Add "peakfinder9"

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);