Fresh branch with up-to-date changes from Main. Changes from fix/rounding have also been implemented here. This commit also includes the changes necessary so that the cluster finder can search for NxN clusters while saving MxM which greatly improves performance and the efficiency of pile-up rejection later down the line

include/aare/ClusterFinder.hpp

@@ -26,11 +26,13 @@ class ClusterFinder {
     const PEDESTAL_TYPE m_nSigma;
     const PEDESTAL_TYPE c2;
     const PEDESTAL_TYPE c3;
+    const uint32_t ClusterSizeX;
+    const uint32_t ClusterSizeY;
     Pedestal<PEDESTAL_TYPE> m_pedestal;
     ClusterVector<ClusterType> m_clusters;
 
-    static const uint8_t ClusterSizeX = ClusterType::cluster_size_x;
-    static const uint8_t ClusterSizeY = ClusterType::cluster_size_y;
+    static const uint8_t SavedClusterSizeX = ClusterType::cluster_size_x;
+    static const uint8_t SavedClusterSizeY = ClusterType::cluster_size_y;
     using CT = typename ClusterType::value_type;
 
   public:
@@ -43,10 +45,12 @@ class ClusterFinder {
      *
      */
     ClusterFinder(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                  size_t capacity = 1000000)
+                  size_t capacity = 1000000,
+                  uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_image_size(image_size), m_nSigma(nSigma),
-          c2(sqrt((ClusterSizeY + 1) / 2 * (ClusterSizeX + 1) / 2)),
-          c3(sqrt(ClusterSizeX * ClusterSizeY)),
+          c2(sqrt((cluster_size_y + 1) / 2 * (cluster_size_x + 1) / 2)),
+          c3(sqrt(cluster_size_x * cluster_size_y)),
+          ClusterSizeX(cluster_size_x), ClusterSizeY(cluster_size_y),
           m_pedestal(image_size[0], image_size[1]), m_clusters(capacity) {
         LOG(logDEBUG) << "ClusterFinder: "
                       << "image_size: " << image_size[0] << "x" << image_size[1]
@@ -83,6 +87,9 @@ class ClusterFinder {
         // //  4,4 -> +/- 2
         int dy = ClusterSizeY / 2;
         int dx = ClusterSizeX / 2;
+        int dy2 = SavedClusterSizeY / 2;
+        int dx2 = SavedClusterSizeX / 2;
+
         int has_center_pixel_x =
             ClusterSizeX %
             2; // for even sized clusters there is no proper cluster center and
@@ -144,8 +151,8 @@ class ClusterFinder {
                     // It's worth redoing the look since most of the time we
                     // don't have a photon
                     int i = 0;
-                    for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                        for (int ic = -dx; ic < dx + has_center_pixel_x; ic++) {
+                    for (int ir = -dy2; ir < dy2 + has_center_pixel_y; ir++) {
+                        for (int ic = -dx2; ic < dx2 + has_center_pixel_x; ic++) {
                             if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                                 iy + ir >= 0 && iy + ir < frame.shape(0)) {
 

include/aare/ClusterFinderMT.hpp

@@ -126,7 +126,8 @@ class ClusterFinderMT {
      * @param n_threads number of threads to use
      */
     ClusterFinderMT(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                    size_t capacity = 2000, size_t n_threads = 3)
+                    size_t capacity = 2000, size_t n_threads = 3,
+                    uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_n_threads(n_threads) {
 
         LOG(logDEBUG1) << "ClusterFinderMT: "
@@ -139,7 +140,7 @@ class ClusterFinderMT {
             m_cluster_finders.push_back(
                 std::make_unique<
                     ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>>(
-                    image_size, nSigma, capacity));
+                    image_size, nSigma, capacity, cluster_size_x, cluster_size_y));
         }
         for (size_t i = 0; i < n_threads; i++) {
             m_input_queues.emplace_back(std::make_unique<InputQueue>(200));

python/aare/ClusterFinder.py

@@ -29,24 +29,24 @@ def _get_class(name, cluster_size, dtype):
 
 
 
-def ClusterFinder(image_size, cluster_size=(3,3), n_sigma=5, dtype = np.int32, capacity = 1024):
+def ClusterFinder(image_size, saved_cluster_size=(3,3), checked_cluster_size=(3,3), n_sigma=5, dtype = np.int32, capacity = 1024):
     """
     Factory function to create a ClusterFinder object. Provides a cleaner syntax for 
     the templated ClusterFinder in C++.
     """
-    cls = _get_class("ClusterFinder", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity)
+    cls = _get_class("ClusterFinder", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 
-def ClusterFinderMT(image_size, cluster_size = (3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3): 
+def ClusterFinderMT(image_size, saved_cluster_size=(3,3), checked_cluster_size=(3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3): 
     """ 
     Factory function to create a ClusterFinderMT object. Provides a cleaner syntax for 
     the templated ClusterFinderMT in C++.
     """
 
-    cls = _get_class("ClusterFinderMT", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads)
+    cls = _get_class("ClusterFinderMT", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads, cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 def ClusterCollector(clusterfindermt, dtype=np.int32): 

python/src/bind_ClusterFinder.hpp

@@ -31,8 +31,9 @@ void define_ClusterFinder(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinder<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t>(), py::arg("image_size"),
-             py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000)
+        .def(py::init<Shape<2>, pd_type, size_t, uint32_t, uint32_t>(), py::arg("image_size"),
+             py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {

python/src/bind_ClusterFinderMT.hpp

@@ -31,9 +31,10 @@ void define_ClusterFinderMT(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinderMT<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t, size_t>(),
+        .def(py::init<Shape<2>, pd_type, size_t, size_t, uint32_t, uint32_t>(),
              py::arg("image_size"), py::arg("n_sigma") = 5.0,
-             py::arg("capacity") = 2048, py::arg("n_threads") = 3)
+             py::arg("capacity") = 2048, py::arg("n_threads") = 3,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {