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-rw-r--r--libcrystfel/src/peaks.c106
-rw-r--r--libcrystfel/src/peaks.h6
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);