No idea. Bug Fixes probably

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

CMakeLists.txt

@@ -368,6 +368,7 @@ set(PUBLICHEADERS
 
 
 set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/calibration.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
@@ -437,6 +438,7 @@ endif()
 if(AARE_TESTS)
     set(TestSources
             ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/calibration.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp

RELEASE.md

@@ -5,6 +5,15 @@
 
 Features:
 
+- Apply calibration works in G0 if passes a 2D calibration and pedestal
+- count pixels that switch
+- calculate pedestal (also g0 version)
+
+
+### 2025.07.18
+
+Features:
+
 - Cluster finder now works with 5x5, 7x7 and 9x9 clusters
 - Added ClusterVector::empty() member
 - Added apply_calibration function for Jungfrau data

VERSION

@@ -1 +1 @@
-2025.5.22
+2025.7.18

benchmarks/CMakeLists.txt

@@ -15,7 +15,7 @@ FetchContent_MakeAvailable(benchmark)
 
 add_executable(benchmarks)
 
-target_sources(benchmarks PRIVATE ndarray_benchmark.cpp calculateeta_benchmark.cpp reduce_benchmark.cpp)
+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)

benchmarks/reduce_benchmark.cpp

@@ -1,168 +0,0 @@
-#include "aare/Cluster.hpp"
-#include <benchmark/benchmark.h>
-
-using namespace aare;
-
-class ClustersForReduceFixture : public benchmark::Fixture {
-  public:
-    Cluster<int, 5, 5> cluster_5x5{};
-    Cluster<int, 3, 3> cluster_3x3{};
-
-  private:
-    using benchmark::Fixture::SetUp;
-
-    void SetUp([[maybe_unused]] const benchmark::State &state) override {
-        int temp_data[25] = {1, 1, 1, 1, 1, 1, 1, 2, 1, 1,
-                             1, 2, 3, 1, 2, 1, 1, 1, 1, 2};
-        std::copy(std::begin(temp_data), std::end(temp_data),
-                  std::begin(cluster_5x5.data));
-
-        cluster_5x5.x = 5;
-        cluster_5x5.y = 5;
-
-        int temp_data2[9] = {1, 1, 1, 2, 3, 1, 2, 2, 1};
-        std::copy(std::begin(temp_data2), std::end(temp_data2),
-                  std::begin(cluster_3x3.data));
-
-        cluster_3x3.x = 5;
-        cluster_3x3.y = 5;
-    }
-
-    // void TearDown(::benchmark::State& state) {
-    // }
-};
-
-template <typename T>
-Cluster<T, 3, 3, int16_t> reduce_to_3x3(const Cluster<T, 5, 5, int16_t> &c) {
-    Cluster<T, 3, 3, int16_t> result;
-
-    // Write out the sums in the hope that the compiler can optimize this
-    std::array<T, 9> sum_3x3_subclusters;
-
-    // Write out the sums in the hope that the compiler can optimize this
-    sum_3x3_subclusters[0] = c.data[0] + c.data[1] + c.data[2] + c.data[5] +
-                             c.data[6] + c.data[7] + c.data[10] + c.data[11] +
-                             c.data[12];
-    sum_3x3_subclusters[1] = c.data[1] + c.data[2] + c.data[3] + c.data[6] +
-                             c.data[7] + c.data[8] + c.data[11] + c.data[12] +
-                             c.data[13];
-    sum_3x3_subclusters[2] = c.data[2] + c.data[3] + c.data[4] + c.data[7] +
-                             c.data[8] + c.data[9] + c.data[12] + c.data[13] +
-                             c.data[14];
-    sum_3x3_subclusters[3] = c.data[5] + c.data[6] + c.data[7] + c.data[10] +
-                             c.data[11] + c.data[12] + c.data[15] + c.data[16] +
-                             c.data[17];
-    sum_3x3_subclusters[4] = c.data[6] + c.data[7] + c.data[8] + c.data[11] +
-                             c.data[12] + c.data[13] + c.data[16] + c.data[17] +
-                             c.data[18];
-    sum_3x3_subclusters[5] = c.data[7] + c.data[8] + c.data[9] + c.data[12] +
-                             c.data[13] + c.data[14] + c.data[17] + c.data[18] +
-                             c.data[19];
-    sum_3x3_subclusters[6] = c.data[10] + c.data[11] + c.data[12] + c.data[15] +
-                             c.data[16] + c.data[17] + c.data[20] + c.data[21] +
-                             c.data[22];
-    sum_3x3_subclusters[7] = c.data[11] + c.data[12] + c.data[13] + c.data[16] +
-                             c.data[17] + c.data[18] + c.data[21] + c.data[22] +
-                             c.data[23];
-    sum_3x3_subclusters[8] = c.data[12] + c.data[13] + c.data[14] + c.data[17] +
-                             c.data[18] + c.data[19] + c.data[22] + c.data[23] +
-                             c.data[24];
-
-    auto index = std::max_element(sum_3x3_subclusters.begin(),
-                                  sum_3x3_subclusters.end()) -
-                 sum_3x3_subclusters.begin();
-
-    switch (index) {
-    case 0:
-        result.x = c.x - 1;
-        result.y = c.y + 1;
-        result.data = {c.data[0], c.data[1],  c.data[2],  c.data[5], c.data[6],
-                       c.data[7], c.data[10], c.data[11], c.data[12]};
-        break;
-    case 1:
-        result.x = c.x;
-        result.y = c.y + 1;
-        result.data = {c.data[1], c.data[2],  c.data[3],  c.data[6], c.data[7],
-                       c.data[8], c.data[11], c.data[12], c.data[13]};
-        break;
-    case 2:
-        result.x = c.x + 1;
-        result.y = c.y + 1;
-        result.data = {c.data[2], c.data[3],  c.data[4],  c.data[7], c.data[8],
-                       c.data[9], c.data[12], c.data[13], c.data[14]};
-        break;
-    case 3:
-        result.x = c.x - 1;
-        result.y = c.y;
-        result.data = {c.data[5],  c.data[6],  c.data[7],
-                       c.data[10], c.data[11], c.data[12],
-                       c.data[15], c.data[16], c.data[17]};
-        break;
-    case 4:
-        result.x = c.x + 1;
-        result.y = c.y;
-        result.data = {c.data[6],  c.data[7],  c.data[8],
-                       c.data[11], c.data[12], c.data[13],
-                       c.data[16], c.data[17], c.data[18]};
-        break;
-    case 5:
-        result.x = c.x + 1;
-        result.y = c.y;
-        result.data = {c.data[7],  c.data[8],  c.data[9],
-                       c.data[12], c.data[13], c.data[14],
-                       c.data[17], c.data[18], c.data[19]};
-        break;
-    case 6:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[10], c.data[11], c.data[12],
-                       c.data[15], c.data[16], c.data[17],
-                       c.data[20], c.data[21], c.data[22]};
-        break;
-    case 7:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[11], c.data[12], c.data[13],
-                       c.data[16], c.data[17], c.data[18],
-                       c.data[21], c.data[22], c.data[23]};
-        break;
-    case 8:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[12], c.data[13], c.data[14],
-                       c.data[17], c.data[18], c.data[19],
-                       c.data[22], c.data[23], c.data[24]};
-        break;
-    }
-    return result;
-}
-
-BENCHMARK_F(ClustersForReduceFixture, Reduce2x2)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_2x2<int, 3, 3, int16_t>(
-            cluster_3x3)); // make sure compiler evaluates the expression
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, SpecificReduce2x2)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_2x2<int>(cluster_3x3));
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, Reduce3x3)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(
-            reduce_to_3x3<int, 5, 5, int16_t>(cluster_5x5));
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, SpecificReduce3x3)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_3x3<int>(cluster_5x5));
-    }
-}

docs/src/ClusterVector.rst

@@ -12,11 +12,4 @@ ClusterVector
    :members:
    :undoc-members:
    :private-members:
-   
-
-**Free Functions:** 
-
-.. doxygenfunction:: aare::reduce_to_3x3(const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>&)
-   
-.. doxygenfunction:: aare::reduce_to_2x2(const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>&)
    

docs/src/pyClusterVector.rst

@@ -33,17 +33,4 @@ C++ functions that support the ClusterVector or to view it as a numpy array.
     :members:
     :undoc-members:
     :show-inheritance:
-    :inherited-members:
-
-
-**Free Functions:** 
-
-.. autofunction:: reduce_to_3x3
-   :noindex:
-
-   Reduce a single Cluster to 3x3 by taking the 3x3 subcluster with highest photon energy.
-
-.. autofunction:: reduce_to_2x2
-   :noindex:
-
-   Reduce a single Cluster to 2x2 by taking the 2x2 subcluster with highest photon energy.
+    :inherited-members:

docs/src/pycalibration.rst

@@ -17,8 +17,24 @@ Functions for applying calibration to data.
     # Apply calibration to raw data to convert from raw ADC values to keV
     data = aare.apply_calibration(raw_data, pd=pedestal, cal=calibration)
 
+    # If you pass a 2D pedestal and calibration only G0 will be used for the conversion
+    # Pixels that switched to G1 or G2 will be set to 0
+    data = aare.apply_calibration(raw_data, pd=pedestal[0], cal=calibration[0])
+
+    
+
 .. py:currentmodule:: aare
 
 .. autofunction:: apply_calibration
 
 .. autofunction:: load_calibration
+
+.. autofunction:: calculate_pedestal
+
+.. autofunction:: calculate_pedestal_float
+
+.. autofunction:: calculate_pedestal_g0
+
+.. autofunction:: calculate_pedestal_g0_float
+
+.. autofunction:: count_switching_pixels

include/aare/CalculateEta.hpp

@@ -28,7 +28,7 @@ enum class pixel : int {
 template <typename T> struct Eta2 {
     double x;
     double y;
-    int c{0};
+    int c;
     T sum;
 };
 
@@ -70,8 +70,6 @@ calculate_eta2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
     size_t index_bottom_left_max_2x2_subcluster =
         (int(c / (ClusterSizeX - 1))) * ClusterSizeX + c % (ClusterSizeX - 1);
 
-    // calculate direction of gradient
-
     // 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 &&
@@ -130,15 +128,12 @@ 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]); // between (0,1) the closer to zero
-                                           // left value probably larger
+        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]); // between (0,1) the closer to zero
-                                           // bottom value probably larger
+        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;
 }
 
@@ -155,11 +150,13 @@ template <typename T> Eta2<T> calculate_eta3(const Cluster<T, 3, 3> &cl) {
 
     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]); // (-1,1)
+                (cl.data[3] + cl.data[4] + cl.data[5]);
 
     if ((cl.data[1] + cl.data[4] + cl.data[7]) != 0)
 

include/aare/ChunkedPedestal.hpp

@@ -0,0 +1,152 @@
+#pragma once
+#include "aare/Frame.hpp"
+#include "aare/NDArray.hpp"
+#include "aare/NDView.hpp"
+#include <cstddef>
+
+//JMulvey
+//This is a new way to do pedestals (inspired by Dominic's cluster finder)
+//Instead of pedestal tracking, we split the data (photon data) up into chunks (say 50K frames)
+//For each chunk, we look at the spectra and fit to the noise peak. When we run the cluster finder, we then use this chunked pedestal data
+//The smaller the chunk size, the more accurate, but also the longer it takes to process.
+//It is essentially a pre-processing step.
+//Ideally this new class will do that processing. 
+//But for now we will just implement a method to pass in the chunked pedestal values directly (I have my own script which does it for now)
+//I've cut this down a lot, knowing full well it'll need changing if we want to merge it with main (happy to do that once I get it work for what I need)
+
+namespace aare {
+
+/**
+ * @brief Calculate the pedestal of a series of frames. Can be used as
+ * standalone but mostly used in the ClusterFinder.
+ *
+ * @tparam SUM_TYPE type of the sum
+ */
+template <typename SUM_TYPE = double> class ChunkedPedestal {
+    uint32_t m_rows;
+    uint32_t m_cols;
+    uint32_t m_n_chunks;
+    uint64_t m_current_frame_number;
+    uint64_t m_current_chunk_number;
+
+    NDArray<SUM_TYPE, 3> m_mean;
+    NDArray<SUM_TYPE, 3> m_std;
+    uint32_t m_chunk_size;
+
+  public:
+    ChunkedPedestal(uint32_t rows, uint32_t cols, uint32_t chunk_size = 50000, uint32_t n_chunks = 10)
+        : m_rows(rows), m_cols(cols), m_chunk_size(chunk_size), m_n_chunks(n_chunks),    
+          m_mean(NDArray<SUM_TYPE, 3>({n_chunks, rows, cols})), m_std(NDArray<SUM_TYPE, 3>({n_chunks, rows, cols})) {
+        assert(rows > 0 && cols > 0 && chunk_size > 0);
+        m_mean = 0;
+        m_std = 0;
+        m_current_frame_number = 0;
+        m_current_chunk_number = 0;
+    }
+    ~ChunkedPedestal() = default;
+
+    NDArray<SUM_TYPE, 3> mean() { return m_mean; }
+    NDArray<SUM_TYPE, 3> std() { return m_std; }
+
+    void set_frame_number (uint64_t frame_number) {
+        m_current_frame_number = frame_number;
+        m_current_chunk_number = std::floor(frame_number / m_chunk_size);
+
+        //Debug
+        // if (frame_number % 10000 == 0)
+        // {
+        //     std::cout << "frame_number: " << frame_number << " -> chunk_number: " << m_current_chunk_number << " pedestal at (100, 100): " << m_mean(m_current_chunk_number, 100, 100) << std::endl;
+        // }
+
+        if (m_current_chunk_number >= m_n_chunks) 
+        {
+            m_current_chunk_number = 0;
+            throw std::runtime_error(
+                "Chunk number exceeds the number of chunks");
+        }
+    }
+
+    SUM_TYPE mean(const uint32_t row, const uint32_t col) const {    
+        return m_mean(m_current_chunk_number, row, col);
+    }
+
+    SUM_TYPE std(const uint32_t row, const uint32_t col) const {
+        return m_std(m_current_chunk_number, row, col);
+    }
+
+    SUM_TYPE* get_mean_chunk_ptr() {
+        return &m_mean(m_current_chunk_number, 0, 0);
+    }
+
+    SUM_TYPE* get_std_chunk_ptr() {
+        return &m_std(m_current_chunk_number, 0, 0);
+    }
+
+    void clear() {
+        m_mean = 0;
+        m_std = 0;
+        m_n_chunks = 0;
+    }
+
+    //Probably don't need to do this one at a time, but let's keep it simple for now
+    template <typename T> void push_mean(NDView<T, 2> frame, uint32_t chunk_number) {
+        assert(frame.size() == m_rows * m_cols);
+
+        if (chunk_number >= m_n_chunks)
+            throw std::runtime_error(
+                "Chunk number is larger than the number of chunks");
+
+        // TODO! move away from m_rows, m_cols
+        if (frame.shape() != std::array<ssize_t, 2>{m_rows, m_cols}) {
+            throw std::runtime_error(
+                "Frame shape does not match pedestal shape");
+        }
+
+        for (size_t row = 0; row < m_rows; row++) {
+            for (size_t col = 0; col < m_cols; col++) {
+                push_mean<T>(row, col, chunk_number, frame(row, col));
+            }
+        }
+       
+    }
+    
+    template <typename T> void push_std(NDView<T, 2> frame, uint32_t chunk_number) {
+        assert(frame.size() == m_rows * m_cols);
+
+        if (chunk_number >= m_n_chunks)
+            throw std::runtime_error(
+                "Chunk number is larger than the number of chunks");
+
+        // TODO! move away from m_rows, m_cols
+        if (frame.shape() != std::array<ssize_t, 2>{m_rows, m_cols}) {
+            throw std::runtime_error(
+                "Frame shape does not match pedestal shape");
+        }
+
+        for (size_t row = 0; row < m_rows; row++) {
+            for (size_t col = 0; col < m_cols; col++) {
+                push_std<T>(row, col, chunk_number, frame(row, col));
+            }
+        }
+        
+    }
+
+    // pixel level operations (should be refactored to allow users to implement
+    // their own pixel level operations)
+    template <typename T>
+    void push_mean(const uint32_t row, const uint32_t col, const uint32_t chunk_number, const T val_) {        
+        m_mean(chunk_number, row, col) = val_;
+    }
+
+    template <typename T>
+    void push_std(const uint32_t row, const uint32_t col, const uint32_t chunk_number, const T val_) {        
+        m_std(chunk_number, row, col) = val_;
+    }
+
+    // getter functions
+    uint32_t rows() const { return m_rows; }
+    uint32_t cols() const { return m_cols; }
+
+};
+
+} // namespace aare

include/aare/Cluster.hpp

@@ -8,7 +8,6 @@
 
 #pragma once
 
-#include "logger.hpp"
 #include <algorithm>
 #include <array>
 #include <cstdint>
@@ -75,163 +74,6 @@ struct Cluster {
     }
 };
 
-/**
- * @brief Reduce a cluster to a 2x2 cluster by selecting the 2x2 block with the
- * highest sum.
- * @param c Cluster to reduce
- * @return reduced cluster
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-Cluster<T, 2, 2, CoordType>
-reduce_to_2x2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &c) {
-
-    static_assert(ClusterSizeX >= 2 && ClusterSizeY >= 2,
-                  "Cluster sizes must be at least 2x2 for reduction to 2x2");
-
-    // TODO maybe add sanity check and check that center is in max subcluster
-    Cluster<T, 2, 2, CoordType> result;
-
-    auto [sum, index] = c.max_sum_2x2();
-
-    int16_t cluster_center_index =
-        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
-
-    int16_t index_bottom_left_max_2x2_subcluster =
-        (int(index / (ClusterSizeX - 1))) * ClusterSizeX +
-        index % (ClusterSizeX - 1);
-
-    result.x =
-        c.x + (index_bottom_left_max_2x2_subcluster - cluster_center_index) %
-                  ClusterSizeX;
-
-    result.y =
-        c.y - (index_bottom_left_max_2x2_subcluster - cluster_center_index) /
-                  ClusterSizeX;
-    result.data = {
-        c.data[index_bottom_left_max_2x2_subcluster],
-        c.data[index_bottom_left_max_2x2_subcluster + 1],
-        c.data[index_bottom_left_max_2x2_subcluster + ClusterSizeX],
-        c.data[index_bottom_left_max_2x2_subcluster + ClusterSizeX + 1]};
-    return result;
-}
-
-template <typename T>
-Cluster<T, 2, 2, int16_t> reduce_to_2x2(const Cluster<T, 3, 3, int16_t> &c) {
-    Cluster<T, 2, 2, int16_t> result;
-
-    auto [s, i] = c.max_sum_2x2();
-    switch (i) {
-    case 0:
-        result.x = c.x - 1;
-        result.y = c.y + 1;
-        result.data = {c.data[0], c.data[1], c.data[3], c.data[4]};
-        break;
-    case 1:
-        result.x = c.x;
-        result.y = c.y + 1;
-        result.data = {c.data[1], c.data[2], c.data[4], c.data[5]};
-        break;
-    case 2:
-        result.x = c.x - 1;
-        result.y = c.y;
-        result.data = {c.data[3], c.data[4], c.data[6], c.data[7]};
-        break;
-    case 3:
-        result.x = c.x;
-        result.y = c.y;
-        result.data = {c.data[4], c.data[5], c.data[7], c.data[8]};
-        break;
-    }
-
-    return result;
-}
-
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-inline std::pair<T, uint16_t>
-max_3x3_sum(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cluster) {
-
-    if constexpr (ClusterSizeX == 3 && ClusterSizeY == 3) {
-        return std::make_pair(cluster.sum(), 0);
-    } else {
-
-        size_t index = 0;
-        T max_3x3_subcluster_sum = 0;
-        for (size_t i = 0; i < ClusterSizeY - 2; ++i) {
-            for (size_t j = 0; j < ClusterSizeX - 2; ++j) {
-
-                T sum = cluster.data[i * ClusterSizeX + j] +
-                        cluster.data[i * ClusterSizeX + j + 1] +
-                        cluster.data[i * ClusterSizeX + j + 2] +
-                        cluster.data[(i + 1) * ClusterSizeX + j] +
-                        cluster.data[(i + 1) * ClusterSizeX + j + 1] +
-                        cluster.data[(i + 1) * ClusterSizeX + j + 2] +
-                        cluster.data[(i + 2) * ClusterSizeX + j] +
-                        cluster.data[(i + 2) * ClusterSizeX + j + 1] +
-                        cluster.data[(i + 2) * ClusterSizeX + j + 2];
-                if (sum > max_3x3_subcluster_sum) {
-                    max_3x3_subcluster_sum = sum;
-                    index = i * (ClusterSizeX - 2) + j;
-                }
-            }
-        }
-
-        return std::make_pair(max_3x3_subcluster_sum, index);
-    }
-}
-
-/**
- * @brief Reduce a cluster to a 3x3 cluster by selecting the 3x3 block with the
- * highest sum.
- * @param c Cluster to reduce
- * @return reduced cluster
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-Cluster<T, 3, 3, CoordType>
-reduce_to_3x3(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &c) {
-
-    static_assert(ClusterSizeX >= 3 && ClusterSizeY >= 3,
-                  "Cluster sizes must be at least 3x3 for reduction to 3x3");
-
-    Cluster<T, 3, 3, CoordType> result;
-
-    // TODO maybe add sanity check and check that center is in max subcluster
-
-    auto [sum, index] = max_3x3_sum(c);
-
-    int16_t cluster_center_index =
-        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
-
-    int16_t index_center_max_3x3_subcluster =
-        (int(index / (ClusterSizeX - 2))) * ClusterSizeX + ClusterSizeX +
-        index % (ClusterSizeX - 2) + 1;
-
-    int16_t index_3x3_subcluster_cluster_center =
-        int((cluster_center_index - 1 - ClusterSizeX) / ClusterSizeX) *
-            (ClusterSizeX - 2) +
-        (cluster_center_index - 1 - ClusterSizeX) % ClusterSizeX;
-
-    result.x =
-        c.x + (index % (ClusterSizeX - 2) -
-               (index_3x3_subcluster_cluster_center % (ClusterSizeX - 2)));
-    result.y =
-        c.y - (index / (ClusterSizeX - 2) -
-               (index_3x3_subcluster_cluster_center / (ClusterSizeX - 2)));
-
-    result.data = {c.data[index_center_max_3x3_subcluster - ClusterSizeX - 1],
-                   c.data[index_center_max_3x3_subcluster - ClusterSizeX],
-                   c.data[index_center_max_3x3_subcluster - ClusterSizeX + 1],
-                   c.data[index_center_max_3x3_subcluster - 1],
-                   c.data[index_center_max_3x3_subcluster],
-                   c.data[index_center_max_3x3_subcluster + 1],
-                   c.data[index_center_max_3x3_subcluster + ClusterSizeX - 1],
-                   c.data[index_center_max_3x3_subcluster + ClusterSizeX],
-                   c.data[index_center_max_3x3_subcluster + ClusterSizeX + 1]};
-    return result;
-}
-
 // Type Traits for is_cluster_type
 template <typename T>
 struct is_cluster : std::false_type {}; // Default case: Not a Cluster

include/aare/ClusterFinder.hpp

@@ -4,9 +4,11 @@
 #include "aare/Dtype.hpp"
 #include "aare/NDArray.hpp"
 #include "aare/NDView.hpp"
-#include "aare/Pedestal.hpp"
+// #include "aare/Pedestal.hpp"
+#include "aare/ChunkedPedestal.hpp"
 #include "aare/defs.hpp"
 #include <cstddef>
+#include <iostream>
 
 namespace aare {
 
@@ -17,11 +19,13 @@ class ClusterFinder {
     const PEDESTAL_TYPE m_nSigma;
     const PEDESTAL_TYPE c2;
     const PEDESTAL_TYPE c3;
-    Pedestal<PEDESTAL_TYPE> m_pedestal;
+    ChunkedPedestal<PEDESTAL_TYPE> m_pedestal;
     ClusterVector<ClusterType> m_clusters;
+    const uint32_t ClusterSizeX;
+    const uint32_t ClusterSizeY;
 
-    static const uint8_t ClusterSizeX = ClusterType::cluster_size_x;
-    static const uint8_t ClusterSizeY = ClusterType::cluster_size_y;
+    static const uint8_t SavedClusterSizeX = ClusterType::cluster_size_x;
+    static const uint8_t SavedClusterSizeY = ClusterType::cluster_size_y;
     using CT = typename ClusterType::value_type;
 
   public:
@@ -34,25 +38,36 @@ class ClusterFinder {
      *
      */
     ClusterFinder(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                  size_t capacity = 1000000)
+                  size_t capacity = 1000000,
+                  uint32_t chunk_size = 50000, uint32_t n_chunks = 10,
+                  uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_image_size(image_size), m_nSigma(nSigma),
-          c2(sqrt((ClusterSizeY + 1) / 2 * (ClusterSizeX + 1) / 2)),
-          c3(sqrt(ClusterSizeX * ClusterSizeY)),
-          m_pedestal(image_size[0], image_size[1]), m_clusters(capacity) {
+          c2(sqrt((cluster_size_y + 1) / 2 * (cluster_size_x + 1) / 2)),
+          c3(sqrt(cluster_size_x * cluster_size_y)),
+          ClusterSizeX(cluster_size_x), ClusterSizeY(cluster_size_y),
+          m_pedestal(image_size[0], image_size[1], chunk_size, n_chunks), m_clusters(capacity) {
         LOG(logDEBUG) << "ClusterFinder: "
                       << "image_size: " << image_size[0] << "x" << image_size[1]
                       << ", nSigma: " << nSigma << ", capacity: " << capacity;
     }
 
-    void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {
-        m_pedestal.push(frame);
+    // void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {
+    //     m_pedestal.push(frame);
+    // }
+    void push_pedestal_mean(NDView<PEDESTAL_TYPE, 2> frame, uint32_t chunk_number) {
+        m_pedestal.push_mean(frame, chunk_number);
     }
+    void push_pedestal_std(NDView<PEDESTAL_TYPE, 2> frame, uint32_t chunk_number) {
+        m_pedestal.push_std(frame, chunk_number);
+    }
+    //This is here purely to keep the compiler happy for now
+    void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {}
 
     NDArray<PEDESTAL_TYPE, 2> pedestal() { return m_pedestal.mean(); }
     NDArray<PEDESTAL_TYPE, 2> noise() { return m_pedestal.std(); }
     void clear_pedestal() { m_pedestal.clear(); }
 
-    /**
+     /**
      * @brief Move the clusters from the ClusterVector in the ClusterFinder to a
      * new ClusterVector and return it.
      * @param realloc_same_capacity if true the new ClusterVector will have the
@@ -69,11 +84,13 @@ class ClusterFinder {
         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 = ClusterSizeY / 2;
         int dx = ClusterSizeX / 2;
+        int dy2 = SavedClusterSizeY / 2;
+        int dx2 = SavedClusterSizeX / 2;
+
         int has_center_pixel_x =
             ClusterSizeX %
             2; // for even sized clusters there is no proper cluster center and
@@ -81,27 +98,39 @@ class ClusterFinder {
         int has_center_pixel_y = ClusterSizeY % 2;
 
         m_clusters.set_frame_number(frame_number);
+        m_pedestal.set_frame_number(frame_number);
+        auto mean_ptr = m_pedestal.get_mean_chunk_ptr();
+        auto std_ptr = m_pedestal.get_std_chunk_ptr();
+
         for (int iy = 0; iy < frame.shape(0); iy++) {
+            size_t row_offset = iy * frame.shape(1); 
             for (int ix = 0; ix < frame.shape(1); ix++) {
 
+                // PEDESTAL_TYPE rms = m_pedestal.std(iy, ix);
+                PEDESTAL_TYPE rms = std_ptr[row_offset + ix];
+                if (rms == 0) continue;
+
                 PEDESTAL_TYPE max = std::numeric_limits<FRAME_TYPE>::min();
                 PEDESTAL_TYPE total = 0;
 
-                // What can we short circuit here?
-                PEDESTAL_TYPE rms = m_pedestal.std(iy, ix);
-                PEDESTAL_TYPE value = (frame(iy, ix) - m_pedestal.mean(iy, ix));
+                // What can we short circuit here?                
+                // PEDESTAL_TYPE value = (frame(iy, ix) - m_pedestal.mean(iy, ix));
+                PEDESTAL_TYPE value = (frame(iy, ix) - mean_ptr[row_offset + ix]);
 
                 if (value < -m_nSigma * rms)
                     continue; // NEGATIVE_PEDESTAL go to next pixel
                               // TODO! No pedestal update???
 
                 for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
+                    size_t inner_row_offset = row_offset + (ir * frame.shape(1));
                     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 =
-                                frame(iy + ir, ix + ic) -
-                                m_pedestal.mean(iy + ir, ix + ic);
+                            // if (m_pedestal.std(iy + ir, ix + ic) == 0) continue;
+                            if (std_ptr[inner_row_offset + ix + ic] == 0) continue;
+
+                            // PEDESTAL_TYPE val = frame(iy + ir, ix + ic) - m_pedestal.mean(iy + ir, ix + ic);
+                            PEDESTAL_TYPE val = frame(iy + ir, ix + ic) - mean_ptr[inner_row_offset + ix + ic];
 
                             total += val;
                             max = std::max(max, val);
@@ -109,24 +138,64 @@ class ClusterFinder {
                     }
                 }
 
-                if ((max > m_nSigma * rms)) {
-                    if (value < max)
-                        continue; // Not max go to the next pixel
-                                  // but also no pedestal update
-                } else if (total > c3 * m_nSigma * rms) {
+//                 if (frame_number < 1)
+//                     if ( (ix == 115 && iy == 122) )
+//                     if ( (ix == 175 && iy == 175) )
+//                     {
+// //                         std::cout << std::endl;
+// //                         std::cout << std::endl;
+// //                         std::cout << "frame_number: " << frame_number << std::endl;
+// //                         std::cout << "(" << ix << ", " << iy << "): " << std::endl;
+// //                         std::cout << "frame.shape: (" << frame.shape(0) << ", " << frame.shape(1) << "): " << std::endl;
+// //                         std::cout << "frame(175, 175): " << frame(175, 175) << std::endl;
+// //                         std::cout << "frame(77, 98): " << frame(77, 98) << std::endl;
+// //                         std::cout << "frame(82, 100): " << frame(82, 100) << std::endl;
+// //                         std::cout << "frame(iy, ix): " << frame(iy, ix) << std::endl;
+// //                         std::cout << "mean_ptr[row_offset + ix]: " << mean_ptr[row_offset + ix] << std::endl;
+// //                         std::cout << "total: " << total << std::endl;
+
+//                         std::cout << "(" << ix << ", " << iy << "): " << frame(iy, ix) << std::endl;
+//                     }
+
+                // if ((max > m_nSigma * rms)) {
+                //     if (value < max)
+                //         continue; // Not max go to the next pixel
+                //                   // but also no pedestal update
+                // } else 
+                if (total > c3 * m_nSigma * rms) {
                     // 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
+
+                    //Not needed for chunked pedestal
+                    // 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) {
+                    
+                    // if (total < 0)
+                    // {
+                    //     std::cout << "" << std::endl;   
+                    //     std::cout << "frame_number: " << frame_number << std::endl;                                        
+                    //     std::cout << "ix: " << ix << std::endl;
+                    //     std::cout << "iy: " << iy << std::endl;
+                    //     std::cout << "frame(iy, ix): " << frame(iy, ix) << std::endl;
+                    //     std::cout << "m_pedestal.mean(iy, ix): " << m_pedestal.mean(iy, ix) << std::endl;
+                    //     std::cout << "m_pedestal.std(iy, ix): " << m_pedestal.std(iy, ix) << std::endl;
+                    //     std::cout << "max: " << max << std::endl;
+                    //     std::cout << "value: " << value << std::endl;
+                    //     std::cout << "m_nSigma * rms: " << (m_nSigma * rms) << std::endl;
+                    //     std::cout << "total: " << total << std::endl;
+                    //     std::cout << "c3 * m_nSigma * rms: " << (c3 * m_nSigma * rms) << std::endl;
+                    // }                    
+
                     ClusterType cluster{};
                     cluster.x = ix;
                     cluster.y = iy;
@@ -135,18 +204,24 @@ class ClusterFinder {
                     // It's worth redoing the look since most of the time we
                     // don't have a photon
                     int i = 0;
-                    for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                        for (int ic = -dx; ic < dx + has_center_pixel_y; ic++) {
+                    for (int ir = -dy2; ir < dy2 + has_center_pixel_y; ir++) {
+                        size_t inner_row_offset = row_offset + (ir * frame.shape(1));
+                        for (int ic = -dx2; ic < dx2 + has_center_pixel_y; ic++) {
                             if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                                 iy + ir >= 0 && iy + ir < frame.shape(0)) {
-                                CT tmp =
-                                    static_cast<CT>(frame(iy + ir, ix + ic)) -
-                                    static_cast<CT>(
-                                        m_pedestal.mean(iy + ir, ix + ic));
-                                cluster.data[i] =
-                                    tmp; // Watch for out of bounds access
-                                i++;
+                                // if (m_pedestal.std(iy + ir, ix + ic) == 0) continue;
+                                // if (std_ptr[inner_row_offset + ix + ic] == 0) continue;
+
+                                // CT tmp = static_cast<CT>(frame(iy + ir, ix + ic)) - static_cast<CT>(m_pedestal.mean(iy + ir, ix + ic));
+
+                                // CT tmp = 0;
+                                if (std_ptr[inner_row_offset + ix + ic] != 0)
+                                {                                
+                                    CT tmp = static_cast<CT>(frame(iy + ir, ix + ic)) - static_cast<CT>(mean_ptr[inner_row_offset + ix + ic]);                                
+                                    cluster.data[i] = tmp; // Watch for out of bounds access                                
+                                }
                             }
+                            i++;
                         }
                     }
 
@@ -158,4 +233,4 @@ class ClusterFinder {
     }
 };
 
-} // namespace aare
+} // namespace aare

include/aare/ClusterFinderMT.hpp

@@ -20,9 +20,15 @@ enum class FrameType {
 struct FrameWrapper {
     FrameType type;
     uint64_t frame_number;
+    // NDArray<T, 2> data;
     NDArray<uint16_t, 2> data;
+    // NDArray<double, 2> data;
+    // void* data_ptr;
+    // std::type_index data_type;
+    uint32_t chunk_number;
 };
 
+
 /**
  * @brief ClusterFinderMT is a multi-threaded version of ClusterFinder. It uses
  * a producer-consumer queue to distribute the frames to the threads. The
@@ -68,6 +74,7 @@ class ClusterFinderMT {
         while (!m_stop_requested || !q->isEmpty()) {
             if (FrameWrapper *frame = q->frontPtr(); frame != nullptr) {
 
+
                 switch (frame->type) {
                 case FrameType::DATA:
                     cf->find_clusters(frame->data.view(), frame->frame_number);
@@ -121,7 +128,9 @@ class ClusterFinderMT {
      * @param n_threads number of threads to use
      */
     ClusterFinderMT(Shape<2> image_size, PEDESTAL_TYPE nSigma = 5.0,
-                    size_t capacity = 2000, size_t n_threads = 3)
+                    size_t capacity = 2000, size_t n_threads = 3,
+                    uint32_t chunk_size = 50000, uint32_t n_chunks = 10,
+                    uint32_t cluster_size_x = 3, uint32_t cluster_size_y = 3)
         : m_n_threads(n_threads) {
 
         LOG(logDEBUG1) << "ClusterFinderMT: "
@@ -134,7 +143,7 @@ class ClusterFinderMT {
             m_cluster_finders.push_back(
                 std::make_unique<
                     ClusterFinder<ClusterType, FRAME_TYPE, PEDESTAL_TYPE>>(
-                    image_size, nSigma, capacity));
+                    image_size, nSigma, capacity, chunk_size, n_chunks, cluster_size_x, cluster_size_y));
         }
         for (size_t i = 0; i < n_threads; i++) {
             m_input_queues.emplace_back(std::make_unique<InputQueue>(200));
@@ -208,7 +217,7 @@ class ClusterFinderMT {
      */
     void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {
         FrameWrapper fw{FrameType::PEDESTAL, 0,
-                        NDArray(frame)}; // TODO! copies the data!
+                        NDArray(frame), 0}; // TODO! copies the data!
 
         for (auto &queue : m_input_queues) {
             while (!queue->write(fw)) {
@@ -217,6 +226,23 @@ class ClusterFinderMT {
         }
     }
 
+    void push_pedestal_mean(NDView<PEDESTAL_TYPE, 2> frame, uint32_t chunk_number) {
+        if (!m_processing_threads_stopped) {
+            throw std::runtime_error("ClusterFinderMT is still running");
+        }
+        for (auto &cf : m_cluster_finders) {
+            cf->push_pedestal_mean(frame, chunk_number);
+        }
+    }
+    void push_pedestal_std(NDView<PEDESTAL_TYPE, 2> frame, uint32_t chunk_number) {
+        if (!m_processing_threads_stopped) {
+            throw std::runtime_error("ClusterFinderMT is still running");
+        }
+        for (auto &cf : m_cluster_finders) {
+            cf->push_pedestal_std(frame, chunk_number);
+        }
+    }
+
     /**
      * @brief Push the frame to the queue of the next available thread. Function
      * returns once the frame is in a queue.
@@ -224,7 +250,10 @@ class ClusterFinderMT {
      */
     void find_clusters(NDView<FRAME_TYPE, 2> frame, uint64_t frame_number = 0) {
         FrameWrapper fw{FrameType::DATA, frame_number,
-                        NDArray(frame)}; // TODO! copies the data!
+                        NDArray(frame), 0}; // TODO! copies the data!
+
+        // std::cout << "frame(122, 115): " << frame(122, 115) << std::endl;
+
         while (!m_input_queues[m_current_thread % m_n_threads]->write(fw)) {
             std::this_thread::sleep_for(m_default_wait);
         }
@@ -281,4 +310,4 @@ class ClusterFinderMT {
     // }
 };
 
-} // namespace aare
+} // namespace aare

include/aare/ClusterVector.hpp

@@ -32,7 +32,8 @@ class ClusterVector; // Forward declaration
  */
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType>
-class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
+class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> 
+{
 
     std::vector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> m_data{};
     int32_t m_frame_number{0}; // TODO! Check frame number size and type
@@ -172,40 +173,4 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
     }
 };
 
-/**
- * @brief Reduce a cluster to a 2x2 cluster by selecting the 2x2 block with the
- * highest sum.
- * @param cv Clustervector containing clusters to reduce
- * @return Clustervector with reduced clusters
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-ClusterVector<Cluster<T, 2, 2, CoordType>> reduce_to_2x2(
-    const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>
-        &cv) {
-    ClusterVector<Cluster<T, 2, 2, CoordType>> result;
-    for (const auto &c : cv) {
-        result.push_back(reduce_to_2x2(c));
-    }
-    return result;
-}
-
-/**
- * @brief Reduce a cluster to a 3x3 cluster by selecting the 3x3 block with the
- * highest sum.
- * @param cv Clustervector containing clusters to reduce
- * @return Clustervector with reduced clusters
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-ClusterVector<Cluster<T, 3, 3, CoordType>> reduce_to_3x3(
-    const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>
-        &cv) {
-    ClusterVector<Cluster<T, 3, 3, CoordType>> result;
-    for (const auto &c : cv) {
-        result.push_back(reduce_to_3x3(c));
-    }
-    return result;
-}
-
 } // namespace aare

include/aare/NDArray.hpp

@@ -25,7 +25,7 @@ template <typename T, ssize_t Ndim = 2>
 class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
     std::array<ssize_t, Ndim> shape_;
     std::array<ssize_t, Ndim> strides_;
-    size_t size_{};
+    size_t size_{}; //TODO! do we need to store size when we have shape?
     T *data_;
 
   public:
@@ -33,7 +33,7 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
      * @brief Default constructor. Will construct an empty NDArray.
      *
      */
-    NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), data_(nullptr){};
+    NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), data_(nullptr) {};
 
     /**
      * @brief Construct a new NDArray object with a given shape.
@@ -43,8 +43,7 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
      */
     explicit NDArray(std::array<ssize_t, Ndim> shape)
         : shape_(shape), strides_(c_strides<Ndim>(shape_)),
-          size_(std::accumulate(shape_.begin(), shape_.end(), 1,
-                                std::multiplies<>())),
+          size_(num_elements(shape_)),
           data_(new T[size_]) {}
 
     /**
@@ -79,6 +78,24 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
         other.reset(); // TODO! is this necessary?
     }
 
+
+    //Move constructor from an an array with Ndim + 1
+    template <ssize_t M, typename = std::enable_if_t<(M == Ndim + 1)>>
+    NDArray(NDArray<T, M> &&other) 
+        : shape_(drop_first_dim(other.shape())),
+          strides_(c_strides<Ndim>(shape_)), size_(num_elements(shape_)),
+          data_(other.data()) {
+
+            // For now only allow move if the size matches, to avoid unreachable data
+            // if the use case arises we can remove this check
+            if(size() != other.size()) {
+                data_ = nullptr; // avoid double free, other will clean up the memory in it's destructor
+                throw std::runtime_error(LOCATION +
+                                         "Size mismatch in move constructor of NDArray<T, Ndim-1>");
+            }
+        other.reset();
+    }
+
     // Copy constructor
     NDArray(const NDArray &other)
         : shape_(other.shape_), strides_(c_strides<Ndim>(shape_)),
@@ -380,12 +397,6 @@ NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
     result *= value;
     return result;
 }
-// template <typename T, ssize_t Ndim> void NDArray<T, Ndim>::Print() {
-//     if (shape_[0] < 20 && shape_[1] < 20)
-//         Print_all();
-//     else
-//         Print_some();
-// }
 
 template <typename T, ssize_t Ndim>
 std::ostream &operator<<(std::ostream &os, const NDArray<T, Ndim> &arr) {
@@ -437,4 +448,23 @@ NDArray<T, Ndim> load(const std::string &pathname,
     return img;
 }
 
+template <typename RT, typename NT, typename DT, ssize_t Ndim>
+NDArray<RT, Ndim> safe_divide(const NDArray<NT, Ndim> &numerator,
+                              const NDArray<DT, Ndim> &denominator) {
+    if (numerator.shape() != denominator.shape()) {
+        throw std::runtime_error(
+            "Shapes of numerator and denominator must match");
+    }
+    NDArray<RT, Ndim> result(numerator.shape());
+    for (ssize_t i = 0; i < numerator.size(); ++i) {
+        if (denominator[i] != 0) {
+            result[i] =
+                static_cast<RT>(numerator[i]) / static_cast<RT>(denominator[i]);
+        } else {
+            result[i] = RT{0}; // or handle division by zero as needed
+        }
+    }
+    return result;
+}
+
 } // namespace aare

include/aare/NDView.hpp

@@ -26,6 +26,33 @@ Shape<Ndim> make_shape(const std::vector<size_t> &shape) {
     return arr;
 }
 
+
+/**
+ * @brief Helper function to drop the first dimension of a shape.
+ * This is useful when you want to create a 2D view from a 3D array.
+ * @param shape The shape to drop the first dimension from.
+ * @return A new shape with the first dimension dropped.
+ */
+template<size_t Ndim>
+Shape<Ndim-1> drop_first_dim(const Shape<Ndim> &shape) {
+    static_assert(Ndim > 1, "Cannot drop first dimension from a 1D shape");
+    Shape<Ndim - 1> new_shape;
+    std::copy(shape.begin() + 1, shape.end(), new_shape.begin());
+    return new_shape;
+}
+
+/**
+ * @brief Helper function when constructing NDArray/NDView. Calculates the number
+ * of elements in the resulting array from a shape.
+ * @param shape The shape to calculate the number of elements for.
+ * @return The number of elements in and NDArray/NDView of that shape.
+ */
+template <size_t Ndim>
+size_t num_elements(const Shape<Ndim> &shape) {
+    return std::accumulate(shape.begin(), shape.end(), 1,
+                           std::multiplies<size_t>());
+}
+
 template <ssize_t Dim = 0, typename Strides>
 ssize_t element_offset(const Strides & /*unused*/) {
     return 0;
@@ -66,17 +93,28 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
         : buffer_(buffer), strides_(c_strides<Ndim>(shape)), shape_(shape),
           size_(std::accumulate(std::begin(shape), std::end(shape), 1,
                                 std::multiplies<>())) {}
-
+                   
     template <typename... Ix>
     std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) {
         return buffer_[element_offset(strides_, index...)];
     }
 
     template <typename... Ix>
-    const std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) const {
+    std::enable_if_t<sizeof...(Ix) == 1 && (Ndim > 1), NDView<T, Ndim - 1>> operator()(Ix... index) {
+        // return a view of the next dimension
+        std::array<ssize_t, Ndim - 1> new_shape{};
+        std::copy_n(shape_.begin() + 1, Ndim - 1, new_shape.begin());
+        return NDView<T, Ndim - 1>(&buffer_[element_offset(strides_, index...)],
+                                   new_shape);
+        
+    }
+
+    template <typename... Ix>
+    std::enable_if_t<sizeof...(Ix) == Ndim, const T &> operator()(Ix... index) const {
         return buffer_[element_offset(strides_, index...)];
     }
 
+
     ssize_t size() const { return static_cast<ssize_t>(size_); }
     size_t total_bytes() const { return size_ * sizeof(T); }
     std::array<ssize_t, Ndim> strides() const noexcept { return strides_; }
@@ -85,9 +123,19 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
     T *end() { return buffer_ + size_; }
     T const *begin() const { return buffer_; }
     T const *end() const { return buffer_ + size_; }
-    T &operator()(ssize_t i)  { return buffer_[i]; }
+    
+    
+
+
+
+    /**
+     * @brief Access element at index i.
+     */
     T &operator[](ssize_t i)  { return buffer_[i]; }
-    const T &operator()(ssize_t i) const { return buffer_[i]; }
+
+    /**
+     * @brief Access element at index i.
+     */
     const T &operator[](ssize_t i) const { return buffer_[i]; }
 
     bool operator==(const NDView &other) const {
@@ -157,6 +205,22 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
     const T *data() const { return buffer_; }
     void print_all() const;
 
+    /**
+     * @brief Create a subview of a range of the first dimension. 
+     * This is useful for splitting a batches of frames in parallel processing.
+     * @param first The first index of the subview (inclusive).
+     * @param last The last index of the subview (exclusive).
+     * @return A new NDView that is a subview of the current view.
+     * @throws std::runtime_error if the range is invalid.
+     */
+    NDView sub_view(ssize_t first, ssize_t last) const {
+        if (first < 0 || last > shape_[0] || first >= last)
+            throw std::runtime_error(LOCATION + "Invalid sub_view range");
+        auto new_shape = shape_;
+        new_shape[0] = last - first;
+        return NDView(buffer_ + first * strides_[0], new_shape);
+    }
+
   private:
     T *buffer_{nullptr};
     std::array<ssize_t, Ndim> strides_{};

include/aare/VarClusterFinder.hpp

@@ -240,14 +240,14 @@ template <typename T> void VarClusterFinder<T>::first_pass() {
 
     for (ssize_t i = 0; i < original_.size(); ++i) {
         if (use_noise_map)
-            threshold_ = 5 * noiseMap(i);
-        binary_(i) = (original_(i) > threshold_);
+            threshold_ = 5 * noiseMap[i];
+        binary_[i] = (original_[i] > threshold_);
     }
 
     for (int i = 0; i < shape_[0]; ++i) {
         for (int j = 0; j < shape_[1]; ++j) {
 
-            // do we have someting to process?
+            // do we have something to process?
             if (binary_(i, j)) {
                 auto tmp = check_neighbours(i, j);
                 if (tmp != 0) {

include/aare/calibration.hpp

@@ -1,6 +1,9 @@
 #pragma once
 
+#include "aare/NDArray.hpp"
+#include "aare/NDView.hpp"
 #include "aare/defs.hpp"
+#include "aare/utils/par.hpp"
 #include "aare/utils/task.hpp"
 #include <cstdint>
 #include <future>
@@ -55,32 +58,152 @@ ALWAYS_INLINE std::pair<uint16_t, int16_t> get_value_and_gain(uint16_t raw) {
 
 template <class T>
 void apply_calibration_impl(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
-                       NDView<T, 3> ped, NDView<T, 3> cal, int start,
-                       int stop) {
+                            NDView<T, 3> ped, NDView<T, 3> cal, int start,
+                            int stop) {
 
     for (int frame_nr = start; frame_nr != stop; ++frame_nr) {
         for (int row = 0; row != raw_data.shape(1); ++row) {
             for (int col = 0; col != raw_data.shape(2); ++col) {
-                auto [value, gain] = get_value_and_gain(raw_data(frame_nr, row, col));
+                auto [value, gain] =
+                    get_value_and_gain(raw_data(frame_nr, row, col));
+
+                // Using multiplication does not seem to speed up the code here
+                // ADU/keV is the standard unit for the calibration which
+                // means rewriting the formula is not worth it.
                 res(frame_nr, row, col) =
-                    (value - ped(gain, row, col)) / cal(gain, row, col); //TODO! use multiplication
+                    (value - ped(gain, row, col)) / cal(gain, row, col);
             }
         }
     }
 }
 
 template <class T>
+void apply_calibration_impl(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
+                            NDView<T, 2> ped, NDView<T, 2> cal, int start,
+                            int stop) {
+
+    for (int frame_nr = start; frame_nr != stop; ++frame_nr) {
+        for (int row = 0; row != raw_data.shape(1); ++row) {
+            for (int col = 0; col != raw_data.shape(2); ++col) {
+                auto [value, gain] =
+                    get_value_and_gain(raw_data(frame_nr, row, col));
+
+                // Using multiplication does not seem to speed up the code here
+                // ADU/keV is the standard unit for the calibration which
+                // means rewriting the formula is not worth it.
+
+                // Set the value to 0 if the gain is not 0
+                if (gain == 0)
+                    res(frame_nr, row, col) =
+                        (value - ped(row, col)) / cal(row, col);
+                else
+                    res(frame_nr, row, col) = 0;
+            }
+        }
+    }
+}
+
+template <class T, ssize_t Ndim = 3>
 void apply_calibration(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
-                       NDView<T, 3> ped, NDView<T, 3> cal,
+                       NDView<T, Ndim> ped, NDView<T, Ndim> cal,
                        ssize_t n_threads = 4) {
     std::vector<std::future<void>> futures;
     futures.reserve(n_threads);
     auto limits = split_task(0, raw_data.shape(0), n_threads);
     for (const auto &lim : limits)
-        futures.push_back(std::async(&apply_calibration_impl<T>, res, raw_data, ped, cal,
-                                     lim.first, lim.second));
+        futures.push_back(std::async(
+            static_cast<void (*)(NDView<T, 3>, NDView<uint16_t, 3>,
+                                 NDView<T, Ndim>, NDView<T, Ndim>, int, int)>(
+                apply_calibration_impl),
+            res, raw_data, ped, cal, lim.first, lim.second));
     for (auto &f : futures)
         f.get();
 }
 
+template <bool only_gain0>
+std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>>
+sum_and_count_per_gain(NDView<uint16_t, 3> raw_data) {
+    constexpr ssize_t num_gains = only_gain0 ? 1 : 3;
+    NDArray<size_t, 3> accumulator(
+        std::array<ssize_t, 3>{num_gains, raw_data.shape(1), raw_data.shape(2)},
+        0);
+    NDArray<size_t, 3> count(
+        std::array<ssize_t, 3>{num_gains, raw_data.shape(1), raw_data.shape(2)},
+        0);
+    for (int frame_nr = 0; frame_nr != raw_data.shape(0); ++frame_nr) {
+        for (int row = 0; row != raw_data.shape(1); ++row) {
+            for (int col = 0; col != raw_data.shape(2); ++col) {
+                auto [value, gain] =
+                    get_value_and_gain(raw_data(frame_nr, row, col));
+                if (gain != 0 && only_gain0)
+                    continue;
+                accumulator(gain, row, col) += value;
+                count(gain, row, col) += 1;
+            }
+        }
+    }
+
+    return {std::move(accumulator), std::move(count)};
+}
+
+template <typename T, bool only_gain0 = false>
+NDArray<T, 3 - static_cast<ssize_t>(only_gain0)>
+calculate_pedestal(NDView<uint16_t, 3> raw_data, ssize_t n_threads) {
+
+    constexpr ssize_t num_gains = only_gain0 ? 1 : 3;
+    std::vector<std::future<std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>>>>
+        futures;
+    futures.reserve(n_threads);
+
+    auto subviews = make_subviews(raw_data, n_threads);
+
+    for (auto view : subviews) {
+        futures.push_back(std::async(
+            static_cast<std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>> (*)(
+                NDView<uint16_t, 3>)>(&sum_and_count_per_gain<only_gain0>),
+            view));
+    }
+    Shape<3> shape{num_gains, raw_data.shape(1), raw_data.shape(2)};
+    NDArray<size_t, 3> accumulator(shape, 0);
+    NDArray<size_t, 3> count(shape, 0);
+
+    // Combine the results from the futures
+    for (auto &f : futures) {
+        auto [acc, cnt] = f.get();
+        accumulator += acc;
+        count += cnt;
+    }
+
+
+    // Will move to a NDArray<T, 3 - static_cast<ssize_t>(only_gain0)>
+    // if only_gain0 is true
+    return safe_divide<T>(accumulator, count);
+
+}
+
+/**
+ * @brief Count the number of switching pixels in the raw data.
+ * This function counts the number of pixels that switch between G1 and G2 gain.
+ * It returns an NDArray with the number of switching pixels per pixel.
+ * @param raw_data The NDView containing the raw data
+ * @return An NDArray with the number of switching pixels per pixel
+ */
+NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data);
+
+/**
+ * @brief Count the number of switching pixels in the raw data.
+ * This function counts the number of pixels that switch between G1 and G2 gain.
+ * It returns an NDArray with the number of switching pixels per pixel.
+ * @param raw_data The NDView containing the raw data
+ * @param n_threads The number of threads to use for parallel processing
+ * @return An NDArray with the number of switching pixels per pixel
+ */
+NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data,
+                                       ssize_t n_threads);
+
+template <typename T>
+auto calculate_pedestal_g0(NDView<uint16_t, 3> raw_data, ssize_t n_threads) {
+    return calculate_pedestal<T, true>(raw_data, n_threads);
+}
+
 } // namespace aare

include/aare/utils/par.hpp

@@ -1,7 +1,10 @@
+#pragma once
 #include <thread>
 #include <utility>
 #include <vector>
 
+#include "aare/utils/task.hpp"
+
 namespace aare {
 
 template <typename F>
@@ -15,4 +18,17 @@ void RunInParallel(F func, const std::vector<std::pair<int, int>> &tasks) {
         thread.join();
     }
 }
+
+
+template <typename T>
+std::vector<NDView<T,3>> make_subviews(NDView<T, 3> &data, ssize_t n_threads) {
+    std::vector<NDView<T, 3>> subviews;
+    subviews.reserve(n_threads);
+    auto limits = split_task(0, data.shape(0), n_threads);
+    for (const auto &lim : limits) {
+        subviews.push_back(data.sub_view(lim.first, lim.second));
+    }
+    return subviews;
+}
+
 } // namespace aare

include/aare/utils/task.hpp

@@ -1,4 +1,4 @@
-
+#pragma once
 #include <utility>
 #include <vector>
 

python/aare/ClusterFinder.py

@@ -26,24 +26,24 @@ def _get_class(name, cluster_size, dtype):
 
 
 
-def ClusterFinder(image_size, cluster_size, n_sigma=5, dtype = np.int32, capacity = 1024):
+def ClusterFinder(image_size, saved_cluster_size, checked_cluster_size, n_sigma=5, dtype = np.int32, capacity = 1024, chunk_size=50000, n_chunks = 10):
     """
     Factory function to create a ClusterFinder object. Provides a cleaner syntax for 
     the templated ClusterFinder in C++.
     """
-    cls = _get_class("ClusterFinder", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity)
+    cls = _get_class("ClusterFinder", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, chunk_size=chunk_size, n_chunks=n_chunks, cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 
-def ClusterFinderMT(image_size, cluster_size = (3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3): 
+def ClusterFinderMT(image_size, saved_cluster_size = (3,3), checked_cluster_size = (3,3), dtype=np.int32, n_sigma=5, capacity = 1024, n_threads = 3, chunk_size=50000, n_chunks = 10): 
     """ 
     Factory function to create a ClusterFinderMT object. Provides a cleaner syntax for 
     the templated ClusterFinderMT in C++.
     """
 
-    cls = _get_class("ClusterFinderMT", cluster_size, dtype)
-    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads)
+    cls = _get_class("ClusterFinderMT", saved_cluster_size, dtype)
+    return cls(image_size, n_sigma=n_sigma, capacity=capacity, n_threads=n_threads, chunk_size=chunk_size, n_chunks=n_chunks,  cluster_size_x=checked_cluster_size[0], cluster_size_y=checked_cluster_size[1])
 
 
 

python/aare/__init__.py

@@ -17,7 +17,7 @@ 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 reduce_to_2x2, reduce_to_3x3
+
 
 from ._aare import apply_custom_weights
 
@@ -32,6 +32,7 @@ from .utils import random_pixels, random_pixel, flat_list, add_colorbar
 from .func import *
 
 from .calibration import *
-from ._aare import apply_calibration
+from ._aare import apply_calibration, count_switching_pixels
+from ._aare import calculate_pedestal, calculate_pedestal_float, calculate_pedestal_g0, calculate_pedestal_g0_float
 
 from ._aare import VarClusterFinder

python/src/bind_Cluster.hpp

@@ -24,8 +24,7 @@ void define_Cluster(py::module &m, const std::string &typestr) {
     py::class_<Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>>(
         m, class_name.c_str(), py::buffer_protocol())
 
-        .def(py::init([](uint8_t x, uint8_t y,
-                         py::array_t<Type, py::array::forcecast> data) {
+        .def(py::init([](uint8_t x, uint8_t y, py::array_t<Type> data) {
             py::buffer_info buf_info = data.request();
             Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType> cluster;
             cluster.x = x;
@@ -35,58 +34,31 @@ void define_Cluster(py::module &m, const std::string &typestr) {
                 cluster.data[i] = r(i);
             }
             return cluster;
-        }))
+        }));
 
-        // TODO! Review if to keep or not
-        .def_property_readonly(
-            "data",
-            [](Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType> &c)
-                -> py::array {
-                return py::array(py::buffer_info(
-                    c.data.data(), sizeof(Type),
-                    py::format_descriptor<Type>::format(), // Type
-                                                           // format
-                    2, // Number of dimensions
-                    {static_cast<ssize_t>(ClusterSizeX),
-                     static_cast<ssize_t>(ClusterSizeY)}, // Shape (flattened)
-                    {sizeof(Type) * ClusterSizeY, sizeof(Type)}
-                    // Stride (step size between elements)
-                    ));
-            })
-
-        .def_readonly("x",
-                      &Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>::x)
-
-        .def_readonly("y",
-                      &Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>::y);
-}
-
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-void reduce_to_3x3(py::module &m) {
-
-    m.def(
-        "reduce_to_3x3",
-        [](const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-            return reduce_to_3x3(cl);
+    /*
+    //TODO! Review if to keep or not
+    .def_property(
+        "data",
+        [](ClusterType &c) -> py::array {
+            return py::array(py::buffer_info(
+                c.data, sizeof(Type),
+                py::format_descriptor<Type>::format(), // Type
+                                                       // format
+                1, // Number of dimensions
+                {static_cast<ssize_t>(ClusterSizeX *
+                                      ClusterSizeY)}, // Shape (flattened)
+                {sizeof(Type)} // Stride (step size between elements)
+                ));
         },
-        py::return_value_policy::move,
-        "Reduce cluster to 3x3 subcluster by taking the 3x3 subcluster with "
-        "the highest photon energy.");
-}
+        [](ClusterType &c, py::array_t<Type> arr) {
+            py::buffer_info buf_info = arr.request();
+            Type *ptr = static_cast<Type *>(buf_info.ptr);
+            std::copy(ptr, ptr + ClusterSizeX * ClusterSizeY,
+                      c.data); // TODO dont iterate over centers!!!
 
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-void reduce_to_2x2(py::module &m) {
-
-    m.def(
-        "reduce_to_2x2",
-        [](const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-            return reduce_to_2x2(cl);
-        },
-        py::return_value_policy::move,
-        "Reduce cluster to 2x2 subcluster by taking the 2x2 subcluster with "
-        "the highest photon energy.");
+        });
+    */
 }
 
 #pragma GCC diagnostic pop

python/src/bind_ClusterFinder.hpp

@@ -30,14 +30,30 @@ void define_ClusterFinder(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinder<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t>(), py::arg("image_size"),
-             py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000)
+        .def(py::init<Shape<2>, pd_type, size_t, uint32_t, uint32_t, uint32_t, uint32_t>(),
+             py::arg("image_size"), py::arg("n_sigma") = 5.0, py::arg("capacity") = 1'000'000,
+             py::arg("chunk_size") = 50'000, py::arg("n_chunks") = 10,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {
                  auto view = make_view_2d(frame);
                  self.push_pedestal_frame(view);
              })
+
+        .def("push_pedestal_mean",
+             [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
+                py::array_t<double> frame, uint32_t chunk_number) {            
+                 auto view = make_view_2d(frame);             
+                 self.push_pedestal_mean(view, chunk_number);
+             })
+        .def("push_pedestal_std",
+             [](ClusterFinder<ClusterType, uint16_t, pd_type> &self,
+                py::array_t<double> frame, uint32_t chunk_number) {
+                 auto view = make_view_2d(frame);
+                 self.push_pedestal_std(view, chunk_number);
+             })
+
         .def("clear_pedestal",
              &ClusterFinder<ClusterType, uint16_t, pd_type>::clear_pedestal)
         .def_property_readonly(

python/src/bind_ClusterFinderMT.hpp

@@ -30,15 +30,31 @@ void define_ClusterFinderMT(py::module &m, const std::string &typestr) {
 
     py::class_<ClusterFinderMT<ClusterType, uint16_t, pd_type>>(
         m, class_name.c_str())
-        .def(py::init<Shape<2>, pd_type, size_t, size_t>(),
+        .def(py::init<Shape<2>, pd_type, size_t, size_t, uint32_t, uint32_t, uint32_t, uint32_t>(),
              py::arg("image_size"), py::arg("n_sigma") = 5.0,
-             py::arg("capacity") = 2048, py::arg("n_threads") = 3)
+             py::arg("capacity") = 2048, py::arg("n_threads") = 3,
+             py::arg("chunk_size") = 50'000, py::arg("n_chunks") = 10,
+             py::arg("cluster_size_x") = 3, py::arg("cluster_size_y") = 3)
         .def("push_pedestal_frame",
              [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
                 py::array_t<uint16_t> frame) {
                  auto view = make_view_2d(frame);
                  self.push_pedestal_frame(view);
              })
+
+        .def("push_pedestal_mean",
+             [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
+                py::array_t<double> frame, uint32_t chunk_number) {
+                 auto view = make_view_2d(frame);                 
+                 self.push_pedestal_mean(view, chunk_number);
+             })
+        .def("push_pedestal_std",
+             [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,
+                py::array_t<double> frame, uint32_t chunk_number) {
+                 auto view = make_view_2d(frame);
+                 self.push_pedestal_std(view, chunk_number);
+             })
+
         .def(
             "find_clusters",
             [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self,

python/src/bind_ClusterVector.hpp

@@ -104,47 +104,4 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
           });
 }
 
-template <typename Type, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-void define_2x2_reduction(py::module &m) {
-    m.def(
-        "reduce_to_2x2",
-        [](const ClusterVector<
-            Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>> &cv) {
-            return new ClusterVector<Cluster<Type, 2, 2, CoordType>>(
-                reduce_to_2x2(cv));
-        },
-        R"(
-        
-        Reduce cluster to 2x2 subcluster by taking the 2x2 subcluster with 
-        the highest photon energy."
-        Parameters
-        ----------
-        cv : ClusterVector   
-        )",
-        py::arg("clustervector"));
-}
-
-template <typename Type, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-void define_3x3_reduction(py::module &m) {
-
-    m.def(
-        "reduce_to_3x3",
-        [](const ClusterVector<
-            Cluster<Type, ClusterSizeX, ClusterSizeY, CoordType>> &cv) {
-            return new ClusterVector<Cluster<Type, 3, 3, CoordType>>(
-                reduce_to_3x3(cv));
-        },
-        R"(
-        
-        Reduce cluster to 3x3 subcluster by taking the 3x3 subcluster with 
-        the highest photon energy."
-        Parameters
-        ----------
-        cv : ClusterVector   
-        )",
-        py::arg("clustervector"));
-}
-
 #pragma GCC diagnostic pop

python/src/bind_calibration.hpp

@@ -17,27 +17,137 @@ py::array_t<DataType> pybind_apply_calibration(
         calibration,
     int n_threads = 4) {
 
-    auto data_span = make_view_3d(data);
-    auto ped = make_view_3d(pedestal);
-    auto cal = make_view_3d(calibration);
-
+    auto data_span = make_view_3d(data); // data is always 3D
     /* No pointer is passed, so NumPy will allocate the buffer */
     auto result = py::array_t<DataType>(data_span.shape());
     auto res = make_view_3d(result);
-
-    aare::apply_calibration<DataType>(res, data_span, ped, cal, n_threads);
-
+    if (data.ndim() == 3 && pedestal.ndim() == 3 && calibration.ndim() == 3) {
+        auto ped = make_view_3d(pedestal);
+        auto cal = make_view_3d(calibration);
+        aare::apply_calibration<DataType, 3>(res, data_span, ped, cal,
+                                             n_threads);
+    } else if (data.ndim() == 3 && pedestal.ndim() == 2 &&
+               calibration.ndim() == 2) {
+        auto ped = make_view_2d(pedestal);
+        auto cal = make_view_2d(calibration);
+        aare::apply_calibration<DataType, 2>(res, data_span, ped, cal,
+                                             n_threads);
+    } else {
+        throw std::runtime_error(
+            "Invalid number of dimensions for data, pedestal or calibration");
+    }
     return result;
 }
 
+py::array_t<int> pybind_count_switching_pixels(
+    py::array_t<uint16_t, py::array::c_style | py::array::forcecast> data,
+    ssize_t n_threads = 4) {
+
+    auto data_span = make_view_3d(data);
+    auto arr = new NDArray<int, 2>{};
+    *arr = aare::count_switching_pixels(data_span, n_threads);
+    return return_image_data(arr);
+}
+
+template <typename T>
+py::array_t<T> pybind_calculate_pedestal(
+    py::array_t<uint16_t, py::array::c_style | py::array::forcecast> data,
+    ssize_t n_threads) {
+
+    auto data_span = make_view_3d(data);
+    auto arr = new NDArray<T, 3>{};
+    *arr = aare::calculate_pedestal<T, false>(data_span, n_threads);
+    return return_image_data(arr);
+}
+
+template <typename T>
+py::array_t<T> pybind_calculate_pedestal_g0(
+    py::array_t<uint16_t, py::array::c_style | py::array::forcecast> data,
+    ssize_t n_threads) {
+
+    auto data_span = make_view_3d(data);
+    auto arr = new NDArray<T, 2>{};
+    *arr = aare::calculate_pedestal<T, true>(data_span, n_threads);
+    return return_image_data(arr);
+}
+
 void bind_calibration(py::module &m) {
+    m.def("apply_calibration", &pybind_apply_calibration<double>,
+          py::arg("raw_data").noconvert(), py::kw_only(),
+          py::arg("pd").noconvert(), py::arg("cal").noconvert(),
+          py::arg("n_threads") = 4);
+
     m.def("apply_calibration", &pybind_apply_calibration<float>,
           py::arg("raw_data").noconvert(), py::kw_only(),
           py::arg("pd").noconvert(), py::arg("cal").noconvert(),
           py::arg("n_threads") = 4);
 
-    m.def("apply_calibration", &pybind_apply_calibration<double>,
+    m.def("count_switching_pixels", &pybind_count_switching_pixels,
+          R"(
+        Count the number of time each pixel switches to G1 or G2.
+
+        Parameters
+        ----------
+        raw_data : array_like
+            3D array of shape (frames, rows, cols) to count the switching pixels from.
+        n_threads : int 
+            The number of threads to use for the calculation.
+        )",
           py::arg("raw_data").noconvert(), py::kw_only(),
-          py::arg("pd").noconvert(), py::arg("cal").noconvert(),
           py::arg("n_threads") = 4);
+
+    m.def("calculate_pedestal", &pybind_calculate_pedestal<double>,
+          R"(
+        Calculate the pedestal for all three gains and return the result as a 3D array of doubles.
+
+        Parameters
+        ----------
+        raw_data : array_like
+            3D array of shape (frames, rows, cols) to calculate the pedestal from.
+            Needs to contain data for all three gains (G0, G1, G2).
+        n_threads : int 
+            The number of threads to use for the calculation.
+        )",
+          py::arg("raw_data").noconvert(), py::arg("n_threads") = 4);
+
+    m.def("calculate_pedestal_float", &pybind_calculate_pedestal<float>,
+          R"(
+        Same as `calculate_pedestal` but returns a 3D array of floats.
+
+        Parameters
+        ----------
+        raw_data : array_like
+            3D array of shape (frames, rows, cols) to calculate the pedestal from.
+            Needs to contain data for all three gains (G0, G1, G2).
+        n_threads : int 
+            The number of threads to use for the calculation.
+        )",
+          py::arg("raw_data").noconvert(), py::arg("n_threads") = 4);
+
+    m.def("calculate_pedestal_g0", &pybind_calculate_pedestal_g0<double>,
+          R"(
+        Calculate the pedestal for G0 and return the result as a 2D array of doubles.
+        Pixels in G1 and G2 are ignored.
+
+        Parameters
+        ----------
+        raw_data : array_like
+            3D array of shape (frames, rows, cols) to calculate the pedestal from.
+        n_threads : int 
+            The number of threads to use for the calculation.
+        )",
+          py::arg("raw_data").noconvert(), py::arg("n_threads") = 4);
+
+    m.def("calculate_pedestal_g0_float", &pybind_calculate_pedestal_g0<float>,
+          R"(
+        Same as `calculate_pedestal_g0` but returns a 2D array of floats.
+
+        Parameters
+        ----------
+        raw_data : array_like
+            3D array of shape (frames, rows, cols) to calculate the pedestal from.
+        n_threads : int 
+            The number of threads to use for the calculation.
+        )",
+          py::arg("raw_data").noconvert(), py::arg("n_threads") = 4);
 }

python/src/module.cpp

@@ -47,9 +47,7 @@ double, 'f' for float)
     define_ClusterFileSink<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);     \
     define_ClusterCollector<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);    \
     define_Cluster<T, N, M, U>(m, #N "x" #M #TYPE_CODE);                       \
-    register_calculate_eta<T, N, M, U>(m);                                     \
-    define_2x2_reduction<T, N, M, U>(m);                                       \
-    reduce_to_2x2<T, N, M, U>(m);
+    register_calculate_eta<T, N, M, U>(m);
 
 PYBIND11_MODULE(_aare, m) {
     define_file_io_bindings(m);
@@ -86,30 +84,4 @@ PYBIND11_MODULE(_aare, m) {
     DEFINE_CLUSTER_BINDINGS(int, 9, 9, uint16_t, i);
     DEFINE_CLUSTER_BINDINGS(double, 9, 9, uint16_t, d);
     DEFINE_CLUSTER_BINDINGS(float, 9, 9, uint16_t, f);
-
-    define_3x3_reduction<int, 3, 3, uint16_t>(m);
-    define_3x3_reduction<double, 3, 3, uint16_t>(m);
-    define_3x3_reduction<float, 3, 3, uint16_t>(m);
-    define_3x3_reduction<int, 5, 5, uint16_t>(m);
-    define_3x3_reduction<double, 5, 5, uint16_t>(m);
-    define_3x3_reduction<float, 5, 5, uint16_t>(m);
-    define_3x3_reduction<int, 7, 7, uint16_t>(m);
-    define_3x3_reduction<double, 7, 7, uint16_t>(m);
-    define_3x3_reduction<float, 7, 7, uint16_t>(m);
-    define_3x3_reduction<int, 9, 9, uint16_t>(m);
-    define_3x3_reduction<double, 9, 9, uint16_t>(m);
-    define_3x3_reduction<float, 9, 9, uint16_t>(m);
-
-    reduce_to_3x3<int, 3, 3, uint16_t>(m);
-    reduce_to_3x3<double, 3, 3, uint16_t>(m);
-    reduce_to_3x3<float, 3, 3, uint16_t>(m);
-    reduce_to_3x3<int, 5, 5, uint16_t>(m);
-    reduce_to_3x3<double, 5, 5, uint16_t>(m);
-    reduce_to_3x3<float, 5, 5, uint16_t>(m);
-    reduce_to_3x3<int, 7, 7, uint16_t>(m);
-    reduce_to_3x3<double, 7, 7, uint16_t>(m);
-    reduce_to_3x3<float, 7, 7, uint16_t>(m);
-    reduce_to_3x3<int, 9, 9, uint16_t>(m);
-    reduce_to_3x3<double, 9, 9, uint16_t>(m);
-    reduce_to_3x3<float, 9, 9, uint16_t>(m);
 }

python/tests/test_Cluster.py

@@ -101,27 +101,6 @@ def test_cluster_finder():
     assert clusters.size == 0
 
 
-def test_2x2_reduction(): 
-    """Test 2x2 Reduction"""
-    cluster = _aare.Cluster3x3i(5,5,np.array([1, 1, 1, 2, 3, 1, 2, 2, 1], dtype=np.int32))
-
-    reduced_cluster = _aare.reduce_to_2x2(cluster) 
-
-    assert reduced_cluster.x == 4
-    assert reduced_cluster.y == 5
-    assert (reduced_cluster.data == np.array([[2, 3], [2, 2]], dtype=np.int32)).all()
-    
-    
-def test_3x3_reduction(): 
-    """Test 3x3 Reduction"""
-    cluster = _aare.Cluster5x5d(5,5,np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 2.0, 2.0, 3.0,
-                                   1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], dtype=np.double))
-
-    reduced_cluster = _aare.reduce_to_3x3(cluster) 
-
-    assert reduced_cluster.x == 4
-    assert reduced_cluster.y == 5
-    assert (reduced_cluster.data == np.array([[1.0, 2.0, 1.0], [2.0, 2.0, 3.0], [1.0, 2.0, 1.0]], dtype=np.double)).all()
 
 
 

python/tests/test_ClusterVector.py

@@ -5,7 +5,7 @@ import time
 from pathlib import Path
 import pickle
 
-from aare import ClusterFile, ClusterVector
+from aare import ClusterFile
 from aare import _aare
 from conftest import test_data_path
 
@@ -51,36 +51,4 @@ def test_make_a_hitmap_from_cluster_vector():
     # print(img)
     # print(ref)
     assert (img == ref).all()
-
-
-def test_2x2_reduction(): 
-    cv = ClusterVector((3,3))
-
-    cv.push_back(_aare.Cluster3x3i(5, 5, np.array([1, 1, 1, 2, 3, 1, 2, 2, 1], dtype=np.int32)))
-    cv.push_back(_aare.Cluster3x3i(5, 5, np.array([2, 2, 1, 2, 3, 1, 1, 1, 1], dtype=np.int32)))
-
-    reduced_cv = np.array(_aare.reduce_to_2x2(cv), copy=False) 
-
-    assert reduced_cv.size == 2
-    assert reduced_cv[0]["x"] == 4
-    assert reduced_cv[0]["y"] == 5
-    assert (reduced_cv[0]["data"] == np.array([[2, 3], [2, 2]], dtype=np.int32)).all()
-    assert reduced_cv[1]["x"] == 4
-    assert reduced_cv[1]["y"] == 6
-    assert (reduced_cv[1]["data"] == np.array([[2, 2], [2, 3]], dtype=np.int32)).all()
-    
-    
-def test_3x3_reduction(): 
-    cv = _aare.ClusterVector_Cluster5x5d()
-    
-    cv.push_back(_aare.Cluster5x5d(5,5,np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 2.0, 2.0, 3.0,
-                                   1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], dtype=np.double)))
-    cv.push_back(_aare.Cluster5x5d(5,5,np.array([1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 2.0, 2.0, 3.0,
-                                   1.0, 1.0, 1.0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], dtype=np.double)))
-    
-    reduced_cv = np.array(_aare.reduce_to_3x3(cv), copy=False)  
-
-    assert reduced_cv.size == 2
-    assert reduced_cv[0]["x"] == 4
-    assert reduced_cv[0]["y"] == 5
-    assert (reduced_cv[0]["data"] == np.array([[1.0, 2.0, 1.0], [2.0, 2.0, 3.0], [1.0, 2.0, 1.0]], dtype=np.double)).all()
+    

python/tests/test_calibration.py

@@ -1,6 +1,7 @@
 import pytest 
 import numpy as np
-from aare import apply_calibration
+
+import aare
 
 def test_apply_calibration_small_data():
     # The raw data consists of 10 4x5 images
@@ -27,7 +28,7 @@ def test_apply_calibration_small_data():
 
     
 
-    data = apply_calibration(raw, pd = pedestal, cal = calibration)
+    data = aare.apply_calibration(raw, pd = pedestal, cal = calibration)
 
 
     # The formula that is applied is:
@@ -41,3 +42,94 @@ def test_apply_calibration_small_data():
     assert data[2,2,2] == 0
     assert data[0,1,1] == 0
     assert data[1,3,0] == 0
+
+
+@pytest.fixture
+def raw_data_3x2x2():
+    raw = np.zeros((3, 2, 2), dtype=np.uint16)
+    raw[0, 0, 0] = 100
+    raw[1,0, 0] =  200
+    raw[2, 0, 0] = 300
+
+    raw[0, 0, 1] = (1<<14) + 100
+    raw[1, 0, 1] = (1<<14) + 200
+    raw[2, 0, 1] = (1<<14) + 300
+
+    raw[0, 1, 0] = (1<<14) + 37
+    raw[1, 1, 0] =  38
+    raw[2, 1, 0] = (3<<14) + 39
+
+    raw[0, 1, 1] = (3<<14) + 100
+    raw[1, 1, 1] = (3<<14) + 200
+    raw[2, 1, 1] = (3<<14) + 300
+    return raw
+
+def test_calculate_pedestal(raw_data_3x2x2):
+    # Calculate the pedestal
+    pd = aare.calculate_pedestal(raw_data_3x2x2)
+    assert pd.shape == (3, 2, 2)
+    assert pd.dtype == np.float64
+    assert pd[0, 0, 0] == 200
+    assert pd[1, 0, 0] == 0
+    assert pd[2, 0, 0] == 0
+
+    assert pd[0, 0, 1] == 0
+    assert pd[1, 0, 1] == 200
+    assert pd[2, 0, 1] == 0
+
+    assert pd[0, 1, 0] == 38
+    assert pd[1, 1, 0] == 37
+    assert pd[2, 1, 0] == 39
+
+    assert pd[0, 1, 1] == 0
+    assert pd[1, 1, 1] == 0
+    assert pd[2, 1, 1] == 200
+
+def test_calculate_pedestal_float(raw_data_3x2x2):
+    #results should be the same for float
+    pd2 = aare.calculate_pedestal_float(raw_data_3x2x2)
+    assert pd2.shape == (3, 2, 2)
+    assert pd2.dtype == np.float32
+    assert pd2[0, 0, 0] == 200
+    assert pd2[1, 0, 0] == 0
+    assert pd2[2, 0, 0] == 0
+
+    assert pd2[0, 0, 1] == 0
+    assert pd2[1, 0, 1] == 200
+    assert pd2[2, 0, 1] == 0
+
+    assert pd2[0, 1, 0] == 38
+    assert pd2[1, 1, 0] == 37
+    assert pd2[2, 1, 0] == 39
+
+    assert pd2[0, 1, 1] == 0
+    assert pd2[1, 1, 1] == 0
+    assert pd2[2, 1, 1] == 200
+
+def test_calculate_pedestal_g0(raw_data_3x2x2):
+    pd = aare.calculate_pedestal_g0(raw_data_3x2x2)
+    assert pd.shape == (2, 2)
+    assert pd.dtype == np.float64
+    assert pd[0, 0] == 200
+    assert pd[1, 0] == 38
+    assert pd[0, 1] == 0
+    assert pd[1, 1] == 0
+
+def test_calculate_pedestal_g0_float(raw_data_3x2x2):
+    pd = aare.calculate_pedestal_g0_float(raw_data_3x2x2)
+    assert pd.shape == (2, 2)
+    assert pd.dtype == np.float32
+    assert pd[0, 0] == 200
+    assert pd[1, 0] == 38
+    assert pd[0, 1] == 0
+    assert pd[1, 1] == 0
+
+def test_count_switching_pixels(raw_data_3x2x2):
+    # Count the number of pixels that switched gain
+    count = aare.count_switching_pixels(raw_data_3x2x2)
+    assert count.shape == (2, 2)
+    assert count.sum() == 8
+    assert count[0, 0] == 0 
+    assert count[1, 0] == 2 
+    assert count[0, 1] == 3 
+    assert count[1, 1] == 3

src/Cluster.test.cpp

@@ -18,86 +18,4 @@ TEST_CASE("Test sum of Cluster", "[.cluster]") {
     Cluster<int, 2, 2> cluster{0, 0, {1, 2, 3, 4}};
 
     CHECK(cluster.sum() == 10);
-}
-
-using ClusterTypes = std::variant<Cluster<int, 2, 2>, Cluster<int, 3, 3>,
-                                  Cluster<int, 5, 5>, Cluster<int, 2, 3>>;
-
-using ClusterTypesLargerThan2x2 =
-    std::variant<Cluster<int, 3, 3>, Cluster<int, 4, 4>, Cluster<int, 5, 5>>;
-
-TEST_CASE("Test reduce to 2x2 Cluster", "[.cluster]") {
-    auto [cluster, expected_reduced_cluster] = GENERATE(
-        std::make_tuple(ClusterTypes{Cluster<int, 2, 2>{5, 5, {1, 2, 3, 4}}},
-                        Cluster<int, 2, 2>{4, 6, {1, 2, 3, 4}}),
-        std::make_tuple(
-            ClusterTypes{Cluster<int, 3, 3>{5, 5, {1, 1, 1, 1, 3, 2, 1, 2, 2}}},
-            Cluster<int, 2, 2>{5, 5, {3, 2, 2, 2}}),
-        std::make_tuple(
-            ClusterTypes{Cluster<int, 3, 3>{5, 5, {1, 1, 1, 2, 3, 1, 2, 2, 1}}},
-            Cluster<int, 2, 2>{4, 5, {2, 3, 2, 2}}),
-        std::make_tuple(
-            ClusterTypes{Cluster<int, 3, 3>{5, 5, {2, 2, 1, 2, 3, 1, 1, 1, 1}}},
-            Cluster<int, 2, 2>{4, 6, {2, 2, 2, 3}}),
-        std::make_tuple(
-            ClusterTypes{Cluster<int, 3, 3>{5, 5, {1, 2, 2, 1, 3, 2, 1, 1, 1}}},
-            Cluster<int, 2, 2>{5, 6, {2, 2, 3, 2}}),
-        std::make_tuple(ClusterTypes{Cluster<int, 5, 5>{
-                            5, 5, {1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3,
-                                   2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}}},
-                        Cluster<int, 2, 2>{5, 6, {2, 2, 3, 2}}),
-        std::make_tuple(ClusterTypes{Cluster<int, 5, 5>{
-                            5, 5, {1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 3,
-                                   1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}}},
-                        Cluster<int, 2, 2>{4, 6, {2, 2, 2, 3}}),
-        std::make_tuple(
-            ClusterTypes{Cluster<int, 2, 3>{5, 5, {2, 2, 3, 2, 1, 1}}},
-            Cluster<int, 2, 2>{4, 6, {2, 2, 3, 2}}));
-
-    auto reduced_cluster = std::visit(
-        [](const auto &clustertype) { return reduce_to_2x2(clustertype); },
-        cluster);
-
-    CHECK(reduced_cluster.x == expected_reduced_cluster.x);
-    CHECK(reduced_cluster.y == expected_reduced_cluster.y);
-    CHECK(std::equal(reduced_cluster.data.begin(),
-                     reduced_cluster.data.begin() + 4,
-                     expected_reduced_cluster.data.begin()));
-}
-
-TEST_CASE("Test reduce to 3x3 Cluster", "[.cluster]") {
-    auto [cluster, expected_reduced_cluster] = GENERATE(
-        std::make_tuple(ClusterTypesLargerThan2x2{Cluster<int, 3, 3>{
-                            5, 5, {1, 1, 1, 1, 3, 1, 1, 1, 1}}},
-                        Cluster<int, 3, 3>{5, 5, {1, 1, 1, 1, 3, 1, 1, 1, 1}}),
-        std::make_tuple(
-            ClusterTypesLargerThan2x2{Cluster<int, 4, 4>{
-                5, 5, {2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1}}},
-            Cluster<int, 3, 3>{4, 6, {2, 2, 1, 2, 2, 1, 1, 1, 3}}),
-        std::make_tuple(
-            ClusterTypesLargerThan2x2{Cluster<int, 4, 4>{
-                5, 5, {1, 1, 2, 2, 1, 1, 2, 2, 1, 1, 3, 1, 1, 1, 1, 1}}},
-            Cluster<int, 3, 3>{5, 6, {1, 2, 2, 1, 2, 2, 1, 3, 1}}),
-        std::make_tuple(
-            ClusterTypesLargerThan2x2{Cluster<int, 4, 4>{
-                5, 5, {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 2, 1, 1, 2, 2}}},
-            Cluster<int, 3, 3>{5, 5, {1, 1, 1, 1, 3, 2, 1, 2, 2}}),
-        std::make_tuple(
-            ClusterTypesLargerThan2x2{Cluster<int, 4, 4>{
-                5, 5, {1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 1, 2, 2, 1, 1}}},
-            Cluster<int, 3, 3>{4, 5, {1, 1, 1, 2, 2, 3, 2, 2, 1}}),
-        std::make_tuple(ClusterTypesLargerThan2x2{Cluster<int, 5, 5>{
-                            5, 5, {1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 3,
-                                   1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1}}},
-                        Cluster<int, 3, 3>{4, 5, {1, 2, 1, 2, 2, 3, 1, 2, 1}}));
-
-    auto reduced_cluster = std::visit(
-        [](const auto &clustertype) { return reduce_to_3x3(clustertype); },
-        cluster);
-
-    CHECK(reduced_cluster.x == expected_reduced_cluster.x);
-    CHECK(reduced_cluster.y == expected_reduced_cluster.y);
-    CHECK(std::equal(reduced_cluster.data.begin(),
-                     reduced_cluster.data.begin() + 9,
-                     expected_reduced_cluster.data.begin()));
 }

src/NDArray.test.cpp

@@ -25,13 +25,13 @@ TEST_CASE("Construct from an NDView") {
     REQUIRE(image.data() != view.data());
 
     for (uint32_t i = 0; i < image.size(); ++i) {
-        REQUIRE(image(i) == view(i));
+        REQUIRE(image[i] == view[i]);
     }
 
     // Changing the image doesn't change the view
     image = 43;
     for (uint32_t i = 0; i < image.size(); ++i) {
-        REQUIRE(image(i) != view(i));
+        REQUIRE(image[i] != view[i]);
     }
 }
 
@@ -427,4 +427,30 @@ TEST_CASE("Construct an NDArray from an std::array") {
     for (uint32_t i = 0; i < a.size(); ++i) {
         REQUIRE(a(i) == b[i]);
     }
-}
+}
+
+
+
+TEST_CASE("Move construct from an array with Ndim + 1") {
+    NDArray<int, 3> a({{1,2,2}}, 0);
+    a(0, 0, 0) = 1;
+    a(0, 0, 1) = 2;
+    a(0, 1, 0) = 3;
+    a(0, 1, 1) = 4;
+
+
+    NDArray<int, 2> b(std::move(a));
+    REQUIRE(b.shape() == Shape<2>{2,2});
+    REQUIRE(b.size() == 4);
+    REQUIRE(b(0, 0) == 1);
+    REQUIRE(b(0, 1) == 2);
+    REQUIRE(b(1, 0) == 3);
+    REQUIRE(b(1, 1) == 4);
+
+}
+
+TEST_CASE("Move construct from an array with Ndim + 1 throws on size mismatch") {
+    NDArray<int, 3> a({{2,2,2}}, 0);
+    REQUIRE_THROWS(NDArray<int, 2>(std::move(a)));
+}
+

src/calibration.cpp

@@ -0,0 +1,44 @@
+#include "aare/calibration.hpp"
+
+namespace aare {
+
+NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data) {
+    NDArray<int, 2> switched(
+        std::array<ssize_t, 2>{raw_data.shape(1), raw_data.shape(2)}, 0);
+    for (int frame_nr = 0; frame_nr != raw_data.shape(0); ++frame_nr) {
+        for (int row = 0; row != raw_data.shape(1); ++row) {
+            for (int col = 0; col != raw_data.shape(2); ++col) {
+                auto [value, gain] =
+                    get_value_and_gain(raw_data(frame_nr, row, col));
+                if (gain != 0) {
+                    switched(row, col) += 1;
+                }
+            }
+        }
+    }
+    return switched;
+}
+
+NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data,
+                                       ssize_t n_threads) {
+    NDArray<int, 2> switched(
+        std::array<ssize_t, 2>{raw_data.shape(1), raw_data.shape(2)}, 0);
+    std::vector<std::future<NDArray<int, 2>>> futures;
+    futures.reserve(n_threads);
+
+    auto subviews = make_subviews(raw_data, n_threads);
+
+    for (auto view : subviews) {
+        futures.push_back(
+            std::async(static_cast<NDArray<int, 2> (*)(NDView<uint16_t, 3>)>(
+                           &count_switching_pixels),
+                       view));
+    }
+
+    for (auto &f : futures) {
+        switched += f.get();
+    }
+    return switched;
+}
+
+} // namespace aare

src/calibration.test.cpp

@@ -0,0 +1,49 @@
+/************************************************
+ * @file test-Cluster.cpp
+ * @short test case for generic Cluster, ClusterVector, and calculate_eta2
+ ***********************************************/
+
+#include "aare/calibration.hpp"
+
+// #include "catch.hpp"
+#include <array>
+#include <catch2/catch_all.hpp>
+#include <catch2/catch_test_macros.hpp>
+
+using namespace aare;
+
+TEST_CASE("Test Pedestal Generation", "[.calibration]") {
+    NDArray<uint16_t, 3> raw(std::array<ssize_t, 3>{3, 2, 2}, 0);
+
+    // gain 0
+    raw(0, 0, 0) = 100;
+    raw(1, 0, 0) = 200;
+    raw(2, 0, 0) = 300;
+
+    // gain 1
+    raw(0, 0, 1) = (1 << 14) + 100;
+    raw(1, 0, 1) = (1 << 14) + 200;
+    raw(2, 0, 1) = (1 << 14) + 300;
+
+    raw(0, 1, 0) = (1 << 14) + 37;
+    raw(1, 1, 0) = 38;
+    raw(2, 1, 0) = (3 << 14) + 39;
+
+    // gain 2
+    raw(0, 1, 1) = (3 << 14) + 100;
+    raw(1, 1, 1) = (3 << 14) + 200;
+    raw(2, 1, 1) = (3 << 14) + 300;
+
+    auto pedestal = calculate_pedestal<double>(raw.view(), 4);
+
+    REQUIRE(pedestal.size() == raw.size());
+    CHECK(pedestal(0, 0, 0) == 200);
+    CHECK(pedestal(1, 0, 0) == 0);
+    CHECK(pedestal(1, 0, 1) == 200);
+
+    auto pedestal_gain0 = calculate_pedestal_g0<double>(raw.view(), 4);
+
+    REQUIRE(pedestal_gain0.size() == 4);
+    CHECK(pedestal_gain0(0, 0) == 200);
+    CHECK(pedestal_gain0(1, 0) == 38);
+}