Added ability to save a cluster larger than we search for

- NDView operator()(size_t) now returns a view with one less dimension
- Apply calibration takes also a 2D array and then ignores pixels that
switch
- Calculate pedestal from a dataset which contains all three gains 
- G0 variant of pedestal
- Function to count pixels switching

include/aare/ClusterFinder.hpp

@@ -19,9 +19,11 @@ class ClusterFinder {
     const PEDESTAL_TYPE c3;
     Pedestal<PEDESTAL_TYPE> m_pedestal;
     ClusterVector<ClusterType> m_clusters;
+    const uint32_t ClusterSizeX;
+    const uint32_t ClusterSizeY;
 
-    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:
@@ -34,10 +36,12 @@ 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]
@@ -74,6 +78,9 @@ 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
@@ -135,18 +142,16 @@ 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_y; ic++) {
+                    for (int ir = -dy2; ir < dy2 + has_center_pixel_y; ir++) {
+                        for (int ic = -dx2; ic < dx2 + has_center_pixel_y; ic++) {
                             if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                                 iy + ir >= 0 && iy + ir < frame.shape(0)) {
-                                CT tmp =
-                                    static_cast<CT>(frame(iy + ir, ix + ic)) -
-                                    static_cast<CT>(
-                                        m_pedestal.mean(iy + ir, ix + ic));
-                                cluster.data[i] =
-                                    tmp; // Watch for out of bounds access
-                                i++;
+                                    
+                                CT tmp = static_cast<CT>(frame(iy + ir, ix + ic)) - static_cast<CT>(m_pedestal.mean(iy + ir, ix + ic));
+                                cluster.data[i] = tmp; // Watch for out of bounds access
+                                
                             }
+                            i++;
                         }
                     }
 

include/aare/ClusterFinderMT.hpp

@@ -121,7 +121,8 @@ 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: "
@@ -134,7 +135,7 @@ 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

@@ -26,24 +26,24 @@ def _get_class(name, cluster_size, dtype):
 
 
 
-def ClusterFinder(image_size, cluster_size, n_sigma=5, dtype = np.int32, capacity = 1024):
+def ClusterFinder(image_size, saved_cluster_size, checked_cluster_size, 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])
 
 
 

python/src/bind_ClusterFinder.hpp

@@ -30,8 +30,9 @@ 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

@@ -30,9 +30,10 @@ 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) {

python/src/module.cpp

@@ -84,4 +84,9 @@ PYBIND11_MODULE(_aare, m) {
     DEFINE_CLUSTER_BINDINGS(int, 9, 9, uint16_t, i);
     DEFINE_CLUSTER_BINDINGS(double, 9, 9, uint16_t, d);
     DEFINE_CLUSTER_BINDINGS(float, 9, 9, uint16_t, f);
+
+    DEFINE_CLUSTER_BINDINGS(int, 21, 21, uint16_t, i);
+    DEFINE_CLUSTER_BINDINGS(double, 21, 21, uint16_t, d);
+    DEFINE_CLUSTER_BINDINGS(float, 21, 21, uint16_t, f);
+    
 }