No idea. Bug Fixes probably

CMakeLists.txt

@@ -388,7 +388,7 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
-) 
+)
 
 add_library(aare_core STATIC ${SourceFiles})
 target_include_directories(aare_core PUBLIC 
@@ -412,8 +412,6 @@ target_link_libraries(
 
 )
 
-set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON)
-
 if(AARE_TESTS)
     target_compile_definitions(aare_core PRIVATE AARE_TESTS)
 endif()
@@ -433,6 +431,10 @@ set_target_properties(aare_core PROPERTIES
     PUBLIC_HEADER "${PUBLICHEADERS}"
 )
 
+if (AARE_PYTHON_BINDINGS)
+    set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON)
+endif()
+
 if(AARE_TESTS)
     set(TestSources
             ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp
@@ -463,7 +465,6 @@ if(AARE_TESTS)
     target_sources(tests PRIVATE ${TestSources} )
 endif()
 
-
 if(AARE_MASTER_PROJECT)
     install(TARGETS aare_core aare_compiler_flags 
         EXPORT "${TARGETS_EXPORT_NAME}"
@@ -473,6 +474,7 @@ if(AARE_MASTER_PROJECT)
     )
 endif()
 
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_INSTALL_RPATH $ORIGIN)
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 

RELEASE.md

@@ -1,27 +1,16 @@
 # Release notes
 
-### 2025.10.1
 
-Bugfixes: 
-
-- File supports reading new master json file format (multiple ROI's not supported yet)
-
-### 2025.8.22
+### head
 
 Features:
 
 - Apply calibration works in G0 if passes a 2D calibration and pedestal
 - count pixels that switch
 - calculate pedestal (also g0 version)
-- NDArray::view() needs an lvalue to reduce issues with the view outliving the array
 
 
-Bugfixes:
-
-- Now using glibc 2.17 in conda builds (was using the host)
-- Fixed shifted pixels in clusters close to the edge of a frame
-
-### 2025.7.18
+### 2025.07.18
 
 Features:
 
@@ -35,7 +24,7 @@ Bugfixes:
 - Removed unused file: ClusterFile.cpp 
 
 
-### 2025.5.22
+### 2025.05.22
 
 Features:
 
@@ -48,6 +37,3 @@ Bugfixes:
 
 
 
-
-
-

VERSION

@@ -1 +1 @@
-2025.8.22
+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));
-    }
-}

conda-recipe/conda_build_config.yaml

@@ -3,14 +3,3 @@ python:
     - 3.12
     - 3.13
 
-c_compiler:
-  - gcc                        # [linux]
-
-c_stdlib:
-  - sysroot                    # [linux]
-
-cxx_compiler:
-  - gxx                        # [linux]
-
-c_stdlib_version:              # [linux]
-  - 2.17                       # [linux]

conda-recipe/meta.yaml

@@ -16,8 +16,6 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
-    - {{ stdlib("c") }}
     - {{ compiler('cxx') }}
     - cmake
     - ninja

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:

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;
@@ -135,16 +204,22 @@ 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                                
+                                // 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/Frame.hpp

@@ -105,7 +105,7 @@ class Frame {
      * @tparam T type of the pixels
      * @return NDView<T, 2>
      */
-    template <typename T> NDView<T, 2> view() & {
+    template <typename T> NDView<T, 2> view() {
         std::array<ssize_t, 2> shape = {static_cast<ssize_t>(m_rows),
                                         static_cast<ssize_t>(m_cols)};
         T *data = reinterpret_cast<T *>(m_data);

include/aare/NDView.hpp

@@ -93,12 +93,6 @@ 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<>())) {}
-
-    // stride-aware constructor
-    NDView(T* buffer, std::array<ssize_t, Ndim> shape, std::array<ssize_t, Ndim> strides)
-        : buffer_(buffer), shape_(shape), strides_(strides),
-          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) {

include/aare/RawMasterFile.hpp

@@ -42,16 +42,14 @@ class RawFileNameComponents {
 
 class ScanParameters {
     bool m_enabled = false;
-    DACIndex m_dac{};
+    std::string m_dac;
     int m_start = 0;
     int m_stop = 0;
     int m_step = 0;
-    int64_t m_settleTime = 0; // [ns]
+    // TODO! add settleTime, requires string to time conversion
 
   public:
     ScanParameters(const std::string &par);
-    ScanParameters(const bool enabled, const DACIndex dac, const int start,
-                   const int stop, const int step, const int64_t settleTime);
     ScanParameters() = default;
     ScanParameters(const ScanParameters &) = default;
     ScanParameters &operator=(const ScanParameters &) = default;
@@ -59,9 +57,8 @@ class ScanParameters {
     int start() const;
     int stop() const;
     int step() const;
-    DACIndex dac() const;
+    const std::string &dac() const;
     bool enabled() const;
-    int64_t settleTime() const;
     void increment_stop();
 };
 

include/aare/defs.hpp

@@ -215,122 +215,6 @@ enum class DetectorType {
     Unknown
 };
 
-/**
- * @brief Enum class to define the Digital to Analog converter
- * The values are the same as in slsDetectorPackage
- */
-enum DACIndex {
-    DAC_0,
-    DAC_1,
-    DAC_2,
-    DAC_3,
-    DAC_4,
-    DAC_5,
-    DAC_6,
-    DAC_7,
-    DAC_8,
-    DAC_9,
-    DAC_10,
-    DAC_11,
-    DAC_12,
-    DAC_13,
-    DAC_14,
-    DAC_15,
-    DAC_16,
-    DAC_17,
-    VSVP,
-    VTRIM,
-    VRPREAMP,
-    VRSHAPER,
-    VSVN,
-    VTGSTV,
-    VCMP_LL,
-    VCMP_LR,
-    VCAL,
-    VCMP_RL,
-    RXB_RB,
-    RXB_LB,
-    VCMP_RR,
-    VCP,
-    VCN,
-    VISHAPER,
-    VTHRESHOLD,
-    IO_DELAY,
-    VREF_DS,
-    VOUT_CM,
-    VIN_CM,
-    VREF_COMP,
-    VB_COMP,
-    VDD_PROT,
-    VIN_COM,
-    VREF_PRECH,
-    VB_PIXBUF,
-    VB_DS,
-    VREF_H_ADC,
-    VB_COMP_FE,
-    VB_COMP_ADC,
-    VCOM_CDS,
-    VREF_RSTORE,
-    VB_OPA_1ST,
-    VREF_COMP_FE,
-    VCOM_ADC1,
-    VREF_L_ADC,
-    VREF_CDS,
-    VB_CS,
-    VB_OPA_FD,
-    VCOM_ADC2,
-    VCASSH,
-    VTH2,
-    VRSHAPER_N,
-    VIPRE_OUT,
-    VTH3,
-    VTH1,
-    VICIN,
-    VCAS,
-    VCAL_N,
-    VIPRE,
-    VCAL_P,
-    VDCSH,
-    VBP_COLBUF,
-    VB_SDA,
-    VCASC_SFP,
-    VIPRE_CDS,
-    IBIAS_SFP,
-    ADC_VPP,
-    HIGH_VOLTAGE,
-    TEMPERATURE_ADC,
-    TEMPERATURE_FPGA,
-    TEMPERATURE_FPGAEXT,
-    TEMPERATURE_10GE,
-    TEMPERATURE_DCDC,
-    TEMPERATURE_SODL,
-    TEMPERATURE_SODR,
-    TEMPERATURE_FPGA2,
-    TEMPERATURE_FPGA3,
-    TRIMBIT_SCAN,
-    V_POWER_A = 100,
-    V_POWER_B = 101,
-    V_POWER_C = 102,
-    V_POWER_D = 103,
-    V_POWER_IO = 104,
-    V_POWER_CHIP = 105,
-    I_POWER_A = 106,
-    I_POWER_B = 107,
-    I_POWER_C = 108,
-    I_POWER_D = 109,
-    I_POWER_IO = 110,
-    V_LIMIT = 111,
-    SLOW_ADC0 = 1000,
-    SLOW_ADC1,
-    SLOW_ADC2,
-    SLOW_ADC3,
-    SLOW_ADC4,
-    SLOW_ADC5,
-    SLOW_ADC6,
-    SLOW_ADC7,
-    SLOW_ADC_TEMP
-};
-
 enum class TimingMode { Auto, Trigger };
 enum class FrameDiscardPolicy { NoDiscard, Discard, DiscardPartial };
 
@@ -347,15 +231,6 @@ template <> FrameDiscardPolicy StringTo(const std::string & /*mode*/);
 
 using DataTypeVariants = std::variant<uint16_t, uint32_t>;
 
-constexpr uint16_t ADC_MASK =
-    0x3FFF; // used to mask out the gain bits in Jungfrau
-
-/**
- * @brief Convert a string to a DACIndex
- * @param arg string representation of the dacIndex
- * @return DACIndex
- * @throw invalid argument error if the string does not match any DACIndex
- */
-template <> DACIndex StringTo(const std::string &arg);
+constexpr uint16_t ADC_MASK = 0x3FFF; // used to mask out the gain bits in Jungfrau
 
 } // namespace aare

python/aare/ClusterFinder.py

@@ -26,33 +26,34 @@ 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])
 
 
-def ClusterCollector(clusterfindermt, dtype=np.int32): 
+
+def ClusterCollector(clusterfindermt, cluster_size = (3,3), dtype=np.int32): 
     """ 
     Factory function to create a ClusterCollector object. Provides a cleaner syntax for 
     the templated ClusterCollector in C++.
     """
-    
-    cls = _get_class("ClusterCollector", clusterfindermt.cluster_size, dtype)
+
+    cls = _get_class("ClusterCollector", cluster_size, dtype)
     return cls(clusterfindermt)
 
 def ClusterFileSink(clusterfindermt, cluster_file, dtype=np.int32): 

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
 

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/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()
+    

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/ClusterFinderMT.test.cpp

@@ -57,7 +57,6 @@ class ClusterFinderMTWrapper
     size_t m_sink_size() const { return this->m_sink.sizeGuess(); }
 };
 
-
 TEST_CASE("multithreaded cluster finder", "[.with-data]") {
     auto fpath =
         test_data_path() / "raw/moench03/cu_half_speed_master_4.json";
@@ -82,8 +81,7 @@ TEST_CASE("multithreaded cluster finder", "[.with-data]") {
     CHECK(cf.m_input_queues_are_empty() == true);
 
     for (size_t i = 0; i < n_frames_pd; ++i) {
-        auto frame = file.read_frame();
-        cf.find_clusters(frame.view<uint16_t>());
+        cf.find_clusters(file.read_frame().view<uint16_t>());
     }
 
     cf.stop();

src/RawFile.test.cpp

@@ -99,8 +99,7 @@ TEST_CASE("Read data from a jungfrau 500k single port raw file",
 }
 
 TEST_CASE("Read frame numbers from a raw file", "[.with-data]") {
-    auto fpath =
-        test_data_path() / "raw/eiger" / "eiger_500k_16bit_master_0.json";
+    auto fpath = test_data_path() / "raw/eiger" / "eiger_500k_16bit_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     // we know this file has 3 frames with frame numbers 14, 15, 16
@@ -289,7 +288,8 @@ TEST_CASE("check find_geometry", "[.with-data]") {
     }
 }
 
-TEST_CASE("Open multi module file with ROI", "[.with-data]") {
+TEST_CASE("Open multi module file with ROI",
+          "[.with-data]") {
 
     auto fpath = test_data_path() / "raw/SingleChipROI/Data_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -319,4 +319,4 @@ TEST_CASE("Read file with unordered frames", "[.with-data]") {
     REQUIRE(std::filesystem::exists(fpath));
     File f(fpath);
     REQUIRE_THROWS((f.read_frame()));
-}
+}

src/RawMasterFile.cpp

@@ -64,12 +64,6 @@ const std::string &RawFileNameComponents::base_name() const {
 const std::string &RawFileNameComponents::ext() const { return m_ext; }
 int RawFileNameComponents::file_index() const { return m_file_index; }
 
-ScanParameters::ScanParameters(const bool enabled, const DACIndex dac,
-                               const int start, const int stop, const int step,
-                               const int64_t settleTime)
-    : m_enabled(enabled), m_dac(dac), m_start(start), m_stop(stop),
-      m_step(step), m_settleTime(settleTime){};
-
 // "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
 ScanParameters::ScanParameters(const std::string &par) {
     std::istringstream iss(par.substr(1, par.size() - 2));
@@ -78,7 +72,7 @@ ScanParameters::ScanParameters(const std::string &par) {
         if (line == "enabled") {
             m_enabled = true;
         } else if (line.find("dac") != std::string::npos) {
-            m_dac = StringTo<DACIndex>(line.substr(4));
+            m_dac = line.substr(4);
         } else if (line.find("start") != std::string::npos) {
             m_start = std::stoi(line.substr(6));
         } else if (line.find("stop") != std::string::npos) {
@@ -93,9 +87,8 @@ int ScanParameters::start() const { return m_start; }
 int ScanParameters::stop() const { return m_stop; }
 void ScanParameters::increment_stop() { m_stop += 1; }
 int ScanParameters::step() const { return m_step; }
-DACIndex ScanParameters::dac() const { return m_dac; }
+const std::string &ScanParameters::dac() const { return m_dac; }
 bool ScanParameters::enabled() const { return m_enabled; }
-int64_t ScanParameters::settleTime() const { return m_settleTime; }
 
 RawMasterFile::RawMasterFile(const std::filesystem::path &fpath)
     : m_fnc(fpath) {
@@ -177,7 +170,6 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     std::ifstream ifs(fpath);
     json j;
     ifs >> j;
-
     double v = j["Version"];
     m_version = fmt::format("{:.1f}", v);
 
@@ -189,9 +181,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         j["Geometry"]["x"]}; // TODO: isnt it only available for version > 7.1?
                              // - try block default should be 1x1
 
-    m_image_size_in_bytes =
-        v < 8.0 ? j["Image Size in bytes"] : j["Image Size"];
-
+    m_image_size_in_bytes = j["Image Size in bytes"];
     m_frames_in_file = j["Frames in File"];
     m_pixels_y = j["Pixels"]["y"];
     m_pixels_x = j["Pixels"]["x"];
@@ -216,6 +206,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     } catch (const json::out_of_range &e) {
         // keep the optional empty
     }
+
     // ----------------------------------------------------------------
     // Special treatment of analog flag because of Moench03
     try {
@@ -236,6 +227,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         m_analog_flag = 0;
     }
     //-----------------------------------------------------------------
+
     try {
         m_quad = j.at("Quad");
     } catch (const json::out_of_range &e) {
@@ -247,6 +239,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     // }catch (const json::out_of_range &e) {
     //     m_adc_mask = 0;
     // }
+
     try {
         int digital_flag = j.at("Digital Flag");
         if (digital_flag) {
@@ -255,6 +248,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     } catch (const json::out_of_range &e) {
         // keep the optional empty
     }
+
     try {
         m_transceiver_flag = j.at("Transceiver Flag");
         if (m_transceiver_flag) {
@@ -263,20 +257,10 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     } catch (const json::out_of_range &e) {
         // keep the optional empty
     }
+
     try {
-        if (v < 8.0) {
-            std::string scan_parameters = j.at("Scan Parameters");
-            m_scan_parameters = ScanParameters(scan_parameters);
-        } else {
-            auto json_obj = j.at("Scan Parameters");
-            m_scan_parameters = ScanParameters(
-                json_obj.at("enable").get<int>(),
-                static_cast<DACIndex>(json_obj.at("dacInd").get<int>()),
-                json_obj.at("start offset").get<int>(),
-                json_obj.at("stop offset").get<int>(),
-                json_obj.at("step size").get<int>(),
-                json_obj.at("dac settle time ns").get<int>());
-        }
+        std::string scan_parameters = j.at("Scan Parameters");
+        m_scan_parameters = ScanParameters(scan_parameters);
         if (v < 7.21) {
             m_scan_parameters
                 .increment_stop(); // adjust for endpoint being included
@@ -284,7 +268,6 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     } catch (const json::out_of_range &e) {
         // not a scan
     }
-
     try {
         m_udp_interfaces_per_module = {j.at("Number of UDP Interfaces"), 1};
     } catch (const json::out_of_range &e) {
@@ -294,22 +277,14 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
             m_udp_interfaces_per_module = {1, 2};
         }
     }
+
     try {
         ROI tmp_roi;
-        if (v < 8.0) {
-            auto obj = j.at("Receiver Roi");
-            tmp_roi.xmin = obj.at("xmin");
-            tmp_roi.xmax = obj.at("xmax");
-            tmp_roi.ymin = obj.at("ymin");
-            tmp_roi.ymax = obj.at("ymax");
-        } else {
-            // TODO: for now only handle single ROI
-            auto obj = j.at("Receiver Rois");
-            tmp_roi.xmin = obj[0].at("xmin");
-            tmp_roi.xmax = obj[0].at("xmax");
-            tmp_roi.ymin = obj[0].at("ymin");
-            tmp_roi.ymax = obj[0].at("ymax");
-        }
+        auto obj = j.at("Receiver Roi");
+        tmp_roi.xmin = obj.at("xmin");
+        tmp_roi.xmax = obj.at("xmax");
+        tmp_roi.ymin = obj.at("ymin");
+        tmp_roi.ymax = obj.at("ymax");
 
         // if any of the values are set update the roi
         if (tmp_roi.xmin != 4294967295 || tmp_roi.xmax != 4294967295 ||
@@ -323,10 +298,14 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         }
 
     } catch (const json::out_of_range &e) {
-        LOG(TLogLevel::logERROR) << e.what() << std::endl;
+        std::cout << e.what() << std::endl;
         // leave the optional empty
     }
 
+    // if we have an roi we need to update the geometry for the subfiles
+    if (m_roi) {
+    }
+
 // Update detector type for Moench
 // TODO! How does this work with old .raw master files?
 #ifdef AARE_VERBOSE

src/RawMasterFile.test.cpp

@@ -51,7 +51,7 @@ TEST_CASE("Parse scan parameters") {
     ScanParameters s("[enabled\ndac dac 4\nstart 500\nstop 2200\nstep "
                      "5\nsettleTime 100us\n]");
     REQUIRE(s.enabled());
-    REQUIRE(s.dac() == DACIndex::DAC_4);
+    REQUIRE(s.dac() == "dac 4");
     REQUIRE(s.start() == 500);
     REQUIRE(s.stop() == 2200);
     REQUIRE(s.step() == 5);
@@ -60,7 +60,7 @@ TEST_CASE("Parse scan parameters") {
 TEST_CASE("A disabled scan") {
     ScanParameters s("[disabled]");
     REQUIRE_FALSE(s.enabled());
-    REQUIRE(s.dac() == DACIndex::DAC_0);
+    REQUIRE(s.dac() == "");
     REQUIRE(s.start() == 0);
     REQUIRE(s.stop() == 0);
     REQUIRE(s.step() == 0);
@@ -68,7 +68,7 @@ TEST_CASE("A disabled scan") {
 
 TEST_CASE("Parse a master file in .json format", "[.integration]") {
     auto fpath =
-        test_data_path() / "raw" / "jungfrau" / "jungfrau_single_master_0.json";
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
 
@@ -224,41 +224,6 @@ TEST_CASE("Parse a master file in .raw format", "[.integration]") {
     // Packets Caught Mask        : 64 bytes
 }
 
-TEST_CASE("Parse a master file in new .json format",
-          "[.integration][.width-data]") {
-
-    auto file_path =
-        test_data_path() / "raw" / "newmythen03" / "run_87_master_0.json";
-    REQUIRE(std::filesystem::exists(file_path));
-
-    RawMasterFile f(file_path);
-
-    // Version                    : 8.0
-    REQUIRE(f.version() == "8.0");
-
-    REQUIRE(f.detector_type() == DetectorType::Mythen3);
-    // Timing Mode                : auto
-    REQUIRE(f.timing_mode() == TimingMode::Auto);
-    // Geometry                   : [2, 1]
-    REQUIRE(f.geometry().col == 2);
-    REQUIRE(f.geometry().row == 1);
-    // Image Size                 : 5120 bytes
-    REQUIRE(f.image_size_in_bytes() == 5120);
-
-    REQUIRE(f.scan_parameters().enabled() == false);
-    REQUIRE(f.scan_parameters().dac() == DACIndex::DAC_0);
-    REQUIRE(f.scan_parameters().start() == 0);
-    REQUIRE(f.scan_parameters().stop() == 0);
-    REQUIRE(f.scan_parameters().step() == 0);
-    REQUIRE(f.scan_parameters().settleTime() == 0);
-
-    auto roi = f.roi().value();
-    REQUIRE(roi.xmin == 0);
-    REQUIRE(roi.xmax == 2559);
-    REQUIRE(roi.ymin == -1);
-    REQUIRE(roi.ymax == -1);
-}
-
 TEST_CASE("Read eiger master file", "[.integration]") {
     auto fpath = test_data_path() / "eiger" / "eiger_500k_32bit_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -327,4 +292,4 @@ TEST_CASE("Read eiger master file", "[.integration]") {
     //         "Packets Caught Mask": "64 bytes"
     //     }
     // }
-}
+}

src/defs.cpp

@@ -115,186 +115,4 @@ template <> FrameDiscardPolicy StringTo(const std::string &arg) {
 
 // template <> TimingMode StringTo<TimingMode>(std::string mode);
 
-template <> DACIndex StringTo(const std::string &arg) {
-    if (arg == "dac 0")
-        return DACIndex::DAC_0;
-    else if (arg == "dac 1")
-        return DACIndex::DAC_1;
-    else if (arg == "dac 2")
-        return DACIndex::DAC_2;
-    else if (arg == "dac 3")
-        return DACIndex::DAC_3;
-    else if (arg == "dac 4")
-        return DACIndex::DAC_4;
-    else if (arg == "dac 5")
-        return DACIndex::DAC_5;
-    else if (arg == "dac 6")
-        return DACIndex::DAC_6;
-    else if (arg == "dac 7")
-        return DACIndex::DAC_7;
-    else if (arg == "dac 8")
-        return DACIndex::DAC_8;
-    else if (arg == "dac 9")
-        return DACIndex::DAC_9;
-    else if (arg == "dac 10")
-        return DACIndex::DAC_10;
-    else if (arg == "dac 11")
-        return DACIndex::DAC_11;
-    else if (arg == "dac 12")
-        return DACIndex::DAC_12;
-    else if (arg == "dac 13")
-        return DACIndex::DAC_13;
-    else if (arg == "dac 14")
-        return DACIndex::DAC_14;
-    else if (arg == "dac 15")
-        return DACIndex::DAC_15;
-    else if (arg == "dac 16")
-        return DACIndex::DAC_16;
-    else if (arg == "dac 17")
-        return DACIndex::DAC_17;
-    else if (arg == "vsvp")
-        return DACIndex::VSVP;
-    else if (arg == "vtrim")
-        return DACIndex::VTRIM;
-    else if (arg == "vrpreamp")
-        return DACIndex::VRPREAMP;
-    else if (arg == "vrshaper")
-        return DACIndex::VRSHAPER;
-    else if (arg == "vsvn")
-        return DACIndex::VSVN;
-    else if (arg == "vtgstv")
-        return DACIndex::VTGSTV;
-    else if (arg == "vcmp_ll")
-        return DACIndex::VCMP_LL;
-    else if (arg == "vcmp_lr")
-        return DACIndex::VCMP_LR;
-    else if (arg == "vcal")
-        return DACIndex::VCAL;
-    else if (arg == "vcmp_rl")
-        return DACIndex::VCMP_RL;
-    else if (arg == "rxb_rb")
-        return DACIndex::RXB_RB;
-    else if (arg == "rxb_lb")
-        return DACIndex::RXB_LB;
-    else if (arg == "vcmp_rr")
-        return DACIndex::VCMP_RR;
-    else if (arg == "vcp")
-        return DACIndex::VCP;
-    else if (arg == "vcn")
-        return DACIndex::VCN;
-    else if (arg == "vishaper")
-        return DACIndex::VISHAPER;
-    else if (arg == "vthreshold")
-        return DACIndex::VTHRESHOLD;
-    else if (arg == "vref_ds")
-        return DACIndex::VREF_DS;
-    else if (arg == "vout_cm")
-        return DACIndex::VOUT_CM;
-    else if (arg == "vin_cm")
-        return DACIndex::VIN_CM;
-    else if (arg == "vref_comp")
-        return DACIndex::VREF_COMP;
-    else if (arg == "vb_comp")
-        return DACIndex::VB_COMP;
-    else if (arg == "vdd_prot")
-        return DACIndex::VDD_PROT;
-    else if (arg == "vin_com")
-        return DACIndex::VIN_COM;
-    else if (arg == "vref_prech")
-        return DACIndex::VREF_PRECH;
-    else if (arg == "vb_pixbuf")
-        return DACIndex::VB_PIXBUF;
-    else if (arg == "vb_ds")
-        return DACIndex::VB_DS;
-    else if (arg == "vref_h_adc")
-        return DACIndex::VREF_H_ADC;
-    else if (arg == "vb_comp_fe")
-        return DACIndex::VB_COMP_FE;
-    else if (arg == "vb_comp_adc")
-        return DACIndex::VB_COMP_ADC;
-    else if (arg == "vcom_cds")
-        return DACIndex::VCOM_CDS;
-    else if (arg == "vref_rstore")
-        return DACIndex::VREF_RSTORE;
-    else if (arg == "vb_opa_1st")
-        return DACIndex::VB_OPA_1ST;
-    else if (arg == "vref_comp_fe")
-        return DACIndex::VREF_COMP_FE;
-    else if (arg == "vcom_adc1")
-        return DACIndex::VCOM_ADC1;
-    else if (arg == "vref_l_adc")
-        return DACIndex::VREF_L_ADC;
-    else if (arg == "vref_cds")
-        return DACIndex::VREF_CDS;
-    else if (arg == "vb_cs")
-        return DACIndex::VB_CS;
-    else if (arg == "vb_opa_fd")
-        return DACIndex::VB_OPA_FD;
-    else if (arg == "vcom_adc2")
-        return DACIndex::VCOM_ADC2;
-    else if (arg == "vcassh")
-        return DACIndex::VCASSH;
-    else if (arg == "vth2")
-        return DACIndex::VTH2;
-    else if (arg == "vrshaper_n")
-        return DACIndex::VRSHAPER_N;
-    else if (arg == "vipre_out")
-        return DACIndex::VIPRE_OUT;
-    else if (arg == "vth3")
-        return DACIndex::VTH3;
-    else if (arg == "vth1")
-        return DACIndex::VTH1;
-    else if (arg == "vicin")
-        return DACIndex::VICIN;
-    else if (arg == "vcas")
-        return DACIndex::VCAS;
-    else if (arg == "vcal_n")
-        return DACIndex::VCAL_N;
-    else if (arg == "vipre")
-        return DACIndex::VIPRE;
-    else if (arg == "vcal_p")
-        return DACIndex::VCAL_P;
-    else if (arg == "vdcsh")
-        return DACIndex::VDCSH;
-    else if (arg == "vbp_colbuf")
-        return DACIndex::VBP_COLBUF;
-    else if (arg == "vb_sda")
-        return DACIndex::VB_SDA;
-    else if (arg == "vcasc_sfp")
-        return DACIndex::VCASC_SFP;
-    else if (arg == "vipre_cds")
-        return DACIndex::VIPRE_CDS;
-    else if (arg == "ibias_sfp")
-        return DACIndex::IBIAS_SFP;
-    else if (arg == "trimbits")
-        return DACIndex::TRIMBIT_SCAN;
-    else if (arg == "highvoltage")
-        return DACIndex::HIGH_VOLTAGE;
-    else if (arg == "iodelay")
-        return DACIndex::IO_DELAY;
-    else if (arg == "temp_adc")
-        return DACIndex::TEMPERATURE_ADC;
-    else if (arg == "temp_fpga")
-        return DACIndex::TEMPERATURE_FPGA;
-    else if (arg == "temp_fpgaext")
-        return DACIndex::TEMPERATURE_FPGAEXT;
-    else if (arg == "temp_10ge")
-        return DACIndex::TEMPERATURE_10GE;
-    else if (arg == "temp_dcdc")
-        return DACIndex::TEMPERATURE_DCDC;
-    else if (arg == "temp_sodl")
-        return DACIndex::TEMPERATURE_SODL;
-    else if (arg == "temp_sodr")
-        return DACIndex::TEMPERATURE_SODR;
-    else if (arg == "temp_fpgafl")
-        return DACIndex::TEMPERATURE_FPGA2;
-    else if (arg == "temp_fpgafr")
-        return DACIndex::TEMPERATURE_FPGA3;
-    else if (arg == "temp_slowadc")
-        return DACIndex::SLOW_ADC_TEMP;
-    else
-        throw std::invalid_argument("Could not decode DACIndex from: \"" + arg +
-                                    "\"");
-}
-
 } // namespace aare

update_version.py

@@ -7,7 +7,6 @@ Script to update VERSION file with semantic versioning if provided as an argumen
 import sys
 import os
 import re
-from datetime import datetime
 
 from packaging.version import Version, InvalidVersion
 
@@ -27,9 +26,9 @@ def get_version():
 
     # Check at least one argument is passed
     if len(sys.argv) < 2:
-        version =   datetime.today().strftime('%Y.%-m.%-d')
-    else: 
-        version = sys.argv[1]
+        return "0.0.0"
+
+    version = sys.argv[1]
 
     try:
         v = Version(version)  # normalize check if version follows PEP 440 specification
@@ -55,4 +54,4 @@ def write_version_to_file(version):
 if __name__ == "__main__":
 
     version = get_version()
-    write_version_to_file(version)
+    write_version_to_file(version)