missed some refactoring of datatypes

include/aare/Cluster.hpp

@@ -100,8 +100,8 @@ struct is_cluster<Cluster<T, X, Y, CoordType>> : std::true_type {}; // Cluster
 
 template <typename T> constexpr bool is_cluster_v = is_cluster<T>::value;
 
-template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
+template <typename ClusterType>
+// typename = std::enable_if_t<is_cluster_v<ClusterType>>>
 struct extract_template_arguments; // Forward declaration
 
 // helper struct to extract template argument
@@ -110,7 +110,7 @@ template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
 struct extract_template_arguments<
     Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
 
-    using type = T;
+    using value_type = T;
     static constexpr int cluster_size_x = ClusterSizeX;
     static constexpr int cluster_size_y = ClusterSizeY;
     using coordtype = CoordType;

include/aare/ClusterCollector.hpp

@@ -35,7 +35,7 @@ class ClusterCollector {
     }
 
   public:
-    ClusterCollector(ClusterFinderMT<uint16_t, double, int32_t> *source) {
+    ClusterCollector(ClusterFinderMT<ClusterType, uint16_t, double> *source) {
         m_source = source->sink();
         m_thread = std::thread(&ClusterCollector::process, this);
     }

include/aare/ClusterFileSink.hpp

@@ -10,8 +10,8 @@
 namespace aare {
 
 template <typename ClusterType,
-          typename = std::enable_if_t <
-                     is_cluster_v<ClusterType> class ClusterFileSink {
+          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
+class ClusterFileSink {
     ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_stopped{true};
@@ -46,7 +46,7 @@ template <typename ClusterType,
     }
 
   public:
-    ClusterFileSink(ClusterFinderMT<uint16_t, double, int32_t> *source,
+    ClusterFileSink(ClusterFinderMT<ClusterType, uint16_t, double> *source,
                     const std::filesystem::path &fname) {
         m_source = source->sink();
         m_thread = std::thread(&ClusterFileSink::process, this);

include/aare/ClusterFinder.hpp

@@ -10,16 +10,21 @@
 
 namespace aare {
 
-template <typename CT = int32_t, uint8_t ClusterSizeX = 3,
-          uint8_t ClusterSizeY = 3, typename FRAME_TYPE = uint16_t,
-          typename PEDESTAL_TYPE = double>
+template <typename ClusterType = Cluster<int32_t, 3, 3>,
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinder {
     Shape<2> m_image_size;
     const PEDESTAL_TYPE m_nSigma;
     const PEDESTAL_TYPE c2;
     const PEDESTAL_TYPE c3;
     Pedestal<PEDESTAL_TYPE> m_pedestal;
-    ClusterVector<Cluster<CT, ClusterSizeX, ClusterSizeY>> m_clusters;
+    ClusterVector<ClusterType> m_clusters;
+
+    static const uint8_t ClusterSizeX =
+        extract_template_arguments<ClusterType>::cluster_size_x;
+    static const uint8_t ClusterSizeY =
+        extract_template_arguments<ClusterType>::cluster_size_x;
+    using CT = typename extract_template_arguments<ClusterType>::value_type;
 
   public:
     /**
@@ -52,16 +57,13 @@ class ClusterFinder {
      * same capacity as the old one
      *
      */
-    ClusterVector<Cluster<CT, ClusterSizeX, ClusterSizeY>>
+    ClusterVector<ClusterType>
     steal_clusters(bool realloc_same_capacity = false) {
-        ClusterVector<Cluster<CT, ClusterSizeX, ClusterSizeY>> tmp =
-            std::move(m_clusters);
+        ClusterVector<ClusterType> tmp = std::move(m_clusters);
         if (realloc_same_capacity)
-            m_clusters = ClusterVector<Cluster<CT, ClusterSizeX, ClusterSizeY>>(
-                tmp.capacity());
+            m_clusters = ClusterVector<ClusterType>(tmp.capacity());
         else
-            m_clusters =
-                ClusterVector<Cluster<CT, ClusterSizeX, ClusterSizeY>>{};
+            m_clusters = ClusterVector<ClusterType>{};
         return tmp;
     }
     void find_clusters(NDView<FRAME_TYPE, 2> frame, uint64_t frame_number = 0) {
@@ -147,8 +149,7 @@ class ClusterFinder {
 
                     // Add the cluster to the output ClusterVector
                     m_clusters.push_back(
-                        Cluster<CT, ClusterSizeX, ClusterSizeY>{
-                            ix, iy, cluster_data.data()});
+                        ClusterType{ix, iy, cluster_data.data()});
                 }
             }
         }

include/aare/ClusterFinderMT.hpp

@@ -30,14 +30,16 @@ struct FrameWrapper {
  * @tparam PEDESTAL_TYPE type of the pedestal data
  * @tparam CT type of the cluster data
  */
-template <typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double,
-          typename CT = int32_t>
+template <typename ClusterType = Cluster<int32_t, 3, 3>,
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinderMT {
+
+    using CT = typename extract_template_arguments<ClusterType>::value_type;
     size_t m_current_thread{0};
     size_t m_n_threads{0};
-    using Finder = ClusterFinder<FRAME_TYPE, PEDESTAL_TYPE, CT>;
+    using Finder = ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>;
     using InputQueue = ProducerConsumerQueue<FrameWrapper>;
-    using OutputQueue = ProducerConsumerQueue<ClusterVector<int>>;
+    using OutputQueue = ProducerConsumerQueue<ClusterVector<ClusterType>>;
     std::vector<std::unique_ptr<InputQueue>> m_input_queues;
     std::vector<std::unique_ptr<OutputQueue>> m_output_queues;
 
@@ -66,7 +68,8 @@ class ClusterFinderMT {
                 switch (frame->type) {
                 case FrameType::DATA:
                     cf->find_clusters(frame->data.view(), frame->frame_number);
-                    m_output_queues[thread_id]->write(cf->steal_clusters(realloc_same_capacity));
+                    m_output_queues[thread_id]->write(
+                        cf->steal_clusters(realloc_same_capacity));
                     break;
 
                 case FrameType::PEDESTAL:
@@ -127,15 +130,18 @@ class ClusterFinderMT {
             m_input_queues.emplace_back(std::make_unique<InputQueue>(200));
             m_output_queues.emplace_back(std::make_unique<OutputQueue>(200));
         }
-        //TODO! Should we start automatically?
+        // TODO! Should we start automatically?
         start();
     }
 
     /**
      * @brief Return the sink queue where all the clusters are collected
-     * @warning You need to empty this queue otherwise the cluster finder will wait forever
+     * @warning You need to empty this queue otherwise the cluster finder will
+     * wait forever
      */
-    ProducerConsumerQueue<ClusterVector<int>> *sink() { return &m_sink; }
+    ProducerConsumerQueue<ClusterVector<ClusterType>> *sink() {
+        return &m_sink;
+    }
 
     /**
      * @brief Start all processing threads

include/aare/ClusterVector.hpp

@@ -148,6 +148,20 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
         return sums;
     }
 
+    /**
+     * @brief Sum the pixels in the 2x2 subcluster with the biggest pixel sum in
+     * each cluster
+     * @return std::vector<T> vector of sums for each cluster
+     */ //TODO if underlying container is a vector use std::for_each
+    std::vector<T> sum_2x2() {
+        std::vector<T> sums_2x2(m_size);
+
+        for (size_t i = 0; i < m_size; i++) {
+            sums_2x2[i] = at(i).max_sum_2x2;
+        }
+        return sums_2x2;
+    }
+
     /**
      * @brief Return the number of clusters in the vector
      */

include/aare/GainMap.hpp

@@ -26,7 +26,6 @@ class GainMap {
               typename = std::enable_if_t<is_cluster_v<ClusterType>>>
     void apply_gain_map(ClusterVector<ClusterType> &clustervec) {
         // in principle we need to know the size of the image for this lookup
-        // TODO! check orientations
         size_t ClusterSizeX = clustervec.cluster_size_x();
         size_t ClusterSizeY = clustervec.cluster_size_y();