README.md

@@ -25,7 +25,7 @@ conda activate test-dap
 Clone and install dap
 
 ```bash
-git clone https://gitlab.psi.ch/sf-daq/dap.git
+git clone https://gitea.psi.ch/sf-daq/dap.git
 cd dap
 make install
 ```

dap/algos/spiana.py

@@ -1,25 +1,42 @@
+import numpy as np
 
-def calc_spi_analysis(results):
+
+def calc_spi_analysis(results, data):
     do_spi_analysis = results.get("do_spi_analysis", False)
     if not do_spi_analysis:
         return
 
-    for k in ("spi_limit", "roi_intensities_normalised"):
+    for k in ("spi_threshold_photon", "spi_threshold_hit_percentage", "roi_x1", "roi_x2", "roi_y1", "roi_y2"):
         if k not in results:
             return
 
-    spi_limit = results["spi_limit"]
-    roi_intensities_normalised = results["roi_intensities_normalised"]
+    spi_threshold_photon         = results["spi_threshold_photon"]
+    spi_threshold_hit_percentage = results["spi_threshold_hit_percentage"]
 
-    number_of_spots = 0
-    for index, (rin, sl) in enumerate(zip(roi_intensities_normalised, spi_limit)):
-        if rin >= sl:
-            number_of_spots += 25 * (index+1)
+    roi_x1 = results["roi_x1"]
+    roi_x2 = results["roi_x2"]
+    roi_y1 = results["roi_y1"]
+    roi_y2 = results["roi_y2"]
 
-    results["number_of_spots"] = number_of_spots
+    if len(roi_x1) == 0:
+        return
 
-    if number_of_spots > 0:
-        results["is_hit_frame"] = True
+    if not (len(roi_x1) == len(roi_x2) == len(roi_y1) == len(roi_y2)):
+        return
+
+    nphotons = 0
+    npixels = 0
+
+    for ix1, ix2, iy1, iy2 in zip(roi_x1, roi_x2, roi_y1, roi_y2):
+        data_roi = data[iy1:iy2, ix1:ix2]
+        nphotons += np.sum(data_roi > spi_threshold_photon)
+        npixels += data_roi.size
+
+    photon_percentage = nphotons / npixels * 100
+    hit = (photon_percentage > spi_threshold_hit_percentage)
+
+    results["number_of_spots"] = photon_percentage
+    results["is_hit_frame"] = bool(hit) # json does not like numpy bool_ scalars
 
 
 

dap/worker.py

@@ -113,7 +113,7 @@ def work(backend_address, accumulator_host, accumulator_port, visualisation_host
         calc_mask_pixels(pfimage, pixel_mask_pf) # changes pfimage in place
         calc_apply_threshold(results, pfimage) # changes pfimage in place
         calc_roi(results, pfimage, pixel_mask_pf)
-        calc_spi_analysis(results)
+        calc_spi_analysis(results, pfimage)
         calc_peakfinder_analysis(results, pfimage, pixel_mask_pf)
 
 # ???

setup.py

@@ -11,6 +11,7 @@ peakfinder8_ext = Extension(
     include_dirs = [peakfinder8_include_dir, numpy.get_include()],
     library_dirs = [peakfinder8_library_dir],
     libraries = ["peakfinder8"],
+    define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],
     language = "c++"
 )