diff options
Diffstat (limited to 'libcrystfel/src')
| -rw-r--r-- | libcrystfel/src/peaks.c | 106 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.h | 6 |
2 files changed, 112 insertions, 0 deletions
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index 28c79538..7f6e0ba7 100644 --- a/libcrystfel/src/peaks.c +++ b/libcrystfel/src/peaks.c @@ -13,6 +13,7 @@ * 2011 Andrew Martin <andrew.martin@desy.de> * 2011 Richard Kirian * 2017 Valerio Mariani <valerio.mariani@desy.de> + * 2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> * * This file is part of CrystFEL. * @@ -563,6 +564,111 @@ int search_peaks_peakfinder8(struct image *image, int max_n_peaks, } +//#define HAVE_FDIP +#ifdef HAVE_FDIP + +#include "fastDiffractionImageProcessing/adaptions/crystfel/peakFinder9.h" +#include "fastDiffractionImageProcessing/adaptions/crystfel/mask.h" +#include "fastDiffractionImageProcessing/peakList.h" + +#include "fastDiffractionImageProcessing/peakFinder9.h" //debug, only for eclipse +#include "fastDiffractionImageProcessing/detectorRawFormat.h" //debug, only for eclipse + +int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix, + float sig_fac_peak_pix, float sig_fac_whole_peak, float min_sig, + float min_peak_over_neighbour, int window_radius) +{ + if (image->features != NULL) { + image_feature_list_free(image->features); + } + image->features = image_feature_list_new(); + image->num_peaks = 0; + image->num_saturated_peaks = 0; + + peakFinder9_accuracyConstants_t accuracy_consts; + accuracy_consts.sigmaFactorBiggestPixel = sig_fac_biggest_pix; + accuracy_consts.sigmaFactorPeakPixel = sig_fac_peak_pix; + accuracy_consts.sigmaFactorWholePeak = sig_fac_whole_peak; + accuracy_consts.minimumSigma = min_sig; + accuracy_consts.minimumPeakOversizeOverNeighbours = + min_peak_over_neighbour; + accuracy_consts.windowRadius = (unsigned int) window_radius; + + long NpeaksMax = 10000; //more peaks per panel should not appear + + float *data_copy = NULL, *data_copy_new; + peakList_t peakList; + if (allocatePeakList(&peakList, NpeaksMax)) { + return 1; + } + + for (int panel_number = 0; panel_number < image->det->n_panels; + panel_number++) { + + if (image->det->panels[panel_number].no_index) + continue; + + int w = image->det->panels[panel_number].w; + int h = image->det->panels[panel_number].h; + + detectorRawFormat_t det_size_one_panel; + det_size_one_panel.asic_nx = w; + det_size_one_panel.asic_ny = h; + det_size_one_panel.nasics_x = 1; + det_size_one_panel.nasics_y = 1; + det_size_one_panel.pix_nx = w; + det_size_one_panel.pix_ny = h; + det_size_one_panel.pix_nn = w * h; + + data_copy_new = (float*) realloc(data_copy, + w * h * sizeof(*data_copy)); + if (data_copy_new == NULL) { + if (data_copy != NULL) + free(data_copy); + freePeakList(peakList); + return 1; + } + else { + data_copy = data_copy_new; + } + + mergeMaskAndDataIntoDataCopy(image->dp[panel_number], data_copy, + image->bad[panel_number], + &det_size_one_panel); + + peakList.peakCount = 0; + image->num_peaks += peakFinder9_onePanel_noSlab(data_copy, + &accuracy_consts, + &det_size_one_panel, &peakList); + + for (int peak_number = 0; peak_number < peakList.peakCount; + peak_number++) { + image_add_feature(image->features, + peakList.centerOfMass_rawX[peak_number], + peakList.centerOfMass_rawY[peak_number], + &image->det->panels[panel_number], + image, + peakList.totalIntensity[peak_number], + NULL); + } + + } + + freePeakList(peakList); + free(data_copy); + return 0; +} +#else +int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix, + float sig_fac_peak_pix, float sig_fac_whole_peak, float min_sig, + float min_peak_over_neighbour, int window_radius) +{ + ERROR("This copy of CrystFEL was compiled without peakfinder9 support.\n"); + return 0; +} +#endif // HAVE_FDIP + + int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst) { int n_feat = 0; diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h index a5095127..e63287d4 100644 --- a/libcrystfel/src/peaks.h +++ b/libcrystfel/src/peaks.h @@ -9,6 +9,7 @@ * Authors: * 2010-2015 Thomas White <taw@physics.org> * 2017 Valerio Mariani <valerio.mariani@desy.de> + * 2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> * * This file is part of CrystFEL. * @@ -55,6 +56,11 @@ extern int search_peaks_peakfinder8(struct image *image, int max_n_peaks, int local_bg_radius, int min_res, int max_res, int use_saturated); +extern int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix, + float sig_fac_peak_pix, float sig_fac_whole_peak, float min_sig, + float min_peak_over_neighbour, int window_radius); + + extern int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst); |