Merge branch 'developer' into fit_scurve

CMakeLists.txt

@@ -39,7 +39,7 @@ set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
 
 # General options
-option(AARE_PYTHON_BINDINGS "Build python bindings" ON)
+option(AARE_PYTHON_BINDINGS "Build python bindings" OFF)
 option(AARE_TESTS "Build tests" OFF)
 option(AARE_BENCHMARKS "Build benchmarks" OFF)
 option(AARE_EXAMPLES "Build examples" OFF)
@@ -340,6 +340,8 @@ endif()
 
 set(PUBLICHEADERS
     include/aare/ArrayExpr.hpp
+    include/aare/CalculateEta.hpp
+    include/aare/Cluster.hpp
     include/aare/ClusterFinder.hpp
     include/aare/ClusterFile.hpp
     include/aare/CtbRawFile.hpp
@@ -352,6 +354,7 @@ set(PUBLICHEADERS
     include/aare/FileInterface.hpp
     include/aare/FilePtr.hpp
     include/aare/Frame.hpp
+    include/aare/GainMap.hpp
     include/aare/geo_helpers.hpp
     include/aare/JungfrauDataFile.hpp
     include/aare/NDArray.hpp
@@ -365,13 +368,11 @@ set(PUBLICHEADERS
     include/aare/RawSubFile.hpp
     include/aare/VarClusterFinder.hpp
     include/aare/utils/task.hpp
-
 )
 
 
 set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
@@ -393,15 +394,12 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
 )
 
-
 add_library(aare_core STATIC ${SourceFiles})
 target_include_directories(aare_core PUBLIC 
     "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" 
     "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" 
 )
 
-
-
 target_link_libraries(
     aare_core 
     PUBLIC 
@@ -410,7 +408,7 @@ target_link_libraries(
     ${STD_FS_LIB} # from helpers.cmake
     PRIVATE 
     aare_compiler_flags 
-    "$<BUILD_INTERFACE:lmfit>"
+    $<BUILD_INTERFACE:lmfit>
 
 )
 
@@ -436,7 +434,10 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterVector.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Cluster.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/CalculateEta.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinderMT.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Pedestal.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp

benchmarks/CMakeLists.txt

@@ -1,11 +1,27 @@
-find_package(benchmark REQUIRED)
 
-add_executable(ndarray_benchmark ndarray_benchmark.cpp)
+include(FetchContent)
 
-target_link_libraries(ndarray_benchmark benchmark::benchmark aare_core aare_compiler_flags)
-# target_link_libraries(tests PRIVATE aare_core aare_compiler_flags)
 
-set_target_properties(ndarray_benchmark PROPERTIES
+FetchContent_Declare(
-        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+    benchmark
-        # OUTPUT_NAME run_tests
+    GIT_REPOSITORY https://github.com/google/benchmark.git
+    GIT_TAG        v1.8.3 # Change to the latest version if needed
+)
+
+# Ensure Google Benchmark is built correctly
+set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "" FORCE)
+
+FetchContent_MakeAvailable(benchmark)
+
+add_executable(benchmarks)
+
+target_sources(benchmarks PRIVATE ndarray_benchmark.cpp calculateeta_benchmark.cpp)
+
+# Link Google Benchmark and other necessary libraries
+target_link_libraries(benchmarks PRIVATE benchmark::benchmark aare_core aare_compiler_flags)
+
+# Set output properties
+set_target_properties(benchmarks PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+    OUTPUT_NAME run_benchmarks
 )

benchmarks/calculateeta_benchmark.cpp

@@ -0,0 +1,70 @@
+#include "aare/CalculateEta.hpp"
+#include "aare/ClusterFile.hpp"
+#include <benchmark/benchmark.h>
+
+using namespace aare;
+
+class ClusterFixture : public benchmark::Fixture {
+  public:
+    Cluster<int, 2, 2> cluster_2x2{};
+    Cluster<int, 3, 3> cluster_3x3{};
+
+  private:
+    using benchmark::Fixture::SetUp;
+
+    void SetUp([[maybe_unused]] const benchmark::State &state) override {
+        int temp_data[4] = {1, 2, 3, 1};
+        std::copy(std::begin(temp_data), std::end(temp_data),
+                  std::begin(cluster_2x2.data));
+
+        cluster_2x2.x = 0;
+        cluster_2x2.y = 0;
+
+        int temp_data2[9] = {1, 2, 3, 1, 3, 4, 5, 1, 20};
+        std::copy(std::begin(temp_data2), std::end(temp_data2),
+                  std::begin(cluster_3x3.data));
+
+        cluster_3x3.x = 0;
+        cluster_3x3.y = 0;
+    }
+
+    // void TearDown(::benchmark::State& state) {
+    // }
+};
+
+BENCHMARK_F(ClusterFixture, Calculate2x2Eta)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2(cluster_2x2);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+// almost takes double the time
+BENCHMARK_F(ClusterFixture,
+            CalculateGeneralEtaFor2x2Cluster)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2<int, 2, 2>(cluster_2x2);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+BENCHMARK_F(ClusterFixture, Calculate3x3Eta)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2(cluster_3x3);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+// almost takes double the time
+BENCHMARK_F(ClusterFixture,
+            CalculateGeneralEtaFor3x3Cluster)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2<int, 3, 3>(cluster_3x3);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+// BENCHMARK_MAIN();

include/aare/CalculateEta.hpp

@@ -0,0 +1,170 @@
+#pragma once
+
+#include "aare/Cluster.hpp"
+#include "aare/ClusterVector.hpp"
+#include "aare/NDArray.hpp"
+
+namespace aare {
+
+enum class corner : int {
+    cBottomLeft = 0,
+    cBottomRight = 1,
+    cTopLeft = 2,
+    cTopRight = 3
+};
+
+enum class pixel : int {
+    pBottomLeft = 0,
+    pBottom = 1,
+    pBottomRight = 2,
+    pLeft = 3,
+    pCenter = 4,
+    pRight = 5,
+    pTopLeft = 6,
+    pTop = 7,
+    pTopRight = 8
+};
+
+template <typename T> struct Eta2 {
+    double x;
+    double y;
+    int c;
+    T sum;
+};
+
+/**
+ * @brief Calculate the eta2 values for all clusters in a Clustervector
+ */
+template <typename ClusterType,
+          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
+NDArray<double, 2> calculate_eta2(const ClusterVector<ClusterType> &clusters) {
+    NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
+
+    for (size_t i = 0; i < clusters.size(); i++) {
+        auto e = calculate_eta2(clusters[i]);
+        eta2(i, 0) = e.x;
+        eta2(i, 1) = e.y;
+    }
+
+    return eta2;
+}
+
+/**
+ * @brief Calculate the eta2 values for a generic sized cluster and return them
+ * in a Eta2 struct containing etay, etax and the index of the respective 2x2
+ * subcluster.
+ */
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
+          typename CoordType>
+Eta2<T>
+calculate_eta2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
+    Eta2<T> eta{};
+
+    auto max_sum = cl.max_sum_2x2();
+    eta.sum = max_sum.first;
+    auto c = max_sum.second;
+
+    size_t cluster_center_index =
+        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
+
+    size_t index_bottom_left_max_2x2_subcluster =
+        (int(c / (ClusterSizeX - 1))) * ClusterSizeX + c % (ClusterSizeX - 1);
+
+    // check that cluster center is in max subcluster
+    if (cluster_center_index != index_bottom_left_max_2x2_subcluster &&
+        cluster_center_index != index_bottom_left_max_2x2_subcluster + 1 &&
+        cluster_center_index !=
+            index_bottom_left_max_2x2_subcluster + ClusterSizeX &&
+        cluster_center_index !=
+            index_bottom_left_max_2x2_subcluster + ClusterSizeX + 1)
+        throw std::runtime_error("Photon center is not in max 2x2_subcluster");
+
+    if ((cluster_center_index - index_bottom_left_max_2x2_subcluster) %
+            ClusterSizeX ==
+        0) {
+        if ((cl.data[cluster_center_index + 1] +
+             cl.data[cluster_center_index]) != 0)
+
+            eta.x = static_cast<double>(cl.data[cluster_center_index + 1]) /
+                    static_cast<double>((cl.data[cluster_center_index + 1] +
+                                         cl.data[cluster_center_index]));
+    } else {
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index - 1]) != 0)
+
+            eta.x = static_cast<double>(cl.data[cluster_center_index]) /
+                    static_cast<double>((cl.data[cluster_center_index - 1] +
+                                         cl.data[cluster_center_index]));
+    }
+    if ((cluster_center_index - index_bottom_left_max_2x2_subcluster) /
+            ClusterSizeX <
+        1) {
+        assert(cluster_center_index + ClusterSizeX <
+               ClusterSizeX * ClusterSizeY); // suppress warning
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index + ClusterSizeX]) != 0)
+            eta.y = static_cast<double>(
+                        cl.data[cluster_center_index + ClusterSizeX]) /
+                    static_cast<double>(
+                        (cl.data[cluster_center_index] +
+                         cl.data[cluster_center_index + ClusterSizeX]));
+    } else {
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index - ClusterSizeX]) != 0)
+            eta.y = static_cast<double>(cl.data[cluster_center_index]) /
+                    static_cast<double>(
+                        (cl.data[cluster_center_index] +
+                         cl.data[cluster_center_index - ClusterSizeX]));
+    }
+
+    eta.c = c; // TODO only supported for 2x2 and 3x3 clusters -> at least no
+               // underyling enum class
+    return eta;
+}
+
+// TODO! Look up eta2 calculation - photon center should be top right corner
+template <typename T>
+Eta2<T> calculate_eta2(const Cluster<T, 2, 2, int16_t> &cl) {
+    Eta2<T> eta{};
+
+    if ((cl.data[0] + cl.data[1]) != 0)
+        eta.x = static_cast<double>(cl.data[1]) / (cl.data[0] + cl.data[1]);
+    if ((cl.data[0] + cl.data[2]) != 0)
+        eta.y = static_cast<double>(cl.data[2]) / (cl.data[0] + cl.data[2]);
+    eta.sum = cl.sum();
+    eta.c = static_cast<int>(corner::cBottomLeft); // TODO! This is not correct,
+                                                   // but need to put something
+    return eta;
+}
+
+// calculates Eta3 for 3x3 cluster based on code from analyze_cluster
+// TODO only supported for 3x3 Clusters
+template <typename T> Eta2<T> calculate_eta3(const Cluster<T, 3, 3> &cl) {
+
+    Eta2<T> eta{};
+
+    T sum = 0;
+
+    std::for_each(std::begin(cl.data), std::end(cl.data),
+                  [&sum](T x) { sum += x; });
+
+    eta.sum = sum;
+
+    eta.c = corner::cBottomLeft;
+
+    if ((cl.data[3] + cl.data[4] + cl.data[5]) != 0)
+
+        eta.x = static_cast<double>(-cl.data[3] + cl.data[3 + 2]) /
+
+                (cl.data[3] + cl.data[4] + cl.data[5]);
+
+    if ((cl.data[1] + cl.data[4] + cl.data[7]) != 0)
+
+        eta.y = static_cast<double>(-cl.data[1] + cl.data[2 * 3 + 1]) /
+
+                (cl.data[1] + cl.data[4] + cl.data[7]);
+
+    return eta;
+}
+
+} // namespace aare

include/aare/Cluster.hpp

@@ -1,36 +1,86 @@
+
+/************************************************
+ * @file Cluster.hpp
+ * @short definition of cluster, where CoordType (x,y) give
+ * the cluster center coordinates and data the actual cluster data
+ * cluster size is given as template parameters
+ ***********************************************/
+
 #pragma once
 
 #include <algorithm>
 #include <array>
-#include <cstddef>
 #include <cstdint>
 #include <numeric>
+#include <type_traits>
 
 namespace aare {
 
-//TODO! Template this? 
+// requires clause c++20 maybe update
-struct Cluster3x3 {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    int16_t x;
+          typename CoordType = int16_t>
-    int16_t y;
+struct Cluster {
-    int32_t data[9];
 
-    int32_t sum_2x2() const{
+    static_assert(std::is_arithmetic_v<T>, "T needs to be an arithmetic type");
-        std::array<int32_t, 4> total;
+    static_assert(std::is_integral_v<CoordType>,
-        total[0] = data[0] + data[1] + data[3] + data[4];
+                  "CoordType needs to be an integral type");
-        total[1] = data[1] + data[2] + data[4] + data[5];
+    static_assert(ClusterSizeX > 0 && ClusterSizeY > 0,
-        total[2] = data[3] + data[4] + data[6] + data[7];
+                  "Cluster sizes must be bigger than zero");
-        total[3] = data[4] + data[5] + data[7] + data[8];
+
-        return *std::max_element(total.begin(), total.end());
+    CoordType x;
+    CoordType y;
+    std::array<T, ClusterSizeX * ClusterSizeY> data;
+
+    static constexpr uint8_t cluster_size_x = ClusterSizeX;
+    static constexpr uint8_t cluster_size_y = ClusterSizeY;
+    using value_type = T;
+    using coord_type = CoordType;
+
+    T sum() const { return std::accumulate(data.begin(), data.end(), T{}); }
+
+    std::pair<T, int> max_sum_2x2() const {
+
+        if constexpr (cluster_size_x == 3 && cluster_size_y == 3) {
+            std::array<T, 4> sum_2x2_subclusters;
+            sum_2x2_subclusters[0] = data[0] + data[1] + data[3] + data[4];
+            sum_2x2_subclusters[1] = data[1] + data[2] + data[4] + data[5];
+            sum_2x2_subclusters[2] = data[3] + data[4] + data[6] + data[7];
+            sum_2x2_subclusters[3] = data[4] + data[5] + data[7] + data[8];
+            int index = std::max_element(sum_2x2_subclusters.begin(),
+                                         sum_2x2_subclusters.end()) -
+                        sum_2x2_subclusters.begin();
+            return std::make_pair(sum_2x2_subclusters[index], index);
+        } else if constexpr (cluster_size_x == 2 && cluster_size_y == 2) {
+            return std::make_pair(data[0] + data[1] + data[2] + data[3], 0);
+        } else {
+            constexpr size_t num_2x2_subclusters =
+                (ClusterSizeX - 1) * (ClusterSizeY - 1);
+
+            std::array<T, num_2x2_subclusters> sum_2x2_subcluster;
+            for (size_t i = 0; i < ClusterSizeY - 1; ++i) {
+                for (size_t j = 0; j < ClusterSizeX - 1; ++j)
+                    sum_2x2_subcluster[i * (ClusterSizeX - 1) + j] =
+                        data[i * ClusterSizeX + j] +
+                        data[i * ClusterSizeX + j + 1] +
+                        data[(i + 1) * ClusterSizeX + j] +
+                        data[(i + 1) * ClusterSizeX + j + 1];
             }
 
-    int32_t sum() const{
+            int index = std::max_element(sum_2x2_subcluster.begin(),
-        return std::accumulate(data, data + 9, 0);
+                                         sum_2x2_subcluster.end()) -
+                        sum_2x2_subcluster.begin();
+            return std::make_pair(sum_2x2_subcluster[index], index);
+        }
     }
 };
-struct Cluster2x2 {
+
-    int16_t x;
+// Type Traits for is_cluster_type
-    int16_t y;
+template <typename T>
-    int32_t data[4];
+struct is_cluster : std::false_type {}; // Default case: Not a Cluster
-};
+
+template <typename T, uint8_t X, uint8_t Y, typename CoordType>
+struct is_cluster<Cluster<T, X, Y, CoordType>> : std::true_type {}; // Cluster
+
+template <typename T> constexpr bool is_cluster_v = is_cluster<T>::value;
 
 } // namespace aare

include/aare/ClusterCollector.hpp

@@ -2,29 +2,31 @@
 #include <atomic>
 #include <thread>
 
-#include "aare/ProducerConsumerQueue.hpp"
-#include "aare/ClusterVector.hpp"
 #include "aare/ClusterFinderMT.hpp"
+#include "aare/ClusterVector.hpp"
+#include "aare/ProducerConsumerQueue.hpp"
 
 namespace aare {
 
-class ClusterCollector{
+template <typename ClusterType,
-        ProducerConsumerQueue<ClusterVector<int>>* m_source;
+          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
+class ClusterCollector {
+    ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_stopped{true};
     std::chrono::milliseconds m_default_wait{1};
     std::thread m_thread;
-        std::vector<ClusterVector<int>> m_clusters;
+    std::vector<ClusterVector<ClusterType>> m_clusters;
 
-    void process(){
+    void process() {
         m_stopped = false;
         fmt::print("ClusterCollector started\n");
         while (!m_stop_requested || !m_source->isEmpty()) {
-            if (ClusterVector<int> *clusters = m_source->frontPtr();
+            if (ClusterVector<ClusterType> *clusters = m_source->frontPtr();
                 clusters != nullptr) {
                 m_clusters.push_back(std::move(*clusters));
                 m_source->popFront();
-            }else{
+            } else {
                 std::this_thread::sleep_for(m_default_wait);
             }
         }
@@ -33,16 +35,20 @@ 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);
+        m_thread =
+            std::thread(&ClusterCollector::process,
+                        this); // only one process does that so why isnt it
+                               // automatically written to m_cluster in collect
+                               // - instead of writing first to m_sink?
     }
-        void stop(){
+    void stop() {
         m_stop_requested = true;
         m_thread.join();
     }
-        std::vector<ClusterVector<int>> steal_clusters(){
+    std::vector<ClusterVector<ClusterType>> steal_clusters() {
-            if(!m_stopped){
+        if (!m_stopped) {
             throw std::runtime_error("ClusterCollector is still running");
         }
         return std::move(m_clusters);

include/aare/ClusterFile.hpp

@@ -2,6 +2,7 @@
 
 #include "aare/Cluster.hpp"
 #include "aare/ClusterVector.hpp"
+#include "aare/GainMap.hpp"
 #include "aare/NDArray.hpp"
 #include "aare/defs.hpp"
 #include <filesystem>
@@ -10,43 +11,18 @@
 
 namespace aare {
 
+/*
+Binary cluster file. Expects data to be layed out as:
+int32_t frame_number
+uint32_t number_of_clusters
+int16_t x, int16_t y, int32_t data[9] x number_of_clusters
+int32_t frame_number
+uint32_t number_of_clusters
+....
+*/
 
-//TODO! Legacy enums, migrate to enum class
+// TODO: change to support any type of clusters, e.g. header line with
-typedef enum {
+// clsuter_size_x, cluster_size_y,
-    cBottomLeft = 0,
-    cBottomRight = 1,
-    cTopLeft = 2,
-    cTopRight = 3
-} corner;
-
-typedef enum {
-    pBottomLeft = 0,
-    pBottom = 1,
-    pBottomRight = 2,
-    pLeft = 3,
-    pCenter = 4,
-    pRight = 5,
-    pTopLeft = 6,
-    pTop = 7,
-    pTopRight = 8
-} pixel;
-
-struct Eta2 {
-    double x;
-    double y;
-    corner c;
-    int32_t sum;
-};
-
-struct ClusterAnalysis {
-    uint32_t c;
-    int32_t tot;
-    double etax;
-    double etay;
-};
-
-
-
 /**
  * @brief Class to read and write cluster files
  * Expects data to be laid out as:
@@ -59,14 +35,19 @@ struct ClusterAnalysis {
  *       uint32_t number_of_clusters
  *       etc.
  */
+template <typename ClusterType,
+          typename Enable = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterFile {
     FILE *fp{};
+    const std::string m_filename{};
     uint32_t m_num_left{};    /*Number of photons left in frame*/
     size_t m_chunk_size{};    /*Number of clusters to read at a time*/
-    const std::string m_mode;         /*Mode to open the file in*/
+    std::string m_mode;       /*Mode to open the file in*/
     std::optional<ROI> m_roi; /*Region of interest, will be applied if set*/
-    std::optional<NDArray<int32_t, 2>> m_noise_map; /*Noise map to cut photons, will be applied if set*/
+    std::optional<NDArray<int32_t, 2>>
-    std::optional<NDArray<double, 2>> m_gain_map; /*Gain map to apply to the clusters, will be applied if set*/
+        m_noise_map; /*Noise map to cut photons, will be applied if set*/
+    std::optional<InvertedGainMap> m_gain_map; /*Gain map to apply to the
+                                          clusters, will be applied if set*/
 
   public:
     /**
@@ -79,30 +60,81 @@ class ClusterFile {
      * @throws std::runtime_error if the file could not be opened
      */
     ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000,
-                const std::string &mode = "r");
+                const std::string &mode = "r")
 
+        : m_filename(fname.string()), m_chunk_size(chunk_size), m_mode(mode) {
 
-    ~ClusterFile();
+        if (mode == "r") {
+            fp = fopen(m_filename.c_str(), "rb");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for reading: " +
+                                         m_filename);
+            }
+        } else if (mode == "w") {
+            fp = fopen(m_filename.c_str(), "wb");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for writing: " +
+                                         m_filename);
+            }
+        } else if (mode == "a") {
+            fp = fopen(m_filename.c_str(), "ab");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for appending: " +
+                                         m_filename);
+            }
+        } else {
+            throw std::runtime_error("Unsupported mode: " + mode);
+        }
+    }
+
+    ~ClusterFile() { close(); }
 
     /**
-     * @brief Read n_clusters clusters from the file discarding frame numbers.
+     * @brief Read n_clusters clusters from the file discarding
-     * If EOF is reached the returned vector will have less than n_clusters
+     * frame numbers. If EOF is reached the returned vector will
-     * clusters
+     * have less than n_clusters clusters
      */
-    ClusterVector<int32_t> read_clusters(size_t n_clusters);
+    ClusterVector<ClusterType> read_clusters(size_t n_clusters) {
-
+        if (m_mode != "r") {
-    ClusterVector<int32_t> read_clusters(size_t n_clusters, ROI roi);
+            throw std::runtime_error("File not opened for reading");
+        }
+        if (m_noise_map || m_roi) {
+            return read_clusters_with_cut(n_clusters);
+        } else {
+            return read_clusters_without_cut(n_clusters);
+        }
+    }
 
     /**
-     * @brief Read a single frame from the file and return the clusters. The
+     * @brief Read a single frame from the file and return the
-     * cluster vector will have the frame number set.
+     * clusters. The cluster vector will have the frame number
-     * @throws std::runtime_error if the file is not opened for reading or the file pointer not
+     * set.
-     * at the beginning of a frame
+     * @throws std::runtime_error if the file is not opened for
+     * reading or the file pointer not at the beginning of a
+     * frame
      */
-    ClusterVector<int32_t> read_frame();
+    ClusterVector<ClusterType> read_frame() {
+        if (m_mode != "r") {
+            throw std::runtime_error(LOCATION + "File not opened for reading");
+        }
+        if (m_noise_map || m_roi) {
+            return read_frame_with_cut();
+        } else {
+            return read_frame_without_cut();
+        }
+    }
 
+    void write_frame(const ClusterVector<ClusterType> &clusters) {
+        if (m_mode != "w" && m_mode != "a") {
+            throw std::runtime_error("File not opened for writing");
+        }
 
-    void write_frame(const ClusterVector<int32_t> &clusters);
+        int32_t frame_number = clusters.frame_number();
+        fwrite(&frame_number, sizeof(frame_number), 1, fp);
+        uint32_t n_clusters = clusters.size();
+        fwrite(&n_clusters, sizeof(n_clusters), 1, fp);
+        fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp);
+    }
 
     /**
      * @brief Return the chunk size
@@ -110,43 +142,308 @@ class ClusterFile {
     size_t chunk_size() const { return m_chunk_size; }
 
     /**
-     * @brief Set the region of interest to use when reading clusters. If set only clusters within
+     * @brief Set the region of interest to use when reading
-     * the ROI will be read.
+     * clusters. If set only clusters within the ROI will be
+     * read.
      */
-    void set_roi(ROI roi);
+    void set_roi(ROI roi) { m_roi = roi; }
 
     /**
-     * @brief Set the noise map to use when reading clusters. If set clusters below the noise
+     * @brief Set the noise map to use when reading clusters. If
-     * level will be discarded. Selection criteria one of: Central pixel above noise, highest
+     * set clusters below the noise level will be discarded.
-     * 2x2 sum above 2 * noise, total sum above 3 * noise.
+     * Selection criteria one of: Central pixel above noise,
+     * highest 2x2 sum above 2 * noise, total sum above 3 *
+     * noise.
      */
-    void set_noise_map(const NDView<int32_t, 2> noise_map);
+    void set_noise_map(const NDView<int32_t, 2> noise_map) {
+        m_noise_map = NDArray<int32_t, 2>(noise_map);
+    }
 
     /**
-     * @brief Set the gain map to use when reading clusters. If set the gain map will be applied
+     * @brief Set the gain map to use when reading clusters. If set the gain map
-     * to the clusters that pass ROI and noise_map selection. The gain map is expected to be in ADU/energy.
+     * will be applied to the clusters that pass ROI and noise_map selection.
+     * The gain map is expected to be in ADU/energy.
      */
-    void set_gain_map(const NDView<double, 2> gain_map);
+    void set_gain_map(const NDView<double, 2> gain_map) {
+        m_gain_map = InvertedGainMap(gain_map);
+    }
 
+    void set_gain_map(const InvertedGainMap &gain_map) {
+        m_gain_map = gain_map;
+    }
+
+    void set_gain_map(const InvertedGainMap &&gain_map) {
+        m_gain_map = gain_map;
+    }
 
     /**
-     * @brief Close the file. If not closed the file will be closed in the destructor
+     * @brief Close the file. If not closed the file will be
+     * closed in the destructor
      */
-    void close();
+    void close() {
+        if (fp) {
+            fclose(fp);
+            fp = nullptr;
+        }
+    }
+
+    /** @brief Open the file in specific mode
+     *
+     */
+    void open(const std::string &mode) {
+        if (fp) {
+            close();
+        }
+
+        if (mode == "r") {
+            fp = fopen(m_filename.c_str(), "rb");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for reading: " +
+                                         m_filename);
+            }
+            m_mode = "r";
+        } else if (mode == "w") {
+            fp = fopen(m_filename.c_str(), "wb");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for writing: " +
+                                         m_filename);
+            }
+            m_mode = "w";
+        } else if (mode == "a") {
+            fp = fopen(m_filename.c_str(), "ab");
+            if (!fp) {
+                throw std::runtime_error("Could not open file for appending: " +
+                                         m_filename);
+            }
+            m_mode = "a";
+        } else {
+            throw std::runtime_error("Unsupported mode: " + mode);
+        }
+    }
 
   private:
-        ClusterVector<int32_t> read_clusters_with_cut(size_t n_clusters);
+    ClusterVector<ClusterType> read_clusters_with_cut(size_t n_clusters);
-        ClusterVector<int32_t> read_clusters_without_cut(size_t n_clusters);
+    ClusterVector<ClusterType> read_clusters_without_cut(size_t n_clusters);
-        ClusterVector<int32_t> read_frame_with_cut();
+    ClusterVector<ClusterType> read_frame_with_cut();
-        ClusterVector<int32_t> read_frame_without_cut();
+    ClusterVector<ClusterType> read_frame_without_cut();
-        bool is_selected(Cluster3x3 &cl);
+    bool is_selected(ClusterType &cl);
-        Cluster3x3 read_one_cluster();
+    ClusterType read_one_cluster();
 };
 
-//TODO! helper functions that doesn't really belong here
+template <typename ClusterType, typename Enable>
-NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters);
+ClusterVector<ClusterType>
-Eta2 calculate_eta2(Cluster3x3 &cl);
+ClusterFile<ClusterType, Enable>::read_clusters_without_cut(size_t n_clusters) {
-Eta2 calculate_eta2(Cluster2x2 &cl);
+    if (m_mode != "r") {
+        throw std::runtime_error("File not opened for reading");
+    }
 
+    ClusterVector<ClusterType> clusters(n_clusters);
+    clusters.resize(n_clusters);
+
+    int32_t iframe = 0; // frame number needs to be 4 bytes!
+    size_t nph_read = 0;
+    uint32_t nn = m_num_left;
+    uint32_t nph = m_num_left; // number of clusters in frame needs to be 4
+
+    auto buf = clusters.data();
+    // if there are photons left from previous frame read them first
+    if (nph) {
+        if (nph > n_clusters) {
+            // if we have more photons left in the frame then photons to
+            // read we read directly the requested number
+            nn = n_clusters;
+        } else {
+            nn = nph;
+        }
+        nph_read += fread((buf + nph_read), clusters.item_size(), nn, fp);
+        m_num_left = nph - nn; // write back the number of photons left
+    }
+
+    if (nph_read < n_clusters) {
+        // keep on reading frames and photons until reaching n_clusters
+        while (fread(&iframe, sizeof(iframe), 1, fp)) {
+            clusters.set_frame_number(iframe);
+            // read number of clusters in frame
+            if (fread(&nph, sizeof(nph), 1, fp)) {
+                if (nph > (n_clusters - nph_read))
+                    nn = n_clusters - nph_read;
+                else
+                    nn = nph;
+
+                nph_read +=
+                    fread((buf + nph_read), clusters.item_size(), nn, fp);
+                m_num_left = nph - nn;
+            }
+            if (nph_read >= n_clusters)
+                break;
+        }
+    }
+
+    // Resize the vector to the number o f clusters.
+    // No new allocation, only change bounds.
+    clusters.resize(nph_read);
+    if (m_gain_map)
+        m_gain_map->apply_gain_map(clusters);
+    return clusters;
+}
+
+template <typename ClusterType, typename Enable>
+ClusterVector<ClusterType>
+ClusterFile<ClusterType, Enable>::read_clusters_with_cut(size_t n_clusters) {
+    ClusterVector<ClusterType> clusters;
+    clusters.reserve(n_clusters);
+
+    // if there are photons left from previous frame read them first
+    if (m_num_left) {
+        while (m_num_left && clusters.size() < n_clusters) {
+            ClusterType c = read_one_cluster();
+            if (is_selected(c)) {
+                clusters.push_back(c);
+            }
+        }
+    }
+
+    // we did not have enough clusters left in the previous frame
+    // keep on reading frames until reaching n_clusters
+    if (clusters.size() < n_clusters) {
+        // sanity check
+        if (m_num_left) {
+            throw std::runtime_error(
+                LOCATION + "Entered second loop with clusters left\n");
+        }
+
+        int32_t frame_number = 0; // frame number needs to be 4 bytes!
+        while (fread(&frame_number, sizeof(frame_number), 1, fp)) {
+            if (fread(&m_num_left, sizeof(m_num_left), 1, fp)) {
+                clusters.set_frame_number(
+                    frame_number); // cluster vector will hold the last
+                                   // frame number
+                while (m_num_left && clusters.size() < n_clusters) {
+                    ClusterType c = read_one_cluster();
+                    if (is_selected(c)) {
+                        clusters.push_back(c);
+                    }
+                }
+            }
+
+            // we have enough clusters, break out of the outer while loop
+            if (clusters.size() >= n_clusters)
+                break;
+        }
+    }
+    if (m_gain_map)
+        m_gain_map->apply_gain_map(clusters);
+
+    return clusters;
+}
+
+template <typename ClusterType, typename Enable>
+ClusterType ClusterFile<ClusterType, Enable>::read_one_cluster() {
+    ClusterType c;
+    auto rc = fread(&c, sizeof(c), 1, fp);
+    if (rc != 1) {
+        throw std::runtime_error(LOCATION + "Could not read cluster");
+    }
+    --m_num_left;
+    return c;
+}
+
+template <typename ClusterType, typename Enable>
+ClusterVector<ClusterType>
+ClusterFile<ClusterType, Enable>::read_frame_without_cut() {
+    if (m_mode != "r") {
+        throw std::runtime_error("File not opened for reading");
+    }
+    if (m_num_left) {
+        throw std::runtime_error(
+            "There are still photons left in the last frame");
+    }
+    int32_t frame_number;
+    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
+        throw std::runtime_error(LOCATION + "Could not read frame number");
+    }
+
+    int32_t n_clusters; // Saved as 32bit integer in the cluster file
+    if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
+        throw std::runtime_error(LOCATION +
+                                 "Could not read number of clusters");
+    }
+
+    ClusterVector<ClusterType> clusters(n_clusters);
+    clusters.set_frame_number(frame_number);
+
+    clusters.resize(n_clusters);
+
+    if (fread(clusters.data(), clusters.item_size(), n_clusters, fp) !=
+        static_cast<size_t>(n_clusters)) {
+        throw std::runtime_error(LOCATION + "Could not read clusters");
+    }
+
+    if (m_gain_map)
+        m_gain_map->apply_gain_map(clusters);
+    return clusters;
+}
+
+template <typename ClusterType, typename Enable>
+ClusterVector<ClusterType>
+ClusterFile<ClusterType, Enable>::read_frame_with_cut() {
+    if (m_mode != "r") {
+        throw std::runtime_error("File not opened for reading");
+    }
+    if (m_num_left) {
+        throw std::runtime_error(
+            "There are still photons left in the last frame");
+    }
+    int32_t frame_number;
+    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
+        throw std::runtime_error("Could not read frame number");
+    }
+
+    if (fread(&m_num_left, sizeof(m_num_left), 1, fp) != 1) {
+        throw std::runtime_error("Could not read number of clusters");
+    }
+
+    ClusterVector<ClusterType> clusters;
+    clusters.reserve(m_num_left);
+    clusters.set_frame_number(frame_number);
+    while (m_num_left) {
+        ClusterType c = read_one_cluster();
+        if (is_selected(c)) {
+            clusters.push_back(c);
+        }
+    }
+    if (m_gain_map)
+        m_gain_map->apply_gain_map(clusters);
+    return clusters;
+}
+
+template <typename ClusterType, typename Enable>
+bool ClusterFile<ClusterType, Enable>::is_selected(ClusterType &cl) {
+    // Should fail fast
+    if (m_roi) {
+        if (!(m_roi->contains(cl.x, cl.y))) {
+            return false;
+        }
+    }
+
+    size_t cluster_center_index =
+        (ClusterType::cluster_size_x / 2) +
+        (ClusterType::cluster_size_y / 2) * ClusterType::cluster_size_x;
+
+    if (m_noise_map) {
+        auto sum_1x1 = cl.data[cluster_center_index]; // central pixel
+        auto sum_2x2 = cl.max_sum_2x2().first; // highest sum of 2x2 subclusters
+        auto total_sum = cl.sum();             // sum of all pixels
+
+        auto noise =
+            (*m_noise_map)(cl.y, cl.x); // TODO! check if this is correct
+        if (sum_1x1 <= noise || sum_2x2 <= 2 * noise ||
+            total_sum <= 3 * noise) {
+            return false;
+        }
+    }
+    // we passed all checks
+    return true;
+}
 
 } // namespace aare

include/aare/ClusterFileSink.hpp

@@ -3,35 +3,41 @@
 #include <filesystem>
 #include <thread>
 
-#include "aare/ProducerConsumerQueue.hpp"
-#include "aare/ClusterVector.hpp"
 #include "aare/ClusterFinderMT.hpp"
+#include "aare/ClusterVector.hpp"
+#include "aare/ProducerConsumerQueue.hpp"
 
-namespace aare{
+namespace aare {
 
-class ClusterFileSink{
+template <typename ClusterType,
-    ProducerConsumerQueue<ClusterVector<int>>* m_source;
+          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};
     std::chrono::milliseconds m_default_wait{1};
     std::thread m_thread;
     std::ofstream m_file;
 
-
+    void process() {
-    void process(){
         m_stopped = false;
         fmt::print("ClusterFileSink started\n");
         while (!m_stop_requested || !m_source->isEmpty()) {
-            if (ClusterVector<int> *clusters = m_source->frontPtr();
+            if (ClusterVector<ClusterType> *clusters = m_source->frontPtr();
                 clusters != nullptr) {
                 // Write clusters to file
-                int32_t frame_number = clusters->frame_number(); //TODO! Should we store frame number already as int?
+                int32_t frame_number =
+                    clusters->frame_number(); // TODO! Should we store frame
+                                              // number already as int?
                 uint32_t num_clusters = clusters->size();
-                m_file.write(reinterpret_cast<const char*>(&frame_number), sizeof(frame_number));
+                m_file.write(reinterpret_cast<const char *>(&frame_number),
-                m_file.write(reinterpret_cast<const char*>(&num_clusters), sizeof(num_clusters));
+                             sizeof(frame_number));
-                m_file.write(reinterpret_cast<const char*>(clusters->data()), clusters->size() * clusters->item_size());
+                m_file.write(reinterpret_cast<const char *>(&num_clusters),
+                             sizeof(num_clusters));
+                m_file.write(reinterpret_cast<const char *>(clusters->data()),
+                             clusters->size() * clusters->item_size());
                 m_source->popFront();
-            }else{
+            } else {
                 std::this_thread::sleep_for(m_default_wait);
             }
         }
@@ -40,17 +46,17 @@ class ClusterFileSink{
     }
 
   public:
-        ClusterFileSink(ClusterFinderMT<uint16_t, double, int32_t>* source, const std::filesystem::path& fname){
+    ClusterFileSink(ClusterFinderMT<ClusterType, uint16_t, double> *source,
+                    const std::filesystem::path &fname) {
         m_source = source->sink();
         m_thread = std::thread(&ClusterFileSink::process, this);
         m_file.open(fname, std::ios::binary);
     }
-        void stop(){
+    void stop() {
         m_stop_requested = true;
         m_thread.join();
         m_file.close();
     }
 };
 
-
 } // namespace aare

include/aare/ClusterFileV2.hpp

@@ -1,148 +0,0 @@
-#pragma once
-#include "aare/core/defs.hpp"
-#include <filesystem>
-#include <string>
-#include <fmt/format.h>
-
-namespace aare {
-struct ClusterHeader {
-    int32_t frame_number;
-    int32_t n_clusters;
-    std::string to_string() const {
-        return "frame_number: " + std::to_string(frame_number) + ", n_clusters: " + std::to_string(n_clusters);
-    }
-};
-
-struct ClusterV2_ {
-    int16_t x;
-    int16_t y;
-    std::array<int32_t, 9> data;
-    std::string to_string(bool detailed = false) const {
-        if (detailed) {
-            std::string data_str = "[";
-            for (auto &d : data) {
-                data_str += std::to_string(d) + ", ";
-            }
-            data_str += "]";
-            return "x: " + std::to_string(x) + ", y: " + std::to_string(y) + ", data: " + data_str;
-        }
-        return "x: " + std::to_string(x) + ", y: " + std::to_string(y);
-    }
-};
-
-struct ClusterV2 {
-    ClusterV2_ cluster;
-    int32_t frame_number;
-    std::string to_string() const {
-        return "frame_number: " + std::to_string(frame_number) + ", " + cluster.to_string();
-    }
-};
-
-/**
- * @brief
- * important not: fp always points to the clusters header and does not point to individual clusters
- *
- */
-class ClusterFileV2 {
-    std::filesystem::path m_fpath; 
-    std::string m_mode;
-    FILE *fp{nullptr};
-
-    void check_open(){
-        if (!fp)
-            throw std::runtime_error(fmt::format("File: {} not open", m_fpath.string()));
-    }
-
-  public:
-    ClusterFileV2(std::filesystem::path const &fpath, std::string const &mode): m_fpath(fpath), m_mode(mode) {
-        if (m_mode != "r" && m_mode != "w")
-            throw std::invalid_argument("mode must be 'r' or 'w'");
-        if (m_mode == "r" && !std::filesystem::exists(m_fpath))
-            throw std::invalid_argument("File does not exist");
-        if (mode == "r") {
-            fp = fopen(fpath.string().c_str(), "rb");
-        } else if (mode == "w") {
-            if (std::filesystem::exists(fpath)) {
-                fp = fopen(fpath.string().c_str(), "r+b");
-            } else {
-                fp = fopen(fpath.string().c_str(), "wb");
-            }
-        }
-        if (fp == nullptr) {
-            throw std::runtime_error("Failed to open file");
-        }
-    }
-    ~ClusterFileV2() { close(); }
-    std::vector<ClusterV2> read() {
-        check_open();
-
-        ClusterHeader header;
-        fread(&header, sizeof(ClusterHeader), 1, fp); 
-        std::vector<ClusterV2_> clusters_(header.n_clusters);
-        fread(clusters_.data(), sizeof(ClusterV2_), header.n_clusters, fp);
-        std::vector<ClusterV2> clusters;
-        for (auto &c : clusters_) {
-            ClusterV2 cluster;
-            cluster.cluster = std::move(c);
-            cluster.frame_number = header.frame_number;
-            clusters.push_back(cluster);
-        }
-
-        return clusters;
-    }
-    std::vector<std::vector<ClusterV2>> read(int n_frames) {
-        std::vector<std::vector<ClusterV2>> clusters;
-        for (int i = 0; i < n_frames; i++) {
-            clusters.push_back(read());
-        }
-        return clusters;
-    }
-
-    size_t write(std::vector<ClusterV2> const &clusters) {
-        check_open();
-        if (m_mode != "w")
-            throw std::runtime_error("File not opened in write mode");
-        if (clusters.empty())
-            return 0;
-
-        ClusterHeader header;
-        header.frame_number = clusters[0].frame_number;
-        header.n_clusters = clusters.size();
-        fwrite(&header, sizeof(ClusterHeader), 1, fp);
-        for (auto &c : clusters) {
-            fwrite(&c.cluster, sizeof(ClusterV2_), 1, fp);
-        }
-        return clusters.size();
-    }
-
-    size_t write(std::vector<std::vector<ClusterV2>> const &clusters) {
-        check_open();
-        if (m_mode != "w") 
-            throw std::runtime_error("File not opened in write mode");
-
-        size_t n_clusters = 0;
-        for (auto &c : clusters) {
-            n_clusters += write(c);
-        }
-        return n_clusters;
-    }
-
-    int seek_to_begin() { return fseek(fp, 0, SEEK_SET); }
-    int seek_to_end() { return fseek(fp, 0, SEEK_END); }
-
-    int32_t frame_number() {
-        auto pos = ftell(fp);
-        ClusterHeader header;
-        fread(&header, sizeof(ClusterHeader), 1, fp);
-        fseek(fp, pos, SEEK_SET);
-        return header.frame_number;
-    }
-
-    void close() {
-        if (fp) {
-            fclose(fp);
-            fp = nullptr;
-        }
-    }
-};
-} // namespace aare

include/aare/ClusterFinder.hpp

@@ -10,17 +10,19 @@
 
 namespace aare {
 
-template <typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double,
+template <typename ClusterType = Cluster<int32_t, 3, 3>,
-          typename CT = int32_t>
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinder {
     Shape<2> m_image_size;
-    const int m_cluster_sizeX;
-    const int m_cluster_sizeY;
     const PEDESTAL_TYPE m_nSigma;
     const PEDESTAL_TYPE c2;
     const PEDESTAL_TYPE c3;
     Pedestal<PEDESTAL_TYPE> m_pedestal;
-    ClusterVector<CT> m_clusters;
+    ClusterVector<ClusterType> m_clusters;
+
+    static const uint8_t ClusterSizeX = ClusterType::cluster_size_x;
+    static const uint8_t ClusterSizeY = ClusterType::cluster_size_y;
+    using CT = typename ClusterType::value_type;
 
   public:
     /**
@@ -31,15 +33,12 @@ class ClusterFinder {
      * @param capacity initial capacity of the cluster vector
      *
      */
-    ClusterFinder(Shape<2> image_size, Shape<2> cluster_size,
+    ClusterFinder(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                  PEDESTAL_TYPE nSigma = 5.0, size_t capacity = 1000000)
+                  size_t capacity = 1000000)
-        : m_image_size(image_size), m_cluster_sizeX(cluster_size[0]),
+        : m_image_size(image_size), m_nSigma(nSigma),
-          m_cluster_sizeY(cluster_size[1]),
+          c2(sqrt((ClusterSizeY + 1) / 2 * (ClusterSizeX + 1) / 2)),
-          m_nSigma(nSigma),
+          c3(sqrt(ClusterSizeX * ClusterSizeY)),
-          c2(sqrt((m_cluster_sizeY + 1) / 2 * (m_cluster_sizeX + 1) / 2)),
+          m_pedestal(image_size[0], image_size[1]), m_clusters(capacity) {};
-          c3(sqrt(m_cluster_sizeX * m_cluster_sizeY)),
-          m_pedestal(image_size[0], image_size[1]),
-          m_clusters(m_cluster_sizeX, m_cluster_sizeY, capacity) {};
 
     void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {
         m_pedestal.push(frame);
@@ -56,23 +55,28 @@ class ClusterFinder {
      * same capacity as the old one
      *
      */
-    ClusterVector<CT> steal_clusters(bool realloc_same_capacity = false) {
+    ClusterVector<ClusterType>
-        ClusterVector<CT> tmp = std::move(m_clusters);
+    steal_clusters(bool realloc_same_capacity = false) {
+        ClusterVector<ClusterType> tmp = std::move(m_clusters);
         if (realloc_same_capacity)
-            m_clusters = ClusterVector<CT>(m_cluster_sizeX, m_cluster_sizeY,
+            m_clusters = ClusterVector<ClusterType>(tmp.capacity());
-                                           tmp.capacity());
         else
-            m_clusters = ClusterVector<CT>(m_cluster_sizeX, m_cluster_sizeY);
+            m_clusters = ClusterVector<ClusterType>{};
         return tmp;
     }
     void find_clusters(NDView<FRAME_TYPE, 2> frame, uint64_t frame_number = 0) {
         // // TODO! deal with even size clusters
         // // currently 3,3 -> +/- 1
         // //  4,4 -> +/- 2
-        int dy = m_cluster_sizeY / 2;
+        int dy = ClusterSizeY / 2;
-        int dx = m_cluster_sizeX / 2;
+        int dx = ClusterSizeX / 2;
+        int has_center_pixel_x =
+            ClusterSizeX %
+            2; // for even sized clusters there is no proper cluster center and
+               // even amount of pixels around the center
+        int has_center_pixel_y = ClusterSizeY % 2;
+
         m_clusters.set_frame_number(frame_number);
-        std::vector<CT> cluster_data(m_cluster_sizeX * m_cluster_sizeY);
         for (int iy = 0; iy < frame.shape(0); iy++) {
             for (int ix = 0; ix < frame.shape(1); ix++) {
 
@@ -87,8 +91,8 @@ class ClusterFinder {
                     continue; // NEGATIVE_PEDESTAL go to next pixel
                               // TODO! No pedestal update???
 
-                for (int ir = -dy; ir < dy + 1; ir++) {
+                for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                    for (int ic = -dx; ic < dx + 1; ic++) {
+                    for (int ic = -dx; ic < dx + has_center_pixel_x; ic++) {
                         if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                             iy + ir >= 0 && iy + ir < frame.shape(0)) {
                             PEDESTAL_TYPE val =
@@ -109,27 +113,33 @@ class ClusterFinder {
                     // pass
                 } else {
                     // m_pedestal.push(iy, ix, frame(iy, ix));   // Safe option
-                    m_pedestal.push_fast(iy, ix, frame(iy, ix)); // Assume we have reached n_samples in the pedestal, slight performance improvement
+                    m_pedestal.push_fast(
+                        iy, ix,
+                        frame(iy,
+                              ix)); // Assume we have reached n_samples in the
+                                    // pedestal, slight performance improvement
                     continue;       // It was a pedestal value nothing to store
                 }
 
                 // Store cluster
                 if (value == max) {
-                    // Zero out the cluster data
+                    ClusterType cluster{};
-                    std::fill(cluster_data.begin(), cluster_data.end(), 0);
+                    cluster.x = ix;
+                    cluster.y = iy;
 
                     // Fill the cluster data since we have a photon to store
                     // 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 + 1; ir++) {
+                    for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                        for (int ic = -dx; ic < dx + 1; ic++) {
+                        for (int ic = -dx; ic < dx + 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)) -
-                                    m_pedestal.mean(iy + ir, ix + ic);
+                                    static_cast<CT>(
-                                cluster_data[i] =
+                                        m_pedestal.mean(iy + ir, ix + ic));
+                                cluster.data[i] =
                                     tmp; // Watch for out of bounds access
                                 i++;
                             }
@@ -137,9 +147,7 @@ class ClusterFinder {
                     }
 
                     // Add the cluster to the output ClusterVector
-                    m_clusters.push_back(
+                    m_clusters.push_back(cluster);
-                        ix, iy,
-                        reinterpret_cast<std::byte *>(cluster_data.data()));
                 }
             }
         }

include/aare/ClusterFinderMT.hpp

@@ -30,14 +30,17 @@ 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,
+template <typename ClusterType = Cluster<int32_t, 3, 3>,
-          typename CT = int32_t>
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinderMT {
+
+  protected:
+    using CT = typename 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;
 
@@ -48,6 +51,7 @@ class ClusterFinderMT {
     std::thread m_collect_thread;
     std::chrono::milliseconds m_default_wait{1};
 
+  private:
     std::atomic<bool> m_stop_requested{false};
     std::atomic<bool> m_processing_threads_stopped{true};
 
@@ -66,7 +70,8 @@ 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:
@@ -114,28 +119,32 @@ class ClusterFinderMT {
      * expected number of clusters in a frame per frame.
      * @param n_threads number of threads to use
      */
-    ClusterFinderMT(Shape<2> image_size, Shape<2> cluster_size,
+    ClusterFinderMT(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                    PEDESTAL_TYPE nSigma = 5.0, size_t capacity = 2000,
+                    size_t capacity = 2000, size_t n_threads = 3)
-                    size_t n_threads = 3)
         : m_n_threads(n_threads) {
+
         for (size_t i = 0; i < n_threads; i++) {
             m_cluster_finders.push_back(
-                std::make_unique<ClusterFinder<FRAME_TYPE, PEDESTAL_TYPE, CT>>(
+                std::make_unique<
-                    image_size, cluster_size, nSigma, capacity));
+                    ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>>(
+                    image_size, nSigma, capacity));
         }
         for (size_t i = 0; i < n_threads; i++) {
             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

@@ -1,4 +1,5 @@
 #pragma once
+#include "aare/Cluster.hpp" //TODO maybe store in seperate file !!!
 #include <algorithm>
 #include <array>
 #include <cstddef>
@@ -13,292 +14,157 @@
 
 namespace aare {
 
+template <typename ClusterType,
+          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
+class ClusterVector; // Forward declaration
+
 /**
- * @brief ClusterVector is a container for clusters of various sizes. It uses a
+ * @brief ClusterVector is a container for clusters of various sizes. It
- * contiguous memory buffer to store the clusters. It is templated on the data
+ * uses a contiguous memory buffer to store the clusters. It is templated on
- * type and the coordinate type of the clusters.
+ * the data type and the coordinate type of the clusters.
  * @note push_back can invalidate pointers to elements in the container
- * @warning ClusterVector is currently move only to catch unintended copies, but
+ * @warning ClusterVector is currently move only to catch unintended copies,
- * this might change since there are probably use cases where copying is needed.
+ * but this might change since there are probably use cases where copying is
+ * needed.
  * @tparam T data type of the pixels in the cluster
  * @tparam CoordType data type of the x and y coordinates of the cluster
  * (normally int16_t)
  */
-template <typename T, typename CoordType = int16_t> class ClusterVector {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    using value_type = T;
+          typename CoordType>
-    size_t m_cluster_size_x;
+class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
-    size_t m_cluster_size_y;
+
-    std::byte *m_data{};
+    std::vector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> m_data{};
-    size_t m_size{0};
+    int32_t m_frame_number{0}; // TODO! Check frame number size and type
-    size_t m_capacity;
-    uint64_t m_frame_number{0}; // TODO! Check frame number size and type
-    /*
-    Format string used in the python bindings to create a numpy
-    array from the buffer
-    = - native byte order
-    h - short
-    d - double
-    i - int
-    */
-    constexpr static char m_fmt_base[] = "=h:x:\nh:y:\n({},{}){}:data:";
 
   public:
+    using value_type = T;
+    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
+
     /**
      * @brief Construct a new ClusterVector object
-     * @param cluster_size_x size of the cluster in x direction
-     * @param cluster_size_y size of the cluster in y direction
      * @param capacity initial capacity of the buffer in number of clusters
      * @param frame_number frame number of the clusters. Default is 0, which is
      * also used to indicate that the clusters come from many frames
      */
-    ClusterVector(size_t cluster_size_x = 3, size_t cluster_size_y = 3,
+    ClusterVector(size_t capacity = 1024, uint64_t frame_number = 0)
-                  size_t capacity = 1024, uint64_t frame_number = 0)
+        : m_frame_number(frame_number) {
-        : m_cluster_size_x(cluster_size_x), m_cluster_size_y(cluster_size_y),
+        m_data.reserve(capacity);
-          m_capacity(capacity), m_frame_number(frame_number) {
-        allocate_buffer(capacity);
     }
 
-    ~ClusterVector() { delete[] m_data; }
-
     // Move constructor
     ClusterVector(ClusterVector &&other) noexcept
-        : m_cluster_size_x(other.m_cluster_size_x),
+        : m_data(other.m_data), m_frame_number(other.m_frame_number) {
-          m_cluster_size_y(other.m_cluster_size_y), m_data(other.m_data),
+        other.m_data.clear();
-          m_size(other.m_size), m_capacity(other.m_capacity),
-          m_frame_number(other.m_frame_number) {
-        other.m_data = nullptr;
-        other.m_size = 0;
-        other.m_capacity = 0;
     }
 
     // Move assignment operator
     ClusterVector &operator=(ClusterVector &&other) noexcept {
         if (this != &other) {
-            delete[] m_data;
-            m_cluster_size_x = other.m_cluster_size_x;
-            m_cluster_size_y = other.m_cluster_size_y;
             m_data = other.m_data;
-            m_size = other.m_size;
-            m_capacity = other.m_capacity;
             m_frame_number = other.m_frame_number;
-            other.m_data = nullptr;
+            other.m_data.clear();
-            other.m_size = 0;
-            other.m_capacity = 0;
             other.m_frame_number = 0;
         }
         return *this;
     }
 
-    /**
-     * @brief Reserve space for at least capacity clusters
-     * @param capacity number of clusters to reserve space for
-     * @note If capacity is less than the current capacity, the function does
-     * nothing.
-     */
-    void reserve(size_t capacity) {
-        if (capacity > m_capacity) {
-            allocate_buffer(capacity);
-        }
-    }
-
-    /**
-     * @brief Add a cluster to the vector
-     * @param x x-coordinate of the cluster
-     * @param y y-coordinate of the cluster
-     * @param data pointer to the data of the cluster
-     * @warning The data pointer must point to a buffer of size cluster_size_x *
-     * cluster_size_y * sizeof(T)
-     */
-    void push_back(CoordType x, CoordType y, const std::byte *data) {
-        if (m_size == m_capacity) {
-            allocate_buffer(m_capacity * 2);
-        }
-        std::byte *ptr = element_ptr(m_size);
-        *reinterpret_cast<CoordType *>(ptr) = x;
-        ptr += sizeof(CoordType);
-        *reinterpret_cast<CoordType *>(ptr) = y;
-        ptr += sizeof(CoordType);
-
-        std::copy(data, data + m_cluster_size_x * m_cluster_size_y * sizeof(T),
-                  ptr);
-        m_size++;
-    }
-    ClusterVector &operator+=(const ClusterVector &other) {
-        if (m_size + other.m_size > m_capacity) {
-            allocate_buffer(m_capacity + other.m_size);
-        }
-        std::copy(other.m_data, other.m_data + other.m_size * item_size(),
-                  m_data + m_size * item_size());
-        m_size += other.m_size;
-        return *this;
-    }
-
     /**
      * @brief Sum the pixels in each cluster
      * @return std::vector<T> vector of sums for each cluster
      */
     std::vector<T> sum() {
-        std::vector<T> sums(m_size);
+        std::vector<T> sums(m_data.size());
-        const size_t stride = item_size();
+
-        const size_t n_pixels = m_cluster_size_x * m_cluster_size_y;
+        std::transform(
-        std::byte *ptr = m_data + 2 * sizeof(CoordType); // skip x and y
+            m_data.begin(), m_data.end(), sums.begin(),
+            [](const ClusterType &cluster) { return cluster.sum(); });
 
-        for (size_t i = 0; i < m_size; i++) {
-            sums[i] =
-                std::accumulate(reinterpret_cast<T *>(ptr),
-                                reinterpret_cast<T *>(ptr) + n_pixels, T{});
-            ptr += stride;
-        }
         return sums;
     }
 
     /**
-     * @brief Return the maximum sum of the 2x2 subclusters in each cluster
+     * @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
-     * @throws std::runtime_error if the cluster size is not 3x3
-     * @warning Only 3x3 clusters are supported for the 2x2 sum.
      */
     std::vector<T> sum_2x2() {
-        std::vector<T> sums(m_size);
+        std::vector<T> sums_2x2(m_data.size());
-        const size_t stride = item_size();
 
-        if (m_cluster_size_x != 3 || m_cluster_size_y != 3) {
+        std::transform(m_data.begin(), m_data.end(), sums_2x2.begin(),
-            throw std::runtime_error(
+                       [](const ClusterType &cluster) {
-                "Only 3x3 clusters are supported for the 2x2 sum.");
+                           return cluster.max_sum_2x2().first;
-        }
+                       });
-        std::byte *ptr = m_data + 2 * sizeof(CoordType); // skip x and y
 
-        for (size_t i = 0; i < m_size; i++) {
+        return sums_2x2;
-            std::array<T, 4> total;
-            auto T_ptr = reinterpret_cast<T *>(ptr);
-            total[0] = T_ptr[0] + T_ptr[1] + T_ptr[3] + T_ptr[4];
-            total[1] = T_ptr[1] + T_ptr[2] + T_ptr[4] + T_ptr[5];
-            total[2] = T_ptr[3] + T_ptr[4] + T_ptr[6] + T_ptr[7];
-            total[3] = T_ptr[4] + T_ptr[5] + T_ptr[7] + T_ptr[8];
-
-            sums[i] = *std::max_element(total.begin(), total.end());
-            ptr += stride;
     }
 
-        return sums;
+    /**
+     * @brief Reserve space for at least capacity clusters
+     * @param capacity number of clusters to reserve space for
+     * @note If capacity is less than the current capacity, the function does
+     * nothing.
+     */
+    void reserve(size_t capacity) { m_data.reserve(capacity); }
+
+    void resize(size_t size) { m_data.resize(size); }
+
+    void push_back(const ClusterType &cluster) { m_data.push_back(cluster); }
+
+    ClusterVector &operator+=(const ClusterVector &other) {
+        m_data.insert(m_data.end(), other.begin(), other.end());
+
+        return *this;
     }
 
     /**
      * @brief Return the number of clusters in the vector
      */
-    size_t size() const { return m_size; }
+    size_t size() const { return m_data.size(); }
+
+    uint8_t cluster_size_x() const { return ClusterSizeX; }
+
+    uint8_t cluster_size_y() const { return ClusterSizeY; }
 
     /**
      * @brief Return the capacity of the buffer in number of clusters. This is
      * the number of clusters that can be stored in the current buffer without
      * reallocation.
      */
-    size_t capacity() const { return m_capacity; }
+    size_t capacity() const { return m_data.capacity(); }
+
+    const auto begin() const { return m_data.begin(); }
+
+    const auto end() const { return m_data.end(); }
 
     /**
      * @brief Return the size in bytes of a single cluster
      */
     size_t item_size() const {
-        return 2 * sizeof(CoordType) +
+        return sizeof(ClusterType); // 2 * sizeof(CoordType) + ClusterSizeX *
-               m_cluster_size_x * m_cluster_size_y * sizeof(T);
+                                    // ClusterSizeY * sizeof(T);
     }
 
-    /**
+    ClusterType *data() { return m_data.data(); }
-     * @brief Return the offset in bytes for the i-th cluster
+    ClusterType const *data() const { return m_data.data(); }
-     */
-    size_t element_offset(size_t i) const { return item_size() * i; }
-
-    /**
-     * @brief Return a pointer to the i-th cluster
-     */
-    std::byte *element_ptr(size_t i) { return m_data + element_offset(i); }
-
-    /**
-     * @brief Return a pointer to the i-th cluster
-     */
-    const std::byte *element_ptr(size_t i) const {
-        return m_data + element_offset(i);
-    }
-
-    size_t cluster_size_x() const { return m_cluster_size_x; }
-    size_t cluster_size_y() const { return m_cluster_size_y; }
-
-    std::byte *data() { return m_data; }
-    std::byte const *data() const { return m_data; }
 
     /**
      * @brief Return a reference to the i-th cluster casted to type V
      * @tparam V type of the cluster
      */
-    template <typename V> V &at(size_t i) {
+    ClusterType &operator[](size_t i) { return m_data[i]; }
-        return *reinterpret_cast<V *>(element_ptr(i));
-    }
 
-    template <typename V> const V &at(size_t i) const {
+    const ClusterType &operator[](size_t i) const { return m_data[i]; }
-        return *reinterpret_cast<const V *>(element_ptr(i));
-    }
-
-    const std::string_view fmt_base() const {
-        // TODO! how do we match on coord_t?
-        return m_fmt_base;
-    }
 
     /**
      * @brief Return the frame number of the clusters. 0 is used to indicate
      * that the clusters come from many frames
      */
-    uint64_t frame_number() const { return m_frame_number; }
+    int32_t frame_number() const { return m_frame_number; }
 
-    void set_frame_number(uint64_t frame_number) {
+    void set_frame_number(int32_t frame_number) {
         m_frame_number = frame_number;
     }
-
-    /**
-     * @brief Resize the vector to contain new_size clusters. If new_size is
-     * greater than the current capacity, a new buffer is allocated. If the size
-     * is smaller no memory is freed, size is just updated.
-     * @param new_size new size of the vector
-     * @warning The additional clusters are not initialized
-     */
-    void resize(size_t new_size) {
-        // TODO! Should we initialize the new clusters?
-        if (new_size > m_capacity) {
-            allocate_buffer(new_size);
-        }
-        m_size = new_size;
-    }
-
-    void apply_gain_map(const NDView<double> gain_map){
-        //in principle we need to know the size of the image for this lookup
-        //TODO! check orientations
-        std::array<int64_t, 9> xcorr = {-1, 0, 1, -1, 0, 1, -1, 0, 1};
-        std::array<int64_t, 9> ycorr = {-1, -1, -1, 0, 0, 0, 1, 1, 1};
-        for (size_t i=0; i<m_size; i++){
-            auto& cl = at<Cluster3x3>(i);
-
-            if (cl.x > 0 && cl.y > 0 && cl.x < gain_map.shape(1)-1 && cl.y < gain_map.shape(0)-1){
-                for (size_t j=0; j<9; j++){
-                    size_t x = cl.x + xcorr[j];
-                    size_t y = cl.y + ycorr[j];
-                    cl.data[j] = static_cast<T>(cl.data[j] * gain_map(y, x));
-                }
-            }else{
-                memset(cl.data, 0, 9*sizeof(T)); //clear edge clusters
-            }
-
-            
-        }
-    }
-
-  private:
-    void allocate_buffer(size_t new_capacity) {
-        size_t num_bytes = item_size() * new_capacity;
-        std::byte *new_data = new std::byte[num_bytes]{};
-        std::copy(m_data, m_data + item_size() * m_size, new_data);
-        delete[] m_data;
-        m_data = new_data;
-        m_capacity = new_capacity;
-    }
 };
 
 } // namespace aare

include/aare/GainMap.hpp

@@ -0,0 +1,68 @@
+/************************************************
+ * @file GainMap.hpp
+ * @short function to apply gain map of image size to a vector of clusters -
+ *note stored gainmap is inverted for efficient aaplication to images
+ ***********************************************/
+
+#pragma once
+#include "aare/Cluster.hpp"
+#include "aare/ClusterVector.hpp"
+#include "aare/NDArray.hpp"
+#include "aare/NDView.hpp"
+#include <memory>
+
+namespace aare {
+
+class InvertedGainMap {
+
+  public:
+    explicit InvertedGainMap(const NDArray<double, 2> &gain_map)
+        : m_gain_map(gain_map) {
+        for (auto &item : m_gain_map) {
+            item = 1.0 / item;
+        }
+    };
+
+    explicit InvertedGainMap(const NDView<double, 2> gain_map) {
+        m_gain_map = NDArray<double, 2>(gain_map);
+        for (auto &item : m_gain_map) {
+            item = 1.0 / item;
+        }
+    }
+
+    template <typename ClusterType,
+              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
+        size_t ClusterSizeX = clustervec.cluster_size_x();
+        size_t ClusterSizeY = clustervec.cluster_size_y();
+
+        using T = typename ClusterVector<ClusterType>::value_type;
+
+        int64_t index_cluster_center_x = ClusterSizeX / 2;
+        int64_t index_cluster_center_y = ClusterSizeY / 2;
+        for (size_t i = 0; i < clustervec.size(); i++) {
+            auto &cl = clustervec[i];
+
+            if (cl.x > 0 && cl.y > 0 && cl.x < m_gain_map.shape(1) - 1 &&
+                cl.y < m_gain_map.shape(0) - 1) {
+                for (size_t j = 0; j < ClusterSizeX * ClusterSizeY; j++) {
+                    size_t x = cl.x + j % ClusterSizeX - index_cluster_center_x;
+                    size_t y = cl.y + j / ClusterSizeX - index_cluster_center_y;
+                    cl.data[j] = static_cast<T>(
+                        static_cast<double>(cl.data[j]) *
+                        m_gain_map(
+                            y, x)); // cast after conversion to keep precision
+                }
+            } else {
+                // clear edge clusters
+                cl.data.fill(0);
+            }
+        }
+    }
+
+  private:
+    NDArray<double, 2> m_gain_map{};
+};
+
+} // end of namespace aare

include/aare/Interpolator.hpp

@@ -1,29 +1,130 @@
 #pragma once
+
+#include "aare/CalculateEta.hpp"
+#include "aare/Cluster.hpp"
+#include "aare/ClusterFile.hpp" //Cluster_3x3
+#include "aare/ClusterVector.hpp"
 #include "aare/NDArray.hpp"
 #include "aare/NDView.hpp"
-#include "aare/ClusterVector.hpp"
+#include "aare/algorithm.hpp"
-#include "aare/ClusterFile.hpp" //Cluster_3x3
-namespace aare{
 
-struct Photon{
+namespace aare {
+
+struct Photon {
     double x;
     double y;
     double energy;
 };
 
-class Interpolator{
+class Interpolator {
     NDArray<double, 3> m_ietax;
     NDArray<double, 3> m_ietay;
 
     NDArray<double, 1> m_etabinsx;
     NDArray<double, 1> m_etabinsy;
     NDArray<double, 1> m_energy_bins;
-    public:
-        Interpolator(NDView<double, 3> etacube, NDView<double, 1> xbins, NDView<double, 1> ybins, NDView<double, 1> ebins);
-        NDArray<double, 3> get_ietax(){return m_ietax;}
-        NDArray<double, 3> get_ietay(){return m_ietay;}
 
-        std::vector<Photon> interpolate(const ClusterVector<int32_t>& clusters);
+  public:
+    Interpolator(NDView<double, 3> etacube, NDView<double, 1> xbins,
+                 NDView<double, 1> ybins, NDView<double, 1> ebins);
+    NDArray<double, 3> get_ietax() { return m_ietax; }
+    NDArray<double, 3> get_ietay() { return m_ietay; }
+
+    template <typename ClusterType,
+              typename Eanble = std::enable_if_t<is_cluster_v<ClusterType>>>
+    std::vector<Photon> interpolate(const ClusterVector<ClusterType> &clusters);
 };
 
+// TODO: generalize to support any clustertype!!! otherwise add std::enable_if_t
+// to only take Cluster2x2 and Cluster3x3
+template <typename ClusterType, typename Enable>
+std::vector<Photon>
+Interpolator::interpolate(const ClusterVector<ClusterType> &clusters) {
+    std::vector<Photon> photons;
+    photons.reserve(clusters.size());
+
+    if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
+        for (const ClusterType &cluster : clusters) {
+
+            auto eta = calculate_eta2(cluster);
+
+            Photon photon;
+            photon.x = cluster.x;
+            photon.y = cluster.y;
+            photon.energy = eta.sum;
+
+            // auto ie = nearest_index(m_energy_bins, photon.energy)-1;
+            // auto ix = nearest_index(m_etabinsx, eta.x)-1;
+            // auto iy = nearest_index(m_etabinsy, eta.y)-1;
+            // Finding the index of the last element that is smaller
+            // should work fine as long as we have many bins
+            auto ie = last_smaller(m_energy_bins, photon.energy);
+            auto ix = last_smaller(m_etabinsx, eta.x);
+            auto iy = last_smaller(m_etabinsy, eta.y);
+
+            // fmt::print("ex: {}, ix: {}, iy: {}\n", ie, ix, iy);
+
+            double dX, dY;
+            // cBottomLeft = 0,
+            // cBottomRight = 1,
+            // cTopLeft = 2,
+            // cTopRight = 3
+            switch (static_cast<corner>(eta.c)) {
+            case corner::cTopLeft:
+                dX = -1.;
+                dY = 0;
+                break;
+            case corner::cTopRight:;
+                dX = 0;
+                dY = 0;
+                break;
+            case corner::cBottomLeft:
+                dX = -1.;
+                dY = -1.;
+                break;
+            case corner::cBottomRight:
+                dX = 0.;
+                dY = -1.;
+                break;
+            }
+            photon.x += m_ietax(ix, iy, ie) * 2 + dX;
+            photon.y += m_ietay(ix, iy, ie) * 2 + dY;
+            photons.push_back(photon);
+        }
+    } else if (clusters.cluster_size_x() == 2 ||
+               clusters.cluster_size_y() == 2) {
+        for (const ClusterType &cluster : clusters) {
+            auto eta = calculate_eta2(cluster);
+
+            Photon photon;
+            photon.x = cluster.x;
+            photon.y = cluster.y;
+            photon.energy = eta.sum;
+
+            // Now do some actual interpolation.
+            // Find which energy bin the cluster is in
+            //  auto ie = nearest_index(m_energy_bins, photon.energy)-1;
+            //  auto ix = nearest_index(m_etabinsx, eta.x)-1;
+            //  auto iy = nearest_index(m_etabinsy, eta.y)-1;
+            // Finding the index of the last element that is smaller
+            // should work fine as long as we have many bins
+            auto ie = last_smaller(m_energy_bins, photon.energy);
+            auto ix = last_smaller(m_etabinsx, eta.x);
+            auto iy = last_smaller(m_etabinsy, eta.y);
+
+            photon.x += m_ietax(ix, iy, ie) *
+                        2; // eta goes between 0 and 1 but we could move the hit
+                           // anywhere in the 2x2
+            photon.y += m_ietay(ix, iy, ie) * 2;
+            photons.push_back(photon);
+        }
+
+    } else {
+        throw std::runtime_error(
+            "Only 3x3 and 2x2 clusters are supported for interpolation");
+    }
+
+    return photons;
+}
+
 } // namespace aare

python/CMakeLists.txt

@@ -29,6 +29,9 @@ target_link_libraries(_aare PRIVATE aare_core aare_compiler_flags)
 set( PYTHON_FILES
     aare/__init__.py
     aare/CtbRawFile.py
+    aare/ClusterFinder.py
+    aare/ClusterVector.py
+
     aare/func.py
     aare/RawFile.py
     aare/transform.py
@@ -36,6 +39,7 @@ set( PYTHON_FILES
     aare/utils.py
 )
 
+
 # Copy the python files to the build directory
 foreach(FILE ${PYTHON_FILES})
     configure_file(${FILE} ${CMAKE_BINARY_DIR}/${FILE}  )

python/aare/ClusterFinder.py

@@ -0,0 +1,67 @@
+
+from ._aare import ClusterFinder_Cluster3x3i, ClusterFinder_Cluster2x2i, ClusterFinderMT_Cluster3x3i, ClusterFinderMT_Cluster2x2i, ClusterCollector_Cluster3x3i, ClusterCollector_Cluster2x2i
+
+
+from ._aare import ClusterFileSink_Cluster3x3i, ClusterFileSink_Cluster2x2i
+import numpy as np
+
+def ClusterFinder(image_size, 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++.
+    """
+    if dtype == np.int32 and cluster_size == (3,3):
+        return ClusterFinder_Cluster3x3i(image_size, n_sigma = n_sigma, capacity=capacity)
+    elif dtype == np.int32 and cluster_size == (2,2): 
+        return ClusterFinder_Cluster2x2i(image_size, n_sigma = n_sigma, capacity=capacity)
+    else:
+        #TODO! add the other formats
+        raise ValueError(f"Unsupported dtype: {dtype}. Only np.int32 is supported.")
+
+
+def ClusterFinderMT(image_size, 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++.
+    """
+
+    if dtype == np.int32 and cluster_size == (3,3):
+        return ClusterFinderMT_Cluster3x3i(image_size, n_sigma = n_sigma,
+                    capacity = capacity, n_threads = n_threads)
+    elif dtype == np.int32 and cluster_size == (2,2):
+        return ClusterFinderMT_Cluster2x2i(image_size, n_sigma = n_sigma,
+                    capacity = capacity, n_threads = n_threads)
+    else:
+        #TODO! add the other formats
+        raise ValueError(f"Unsupported dtype: {dtype}. Only np.int32 is supported.")
+
+
+def ClusterCollector(clusterfindermt, cluster_size = (3,3), dtype=np.int32): 
+    """ 
+    Factory function to create a ClusterCollector object. Provides a cleaner syntax for 
+    the templated ClusterCollector in C++.
+    """
+
+    if dtype == np.int32 and cluster_size == (3,3): 
+        return ClusterCollector_Cluster3x3i(clusterfindermt)
+    elif dtype == np.int32 and cluster_size == (2,2):
+        return ClusterCollector_Cluster2x2i(clusterfindermt)
+     
+    else: 
+        #TODO! add the other formats
+        raise ValueError(f"Unsupported dtype: {dtype}. Only np.int32 is supported.")
+
+def ClusterFileSink(clusterfindermt, cluster_file, dtype=np.int32): 
+    """ 
+    Factory function to create a ClusterCollector object. Provides a cleaner syntax for 
+    the templated ClusterCollector in C++.
+    """
+
+    if dtype == np.int32 and clusterfindermt.cluster_size == (3,3): 
+        return ClusterFileSink_Cluster3x3i(clusterfindermt, cluster_file)
+    elif dtype == np.int32 and clusterfindermt.cluster_size == (2,2):
+        return ClusterFileSink_Cluster2x2i(clusterfindermt, cluster_file)
+     
+    else: 
+        #TODO! add the other formats
+        raise ValueError(f"Unsupported dtype: {dtype}. Only np.int32 is supported.")

python/aare/ClusterVector.py

@@ -0,0 +1,11 @@
+
+
+from ._aare import ClusterVector_Cluster3x3i
+import numpy as np
+
+def ClusterVector(cluster_size, dtype = np.int32):
+
+    if dtype == np.int32 and cluster_size == (3,3):
+        return ClusterVector_Cluster3x3i()
+    else:
+        raise ValueError(f"Unsupported dtype: {dtype}. Only np.int32 is supported.")

python/aare/__init__.py

@@ -3,16 +3,21 @@ from . import _aare
 
 
 from ._aare import File, RawMasterFile, RawSubFile, JungfrauDataFile
-from ._aare import Pedestal_d, Pedestal_f, ClusterFinder, VarClusterFinder
+from ._aare import Pedestal_d, Pedestal_f, ClusterFinder_Cluster3x3i, VarClusterFinder
 from ._aare import DetectorType
-from ._aare import ClusterFile
+from ._aare import ClusterFile_Cluster3x3i as ClusterFile
 from ._aare import hitmap
 from ._aare import ROI
 
-from ._aare import ClusterFinderMT, ClusterCollector, ClusterFileSink, ClusterVector_i
+# from ._aare import ClusterFinderMT, ClusterCollector, ClusterFileSink, ClusterVector_i
+
+from .ClusterFinder import ClusterFinder, ClusterCollector, ClusterFinderMT, ClusterFileSink
+from .ClusterVector import ClusterVector
+
 
 from ._aare import fit_gaus, fit_pol1, fit_scurve, fit_scurve2
 from ._aare import Interpolator
+from ._aare import calculate_eta2
 
 
 from ._aare import apply_custom_weights

python/src/bind_ClusterVector.hpp

@@ -0,0 +1,104 @@
+#include "aare/ClusterCollector.hpp"
+#include "aare/ClusterFileSink.hpp"
+#include "aare/ClusterFinder.hpp"
+#include "aare/ClusterFinderMT.hpp"
+#include "aare/ClusterVector.hpp"
+#include "aare/NDView.hpp"
+#include "aare/Pedestal.hpp"
+#include "np_helper.hpp"
+
+#include <cstdint>
+#include <filesystem>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <pybind11/stl_bind.h>
+
+namespace py = pybind11;
+using pd_type = double;
+
+using namespace aare;
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wunused-parameter"
+
+template <typename Type, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
+          typename CoordType = uint16_t>
+void define_ClusterVector(py::module &m, const std::string &typestr) {
+    using ClusterType = Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>;
+    auto class_name = fmt::format("ClusterVector_{}", typestr);
+
+    py::class_<ClusterVector<
+        Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>, void>>(
+        m, class_name.c_str(),
+        py::buffer_protocol())
+
+        .def(py::init()) // TODO change!!!
+
+        .def("push_back",
+             [](ClusterVector<ClusterType> &self, const ClusterType &cluster) {
+                 self.push_back(cluster);
+             })
+
+        .def("sum",
+             [](ClusterVector<ClusterType> &self) {
+                 auto *vec = new std::vector<Type>(self.sum());
+                 return return_vector(vec);
+             })
+        .def("sum_2x2", [](ClusterVector<ClusterType> &self){
+            auto *vec = new std::vector<Type>(self.sum_2x2());
+            return return_vector(vec);
+        })
+        .def_property_readonly("size", &ClusterVector<ClusterType>::size)
+        .def("item_size", &ClusterVector<ClusterType>::item_size)
+        .def_property_readonly("fmt",
+                               [typestr](ClusterVector<ClusterType> &self) {
+                                   return fmt_format<ClusterType>;
+                               })
+
+        .def_property_readonly("cluster_size_x",
+                               &ClusterVector<ClusterType>::cluster_size_x)
+        .def_property_readonly("cluster_size_y",
+                               &ClusterVector<ClusterType>::cluster_size_y)
+        .def_property_readonly("capacity",
+                               &ClusterVector<ClusterType>::capacity)
+        .def_property("frame_number", &ClusterVector<ClusterType>::frame_number,
+                      &ClusterVector<ClusterType>::set_frame_number)
+        .def_buffer(
+            [typestr](ClusterVector<ClusterType> &self) -> py::buffer_info {
+                return py::buffer_info(
+                    self.data(),             /* Pointer to buffer */
+                    self.item_size(),        /* Size of one scalar */
+                    fmt_format<ClusterType>, /* Format descriptor */
+                    1,                       /* Number of dimensions */
+                    {self.size()},           /* Buffer dimensions */
+                    {self.item_size()} /* Strides (in bytes) for each index */
+                );
+            });
+
+    // Free functions using ClusterVector
+    m.def("hitmap",
+          [](std::array<size_t, 2> image_size, ClusterVector<ClusterType> &cv) {
+              // Create a numpy array to hold the hitmap
+              // The shape of the array is (image_size[0], image_size[1])
+              // note that the python array is passed as [row, col] which
+              // is the opposite of the clusters [x,y]
+              py::array_t<int32_t> hitmap(image_size);
+              auto r = hitmap.mutable_unchecked<2>();
+
+              // Initialize hitmap to 0
+              for (py::ssize_t i = 0; i < r.shape(0); i++)
+                  for (py::ssize_t j = 0; j < r.shape(1); j++)
+                      r(i, j) = 0;
+
+              // Loop over the clusters and increment the hitmap
+              // Skip out of bound clusters
+              for (const auto &cluster : cv) {
+                  auto x = cluster.x;
+                  auto y = cluster.y;
+                  if (x < image_size[1] && y < image_size[0])
+                      r(cluster.y, cluster.x) += 1;
+              }
+
+              return hitmap;
+          });
+}

python/src/cluster.hpp

@@ -16,194 +16,196 @@
 namespace py = pybind11;
 using pd_type = double;
 
-template <typename T>
+using namespace aare;
-void define_cluster_vector(py::module &m, const std::string &typestr) {
+
-    auto class_name = fmt::format("ClusterVector_{}", typestr);
+#pragma GCC diagnostic push
-    py::class_<ClusterVector<T>>(m, class_name.c_str(), py::buffer_protocol())
+#pragma GCC diagnostic ignored "-Wunused-parameter"
-        .def(py::init<int, int>(),
+
-    py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
+template <typename Type, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-        .def("push_back",
+          typename CoordType>
-             [](ClusterVector<T> &self, int x, int y, py::array_t<T> data) {
+void define_cluster(py::module &m, const std::string &typestr) {
-                //  auto view = make_view_2d(data);
+    auto class_name = fmt::format("Cluster{}", typestr);
-                 self.push_back(x, y, reinterpret_cast<const std::byte*>(data.data()));
+
-             })
+    py::class_<Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>>(
-        .def_property_readonly("size", &ClusterVector<T>::size)
+        m, class_name.c_str(), py::buffer_protocol())
-        .def("item_size", &ClusterVector<T>::item_size)
+
-        .def_property_readonly("fmt",
+        .def(py::init([](uint8_t x, uint8_t y, py::array_t<Type> data) {
-                               [typestr](ClusterVector<T> &self) {
+            py::buffer_info buf_info = data.request();
-                                   return fmt::format(
+            Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType> cluster;
-                                       self.fmt_base(), self.cluster_size_x(),
+            cluster.x = x;
-                                       self.cluster_size_y(), typestr);
+            cluster.y = y;
-                               })
+            auto r = data.template unchecked<1>(); // no bounds checks
-        .def("sum",
+            for (py::ssize_t i = 0; i < data.size(); ++i) {
-             [](ClusterVector<T> &self) {
+                cluster.data[i] = r(i);
-                 auto *vec = new std::vector<T>(self.sum());
+            }
-                 return return_vector(vec);
+            return cluster;
-             })
+        }));
-        .def("sum_2x2", [](ClusterVector<T> &self) {
+
-            auto *vec = new std::vector<T>(self.sum_2x2());
+    /*
-            return return_vector(vec);
+    .def_property(
-        })
+        "data",
-        .def_property_readonly("cluster_size_x", &ClusterVector<T>::cluster_size_x)
+        [](ClusterType &c) -> py::array {
-        .def_property_readonly("cluster_size_y", &ClusterVector<T>::cluster_size_y)
+            return py::array(py::buffer_info(
-        .def_property_readonly("capacity", &ClusterVector<T>::capacity)
+                c.data, sizeof(Type),
-        .def_property("frame_number", &ClusterVector<T>::frame_number,
+                py::format_descriptor<Type>::format(), // Type
-                      &ClusterVector<T>::set_frame_number)
+                                                       // format
-        .def_buffer([typestr](ClusterVector<T> &self) -> py::buffer_info {
+                1, // Number of dimensions
-            return py::buffer_info(
+                {static_cast<ssize_t>(ClusterSizeX *
-                self.data(),      /* Pointer to buffer */
+                                      ClusterSizeY)}, // Shape (flattened)
-                self.item_size(), /* Size of one scalar */
+                {sizeof(Type)} // Stride (step size between elements)
-                fmt::format(self.fmt_base(), self.cluster_size_x(),
+                ));
-                            self.cluster_size_y(),
+        },
-                            typestr), /* Format descriptor */
+        [](ClusterType &c, py::array_t<Type> arr) {
-                1,                    /* Number of dimensions */
+            py::buffer_info buf_info = arr.request();
-                {self.size()},        /* Buffer dimensions */
+            Type *ptr = static_cast<Type *>(buf_info.ptr);
-                {self.item_size()}    /* Strides (in bytes) for each index */
+            std::copy(ptr, ptr + ClusterSizeX * ClusterSizeY,
-            );
+                      c.data); // TODO dont iterate over centers!!!
+
         });
+    */
 }
 
-void define_cluster_finder_mt_bindings(py::module &m) {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    py::class_<ClusterFinderMT<uint16_t, pd_type>>(m, "ClusterFinderMT")
+          typename CoordType = uint16_t>
-        .def(py::init<Shape<2>, Shape<2>, pd_type, size_t, size_t>(),
+void define_cluster_finder_mt_bindings(py::module &m,
-             py::arg("image_size"), py::arg("cluster_size"),
+                                       const std::string &typestr) {
-             py::arg("n_sigma") = 5.0, py::arg("capacity") = 2048,
+    auto class_name = fmt::format("ClusterFinderMT_{}", typestr);
-             py::arg("n_threads") = 3)
+
+    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
+
+    py::class_<ClusterFinderMT<ClusterType, uint16_t, pd_type>>(
+        m, class_name.c_str())
+        .def(py::init<Shape<2>, pd_type, size_t, size_t>(),
+             py::arg("image_size"), py::arg("n_sigma") = 5.0,
+             py::arg("capacity") = 2048, py::arg("n_threads") = 3)
         .def("push_pedestal_frame",
-             [](ClusterFinderMT<uint16_t, pd_type> &self,
+             [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {
                  auto view = make_view_2d(frame);
                  self.push_pedestal_frame(view);
              })
         .def(
             "find_clusters",
-            [](ClusterFinderMT<uint16_t, pd_type> &self,
+            [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
                py::array_t<uint16_t> frame, uint64_t frame_number) {
                 auto view = make_view_2d(frame);
                 self.find_clusters(view, frame_number);
                 return;
             },
             py::arg(), py::arg("frame_number") = 0)
-        .def("clear_pedestal", &ClusterFinderMT<uint16_t, pd_type>::clear_pedestal)
+        .def_property_readonly("cluster_size", [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self){
-        .def("sync", &ClusterFinderMT<uint16_t, pd_type>::sync)
+            return py::make_tuple(ClusterSizeX, ClusterSizeY);
-        .def("stop", &ClusterFinderMT<uint16_t, pd_type>::stop)
+        })
-        .def("start", &ClusterFinderMT<uint16_t, pd_type>::start)
+        .def("clear_pedestal",
-        .def("pedestal",
+             &ClusterFinderMT<ClusterType, uint16_t, pd_type>::clear_pedestal)
-             [](ClusterFinderMT<uint16_t, pd_type> &self, size_t thread_index) {
+        .def("sync", &ClusterFinderMT<ClusterType, uint16_t, pd_type>::sync)
+        .def("stop", &ClusterFinderMT<ClusterType, uint16_t, pd_type>::stop)
+        .def("start", &ClusterFinderMT<ClusterType, uint16_t, pd_type>::start)
+        .def(
+            "pedestal",
+            [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
+               size_t thread_index) {
                 auto pd = new NDArray<pd_type, 2>{};
                 *pd = self.pedestal(thread_index);
                 return return_image_data(pd);
-             },py::arg("thread_index") = 0)
+            },
-        .def("noise",
+            py::arg("thread_index") = 0)
-             [](ClusterFinderMT<uint16_t, pd_type> &self, size_t thread_index) {
+        .def(
+            "noise",
+            [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
+               size_t thread_index) {
                 auto arr = new NDArray<pd_type, 2>{};
                 *arr = self.noise(thread_index);
                 return return_image_data(arr);
-             },py::arg("thread_index") = 0);
+            },
+            py::arg("thread_index") = 0);
 }
 
-void define_cluster_collector_bindings(py::module &m) {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    py::class_<ClusterCollector>(m, "ClusterCollector")
+          typename CoordType = uint16_t>
-        .def(py::init<ClusterFinderMT<uint16_t, double, int32_t> *>())
+void define_cluster_collector_bindings(py::module &m,
-        .def("stop", &ClusterCollector::stop)
+                                       const std::string &typestr) {
+    auto class_name = fmt::format("ClusterCollector_{}", typestr);
+
+    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
+
+    py::class_<ClusterCollector<ClusterType>>(m, class_name.c_str())
+        .def(py::init<ClusterFinderMT<ClusterType, uint16_t, double> *>())
+        .def("stop", &ClusterCollector<ClusterType>::stop)
         .def(
             "steal_clusters",
-            [](ClusterCollector &self) {
+            [](ClusterCollector<ClusterType> &self) {
-                auto v =
+                auto v = new std::vector<ClusterVector<ClusterType>>(
-                    new std::vector<ClusterVector<int>>(self.steal_clusters());
+                    self.steal_clusters());
-                return v;
+                return v; // TODO change!!!
             },
             py::return_value_policy::take_ownership);
 }
 
-void define_cluster_file_sink_bindings(py::module &m) {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    py::class_<ClusterFileSink>(m, "ClusterFileSink")
+          typename CoordType = uint16_t>
-        .def(py::init<ClusterFinderMT<uint16_t, double, int32_t> *,
+void define_cluster_file_sink_bindings(py::module &m,
+                                       const std::string &typestr) {
+    auto class_name = fmt::format("ClusterFileSink_{}", typestr);
+
+    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
+
+    py::class_<ClusterFileSink<ClusterType>>(m, class_name.c_str())
+        .def(py::init<ClusterFinderMT<ClusterType, uint16_t, double> *,
                       const std::filesystem::path &>())
-        .def("stop", &ClusterFileSink::stop);
+        .def("stop", &ClusterFileSink<ClusterType>::stop);
 }
 
-void define_cluster_finder_bindings(py::module &m) {
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-    py::class_<ClusterFinder<uint16_t, pd_type>>(m, "ClusterFinder")
+          typename CoordType = uint16_t>
-        .def(py::init<Shape<2>, Shape<2>, pd_type, size_t>(),
+void define_cluster_finder_bindings(py::module &m, const std::string &typestr) {
-             py::arg("image_size"), py::arg("cluster_size"),
+    auto class_name = fmt::format("ClusterFinder_{}", typestr);
+
+    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
+
+    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("push_pedestal_frame",
-             [](ClusterFinder<uint16_t, pd_type> &self,
+             [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {
                  auto view = make_view_2d(frame);
                  self.push_pedestal_frame(view);
              })
-        .def("clear_pedestal", &ClusterFinder<uint16_t, pd_type>::clear_pedestal)
+        .def("clear_pedestal",
-        .def_property_readonly("pedestal",
+             &ClusterFinder<ClusterType, uint16_t, pd_type>::clear_pedestal)
-                               [](ClusterFinder<uint16_t, pd_type> &self) {
+        .def_property_readonly(
+            "pedestal",
+            [](ClusterFinder<ClusterType, uint16_t, pd_type> &self) {
                 auto pd = new NDArray<pd_type, 2>{};
                 *pd = self.pedestal();
                 return return_image_data(pd);
             })
-        .def_property_readonly("noise",
+        .def_property_readonly(
-                               [](ClusterFinder<uint16_t, pd_type> &self) {
+            "noise",
+            [](ClusterFinder<ClusterType, uint16_t, pd_type> &self) {
                 auto arr = new NDArray<pd_type, 2>{};
                 *arr = self.noise();
                 return return_image_data(arr);
             })
         .def(
             "steal_clusters",
-            [](ClusterFinder<uint16_t, pd_type> &self,
+            [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                bool realloc_same_capacity) {
-                auto v = new ClusterVector<int>(
+                ClusterVector<ClusterType> clusters =
-                    self.steal_clusters(realloc_same_capacity));
+                    self.steal_clusters(realloc_same_capacity);
-                return v;
+                return clusters;
             },
             py::arg("realloc_same_capacity") = false)
         .def(
             "find_clusters",
-            [](ClusterFinder<uint16_t, pd_type> &self,
+            [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                py::array_t<uint16_t> frame, uint64_t frame_number) {
                 auto view = make_view_2d(frame);
                 self.find_clusters(view, frame_number);
                 return;
             },
             py::arg(), py::arg("frame_number") = 0);
-
-    m.def("hitmap",
-          [](std::array<size_t, 2> image_size, ClusterVector<int32_t> &cv) {
-              py::array_t<int32_t> hitmap(image_size);
-              auto r = hitmap.mutable_unchecked<2>();
-
-              // Initialize hitmap to 0
-              for (py::ssize_t i = 0; i < r.shape(0); i++)
-                  for (py::ssize_t j = 0; j < r.shape(1); j++)
-                      r(i, j) = 0;
-
-              size_t stride = cv.item_size();
-              auto ptr = cv.data();
-              for (size_t i = 0; i < cv.size(); i++) {
-                  auto x = *reinterpret_cast<int16_t *>(ptr);
-                  auto y = *reinterpret_cast<int16_t *>(ptr + sizeof(int16_t));
-                  r(y, x) += 1;
-                  ptr += stride;
-              }
-              return hitmap;
-          });
-    define_cluster_vector<int>(m, "i");
-    define_cluster_vector<double>(m, "d");
-    define_cluster_vector<float>(m, "f");
-
-    py::class_<DynamicCluster>(m, "DynamicCluster", py::buffer_protocol())
-        .def(py::init<int, int, Dtype>())
-        .def("size", &DynamicCluster::size)
-        .def("begin", &DynamicCluster::begin)
-        .def("end", &DynamicCluster::end)
-        .def_readwrite("x", &DynamicCluster::x)
-        .def_readwrite("y", &DynamicCluster::y)
-        .def_buffer([](DynamicCluster &c) -> py::buffer_info {
-            return py::buffer_info(c.data(), c.dt.bytes(), c.dt.format_descr(),
-                                   1, {c.size()}, {c.dt.bytes()});
-        })
-
-        .def("__repr__", [](const DynamicCluster &a) {
-            return "<DynamicCluster: x: " + std::to_string(a.x) +
-                   ", y: " + std::to_string(a.y) + ">";
-        });
 }
+#pragma GCC diagnostic pop

python/src/cluster_file.hpp

@@ -1,3 +1,4 @@
+#include "aare/CalculateEta.hpp"
 #include "aare/ClusterFile.hpp"
 #include "aare/defs.hpp"
 
@@ -10,61 +11,81 @@
 #include <pybind11/stl/filesystem.h>
 #include <string>
 
-//Disable warnings for unused parameters, as we ignore some
+// Disable warnings for unused parameters, as we ignore some
-//in the __exit__ method
+// in the __exit__ method
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 
-
 namespace py = pybind11;
 using namespace ::aare;
 
-void define_cluster_file_io_bindings(py::module &m) {
+template <typename Type, uint8_t CoordSizeX, uint8_t CoordSizeY,
-    PYBIND11_NUMPY_DTYPE(Cluster3x3, x, y, data);
+          typename CoordType = uint16_t>
+void define_cluster_file_io_bindings(py::module &m,
+                                     const std::string &typestr) {
 
-    py::class_<ClusterFile>(m, "ClusterFile")
+    using ClusterType = Cluster<Type, CoordSizeX, CoordSizeY, CoordType>;
+
+    auto class_name = fmt::format("ClusterFile_{}", typestr);
+
+    py::class_<ClusterFile<ClusterType>>(m, class_name.c_str())
         .def(py::init<const std::filesystem::path &, size_t,
                       const std::string &>(),
              py::arg(), py::arg("chunk_size") = 1000, py::arg("mode") = "r")
-        .def("read_clusters",
+        .def(
-             [](ClusterFile &self, size_t n_clusters) {
+            "read_clusters",
-                auto v = new ClusterVector<int32_t>(self.read_clusters(n_clusters));
+            [](ClusterFile<ClusterType> &self, size_t n_clusters) {
+                auto v = new ClusterVector<ClusterType>(
+                    self.read_clusters(n_clusters));
                 return v;
-             },py::return_value_policy::take_ownership)
+            },
+            py::return_value_policy::take_ownership)
         .def("read_frame",
-             [](ClusterFile &self) {
+             [](ClusterFile<ClusterType> &self) {
-                auto v = new ClusterVector<int32_t>(self.read_frame());
+                 auto v = new ClusterVector<ClusterType>(self.read_frame());
                  return v;
              })
-        .def("set_roi", &ClusterFile::set_roi)
+        .def("set_roi", &ClusterFile<ClusterType>::set_roi)
-        .def("set_noise_map", [](ClusterFile &self, py::array_t<int32_t> noise_map) {
+        .def(
+            "set_noise_map",
+            [](ClusterFile<ClusterType> &self, py::array_t<int32_t> noise_map) {
                 auto view = make_view_2d(noise_map);
                 self.set_noise_map(view);
             })
-        .def("set_gain_map", [](ClusterFile &self, py::array_t<double> gain_map) {
+
+        .def("set_gain_map",
+             [](ClusterFile<ClusterType> &self, py::array_t<double> gain_map) {
                  auto view = make_view_2d(gain_map);
                  self.set_gain_map(view);
              })
-        .def("close", &ClusterFile::close)
+
-        .def("write_frame", &ClusterFile::write_frame)
+        .def("close", &ClusterFile<ClusterType>::close)
-        .def("__enter__", [](ClusterFile &self) { return &self; })
+        .def("write_frame", &ClusterFile<ClusterType>::write_frame)
+        .def("__enter__", [](ClusterFile<ClusterType> &self) { return &self; })
         .def("__exit__",
-             [](ClusterFile &self,
+             [](ClusterFile<ClusterType> &self,
                 const std::optional<pybind11::type> &exc_type,
                 const std::optional<pybind11::object> &exc_value,
                 const std::optional<pybind11::object> &traceback) {
                  self.close();
              })
-        .def("__iter__", [](ClusterFile &self) { return &self; })
+        .def("__iter__", [](ClusterFile<ClusterType> &self) { return &self; })
-        .def("__next__", [](ClusterFile &self) {
+        .def("__next__", [](ClusterFile<ClusterType> &self) {
-            auto v = new ClusterVector<int32_t>(self.read_clusters(self.chunk_size()));
+            auto v = new ClusterVector<ClusterType>(
+                self.read_clusters(self.chunk_size()));
             if (v->size() == 0) {
                 throw py::stop_iteration();
             }
             return v;
         });
+}
 
-        m.def("calculate_eta2", []( aare::ClusterVector<int32_t> &clusters) {
+template <typename Type, uint8_t CoordSizeX, uint8_t CoordSizeY,
+          typename CoordType = uint16_t>
+void register_calculate_eta(py::module &m) {
+    using ClusterType = Cluster<Type, CoordSizeX, CoordSizeY, CoordType>;
+    m.def("calculate_eta2",
+          [](const aare::ClusterVector<ClusterType> &clusters) {
               auto eta2 = new NDArray<double, 2>(calculate_eta2(clusters));
               return return_image_data(eta2);
           });

python/src/interpolation.hpp

@@ -8,32 +8,56 @@
 #include <pybind11/stl.h>
 
 namespace py = pybind11;
+
+template <typename Type, uint8_t CoordSizeX, uint8_t CoordSizeY,
+          typename CoordType = uint16_t>
+void register_interpolate(py::class_<aare::Interpolator> &interpolator) {
+
+    using ClusterType = Cluster<Type, CoordSizeX, CoordSizeY, CoordType>;
+
+    interpolator.def("interpolate",
+                     [](aare::Interpolator &self,
+                        const ClusterVector<ClusterType> &clusters) {
+                         auto photons = self.interpolate<ClusterType>(clusters);
+                         auto *ptr = new std::vector<Photon>{photons};
+                         return return_vector(ptr);
+                     });
+}
+
 void define_interpolation_bindings(py::module &m) {
 
-    PYBIND11_NUMPY_DTYPE(aare::Photon, x,y,energy);
+    PYBIND11_NUMPY_DTYPE(aare::Photon, x, y, energy);
 
+    auto interpolator =
         py::class_<aare::Interpolator>(m, "Interpolator")
-        .def(py::init([](py::array_t<double, py::array::c_style | py::array::forcecast> etacube, py::array_t<double> xbins,
+            .def(py::init([](py::array_t<double, py::array::c_style |
-                         py::array_t<double> ybins, py::array_t<double> ebins) {
+                                                     py::array::forcecast>
+                                 etacube,
+                             py::array_t<double> xbins,
+                             py::array_t<double> ybins,
+                             py::array_t<double> ebins) {
                 return Interpolator(make_view_3d(etacube), make_view_1d(xbins),
                                     make_view_1d(ybins), make_view_1d(ebins));
             }))
-        .def("get_ietax", [](Interpolator& self){
+            .def("get_ietax",
-            auto*ptr = new NDArray<double,3>{};
+                 [](Interpolator &self) {
+                     auto *ptr = new NDArray<double, 3>{};
                      *ptr = self.get_ietax();
                      return return_image_data(ptr);
                  })
-        .def("get_ietay", [](Interpolator& self){
+            .def("get_ietay", [](Interpolator &self) {
-            auto*ptr = new NDArray<double,3>{};
+                auto *ptr = new NDArray<double, 3>{};
                 *ptr = self.get_ietay();
                 return return_image_data(ptr);
-        })
-        .def("interpolate", [](Interpolator& self, const ClusterVector<int32_t>& clusters){
-            auto photons = self.interpolate(clusters);
-            auto* ptr = new std::vector<Photon>{photons};
-            return return_vector(ptr);
             });
 
+    register_interpolate<int, 3, 3, uint16_t>(interpolator);
+    register_interpolate<float, 3, 3, uint16_t>(interpolator);
+    register_interpolate<double, 3, 3, uint16_t>(interpolator);
+    register_interpolate<int, 2, 2, uint16_t>(interpolator);
+    register_interpolate<float, 2, 2, uint16_t>(interpolator);
+    register_interpolate<double, 2, 2, uint16_t>(interpolator);
+
     // TODO! Evaluate without converting to double
     m.def(
         "hej",

python/src/module.cpp

@@ -1,20 +1,24 @@
-//Files with bindings to the different classes
+// Files with bindings to the different classes
-#include "file.hpp"
+
-#include "raw_file.hpp"
+//New style file naming
-#include "ctb_raw_file.hpp"
+#include "bind_ClusterVector.hpp"
-#include "raw_master_file.hpp"
+
-#include "var_cluster.hpp"
+//TODO! migrate the other names
-#include "pixel_map.hpp"
-#include "pedestal.hpp"
 #include "cluster.hpp"
 #include "cluster_file.hpp"
+#include "ctb_raw_file.hpp"
+#include "file.hpp"
 #include "fit.hpp"
 #include "interpolation.hpp"
 #include "raw_sub_file.hpp"
-
+#include "raw_master_file.hpp"
+#include "raw_file.hpp"
+#include "pixel_map.hpp"
+#include "var_cluster.hpp"
+#include "pedestal.hpp"
 #include "jungfrau_data_file.hpp"
 
-//Pybind stuff
+// Pybind stuff
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
@@ -30,13 +34,63 @@ PYBIND11_MODULE(_aare, m) {
     define_pixel_map_bindings(m);
     define_pedestal_bindings<double>(m, "Pedestal_d");
     define_pedestal_bindings<float>(m, "Pedestal_f");
-    define_cluster_finder_bindings(m);
-    define_cluster_finder_mt_bindings(m);
-    define_cluster_file_io_bindings(m);
-    define_cluster_collector_bindings(m);
-    define_cluster_file_sink_bindings(m);
     define_fit_bindings(m);
     define_interpolation_bindings(m);
     define_jungfrau_data_file_io_bindings(m);
 
+    define_cluster_file_io_bindings<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_cluster_file_io_bindings<double, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_cluster_file_io_bindings<float, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_cluster_file_io_bindings<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_cluster_file_io_bindings<float, 2, 2, uint16_t>(m, "Cluster2x2f");
+    define_cluster_file_io_bindings<double, 2, 2, uint16_t>(m, "Cluster2x2d");
+
+    define_ClusterVector<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_ClusterVector<double, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_ClusterVector<float, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_ClusterVector<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_ClusterVector<double, 2, 2, uint16_t>(m, "Cluster2x2d");
+    define_ClusterVector<float, 2, 2, uint16_t>(m, "Cluster2x2f");
+
+    define_cluster_finder_bindings<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_cluster_finder_bindings<double, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_cluster_finder_bindings<float, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_cluster_finder_bindings<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_cluster_finder_bindings<double, 2, 2, uint16_t>(m, "Cluster2x2d");
+    define_cluster_finder_bindings<float, 2, 2, uint16_t>(m, "Cluster2x2f");
+
+    define_cluster_finder_mt_bindings<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_cluster_finder_mt_bindings<double, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_cluster_finder_mt_bindings<float, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_cluster_finder_mt_bindings<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_cluster_finder_mt_bindings<double, 2, 2, uint16_t>(m, "Cluster2x2d");
+    define_cluster_finder_mt_bindings<float, 2, 2, uint16_t>(m, "Cluster2x2f");
+
+    define_cluster_file_sink_bindings<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_cluster_file_sink_bindings<double, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_cluster_file_sink_bindings<float, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_cluster_file_sink_bindings<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_cluster_file_sink_bindings<double, 2, 2, uint16_t>(m, "Cluster2x2d");
+    define_cluster_file_sink_bindings<float, 2, 2, uint16_t>(m, "Cluster2x2f");
+
+    define_cluster_collector_bindings<int, 3, 3, uint16_t>(m, "Cluster3x3i");
+    define_cluster_collector_bindings<double, 3, 3, uint16_t>(m, "Cluster3x3f");
+    define_cluster_collector_bindings<float, 3, 3, uint16_t>(m, "Cluster3x3d");
+    define_cluster_collector_bindings<int, 2, 2, uint16_t>(m, "Cluster2x2i");
+    define_cluster_collector_bindings<double, 2, 2, uint16_t>(m, "Cluster2x2f");
+    define_cluster_collector_bindings<float, 2, 2, uint16_t>(m, "Cluster2x2d");
+
+    define_cluster<int, 3, 3, uint16_t>(m, "3x3i");
+    define_cluster<float, 3, 3, uint16_t>(m, "3x3f");
+    define_cluster<double, 3, 3, uint16_t>(m, "3x3d");
+    define_cluster<int, 2, 2, uint16_t>(m, "2x2i");
+    define_cluster<float, 2, 2, uint16_t>(m, "2x2f");
+    define_cluster<double, 2, 2, uint16_t>(m, "2x2d");
+
+    register_calculate_eta<int, 3, 3, uint16_t>(m);
+    register_calculate_eta<float, 3, 3, uint16_t>(m);
+    register_calculate_eta<double, 3, 3, uint16_t>(m);
+    register_calculate_eta<int, 2, 2, uint16_t>(m);
+    register_calculate_eta<float, 2, 2, uint16_t>(m);
+    register_calculate_eta<double, 2, 2, uint16_t>(m);
 }

python/src/np_helper.hpp

@@ -10,6 +10,7 @@
 #include "aare/NDView.hpp"
 
 namespace py = pybind11;
+using namespace aare;
 
 // Pass image data back to python as a numpy array
 template <typename T, int64_t Ndim>
@@ -40,25 +41,46 @@ template <typename T> py::array return_vector(std::vector<T> *vec) {
 }
 
 // todo rewrite generic
-template <class T, int Flags> auto get_shape_3d(const py::array_t<T, Flags>& arr) {
+template <class T, int Flags>
+auto get_shape_3d(const py::array_t<T, Flags> &arr) {
     return aare::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)};
 }
 
-template <class T, int Flags> auto make_view_3d(py::array_t<T, Flags>& arr) {
+template <class T, int Flags> auto make_view_3d(py::array_t<T, Flags> &arr) {
     return aare::NDView<T, 3>(arr.mutable_data(), get_shape_3d<T, Flags>(arr));
 }
 
-template <class T, int Flags> auto get_shape_2d(const py::array_t<T, Flags>& arr) {
+template <class T, int Flags>
+auto get_shape_2d(const py::array_t<T, Flags> &arr) {
     return aare::Shape<2>{arr.shape(0), arr.shape(1)};
 }
 
-template <class T, int Flags> auto get_shape_1d(const py::array_t<T, Flags>& arr) {
+template <class T, int Flags>
+auto get_shape_1d(const py::array_t<T, Flags> &arr) {
     return aare::Shape<1>{arr.shape(0)};
 }
 
-template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags>& arr) {
+template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags> &arr) {
     return aare::NDView<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr));
 }
-template <class T, int Flags> auto make_view_1d(py::array_t<T, Flags>& arr) {
+template <class T, int Flags> auto make_view_1d(py::array_t<T, Flags> &arr) {
     return aare::NDView<T, 1>(arr.mutable_data(), get_shape_1d<T, Flags>(arr));
 }
+
+template <typename ClusterType> struct fmt_format_trait; // forward declaration
+
+template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
+          typename CoordType>
+struct fmt_format_trait<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
+
+    static std::string value() {
+        return fmt::format("T{{{}:x:{}:y:{}:data:}}",
+                           py::format_descriptor<CoordType>::format(),
+                           py::format_descriptor<CoordType>::format(),
+                           fmt::format("({},{}){}", ClusterSizeX, ClusterSizeY,
+                                       py::format_descriptor<T>::format()));
+    }
+};
+
+template <typename ClusterType>
+auto fmt_format = fmt_format_trait<ClusterType>::value();

python/tests/conftest.py

@@ -25,5 +25,10 @@ def pytest_collection_modifyitems(config, items):
 
 @pytest.fixture
 def test_data_path():
-    return Path(os.environ["AARE_TEST_DATA"])
+    env_value = os.environ.get("AARE_TEST_DATA")
+    if not env_value:
+        raise RuntimeError("Environment variable AARE_TEST_DATA is not set or is empty")
+
+    return Path(env_value)
+
 

python/tests/test_Cluster.py

@@ -0,0 +1,110 @@
+import pytest 
+import numpy as np
+
+from aare import _aare #import the C++ module
+from conftest import test_data_path
+
+
+def test_cluster_vector_can_be_converted_to_numpy():
+    cv = _aare.ClusterVector_Cluster3x3i()
+    arr = np.array(cv, copy=False)
+    assert arr.shape == (0,)  # 4 for x, y, size, energy and 9 for the cluster data
+
+
+def test_ClusterVector(): 
+    """Test ClusterVector""" 
+
+    clustervector = _aare.ClusterVector_Cluster3x3i()
+    assert clustervector.cluster_size_x == 3
+    assert clustervector.cluster_size_y == 3
+    assert clustervector.item_size() == 4+9*4
+    assert clustervector.frame_number == 0
+    assert clustervector.size == 0
+
+    cluster = _aare.Cluster3x3i(0,0,np.ones(9, dtype=np.int32))
+    
+    clustervector.push_back(cluster) 
+    assert clustervector.size == 1
+
+    with pytest.raises(TypeError):  # Or use the appropriate exception type
+        clustervector.push_back(_aare.Cluster2x2i(0,0,np.ones(4, dtype=np.int32)))
+
+    with pytest.raises(TypeError): 
+        clustervector.push_back(_aare.Cluster3x3f(0,0,np.ones(9, dtype=np.float32))) 
+
+def test_Interpolator(): 
+    """Test Interpolator"""
+
+    ebins = np.linspace(0,10, 20, dtype=np.float64)
+    xbins = np.linspace(0, 5, 30, dtype=np.float64)
+    ybins = np.linspace(0, 5, 30, dtype=np.float64)
+
+    etacube = np.zeros(shape=[30, 30, 20], dtype=np.float64)
+    interpolator = _aare.Interpolator(etacube, xbins, ybins, ebins)
+
+    assert interpolator.get_ietax().shape == (30,30,20)
+    assert interpolator.get_ietay().shape == (30,30,20)
+    clustervector = _aare.ClusterVector_Cluster3x3i()
+    
+    cluster = _aare.Cluster3x3i(0,0, np.ones(9, dtype=np.int32))
+    clustervector.push_back(cluster) 
+
+    interpolated_photons = interpolator.interpolate(clustervector)
+
+    assert interpolated_photons.size == 1
+
+    assert interpolated_photons[0]["x"] == -1 
+    assert interpolated_photons[0]["y"] == -1
+    assert interpolated_photons[0]["energy"] == 4 #eta_sum = 4, dx, dy = -1,-1 m_ietax = 0, m_ietay = 0
+
+    clustervector = _aare.ClusterVector_Cluster2x2i()
+
+    cluster = _aare.Cluster2x2i(0,0, np.ones(4, dtype=np.int32))
+    clustervector.push_back(cluster) 
+
+    interpolated_photons = interpolator.interpolate(clustervector)
+
+    assert interpolated_photons.size == 1
+
+    assert interpolated_photons[0]["x"] == 0
+    assert interpolated_photons[0]["y"] == 0
+    assert interpolated_photons[0]["energy"] == 4
+
+
+
+def test_calculate_eta(): 
+    """Calculate Eta""" 
+    clusters = _aare.ClusterVector_Cluster3x3i() 
+    clusters.push_back(_aare.Cluster3x3i(0,0, np.ones(9, dtype=np.int32)))
+    clusters.push_back(_aare.Cluster3x3i(0,0, np.array([1,1,1,2,2,2,3,3,3])))
+
+    eta2 = _aare.calculate_eta2(clusters)
+
+    assert eta2.shape == (2,2)
+    assert eta2[0,0] == 0.5
+    assert eta2[0,1] == 0.5
+    assert eta2[1,0] == 0.5
+    assert eta2[1,1] == 0.6 #1/5
+
+def test_cluster_finder(): 
+    """Test ClusterFinder""" 
+
+    clusterfinder = _aare.ClusterFinder_Cluster3x3i([100,100])
+
+    #frame = np.random.rand(100,100)
+    frame = np.zeros(shape=[100,100])
+
+    clusterfinder.find_clusters(frame)
+
+    clusters = clusterfinder.steal_clusters(False) #conversion does not work
+
+    assert clusters.size == 0
+
+
+
+
+
+
+
+
+

python/tests/test_ClusterFile.py

@@ -0,0 +1,64 @@
+
+import pytest 
+import numpy as np
+import boost_histogram as bh
+import time
+from pathlib import Path
+import pickle
+
+from aare import ClusterFile
+from conftest import test_data_path
+
+@pytest.mark.files
+def test_cluster_file(test_data_path): 
+    """Test ClusterFile""" 
+    f =  ClusterFile(test_data_path / "clust/single_frame_97_clustrers.clust") 
+    cv = f.read_clusters(10) #conversion does not work
+
+
+    assert cv.frame_number == 135
+    assert cv.size == 10
+
+    #Known data 
+    #frame_number, num_clusters   [135] 97
+    #[  1 200] [0 1 2 3 4 5 6 7 8]
+    #[  2 201] [ 9 10 11 12 13 14 15 16 17]
+    #[  3 202] [18 19 20 21 22 23 24 25 26]
+    #[  4 203] [27 28 29 30 31 32 33 34 35]
+    #[  5 204] [36 37 38 39 40 41 42 43 44]
+    #[  6 205] [45 46 47 48 49 50 51 52 53]
+    #[  7 206] [54 55 56 57 58 59 60 61 62]
+    #[  8 207] [63 64 65 66 67 68 69 70 71]
+    #[  9 208] [72 73 74 75 76 77 78 79 80]
+    #[ 10 209] [81 82 83 84 85 86 87 88 89]
+
+    #conversion to numpy array
+    arr = np.array(cv, copy = False)
+    
+    assert arr.size == 10
+    for i in range(10):
+        assert arr[i]['x'] == i+1
+
+@pytest.mark.files
+def test_read_clusters_and_fill_histogram(test_data_path): 
+    # Create the histogram
+    n_bins = 100
+    xmin = -100
+    xmax = 1e4
+    hist_aare = bh.Histogram(bh.axis.Regular(n_bins, xmin, xmax))
+
+    fname = test_data_path / "clust/beam_En700eV_-40deg_300V_10us_d0_f0_100.clust"
+
+    #Read clusters and fill the histogram with pixel values
+    with ClusterFile(fname, chunk_size = 10000) as f:
+        for clusters in f:
+            arr = np.array(clusters, copy = False)
+            hist_aare.fill(arr['data'].flat)
+
+
+    #Load the histogram from the pickle file
+    with open(fname.with_suffix('.pkl'), 'rb') as f:
+        hist_py = pickle.load(f)
+        
+    #Compare the two histograms
+    assert hist_aare == hist_py

python/tests/test_ClusterVector.py

@@ -0,0 +1,54 @@
+import pytest 
+import numpy as np
+import boost_histogram as bh
+import time
+from pathlib import Path
+import pickle
+
+from aare import ClusterFile
+from aare import _aare
+from conftest import test_data_path
+
+
+def test_create_cluster_vector():
+    cv = _aare.ClusterVector_Cluster3x3i()
+    assert cv.cluster_size_x == 3
+    assert cv.cluster_size_y == 3
+    assert cv.size == 0
+
+
+def test_push_back_on_cluster_vector():
+    cv = _aare.ClusterVector_Cluster2x2i()
+    assert cv.cluster_size_x == 2
+    assert cv.cluster_size_y == 2
+    assert cv.size == 0
+
+    cluster = _aare.Cluster2x2i(19, 22, np.ones(4, dtype=np.int32))
+    cv.push_back(cluster)
+    assert cv.size == 1
+
+    arr = np.array(cv, copy=False)
+    assert arr[0]['x'] == 19
+    assert arr[0]['y'] == 22
+
+
+def test_make_a_hitmap_from_cluster_vector():
+    cv = _aare.ClusterVector_Cluster3x3i()
+
+    # Push back 4 clusters with different positions
+    cv.push_back(_aare.Cluster3x3i(0, 0, np.ones(9, dtype=np.int32)))
+    cv.push_back(_aare.Cluster3x3i(1, 1, np.ones(9, dtype=np.int32)))
+    cv.push_back(_aare.Cluster3x3i(1, 1, np.ones(9, dtype=np.int32)))
+    cv.push_back(_aare.Cluster3x3i(2, 2, np.ones(9, dtype=np.int32)))
+
+    ref = np.zeros((5, 5), dtype=np.int32)
+    ref[0,0] = 1
+    ref[1,1] = 2
+    ref[2,2] = 1
+
+
+    img = _aare.hitmap((5,5), cv)
+    # print(img)
+    # print(ref)
+    assert (img == ref).all()
+    

src/CalculateEta.test.cpp

@@ -0,0 +1,127 @@
+/************************************************
+ * @file CalculateEta.test.cpp
+ * @short test case to calculate_eta2
+ ***********************************************/
+
+#include "aare/CalculateEta.hpp"
+#include "aare/Cluster.hpp"
+#include "aare/ClusterFile.hpp"
+
+// #include "catch.hpp"
+#include <array>
+#include <catch2/catch_all.hpp>
+#include <catch2/catch_test_macros.hpp>
+
+using namespace aare;
+
+using ClusterTypes =
+    std::variant<Cluster<int, 2, 2>, Cluster<int, 3, 3>, Cluster<int, 5, 5>,
+                 Cluster<int, 4, 2>, Cluster<int, 2, 3>>;
+
+auto get_test_parameters() {
+    return GENERATE(
+        std::make_tuple(ClusterTypes{Cluster<int, 2, 2>{0, 0, {1, 2, 3, 1}}},
+                        Eta2<int>{2. / 3, 3. / 4,
+                                  static_cast<int>(corner::cBottomLeft), 7}),
+        std::make_tuple(
+            ClusterTypes{Cluster<int, 3, 3>{0, 0, {1, 2, 3, 4, 5, 6, 1, 2, 7}}},
+            Eta2<int>{6. / 11, 2. / 7, static_cast<int>(corner::cTopRight),
+                      20}),
+        std::make_tuple(ClusterTypes{Cluster<int, 5, 5>{
+                            0, 0, {1, 6, 7, 6, 5, 4, 3, 2, 1, 2, 8, 9, 8,
+                                   1, 4, 5, 6, 7, 8, 4, 1, 1, 1, 1, 1}}},
+                        Eta2<int>{8. / 17, 7. / 15, 9, 30}),
+        std::make_tuple(
+            ClusterTypes{Cluster<int, 4, 2>{0, 0, {1, 4, 7, 2, 5, 6, 4, 3}}},
+            Eta2<int>{4. / 10, 4. / 11, 1, 21}),
+        std::make_tuple(
+            ClusterTypes{Cluster<int, 2, 3>{0, 0, {1, 3, 2, 3, 4, 2}}},
+            Eta2<int>{3. / 5, 2. / 5, 1, 11}));
+}
+
+TEST_CASE("compute_largest_2x2_subcluster", "[eta_calculation]") {
+    auto [cluster, expected_eta] = get_test_parameters();
+
+    auto [sum, index] = std::visit(
+        [](const auto &clustertype) { return clustertype.max_sum_2x2(); },
+        cluster);
+    CHECK(expected_eta.c == index);
+    CHECK(expected_eta.sum == sum);
+}
+
+TEST_CASE("calculate_eta2", "[eta_calculation]") {
+
+    auto [cluster, expected_eta] = get_test_parameters();
+
+    auto eta = std::visit(
+        [](const auto &clustertype) { return calculate_eta2(clustertype); },
+        cluster);
+
+    CHECK(eta.x == expected_eta.x);
+    CHECK(eta.y == expected_eta.y);
+    CHECK(eta.c == expected_eta.c);
+    CHECK(eta.sum == expected_eta.sum);
+}
+
+// 3x3 cluster layout (rotated to match the cBottomLeft enum):
+//  6, 7, 8
+//  3, 4, 5
+//  0, 1, 2
+
+TEST_CASE("Calculate eta2 for a 3x3 int32 cluster with the largest 2x2 sum in "
+          "the bottom left",
+          "[eta_calculation]") {
+
+    // Create a 3x3 cluster
+    Cluster<int32_t, 3, 3> cl;
+    cl.x = 0;
+    cl.y = 0;
+    cl.data[0] = 30;
+    cl.data[1] = 23;
+    cl.data[2] = 5;
+    cl.data[3] = 20;
+    cl.data[4] = 50;
+    cl.data[5] = 3;
+    cl.data[6] = 8;
+    cl.data[7] = 2;
+    cl.data[8] = 3;
+
+    // 8, 2, 3
+    // 20, 50, 3
+    // 30, 23, 5
+
+    auto eta = calculate_eta2(cl);
+    CHECK(eta.c == static_cast<int>(corner::cBottomLeft));
+    CHECK(eta.x == 50.0 / (20 + 50)); // 4/(3+4)
+    CHECK(eta.y == 50.0 / (23 + 50)); // 4/(1+4)
+    CHECK(eta.sum == 30 + 23 + 20 + 50);
+}
+
+TEST_CASE("Calculate eta2 for a 3x3 int32 cluster with the largest 2x2 sum in "
+          "the top left",
+          "[eta_calculation]") {
+
+    // Create a 3x3 cluster
+    Cluster<int32_t, 3, 3> cl;
+    cl.x = 0;
+    cl.y = 0;
+    cl.data[0] = 8;
+    cl.data[1] = 12;
+    cl.data[2] = 5;
+    cl.data[3] = 77;
+    cl.data[4] = 80;
+    cl.data[5] = 3;
+    cl.data[6] = 82;
+    cl.data[7] = 91;
+    cl.data[8] = 3;
+
+    // 82, 91, 3
+    // 77, 80, 3
+    // 8, 12, 5
+
+    auto eta = calculate_eta2(cl);
+    CHECK(eta.c == static_cast<int>(corner::cTopLeft));
+    CHECK(eta.x == 80. / (77 + 80));  // 4/(3+4)
+    CHECK(eta.y == 91.0 / (91 + 80)); // 7/(7+4)
+    CHECK(eta.sum == 77 + 80 + 82 + 91);
+}

src/Cluster.test.cpp

@@ -0,0 +1,21 @@
+/************************************************
+ * @file test-Cluster.cpp
+ * @short test case for generic Cluster, ClusterVector, and calculate_eta2
+ ***********************************************/
+
+#include "aare/Cluster.hpp"
+#include "aare/CalculateEta.hpp"
+#include "aare/ClusterFile.hpp"
+
+// #include "catch.hpp"
+#include <array>
+#include <catch2/catch_all.hpp>
+#include <catch2/catch_test_macros.hpp>
+
+using namespace aare;
+
+TEST_CASE("Test sum of Cluster", "[.cluster]") {
+    Cluster<int, 2, 2> cluster{0, 0, {1, 2, 3, 4}};
+
+    CHECK(cluster.sum() == 10);
+}

src/ClusterFile.cpp

@@ -1,402 +0,0 @@
-#include "aare/ClusterFile.hpp"
-
-#include <algorithm>
-
-namespace aare {
-
-ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
-                         const std::string &mode)
-    : m_chunk_size(chunk_size), m_mode(mode) {
-
-    if (mode == "r") {
-        fp = fopen(fname.c_str(), "rb");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for reading: " +
-                                     fname.string());
-        }
-    } else if (mode == "w") {
-        fp = fopen(fname.c_str(), "wb");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for writing: " +
-                                     fname.string());
-        }
-    } else if (mode == "a") {
-        fp = fopen(fname.c_str(), "ab");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for appending: " +
-                                     fname.string());
-        }
-    } else {
-        throw std::runtime_error("Unsupported mode: " + mode);
-    }
-}
-
-void ClusterFile::set_roi(ROI roi){
-    m_roi = roi;
-}
-
-void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map){
-    m_noise_map = NDArray<int32_t, 2>(noise_map);
-}
-
-void ClusterFile::set_gain_map(const NDView<double, 2> gain_map){
-    m_gain_map = NDArray<double, 2>(gain_map);
-    
-    // Gain map is passed as ADU/keV to avoid dividing in when applying the gain
-    // map we invert it here
-    for (auto &item : m_gain_map->view()) {
-        item = 1.0 / item;
-    }
-}
-
-ClusterFile::~ClusterFile() { close(); }
-
-void ClusterFile::close() {
-    if (fp) {
-        fclose(fp);
-        fp = nullptr;
-    }
-}
-
-void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
-    if (m_mode != "w" && m_mode != "a") {
-        throw std::runtime_error("File not opened for writing");
-    }
-    if (!(clusters.cluster_size_x() == 3) &&
-        !(clusters.cluster_size_y() == 3)) {
-        throw std::runtime_error("Only 3x3 clusters are supported");
-    }
-    //First write the frame number - 4 bytes
-    int32_t frame_number = clusters.frame_number();
-    if(fwrite(&frame_number, sizeof(frame_number), 1, fp)!=1){
-        throw std::runtime_error(LOCATION + "Could not write frame number");
-    }
-
-    //Then write the number of clusters - 4 bytes
-    uint32_t n_clusters = clusters.size();
-    if(fwrite(&n_clusters, sizeof(n_clusters), 1, fp)!=1){
-        throw std::runtime_error(LOCATION + "Could not write number of clusters");
-    }
-
-    //Now write the clusters in the frame
-    if(fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp)!=clusters.size()){
-        throw std::runtime_error(LOCATION + "Could not write clusters");
-    }
-}
-
-
-ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters){
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_noise_map || m_roi){
-        return read_clusters_with_cut(n_clusters);
-    }else{
-        return read_clusters_without_cut(n_clusters);
-    }
-}
-
-ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters) {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    
-    ClusterVector<int32_t> clusters(3,3, n_clusters);
-
-    int32_t iframe = 0; // frame number needs to be 4 bytes!
-    size_t nph_read = 0;
-    uint32_t nn = m_num_left;
-    uint32_t nph = m_num_left; // number of clusters in frame needs to be 4
-
-    // auto buf = reinterpret_cast<Cluster3x3 *>(clusters.data());
-    auto buf = clusters.data();
-    // if there are photons left from previous frame read them first
-    if (nph) {
-        if (nph > n_clusters) {
-            // if we have more photons left in the frame then photons to read we
-            // read directly the requested number
-            nn = n_clusters;
-        } else {
-            nn = nph;
-        }
-        nph_read += fread((buf + nph_read*clusters.item_size()),
-                          clusters.item_size(), nn, fp);
-        m_num_left = nph - nn; // write back the number of photons left
-    }
-
-    if (nph_read < n_clusters) {
-        // keep on reading frames and photons until reaching n_clusters
-        while (fread(&iframe, sizeof(iframe), 1, fp)) {
-            clusters.set_frame_number(iframe);
-            // read number of clusters in frame
-            if (fread(&nph, sizeof(nph), 1, fp)) {
-                if (nph > (n_clusters - nph_read))
-                    nn = n_clusters - nph_read;
-                else
-                    nn = nph;
-
-                nph_read += fread((buf + nph_read*clusters.item_size()),
-                                  clusters.item_size(), nn, fp);
-                m_num_left = nph - nn;
-            }
-            if (nph_read >= n_clusters)
-                break;
-        }
-    }
-
-    // Resize the vector to the number of clusters.
-    // No new allocation, only change bounds.
-    clusters.resize(nph_read);
-    if(m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-
-ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
-    ClusterVector<int32_t> clusters(3,3);
-    clusters.reserve(n_clusters);
-
-    // if there are photons left from previous frame read them first
-    if (m_num_left) {
-        while(m_num_left && clusters.size() < n_clusters){
-            Cluster3x3 c = read_one_cluster();
-            if(is_selected(c)){
-                clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
-            }
-        }
-    }
-
-    // we did not have enough clusters left in the previous frame
-    // keep on reading frames until reaching n_clusters
-    if (clusters.size() < n_clusters) {
-        // sanity check
-        if (m_num_left) {
-            throw std::runtime_error(LOCATION + "Entered second loop with clusters left\n");
-        }
-        
-        int32_t frame_number = 0; // frame number needs to be 4 bytes!
-        while (fread(&frame_number, sizeof(frame_number), 1, fp)) {
-            if (fread(&m_num_left, sizeof(m_num_left), 1, fp)) {
-                clusters.set_frame_number(frame_number); //cluster vector will hold the last frame number
-                while(m_num_left && clusters.size() < n_clusters){
-                    Cluster3x3 c = read_one_cluster();
-                    if(is_selected(c)){
-                        clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
-                    }
-                }
-            }
-
-            // we have enough clusters, break out of the outer while loop
-            if (clusters.size() >= n_clusters)
-                break;
-        }
-
-    }
-    if(m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-
-    return clusters;
-}
-
-Cluster3x3 ClusterFile::read_one_cluster(){
-    Cluster3x3 c;
-    auto rc = fread(&c, sizeof(c), 1, fp);
-    if (rc != 1) {
-        throw std::runtime_error(LOCATION + "Could not read cluster");
-    }
-    --m_num_left;
-    return c;
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame(){
-    if (m_mode != "r") {
-        throw std::runtime_error(LOCATION + "File not opened for reading");
-    }
-    if (m_noise_map || m_roi){
-        return read_frame_with_cut();
-    }else{
-        return read_frame_without_cut();
-    }
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame_without_cut() {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_num_left) {
-        throw std::runtime_error(
-            "There are still photons left in the last frame");
-    }
-    int32_t frame_number;
-    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not read frame number");
-    }
-
-    int32_t n_clusters; // Saved as 32bit integer in the cluster file
-    if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not read number of clusters");
-    }
-
-    ClusterVector<int32_t> clusters(3, 3, n_clusters);
-    clusters.set_frame_number(frame_number);
-
-    if (fread(clusters.data(), clusters.item_size(), n_clusters, fp) !=
-        static_cast<size_t>(n_clusters)) {
-        throw std::runtime_error(LOCATION + "Could not read clusters");
-    }
-    clusters.resize(n_clusters);
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_num_left) {
-        throw std::runtime_error(
-            "There are still photons left in the last frame");
-    }
-    int32_t frame_number;
-    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        throw std::runtime_error("Could not read frame number");
-    }
-
-
-    if (fread(&m_num_left, sizeof(m_num_left), 1, fp) != 1) {
-        throw std::runtime_error("Could not read number of clusters");
-    }
-    
-    ClusterVector<int32_t> clusters(3, 3);
-    clusters.reserve(m_num_left);
-    clusters.set_frame_number(frame_number);
-    while(m_num_left){
-        Cluster3x3 c = read_one_cluster();
-        if(is_selected(c)){
-            clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
-        }
-    }
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-
-
-bool ClusterFile::is_selected(Cluster3x3 &cl) {
-    //Should fail fast
-    if (m_roi) {
-        if (!(m_roi->contains(cl.x, cl.y))) {
-            return false;
-        }
-    }
-    if (m_noise_map){
-        int32_t sum_1x1 = cl.data[4]; // central pixel
-        int32_t sum_2x2 = cl.sum_2x2(); // highest sum of 2x2 subclusters
-        int32_t sum_3x3 = cl.sum(); // sum of all pixels
-
-        auto noise = (*m_noise_map)(cl.y, cl.x); //TODO! check if this is correct
-        if (sum_1x1 <= noise || sum_2x2 <= 2 * noise || sum_3x3 <= 3 * noise) {
-            return false;
-        }
-    }
-    //we passed all checks
-    return true;
-}
-
-NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
-    //TOTO! make work with 2x2 clusters
-    NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
-    
-    if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
-        for (size_t i = 0; i < clusters.size(); i++) {
-            auto e = calculate_eta2(clusters.at<Cluster3x3>(i));
-            eta2(i, 0) = e.x;
-            eta2(i, 1) = e.y;
-        }
-    }else if(clusters.cluster_size_x() == 2 || clusters.cluster_size_y() == 2){
-        for (size_t i = 0; i < clusters.size(); i++) {
-            auto e = calculate_eta2(clusters.at<Cluster2x2>(i));
-            eta2(i, 0) = e.x;
-            eta2(i, 1) = e.y;
-        }
-    }else{
-        throw std::runtime_error("Only 3x3 and 2x2 clusters are supported");
-    }
-    
-    return eta2;
-}
-
-/** 
- * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2 struct
- * containing etay, etax and the corner of the cluster. 
-*/
-Eta2 calculate_eta2(Cluster3x3 &cl) {
-    Eta2 eta{};
-
-    std::array<int32_t, 4> tot2;
-    tot2[0] = cl.data[0] + cl.data[1] + cl.data[3] + cl.data[4];
-    tot2[1] = cl.data[1] + cl.data[2] + cl.data[4] + cl.data[5];
-    tot2[2] = cl.data[3] + cl.data[4] + cl.data[6] + cl.data[7];
-    tot2[3] = cl.data[4] + cl.data[5] + cl.data[7] + cl.data[8];
-
-    auto c = std::max_element(tot2.begin(), tot2.end()) - tot2.begin();
-    eta.sum = tot2[c];
-    switch (c) {
-    case cBottomLeft:
-        if ((cl.data[3] + cl.data[4]) != 0)
-            eta.x =
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-        if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-        eta.c = cBottomLeft;
-        break;
-    case cBottomRight:
-        if ((cl.data[2] + cl.data[5]) != 0)
-            eta.x =
-                static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
-        if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-        eta.c = cBottomRight;
-        break;
-    case cTopLeft:
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.x =
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-        eta.c = cTopLeft;
-        break;
-    case cTopRight:
-        if ((cl.data[5] + cl.data[4]) != 0)
-            eta.x =
-                static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-        eta.c = cTopRight;
-        break;
-    // no default to allow compiler to warn about missing cases
-    }
-    return eta;
-}
-
-
-Eta2 calculate_eta2(Cluster2x2 &cl) {
-    Eta2 eta{};
-    if ((cl.data[0] + cl.data[1]) != 0)
-        eta.x = static_cast<double>(cl.data[1]) / (cl.data[0] + cl.data[1]);
-    if ((cl.data[0] + cl.data[2]) != 0)
-        eta.y = static_cast<double>(cl.data[2]) / (cl.data[0] + cl.data[2]);
-    eta.sum = cl.data[0] + cl.data[1] + cl.data[2]+ cl.data[3];
-    eta.c = cBottomLeft; //TODO! This is not correct, but need to put something
-    return eta;
-}
-
-
-} // namespace aare

src/ClusterFile.test.cpp

@@ -1,35 +1,39 @@
 #include "aare/ClusterFile.hpp"
 #include "test_config.hpp"
 
-
 #include "aare/defs.hpp"
+#include <algorithm>
 #include <catch2/catch_test_macros.hpp>
 #include <filesystem>
 
-
+using aare::Cluster;
-
-
 using aare::ClusterFile;
+using aare::ClusterVector;
 
 
-TEST_CASE("Read one frame from a a cluster file", "[.files]") {
+TEST_CASE("Read one frame from a cluster file", "[.files]") {
     //We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
     REQUIRE(std::filesystem::exists(fpath));
 
-    ClusterFile f(fpath);
+    ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
     auto clusters = f.read_frame();
-    REQUIRE(clusters.size() == 97);
+    CHECK(clusters.size() == 97);
-    REQUIRE(clusters.frame_number() == 135);
+    CHECK(clusters.frame_number() == 135);
+    CHECK(clusters[0].x == 1);
+    CHECK(clusters[0].y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters[0].data), std::end(clusters[0].data),
+                     std::begin(expected_cluster_data)));
 }
 
 
 TEST_CASE("Read one frame using ROI", "[.files]") {
-    //We know that the frame has 97 clusters
+    // We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
     REQUIRE(std::filesystem::exists(fpath));
 
-    ClusterFile f(fpath);
+    ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
     aare::ROI roi;
     roi.xmin = 0;
     roi.xmax = 50;
@@ -40,45 +44,308 @@ TEST_CASE("Read one frame using ROI", "[.files]") {
     REQUIRE(clusters.size() == 49);
     REQUIRE(clusters.frame_number() == 135);
 
-    //Check that all clusters are within the ROI
+    // Check that all clusters are within the ROI
     for (size_t i = 0; i < clusters.size(); i++) {
-        auto c = clusters.at<aare::Cluster3x3>(i);
+        auto c = clusters[i];
         REQUIRE(c.x >= roi.xmin);
         REQUIRE(c.x <= roi.xmax);
         REQUIRE(c.y >= roi.ymin);
         REQUIRE(c.y <= roi.ymax);
     }
 
+    CHECK(clusters[0].x == 1);
+    CHECK(clusters[0].y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters[0].data), std::end(clusters[0].data),
+                     std::begin(expected_cluster_data)));
 }
 
 
 
 TEST_CASE("Read clusters from single frame file", "[.files]") {
 
+    //  frame_number, num_clusters   [135] 97
+    // [  1 200] [0 1 2 3 4 5 6 7 8]
+    // [  2 201] [ 9 10 11 12 13 14 15 16 17]
+    // [  3 202] [18 19 20 21 22 23 24 25 26]
+    // [  4 203] [27 28 29 30 31 32 33 34 35]
+    // [  5 204] [36 37 38 39 40 41 42 43 44]
+    // [  6 205] [45 46 47 48 49 50 51 52 53]
+    // [  7 206] [54 55 56 57 58 59 60 61 62]
+    // [  8 207] [63 64 65 66 67 68 69 70 71]
+    // [  9 208] [72 73 74 75 76 77 78 79 80]
+    // [ 10 209] [81 82 83 84 85 86 87 88 89]
+    // [ 11 210] [90 91 92 93 94 95 96 97 98]
+    // [ 12 211] [ 99 100 101 102 103 104 105 106 107]
+    // [ 13 212] [108 109 110 111 112 113 114 115 116]
+    // [ 14 213] [117 118 119 120 121 122 123 124 125]
+    // [ 15 214] [126 127 128 129 130 131 132 133 134]
+    // [ 16 215] [135 136 137 138 139 140 141 142 143]
+    // [ 17 216] [144 145 146 147 148 149 150 151 152]
+    // [ 18 217] [153 154 155 156 157 158 159 160 161]
+    // [ 19 218] [162 163 164 165 166 167 168 169 170]
+    // [ 20 219] [171 172 173 174 175 176 177 178 179]
+    // [ 21 220] [180 181 182 183 184 185 186 187 188]
+    // [ 22 221] [189 190 191 192 193 194 195 196 197]
+    // [ 23 222] [198 199 200 201 202 203 204 205 206]
+    // [ 24 223] [207 208 209 210 211 212 213 214 215]
+    // [ 25 224] [216 217 218 219 220 221 222 223 224]
+    // [ 26 225] [225 226 227 228 229 230 231 232 233]
+    // [ 27 226] [234 235 236 237 238 239 240 241 242]
+    // [ 28 227] [243 244 245 246 247 248 249 250 251]
+    // [ 29 228] [252 253 254 255 256 257 258 259 260]
+    // [ 30 229] [261 262 263 264 265 266 267 268 269]
+    // [ 31 230] [270 271 272 273 274 275 276 277 278]
+    // [ 32 231] [279 280 281 282 283 284 285 286 287]
+    // [ 33 232] [288 289 290 291 292 293 294 295 296]
+    // [ 34 233] [297 298 299 300 301 302 303 304 305]
+    // [ 35 234] [306 307 308 309 310 311 312 313 314]
+    // [ 36 235] [315 316 317 318 319 320 321 322 323]
+    // [ 37 236] [324 325 326 327 328 329 330 331 332]
+    // [ 38 237] [333 334 335 336 337 338 339 340 341]
+    // [ 39 238] [342 343 344 345 346 347 348 349 350]
+    // [ 40 239] [351 352 353 354 355 356 357 358 359]
+    // [ 41 240] [360 361 362 363 364 365 366 367 368]
+    // [ 42 241] [369 370 371 372 373 374 375 376 377]
+    // [ 43 242] [378 379 380 381 382 383 384 385 386]
+    // [ 44 243] [387 388 389 390 391 392 393 394 395]
+    // [ 45 244] [396 397 398 399 400 401 402 403 404]
+    // [ 46 245] [405 406 407 408 409 410 411 412 413]
+    // [ 47 246] [414 415 416 417 418 419 420 421 422]
+    // [ 48 247] [423 424 425 426 427 428 429 430 431]
+    // [ 49 248] [432 433 434 435 436 437 438 439 440]
+    // [ 50 249] [441 442 443 444 445 446 447 448 449]
+    // [ 51 250] [450 451 452 453 454 455 456 457 458]
+    // [ 52 251] [459 460 461 462 463 464 465 466 467]
+    // [ 53 252] [468 469 470 471 472 473 474 475 476]
+    // [ 54 253] [477 478 479 480 481 482 483 484 485]
+    // [ 55 254] [486 487 488 489 490 491 492 493 494]
+    // [ 56 255] [495 496 497 498 499 500 501 502 503]
+    // [ 57 256] [504 505 506 507 508 509 510 511 512]
+    // [ 58 257] [513 514 515 516 517 518 519 520 521]
+    // [ 59 258] [522 523 524 525 526 527 528 529 530]
+    // [ 60 259] [531 532 533 534 535 536 537 538 539]
+    // [ 61 260] [540 541 542 543 544 545 546 547 548]
+    // [ 62 261] [549 550 551 552 553 554 555 556 557]
+    // [ 63 262] [558 559 560 561 562 563 564 565 566]
+    // [ 64 263] [567 568 569 570 571 572 573 574 575]
+    // [ 65 264] [576 577 578 579 580 581 582 583 584]
+    // [ 66 265] [585 586 587 588 589 590 591 592 593]
+    // [ 67 266] [594 595 596 597 598 599 600 601 602]
+    // [ 68 267] [603 604 605 606 607 608 609 610 611]
+    // [ 69 268] [612 613 614 615 616 617 618 619 620]
+    // [ 70 269] [621 622 623 624 625 626 627 628 629]
+    // [ 71 270] [630 631 632 633 634 635 636 637 638]
+    // [ 72 271] [639 640 641 642 643 644 645 646 647]
+    // [ 73 272] [648 649 650 651 652 653 654 655 656]
+    // [ 74 273] [657 658 659 660 661 662 663 664 665]
+    // [ 75 274] [666 667 668 669 670 671 672 673 674]
+    // [ 76 275] [675 676 677 678 679 680 681 682 683]
+    // [ 77 276] [684 685 686 687 688 689 690 691 692]
+    // [ 78 277] [693 694 695 696 697 698 699 700 701]
+    // [ 79 278] [702 703 704 705 706 707 708 709 710]
+    // [ 80 279] [711 712 713 714 715 716 717 718 719]
+    // [ 81 280] [720 721 722 723 724 725 726 727 728]
+    // [ 82 281] [729 730 731 732 733 734 735 736 737]
+    // [ 83 282] [738 739 740 741 742 743 744 745 746]
+    // [ 84 283] [747 748 749 750 751 752 753 754 755]
+    // [ 85 284] [756 757 758 759 760 761 762 763 764]
+    // [ 86 285] [765 766 767 768 769 770 771 772 773]
+    // [ 87 286] [774 775 776 777 778 779 780 781 782]
+    // [ 88 287] [783 784 785 786 787 788 789 790 791]
+    // [ 89 288] [792 793 794 795 796 797 798 799 800]
+    // [ 90 289] [801 802 803 804 805 806 807 808 809]
+    // [ 91 290] [810 811 812 813 814 815 816 817 818]
+    // [ 92 291] [819 820 821 822 823 824 825 826 827]
+    // [ 93 292] [828 829 830 831 832 833 834 835 836]
+    // [ 94 293] [837 838 839 840 841 842 843 844 845]
+    // [ 95 294] [846 847 848 849 850 851 852 853 854]
+    // [ 96 295] [855 856 857 858 859 860 861 862 863]
+    // [ 97 296] [864 865 866 867 868 869 870 871 872]
+
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
 
     REQUIRE(std::filesystem::exists(fpath));
 
     SECTION("Read fewer clusters than available") {
-        ClusterFile f(fpath);
+        ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
         auto clusters = f.read_clusters(50);
         REQUIRE(clusters.size() == 50);
         REQUIRE(clusters.frame_number() == 135);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        REQUIRE(clusters[0].x == 1);
+        REQUIRE(clusters[0].y == 200);
+        CHECK(std::equal(std::begin(clusters[0].data),
+                         std::end(clusters[0].data),
+                         std::begin(expected_cluster_data)));
     }
     SECTION("Read more clusters than available") {
-        ClusterFile f(fpath);
+        ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
         // 100 is the maximum number of clusters read
         auto clusters = f.read_clusters(100);
         REQUIRE(clusters.size() == 97);
         REQUIRE(clusters.frame_number() == 135);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        REQUIRE(clusters[0].x == 1);
+        REQUIRE(clusters[0].y == 200);
+        CHECK(std::equal(std::begin(clusters[0].data),
+                         std::end(clusters[0].data),
+                         std::begin(expected_cluster_data)));
     }
     SECTION("Read all clusters") {
-        ClusterFile f(fpath);
+        ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
         auto clusters = f.read_clusters(97);
         REQUIRE(clusters.size() == 97);
         REQUIRE(clusters.frame_number() == 135);
+        REQUIRE(clusters[0].x == 1);
+        REQUIRE(clusters[0].y == 200);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        CHECK(std::equal(std::begin(clusters[0].data),
+                         std::end(clusters[0].data),
+                         std::begin(expected_cluster_data)));
+    }
+}
+
+TEST_CASE("Read clusters from single frame file with ROI", "[.files]") {
+    auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
+
+    aare::ROI roi;
+    roi.xmin = 0;
+    roi.xmax = 50;
+    roi.ymin = 200;
+    roi.ymax = 249;
+    f.set_roi(roi);
+
+    auto clusters = f.read_clusters(10);
+
+    CHECK(clusters.size() == 10);
+    CHECK(clusters.frame_number() == 135);
+    CHECK(clusters[0].x == 1);
+    CHECK(clusters[0].y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters[0].data), std::end(clusters[0].data),
+                     std::begin(expected_cluster_data)));
+}
+
+TEST_CASE("Read cluster from multiple frame file", "[.files]") {
+
+    using ClusterType = Cluster<double, 2, 2>;
+
+    auto fpath =
+        test_data_path() / "clust" / "Two_frames_2x2double_test_clusters.clust";
+
+    REQUIRE(std::filesystem::exists(fpath));
+
+    // Two_frames_2x2double_test_clusters.clust
+    //  frame number, num_clusters 0, 4
+    //[10, 20], {0. ,0., 0., 0.}
+    //[11, 30], {1., 1., 1., 1.}
+    //[12, 40], {2., 2., 2., 2.}
+    //[13, 50], {3., 3., 3., 3.}
+    //  1,4
+    //[10, 20], {4., 4., 4., 4.}
+    //[11, 30], {5., 5., 5., 5.}
+    //[12, 40], {6., 6., 6., 6.}
+    //[13, 50], {7., 7., 7., 7.}
+
+    SECTION("Read clusters from both frames") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(2);
+        REQUIRE(clusters.size() == 2);
+        REQUIRE(clusters.frame_number() == 0);
+
+        auto clusters1 = f.read_clusters(3);
+
+        REQUIRE(clusters1.size() == 3);
+        REQUIRE(clusters1.frame_number() == 1);
     }
 
+    SECTION("Read all clusters") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(8);
+        REQUIRE(clusters.size() == 8);
+        REQUIRE(clusters.frame_number() == 1);
+    }
 
+    SECTION("Read clusters from one frame") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(2);
+        REQUIRE(clusters.size() == 2);
+        REQUIRE(clusters.frame_number() == 0);
 
+        auto clusters1 = f.read_clusters(1);
+
+        REQUIRE(clusters1.size() == 1);
+        REQUIRE(clusters1.frame_number() == 0);
+    }
+}
+
+TEST_CASE("Write cluster with potential padding", "[.files][.ClusterFile]") {
+
+    using ClusterType = Cluster<double, 3, 3>;
+
+    REQUIRE(std::filesystem::exists(test_data_path() / "clust"));
+
+    auto fpath = test_data_path() / "clust" / "single_frame_2_clusters.clust";
+
+    ClusterFile<ClusterType> file(fpath, 1000, "w");
+
+    ClusterVector<ClusterType> clustervec(2);
+    int16_t coordinate = 5;
+    clustervec.push_back(ClusterType{
+        coordinate, coordinate, {0., 0., 0., 0., 0., 0., 0., 0., 0.}});
+    clustervec.push_back(ClusterType{
+        coordinate, coordinate, {0., 0., 0., 0., 0., 0., 0., 0., 0.}});
+
+    file.write_frame(clustervec);
+
+    file.close();
+
+    file.open("r");
+
+    auto read_cluster_vector = file.read_frame();
+
+    CHECK(read_cluster_vector.size() == 2);
+    CHECK(read_cluster_vector.frame_number() == 0);
+
+    CHECK(read_cluster_vector[0].x == clustervec[0].x);
+    CHECK(read_cluster_vector[0].y == clustervec[0].y);
+    CHECK(std::equal(
+        clustervec[0].data.begin(), clustervec[0].data.end(),
+        read_cluster_vector[0].data.begin(), [](double a, double b) {
+            return std::abs(a - b) < std::numeric_limits<double>::epsilon();
+        }));
+
+    CHECK(read_cluster_vector[1].x == clustervec[1].x);
+    CHECK(read_cluster_vector[1].y == clustervec[1].y);
+    CHECK(std::equal(
+        clustervec[1].data.begin(), clustervec[1].data.end(),
+        read_cluster_vector[1].data.begin(), [](double a, double b) {
+            return std::abs(a - b) < std::numeric_limits<double>::epsilon();
+        }));
+}
+
+TEST_CASE("Read frame and modify cluster data", "[.files][.ClusterFile]") {
+    auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
+
+    auto clusters = f.read_frame();
+    CHECK(clusters.size() == 97);
+    CHECK(clusters.frame_number() == 135);
+
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    clusters.push_back(
+        Cluster<int32_t, 3, 3>{0, 0, {0, 1, 2, 3, 4, 5, 6, 7, 8}});
+
+    CHECK(clusters.size() == 98);
+    CHECK(clusters[0].x == 1);
+    CHECK(clusters[0].y == 200);
+
+    CHECK(std::equal(std::begin(clusters[0].data), std::end(clusters[0].data),
+                     std::begin(expected_cluster_data)));
 }

src/ClusterFinder.test.cpp

@@ -1,19 +1,18 @@
 #include "aare/ClusterFinder.hpp"
 #include "aare/Pedestal.hpp"
-#include <catch2/matchers/catch_matchers_floating_point.hpp>
 #include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
 #include <chrono>
 #include <random>
 
 using namespace aare;
 
-//TODO! Find a way to test the cluster finder
+// TODO! Find a way to test the cluster finder
-
-
 
 // class ClusterFinderUnitTest : public ClusterFinder {
 //   public:
-//     ClusterFinderUnitTest(int cluster_sizeX, int cluster_sizeY, double nSigma = 5.0, double threshold = 0.0)
+//     ClusterFinderUnitTest(int cluster_sizeX, int cluster_sizeY, double nSigma
+//     = 5.0, double threshold = 0.0)
 //         : ClusterFinder(cluster_sizeX, cluster_sizeY, nSigma, threshold) {}
 //     double get_c2() { return c2; }
 //     double get_c3() { return c3; }
@@ -37,8 +36,8 @@ using namespace aare;
 //     REQUIRE_THAT(cf.get_c3(), Catch::Matchers::WithinRel(c3, 1e-9));
 // }
 
-TEST_CASE("Construct a cluster finder"){
+TEST_CASE("Construct a cluster finder") {
-    ClusterFinder clusterFinder({400,400}, {3,3});
+    ClusterFinder clusterFinder({400, 400});
     // REQUIRE(clusterFinder.get_cluster_sizeX() == 3);
     // REQUIRE(clusterFinder.get_cluster_sizeY() == 3);
     // REQUIRE(clusterFinder.get_threshold() == 1);
@@ -49,16 +48,17 @@ TEST_CASE("Construct a cluster finder"){
 //     aare::Pedestal pedestal(10, 10, 5);
 //     NDArray<double, 2> frame({10, 10});
 //     frame = 0;
-//     ClusterFinder clusterFinder(3, 3, 1, 1); // 3x3 cluster, 1 nSigma, 1 threshold
+//     ClusterFinder clusterFinder(3, 3, 1, 1); // 3x3 cluster, 1 nSigma, 1
+//     threshold
 
-//     auto clusters = clusterFinder.find_clusters_without_threshold(frame.span(), pedestal);
+//     auto clusters =
+//     clusterFinder.find_clusters_without_threshold(frame.span(), pedestal);
 
 //     REQUIRE(clusters.size() == 0);
 
 //     frame(5, 5) = 10;
-//     clusters = clusterFinder.find_clusters_without_threshold(frame.span(), pedestal);
+//     clusters = clusterFinder.find_clusters_without_threshold(frame.span(),
-//     REQUIRE(clusters.size() == 1);
+//     pedestal); REQUIRE(clusters.size() == 1); REQUIRE(clusters[0].x == 5);
-//     REQUIRE(clusters[0].x == 5);
 //     REQUIRE(clusters[0].y == 5);
 //     for (int i = 0; i < 3; i++) {
 //         for (int j = 0; j < 3; j++) {

src/ClusterFinderMT.test.cpp

@@ -0,0 +1,99 @@
+
+#include "aare/ClusterFinderMT.hpp"
+#include "aare/Cluster.hpp"
+#include "aare/ClusterCollector.hpp"
+#include "aare/File.hpp"
+
+#include "test_config.hpp"
+
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>
+#include <memory>
+
+using namespace aare;
+
+// wrapper function to access private member variables for testing
+template <typename ClusterType, typename FRAME_TYPE = uint16_t,
+          typename PEDESTAL_TYPE = double>
+class ClusterFinderMTWrapper
+    : public ClusterFinderMT<ClusterType, FRAME_TYPE, PEDESTAL_TYPE> {
+
+  public:
+    ClusterFinderMTWrapper(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
+                           size_t capacity = 2000, size_t n_threads = 3)
+        : ClusterFinderMT<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>(
+              image_size, nSigma, capacity, n_threads) {}
+
+    size_t get_m_input_queues_size() const {
+        return this->m_input_queues.size();
+    }
+
+    size_t get_m_output_queues_size() const {
+        return this->m_output_queues.size();
+    }
+
+    size_t get_m_cluster_finders_size() const {
+        return this->m_cluster_finders.size();
+    }
+
+    bool m_output_queues_are_empty() const {
+        for (auto &queue : this->m_output_queues) {
+            if (!queue->isEmpty())
+                return false;
+        }
+        return true;
+    }
+
+    bool m_input_queues_are_empty() const {
+        for (auto &queue : this->m_input_queues) {
+            if (!queue->isEmpty())
+                return false;
+        }
+        return true;
+    }
+
+    bool m_sink_is_empty() const { return this->m_sink.isEmpty(); }
+
+    size_t m_sink_size() const { return this->m_sink.sizeGuess(); }
+};
+
+TEST_CASE("multithreaded cluster finder", "[.files][.ClusterFinder]") {
+    auto fpath = "/mnt/sls_det_storage/matterhorn_data/aare_test_data/"
+                 "Moench03new/cu_half_speed_master_4.json";
+
+    File file(fpath);
+
+    size_t n_threads = 2;
+    size_t n_frames_pd = 10;
+
+    using ClusterType = Cluster<int32_t, 3, 3>;
+
+    ClusterFinderMTWrapper<ClusterType> cf(
+        {static_cast<int64_t>(file.rows()), static_cast<int64_t>(file.cols())},
+        5, 2000, n_threads); // no idea what frame type is!!! default uint16_t
+
+    CHECK(cf.get_m_input_queues_size() == n_threads);
+    CHECK(cf.get_m_output_queues_size() == n_threads);
+    CHECK(cf.get_m_cluster_finders_size() == n_threads);
+    CHECK(cf.m_output_queues_are_empty() == true);
+    CHECK(cf.m_input_queues_are_empty() == true);
+
+    for (size_t i = 0; i < n_frames_pd; ++i) {
+        cf.find_clusters(file.read_frame().view<uint16_t>());
+    }
+
+    cf.stop();
+
+    CHECK(cf.m_output_queues_are_empty() == true);
+    CHECK(cf.m_input_queues_are_empty() == true);
+
+    CHECK(cf.m_sink_size() == n_frames_pd);
+    ClusterCollector<ClusterType> clustercollector(&cf);
+
+    clustercollector.stop();
+
+    CHECK(cf.m_sink_size() == 0);
+
+    auto clustervec = clustercollector.steal_clusters();
+    // CHECK(clustervec.size() == ) //dont know how many clusters to expect
+}

src/ClusterVector.test.cpp

@@ -1,21 +1,52 @@
-#include <cstdint>
 #include "aare/ClusterVector.hpp"
+#include <cstdint>
 
-#include <catch2/matchers/catch_matchers_floating_point.hpp>
+#include <catch2/catch_all.hpp>
 #include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
 
+using aare::Cluster;
 using aare::ClusterVector;
 
-struct Cluster_i2x2 {
+TEST_CASE("item_size return the size of the cluster stored") {
-    int16_t x;
+    using C1 = Cluster<int32_t, 2, 2>;
-    int16_t y;
+    ClusterVector<C1> cv(4);
-    int32_t data[4];
+    CHECK(cv.item_size() == sizeof(C1));
-};
 
-TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read") {
+    // Sanity check
+    // 2*2*4 = 16 bytes of data for the cluster
+    //  2*2 = 4 bytes for the x and y coordinates
+    REQUIRE(cv.item_size() == 20);
 
+    using C2 = Cluster<int32_t, 3, 3>;
+    ClusterVector<C2> cv2(4);
+    CHECK(cv2.item_size() == sizeof(C2));
 
-    ClusterVector<int32_t> cv(2, 2, 4);
+    using C3 = Cluster<double, 2, 3>;
+    ClusterVector<C3> cv3(4);
+    CHECK(cv3.item_size() == sizeof(C3));
+
+    using C4 = Cluster<char, 10, 5>;
+    ClusterVector<C4> cv4(4);
+    CHECK(cv4.item_size() == sizeof(C4));
+
+    using C5 = Cluster<int32_t, 2, 3>;
+    ClusterVector<C5> cv5(4);
+    CHECK(cv5.item_size() == sizeof(C5));
+
+    using C6 = Cluster<double, 5, 5>;
+    ClusterVector<C6> cv6(4);
+    CHECK(cv6.item_size() == sizeof(C6));
+
+    using C7 = Cluster<double, 3, 3>;
+    ClusterVector<C7> cv7(4);
+    CHECK(cv7.item_size() == sizeof(C7));
+}
+
+TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read",
+          "[.ClusterVector]") {
+
+    ClusterVector<Cluster<int32_t, 2, 2>> cv(4);
     REQUIRE(cv.capacity() == 4);
     REQUIRE(cv.size() == 0);
     REQUIRE(cv.cluster_size_x() == 2);
@@ -23,112 +54,102 @@ TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read") {
     // int16_t, int16_t, 2x2 int32_t = 20 bytes
     REQUIRE(cv.item_size() == 20);
 
-    //Create a cluster and push back into the vector
+    // Create a cluster and push back into the vector
-    Cluster_i2x2 c1 = {1, 2, {3, 4, 5, 6}};
+    Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
-    cv.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    cv.push_back(c1);
     REQUIRE(cv.size() == 1);
     REQUIRE(cv.capacity() == 4);
 
-    //Read the cluster back out using copy. TODO! Can we improve the API?
+    auto c2 = cv[0];
-    Cluster_i2x2 c2;
-    std::byte *ptr = cv.element_ptr(0);
-    std::copy(ptr, ptr + cv.item_size(), reinterpret_cast<std::byte*>(&c2));
 
-    //Check that the data is the same
+    // Check that the data is the same
     REQUIRE(c1.x == c2.x);
     REQUIRE(c1.y == c2.y);
-    for(size_t i = 0; i < 4; i++) {
+    for (size_t i = 0; i < 4; i++) {
         REQUIRE(c1.data[i] == c2.data[i]);
     }
 }
 
-TEST_CASE("Summing 3x1 clusters of int64"){
+TEST_CASE("Summing 3x1 clusters of int64", "[.ClusterVector]") {
-    struct Cluster_l3x1{
+    ClusterVector<Cluster<int32_t, 3, 1>> cv(2);
-        int16_t x;
-        int16_t y;
-        int32_t data[3];
-    };
-
-    ClusterVector<int32_t> cv(3, 1, 2);
     REQUIRE(cv.capacity() == 2);
     REQUIRE(cv.size() == 0);
     REQUIRE(cv.cluster_size_x() == 3);
     REQUIRE(cv.cluster_size_y() == 1);
 
-    //Create a cluster and push back into the vector
+    // Create a cluster and push back into the vector
-    Cluster_l3x1 c1 = {1, 2, {3, 4, 5}};
+    Cluster<int32_t, 3, 1> c1 = {1, 2, {3, 4, 5}};
-    cv.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    cv.push_back(c1);
     REQUIRE(cv.capacity() == 2);
     REQUIRE(cv.size() == 1);
 
-    Cluster_l3x1 c2 = {6, 7, {8, 9, 10}};
+    Cluster<int32_t, 3, 1> c2 = {6, 7, {8, 9, 10}};
-    cv.push_back(c2.x, c2.y, reinterpret_cast<std::byte*>(&c2.data[0]));
+    cv.push_back(c2);
     REQUIRE(cv.capacity() == 2);
     REQUIRE(cv.size() == 2);
 
-    Cluster_l3x1 c3 = {11, 12, {13, 14, 15}};
+    Cluster<int32_t, 3, 1> c3 = {11, 12, {13, 14, 15}};
-    cv.push_back(c3.x, c3.y, reinterpret_cast<std::byte*>(&c3.data[0]));
+    cv.push_back(c3);
     REQUIRE(cv.capacity() == 4);
     REQUIRE(cv.size() == 3);
 
+    /*
     auto sums = cv.sum();
     REQUIRE(sums.size() == 3);
     REQUIRE(sums[0] == 12);
     REQUIRE(sums[1] == 27);
     REQUIRE(sums[2] == 42);
+    */
 }
 
-TEST_CASE("Storing floats"){
+TEST_CASE("Storing floats", "[.ClusterVector]") {
-    struct Cluster_f4x2{
+    ClusterVector<Cluster<float, 2, 4>> cv(10);
-        int16_t x;
-        int16_t y;
-        float data[8];
-    };
-
-    ClusterVector<float> cv(2, 4, 10);
     REQUIRE(cv.capacity() == 10);
     REQUIRE(cv.size() == 0);
     REQUIRE(cv.cluster_size_x() == 2);
     REQUIRE(cv.cluster_size_y() == 4);
 
-    //Create a cluster and push back into the vector
+    // Create a cluster and push back into the vector
-    Cluster_f4x2 c1 = {1, 2, {3.0, 4.0, 5.0, 6.0,3.0, 4.0, 5.0, 6.0}};
+    Cluster<float, 2, 4> c1 = {1, 2, {3.0, 4.0, 5.0, 6.0, 3.0, 4.0, 5.0, 6.0}};
-    cv.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    cv.push_back(c1);
     REQUIRE(cv.capacity() == 10);
     REQUIRE(cv.size() == 1);
 
-
+    Cluster<float, 2, 4> c2 = {
-    Cluster_f4x2 c2 = {6, 7, {8.0, 9.0, 10.0, 11.0,8.0, 9.0, 10.0, 11.0}};
+        6, 7, {8.0, 9.0, 10.0, 11.0, 8.0, 9.0, 10.0, 11.0}};
-    cv.push_back(c2.x, c2.y, reinterpret_cast<std::byte*>(&c2.data[0]));
+    cv.push_back(c2);
     REQUIRE(cv.capacity() == 10);
     REQUIRE(cv.size() == 2);
 
+    /*
     auto sums = cv.sum();
     REQUIRE(sums.size() == 2);
     REQUIRE_THAT(sums[0], Catch::Matchers::WithinAbs(36.0, 1e-6));
     REQUIRE_THAT(sums[1], Catch::Matchers::WithinAbs(76.0, 1e-6));
+    */
 }
 
-TEST_CASE("Push back more than initial capacity"){
+TEST_CASE("Push back more than initial capacity", "[.ClusterVector]") {
 
-    ClusterVector<int32_t> cv(2, 2, 2);
+    ClusterVector<Cluster<int32_t, 2, 2>> cv(2);
     auto initial_data = cv.data();
-    Cluster_i2x2 c1 = {1, 2, {3, 4, 5, 6}};
+    Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
-    cv.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    cv.push_back(c1);
     REQUIRE(cv.size() == 1);
     REQUIRE(cv.capacity() == 2);
 
-    Cluster_i2x2 c2 = {6, 7, {8, 9, 10, 11}};
+    Cluster<int32_t, 2, 2> c2 = {6, 7, {8, 9, 10, 11}};
-    cv.push_back(c2.x, c2.y, reinterpret_cast<std::byte*>(&c2.data[0]));
+    cv.push_back(c2);
     REQUIRE(cv.size() == 2);
     REQUIRE(cv.capacity() == 2);
 
-    Cluster_i2x2 c3 = {11, 12, {13, 14, 15, 16}};
+    Cluster<int32_t, 2, 2> c3 = {11, 12, {13, 14, 15, 16}};
-    cv.push_back(c3.x, c3.y, reinterpret_cast<std::byte*>(&c3.data[0]));
+    cv.push_back(c3);
     REQUIRE(cv.size() == 3);
     REQUIRE(cv.capacity() == 4);
 
-    Cluster_i2x2* ptr = reinterpret_cast<Cluster_i2x2*>(cv.data());
+    Cluster<int32_t, 2, 2> *ptr =
+        reinterpret_cast<Cluster<int32_t, 2, 2> *>(cv.data());
     REQUIRE(ptr[0].x == 1);
     REQUIRE(ptr[0].y == 2);
     REQUIRE(ptr[1].x == 6);
@@ -136,29 +157,31 @@ TEST_CASE("Push back more than initial capacity"){
     REQUIRE(ptr[2].x == 11);
     REQUIRE(ptr[2].y == 12);
 
-    //We should have allocated a new buffer, since we outgrew the initial capacity
+    // We should have allocated a new buffer, since we outgrew the initial
+    // capacity
     REQUIRE(initial_data != cv.data());
-
 }
 
-TEST_CASE("Concatenate two cluster vectors where the first has enough capacity"){
+TEST_CASE("Concatenate two cluster vectors where the first has enough capacity",
-    ClusterVector<int32_t> cv1(2, 2, 12);
+          "[.ClusterVector]") {
-    Cluster_i2x2 c1 = {1, 2, {3, 4, 5, 6}};
+    ClusterVector<Cluster<int32_t, 2, 2>> cv1(12);
-    cv1.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
-    Cluster_i2x2 c2 = {6, 7, {8, 9, 10, 11}};
+    cv1.push_back(c1);
-    cv1.push_back(c2.x, c2.y, reinterpret_cast<std::byte*>(&c2.data[0]));
+    Cluster<int32_t, 2, 2> c2 = {6, 7, {8, 9, 10, 11}};
+    cv1.push_back(c2);
 
-    ClusterVector<int32_t> cv2(2, 2, 2);
+    ClusterVector<Cluster<int32_t, 2, 2>> cv2(2);
-    Cluster_i2x2 c3 = {11, 12, {13, 14, 15, 16}};
+    Cluster<int32_t, 2, 2> c3 = {11, 12, {13, 14, 15, 16}};
-    cv2.push_back(c3.x, c3.y, reinterpret_cast<std::byte*>(&c3.data[0]));
+    cv2.push_back(c3);
-    Cluster_i2x2 c4 = {16, 17, {18, 19, 20, 21}};
+    Cluster<int32_t, 2, 2> c4 = {16, 17, {18, 19, 20, 21}};
-    cv2.push_back(c4.x, c4.y, reinterpret_cast<std::byte*>(&c4.data[0]));
+    cv2.push_back(c4);
 
     cv1 += cv2;
     REQUIRE(cv1.size() == 4);
     REQUIRE(cv1.capacity() == 12);
 
-    Cluster_i2x2* ptr = reinterpret_cast<Cluster_i2x2*>(cv1.data());
+    Cluster<int32_t, 2, 2> *ptr =
+        reinterpret_cast<Cluster<int32_t, 2, 2> *>(cv1.data());
     REQUIRE(ptr[0].x == 1);
     REQUIRE(ptr[0].y == 2);
     REQUIRE(ptr[1].x == 6);
@@ -169,24 +192,26 @@ TEST_CASE("Concatenate two cluster vectors where the first has enough capacity")
     REQUIRE(ptr[3].y == 17);
 }
 
-TEST_CASE("Concatenate two cluster vectors where we need to allocate"){
+TEST_CASE("Concatenate two cluster vectors where we need to allocate",
-    ClusterVector<int32_t> cv1(2, 2, 2);
+          "[.ClusterVector]") {
-    Cluster_i2x2 c1 = {1, 2, {3, 4, 5, 6}};
+    ClusterVector<Cluster<int32_t, 2, 2>> cv1(2);
-    cv1.push_back(c1.x, c1.y, reinterpret_cast<std::byte*>(&c1.data[0]));
+    Cluster<int32_t, 2, 2> c1 = {1, 2, {3, 4, 5, 6}};
-    Cluster_i2x2 c2 = {6, 7, {8, 9, 10, 11}};
+    cv1.push_back(c1);
-    cv1.push_back(c2.x, c2.y, reinterpret_cast<std::byte*>(&c2.data[0]));
+    Cluster<int32_t, 2, 2> c2 = {6, 7, {8, 9, 10, 11}};
+    cv1.push_back(c2);
 
-    ClusterVector<int32_t> cv2(2, 2, 2);
+    ClusterVector<Cluster<int32_t, 2, 2>> cv2(2);
-    Cluster_i2x2 c3 = {11, 12, {13, 14, 15, 16}};
+    Cluster<int32_t, 2, 2> c3 = {11, 12, {13, 14, 15, 16}};
-    cv2.push_back(c3.x, c3.y, reinterpret_cast<std::byte*>(&c3.data[0]));
+    cv2.push_back(c3);
-    Cluster_i2x2 c4 = {16, 17, {18, 19, 20, 21}};
+    Cluster<int32_t, 2, 2> c4 = {16, 17, {18, 19, 20, 21}};
-    cv2.push_back(c4.x, c4.y, reinterpret_cast<std::byte*>(&c4.data[0]));
+    cv2.push_back(c4);
 
     cv1 += cv2;
     REQUIRE(cv1.size() == 4);
     REQUIRE(cv1.capacity() == 4);
 
-    Cluster_i2x2* ptr = reinterpret_cast<Cluster_i2x2*>(cv1.data());
+    Cluster<int32_t, 2, 2> *ptr =
+        reinterpret_cast<Cluster<int32_t, 2, 2> *>(cv1.data());
     REQUIRE(ptr[0].x == 1);
     REQUIRE(ptr[0].y == 2);
     REQUIRE(ptr[1].x == 6);
@@ -196,3 +221,48 @@ TEST_CASE("Concatenate two cluster vectors where we need to allocate"){
     REQUIRE(ptr[3].x == 16);
     REQUIRE(ptr[3].y == 17);
 }
+
+struct ClusterTestData {
+    uint8_t ClusterSizeX;
+    uint8_t ClusterSizeY;
+    std::vector<int64_t> index_map_x;
+    std::vector<int64_t> index_map_y;
+};
+
+TEST_CASE("Gain Map Calculation Index Map", "[.ClusterVector][.gain_map]") {
+
+    auto clustertestdata = GENERATE(
+        ClusterTestData{3,
+                        3,
+                        {-1, 0, 1, -1, 0, 1, -1, 0, 1},
+                        {-1, -1, -1, 0, 0, 0, 1, 1, 1}},
+        ClusterTestData{
+            4,
+            4,
+            {-2, -1, 0, 1, -2, -1, 0, 1, -2, -1, 0, 1, -2, -1, 0, 1},
+            {-2, -2, -2, -2, -1, -1, -1, -1, 0, 0, 0, 0, 1, 1, 1, 1}},
+        ClusterTestData{2, 2, {-1, 0, -1, 0}, {-1, -1, 0, 0}},
+        ClusterTestData{5,
+                        5,
+                        {-2, -1, 0,  1,  2, -2, -1, 0,  1,  2, -2, -1, 0,
+                         1,  2,  -2, -1, 0, 1,  2,  -2, -1, 0, 1,  2},
+                        {-2, -2, -2, -2, -2, -1, -1, -1, -1, -1, 0, 0, 0,
+                         0,  0,  1,  1,  1,  1,  1,  2,  2,  2,  2, 2}});
+
+    uint8_t ClusterSizeX = clustertestdata.ClusterSizeX;
+    uint8_t ClusterSizeY = clustertestdata.ClusterSizeY;
+
+    std::vector<int64_t> index_map_x(ClusterSizeX * ClusterSizeY);
+    std::vector<int64_t> index_map_y(ClusterSizeX * ClusterSizeY);
+
+    int64_t index_cluster_center_x = ClusterSizeX / 2;
+    int64_t index_cluster_center_y = ClusterSizeY / 2;
+
+    for (size_t j = 0; j < ClusterSizeX * ClusterSizeY; j++) {
+        index_map_x[j] = j % ClusterSizeX - index_cluster_center_x;
+        index_map_y[j] = j / ClusterSizeX - index_cluster_center_y;
+    }
+
+    CHECK(index_map_x == clustertestdata.index_map_x);
+    CHECK(index_map_y == clustertestdata.index_map_y);
+}

src/Interpolator.cpp

@@ -1,11 +1,11 @@
 #include "aare/Interpolator.hpp"
-#include "aare/algorithm.hpp"
 
 namespace aare {
 
 Interpolator::Interpolator(NDView<double, 3> etacube, NDView<double, 1> xbins,
                            NDView<double, 1> ybins, NDView<double, 1> ebins)
-    : m_ietax(etacube), m_ietay(etacube), m_etabinsx(xbins), m_etabinsy(ybins), m_energy_bins(ebins) {
+    : m_ietax(etacube), m_ietay(etacube), m_etabinsx(xbins), m_etabinsy(ybins),
+      m_energy_bins(ebins) {
     if (etacube.shape(0) != xbins.size() || etacube.shape(1) != ybins.size() ||
         etacube.shape(2) != ebins.size()) {
         throw std::invalid_argument(
@@ -53,87 +53,4 @@ Interpolator::Interpolator(NDView<double, 3> etacube, NDView<double, 1> xbins,
     }
 }
 
-std::vector<Photon> Interpolator::interpolate(const ClusterVector<int32_t>& clusters) {
-    std::vector<Photon> photons;
-    photons.reserve(clusters.size());
-
-    if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
-        for (size_t i = 0; i<clusters.size(); i++){
-
-            auto cluster = clusters.at<Cluster3x3>(i);
-            Eta2 eta= calculate_eta2(cluster);
-    
-            Photon photon;
-            photon.x = cluster.x;
-            photon.y = cluster.y;
-            photon.energy = eta.sum;
-    
-
-            //Finding the index of the last element that is smaller
-            //should work fine as long as we have many bins
-            auto ie = last_smaller(m_energy_bins, photon.energy);
-            auto ix = last_smaller(m_etabinsx, eta.x);
-            auto iy = last_smaller(m_etabinsy, eta.y); 
-            
-            double dX{}, dY{};
-            // cBottomLeft = 0,
-            // cBottomRight = 1,
-            // cTopLeft = 2,
-            // cTopRight = 3
-            switch (eta.c) {
-            case cTopLeft:
-                dX = -1.;
-                dY = 0.;
-                break;
-            case cTopRight:;
-                dX = 0.;
-                dY = 0.;
-                break;
-            case cBottomLeft:
-                dX = -1.;
-                dY = -1.;
-                break;
-            case cBottomRight:
-                dX = 0.; 
-                dY = -1.;
-                break;
-            }
-            photon.x += m_ietax(ix, iy, ie)*2 + dX;
-            photon.y += m_ietay(ix, iy, ie)*2 + dY;
-            photons.push_back(photon);
-        }
-    }else if(clusters.cluster_size_x() == 2 || clusters.cluster_size_y() == 2){
-        for (size_t i = 0; i<clusters.size(); i++){
-            auto cluster = clusters.at<Cluster2x2>(i);
-            Eta2 eta= calculate_eta2(cluster);
-    
-            Photon photon;
-            photon.x = cluster.x;
-            photon.y = cluster.y;
-            photon.energy = eta.sum;
-    
-            //Now do some actual interpolation. 
-            //Find which energy bin the cluster is in
-            // auto ie = nearest_index(m_energy_bins, photon.energy)-1;
-            // auto ix = nearest_index(m_etabinsx, eta.x)-1;
-            // auto iy = nearest_index(m_etabinsy, eta.y)-1;  
-            //Finding the index of the last element that is smaller
-            //should work fine as long as we have many bins
-            auto ie = last_smaller(m_energy_bins, photon.energy);
-            auto ix = last_smaller(m_etabinsx, eta.x);
-            auto iy = last_smaller(m_etabinsy, eta.y); 
-
-            photon.x += m_ietax(ix, iy, ie)*2; //eta goes between 0 and 1 but we could move the hit anywhere in the 2x2
-            photon.y += m_ietay(ix, iy, ie)*2;
-            photons.push_back(photon);
-        }
-        
-    }else{
-        throw std::runtime_error("Only 3x3 and 2x2 clusters are supported for interpolation");
-    }
-  
-
-    return photons;
-}
-
 } // namespace aare

src/algorithm.test.cpp

@@ -1,8 +1,7 @@
 
 
-#include <catch2/catch_test_macros.hpp>
 #include <aare/algorithm.hpp>
-
+#include <catch2/catch_test_macros.hpp>
 
 TEST_CASE("Find the closed index in a 1D array", "[algorithm]") {
     aare::NDArray<double, 1> arr({5});
@@ -17,7 +16,7 @@ TEST_CASE("Find the closed index in a 1D array", "[algorithm]") {
     REQUIRE(aare::nearest_index(arr, -1.0) == 0);
 }
 
-TEST_CASE("Passing integers to nearest_index works", "[algorithm]"){
+TEST_CASE("Passing integers to nearest_index works", "[algorithm]") {
     aare::NDArray<int, 1> arr({5});
     for (ssize_t i = 0; i < arr.size(); i++) {
         arr[i] = i;
@@ -30,8 +29,7 @@ TEST_CASE("Passing integers to nearest_index works", "[algorithm]"){
     REQUIRE(aare::nearest_index(arr, -1) == 0);
 }
 
-
+TEST_CASE("nearest_index works with std::vector", "[algorithm]") {
-TEST_CASE("nearest_index works with std::vector", "[algorithm]"){
     std::vector<double> vec = {0, 1, 2, 3, 4};
     REQUIRE(aare::nearest_index(vec, 2.123) == 2);
     REQUIRE(aare::nearest_index(vec, 2.66) == 3);
@@ -40,7 +38,7 @@ TEST_CASE("nearest_index works with std::vector", "[algorithm]"){
     REQUIRE(aare::nearest_index(vec, -10.0) == 0);
 }
 
-TEST_CASE("nearest index works with std::array", "[algorithm]"){
+TEST_CASE("nearest index works with std::array", "[algorithm]") {
     std::array<double, 5> arr = {0, 1, 2, 3, 4};
     REQUIRE(aare::nearest_index(arr, 2.123) == 2);
     REQUIRE(aare::nearest_index(arr, 2.501) == 3);
@@ -49,18 +47,20 @@ TEST_CASE("nearest index works with std::array", "[algorithm]"){
     REQUIRE(aare::nearest_index(arr, -10.0) == 0);
 }
 
-TEST_CASE("nearest index when there is no different uses the first element", "[algorithm]"){
+TEST_CASE("nearest index when there is no different uses the first element",
+          "[algorithm]") {
     std::vector<int> vec = {5, 5, 5, 5, 5};
     REQUIRE(aare::nearest_index(vec, 5) == 0);
 }
 
-TEST_CASE("nearest index when there is no different uses the first element also when all smaller", "[algorithm]"){
+TEST_CASE("nearest index when there is no different uses the first element "
+          "also when all smaller",
+          "[algorithm]") {
     std::vector<int> vec = {5, 5, 5, 5, 5};
     REQUIRE(aare::nearest_index(vec, 10) == 0);
 }
 
-
+TEST_CASE("last smaller", "[algorithm]") {
-TEST_CASE("last smaller", "[algorithm]"){
     aare::NDArray<double, 1> arr({5});
     for (ssize_t i = 0; i < arr.size(); i++) {
         arr[i] = i;
@@ -72,17 +72,17 @@ TEST_CASE("last smaller", "[algorithm]"){
     REQUIRE(aare::last_smaller(arr, 253.) == 4);
 }
 
-TEST_CASE("returns last bin strictly smaller", "[algorithm]"){
+TEST_CASE("returns last bin strictly smaller", "[algorithm]") {
     aare::NDArray<double, 1> arr({5});
     for (ssize_t i = 0; i < arr.size(); i++) {
         arr[i] = i;
     }
     // arr 0, 1, 2, 3, 4
     REQUIRE(aare::last_smaller(arr, 2.0) == 1);
-
 }
 
-TEST_CASE("last_smaller with all elements smaller returns last element", "[algorithm]"){
+TEST_CASE("last_smaller with all elements smaller returns last element",
+          "[algorithm]") {
     aare::NDArray<double, 1> arr({5});
     for (ssize_t i = 0; i < arr.size(); i++) {
         arr[i] = i;
@@ -91,7 +91,8 @@ TEST_CASE("last_smaller with all elements smaller returns last element", "[algor
     REQUIRE(aare::last_smaller(arr, 50.) == 4);
 }
 
-TEST_CASE("last_smaller with all elements bigger returns first element", "[algorithm]"){
+TEST_CASE("last_smaller with all elements bigger returns first element",
+          "[algorithm]") {
     aare::NDArray<double, 1> arr({5});
     for (ssize_t i = 0; i < arr.size(); i++) {
         arr[i] = i;
@@ -100,38 +101,41 @@ TEST_CASE("last_smaller with all elements bigger returns first element", "[algor
     REQUIRE(aare::last_smaller(arr, -50.) == 0);
 }
 
-TEST_CASE("last smaller with all elements equal returns the first element", "[algorithm]"){
+TEST_CASE("last smaller with all elements equal returns the first element",
-    std::vector<int> vec = {5,5,5,5,5,5,5};
+          "[algorithm]") {
+    std::vector<int> vec = {5, 5, 5, 5, 5, 5, 5};
     REQUIRE(aare::last_smaller(vec, 5) == 0);
 }
 
-
+TEST_CASE("first_lager with vector", "[algorithm]") {
-TEST_CASE("first_lager with vector", "[algorithm]"){
     std::vector<double> vec = {0, 1, 2, 3, 4};
     REQUIRE(aare::first_larger(vec, 2.5) == 3);
 }
 
-TEST_CASE("first_lager with all elements smaller returns last element", "[algorithm]"){
+TEST_CASE("first_lager with all elements smaller returns last element",
+          "[algorithm]") {
     std::vector<double> vec = {0, 1, 2, 3, 4};
     REQUIRE(aare::first_larger(vec, 50.) == 4);
 }
 
-TEST_CASE("first_lager with all elements bigger returns first element", "[algorithm]"){
+TEST_CASE("first_lager with all elements bigger returns first element",
+          "[algorithm]") {
     std::vector<double> vec = {0, 1, 2, 3, 4};
     REQUIRE(aare::first_larger(vec, -50.) == 0);
 }
 
-TEST_CASE("first_lager with all elements the same as the check returns last", "[algorithm]"){
+TEST_CASE("first_lager with all elements the same as the check returns last",
+          "[algorithm]") {
     std::vector<int> vec = {14, 14, 14, 14, 14};
     REQUIRE(aare::first_larger(vec, 14) == 4);
 }
 
-TEST_CASE("first larger with the same element", "[algorithm]"){
+TEST_CASE("first larger with the same element", "[algorithm]") {
-    std::vector<int> vec = {7,8,9,10,11};
+    std::vector<int> vec = {7, 8, 9, 10, 11};
     REQUIRE(aare::first_larger(vec, 9) == 3);
 }
 
-TEST_CASE("cumsum works", "[algorithm]"){
+TEST_CASE("cumsum works", "[algorithm]") {
     std::vector<double> vec = {0, 1, 2, 3, 4};
     auto result = aare::cumsum(vec);
     REQUIRE(result.size() == vec.size());
@@ -141,12 +145,12 @@ TEST_CASE("cumsum works", "[algorithm]"){
     REQUIRE(result[3] == 6);
     REQUIRE(result[4] == 10);
 }
-TEST_CASE("cumsum works with empty vector", "[algorithm]"){
+TEST_CASE("cumsum works with empty vector", "[algorithm]") {
     std::vector<double> vec = {};
     auto result = aare::cumsum(vec);
     REQUIRE(result.size() == 0);
 }
-TEST_CASE("cumsum works with negative numbers", "[algorithm]"){
+TEST_CASE("cumsum works with negative numbers", "[algorithm]") {
     std::vector<double> vec = {0, -1, -2, -3, -4};
     auto result = aare::cumsum(vec);
     REQUIRE(result.size() == vec.size());
@@ -156,4 +160,3 @@ TEST_CASE("cumsum works with negative numbers", "[algorithm]"){
     REQUIRE(result[3] == -6);
     REQUIRE(result[4] == -10);
 }
-