]); + printf("\nmatchedPeaksCount %i from %i\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); + printf("before restoration\n"); + cell_print(uc); + + 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; + printf("after restoration\n"); + cell_print(uc); + + 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)) { + printf("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++; + + printf("crystal %i in image added\n", indexed); + } + else { + break; + } + } while (pinkIndexer_private_data->multi + && indexed <= MAX_MULTI_LATTICE_COUNT + && reciprocalPeaks_1_per_A->peakCount >= pinkIndexer_private_data->min_peaks); + + printf("\n\nfound %i crystals in image\n", indexed); + return indexed; +} + +void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, + struct pinkIndexer_options *pinkIndexer_opts) +{ + printf("preparing pink indexer\n"); + + if (pinkIndexer_opts->beamEnergy == 0.0 || pinkIndexer_opts->detectorDistance <= 0) { + ERROR("ERROR!!!!!! photon_energy and photon_energy_bandwidth must be defined as constants " + "in the geometry file for the pinkIndexer!!!!!!"); + } + if (pinkIndexer_opts->beamBandwidth == 0.0) { + printf("using default bandwidth of 0.01 for pinkIndexer!"); + pinkIndexer_opts->beamBandwidth = 0.01; + } + if (pinkIndexer_opts->detectorDistance == 0.0 && 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); + + printf("reduced cell:\n"); + cell_print(primitiveCell); + + 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 = pinkIndexer_opts->detectorDistance; + float beamEenergy_eV = pinkIndexer_opts->beamEnergy; + float nonMonochromaticity = pinkIndexer_opts->beamBandwidth; + 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) +{ + printf("cleaning up pink indexer\n"); + + 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) +{ + 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 */ diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h new file mode 100644 index 00000000..cd2aaba2 --- /dev/null +++ b/libcrystfel/src/pinkindexer.h @@ -0,0 +1,46 @@ +/* + * pinkIndexer.h + * + * Created on: Nov 27, 2017 + * Author: gevorkov + */ + +#ifndef LIBCRYSTFEL_SRC_PINKINDEXER_H_ +#define LIBCRYSTFEL_SRC_PINKINDEXER_H_ + +#ifdef HAVE_CONFIG_H +#include <config.h> +#endif + +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 beamEnergy; //in eV + float beamBandwidth; //(delta lambda)/lambda + float detectorDistance; //in m + + float reflectionRadius; //in 1/A +}; + +#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); + +extern void pinkIndexer_cleanup(void *pp); + +extern const char *pinkIndexer_probe(UnitCell *cell); + +#endif /* LIBCRYSTFEL_SRC_PINKINDEXER_H_ */ |