changed name of GainMap to InvertedGainMap

include/aare/CalculateEta.hpp

@@ -40,8 +40,8 @@ template <typename ClusterType,
 NDArray<double, 2> calculate_eta2(const ClusterVector<ClusterType> &clusters) {
     NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
 
-    for (const ClusterType &cluster : clusters) {
+    for (size_t i = 0; i < clusters.size(); i++) {
-        auto e = calculate_eta2(cluster);
+        auto e = calculate_eta2(clusters[i]);
         eta2(i, 0) = e.x;
         eta2(i, 1) = e.y;
     }

include/aare/ClusterFile.hpp

@@ -46,8 +46,8 @@ class ClusterFile {
     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<GainMap> m_gain_map; /*Gain map to apply to the clusters, will
+    std::optional<InvertedGainMap> m_gain_map; /*Gain map to apply to the
-                                          be applied if set*/
+                                          clusters, will be applied if set*/
 
   public:
     /**
@@ -160,16 +160,21 @@ class ClusterFile {
     }
 
     /**
-     * @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) {
-        m_gain_map = GainMap(gain_map);
+        m_gain_map = InvertedGainMap(gain_map);
     }
 
-    void set_gain_map(const GainMap &gain_map) { m_gain_map = gain_map; }
+    void set_gain_map(const InvertedGainMap &gain_map) {
+        m_gain_map = gain_map;
+    }
 
-    void set_gain_map(const GainMap &&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

include/aare/ClusterVector.hpp

@@ -76,8 +76,9 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
     std::vector<T> sum() {
         std::vector<T> sums(m_data.size());
 
-        std::transform(m_data.begin(), m_data.end(), sums.begin(),
+        std::transform(
-                       [](const T &cluster) { return cluster.sum(); });
+            m_data.begin(), m_data.end(), sums.begin(),
+            [](const ClusterType &cluster) { return cluster.sum(); });
 
         return sums;
     }
@@ -90,9 +91,10 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
     std::vector<T> sum_2x2() {
         std::vector<T> sums_2x2(m_data.size());
 
-        std::transform(
+        std::transform(m_data.begin(), m_data.end(), sums_2x2.begin(),
-            m_data.begin(), m_data.end(), sums_2x2.begin(),
+                       [](const ClusterType &cluster) {
-            [](const T &cluster) { return cluster.max_sum_2x2().first; });
+                           return cluster.max_sum_2x2().first;
+                       });
 
         return sums_2x2;
     }

include/aare/GainMap.hpp

@@ -1,6 +1,7 @@
 /************************************************
- * @file ApplyGainMap.hpp
+ * @file GainMap.hpp
- * @short function to apply gain map of image size to a vector of clusters
+ * @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
@@ -12,18 +13,17 @@
 
 namespace aare {
 
-class GainMap {
+class InvertedGainMap {
 
   public:
-    explicit GainMap(const NDArray<double, 2> &gain_map)
+    explicit InvertedGainMap(const NDArray<double, 2> &gain_map)
         : m_gain_map(gain_map) {
-            for (auto &item : m_gain_map) {
+        for (auto &item : m_gain_map) {
             item = 1.0 / item;
         }
+    };
 
-        };
+    explicit InvertedGainMap(const NDView<double, 2> gain_map) {
-
-    explicit GainMap(const NDView<double, 2> gain_map) {
         m_gain_map = NDArray<double, 2>(gain_map);
         for (auto &item : m_gain_map) {
             item = 1.0 / item;
@@ -41,14 +41,18 @@ class GainMap {
 
         int64_t index_cluster_center_x = ClusterSizeX / 2;
         int64_t index_cluster_center_y = ClusterSizeY / 2;
-        for (T &cl : clustervec) {
+        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>(cl.data[j] * m_gain_map(y, x)); //cast after conversion to keep precision
+                    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

python/src/cluster_file.hpp

@@ -59,9 +59,6 @@ void define_cluster_file_io_bindings(py::module &m,
                  self.set_gain_map(view);
              })
 
-        // void set_gain_map(const GainMap &gain_map); //TODO do i need a
-        // gainmap constructor?
-
         .def("close", &ClusterFile<ClusterType>::close)
         .def("write_frame", &ClusterFile<ClusterType>::write_frame)
         .def("__enter__", [](ClusterFile<ClusterType> &self) { return &self; })