Merge branch 'api_cluster_vector' into testing_clusters

CMakeLists.txt

@@ -384,7 +384,6 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
 )
 
-
 add_library(aare_core STATIC ${SourceFiles})
 target_include_directories(aare_core PUBLIC 
     "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" 

include/aare/CalculateEta.hpp

@@ -33,7 +33,7 @@ template <typename T> struct Eta2 {
 };
 
 /**
- * @brief Calculate the eta2 values for all clusters in a Clsutervector
+ * @brief Calculate the eta2 values for all clusters in a Clustervector
  */
 template <typename ClusterType,
           typename = std::enable_if_t<is_cluster_v<ClusterType>>>

include/aare/ClusterFile.hpp

@@ -39,9 +39,10 @@ template <typename ClusterType,
           typename Enable = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterFile {
     FILE *fp{};
+    const std::string m_filename{};
     uint32_t m_num_left{};    /*Number of photons left in frame*/
     size_t m_chunk_size{};    /*Number of clusters to read at a time*/
-    const std::string m_mode; /*Mode to open the file in*/
+    std::string m_mode;       /*Mode to open the file in*/
     std::optional<ROI> m_roi; /*Region of interest, will be applied if set*/
     std::optional<NDArray<int32_t, 2>>
         m_noise_map; /*Noise map to cut photons, will be applied if set*/
@@ -115,6 +116,11 @@ class ClusterFile {
      */
     void close();
 
+    /** @brief Open the file in specific mode
+     *
+     */
+    void open(const std::string &mode);
+
   private:
     ClusterVector<ClusterType> read_clusters_with_cut(size_t n_clusters);
     ClusterVector<ClusterType> read_clusters_without_cut(size_t n_clusters);
@@ -128,25 +134,25 @@ template <typename ClusterType, typename Enable>
 ClusterFile<ClusterType, Enable>::ClusterFile(
     const std::filesystem::path &fname, size_t chunk_size,
     const std::string &mode)
-    : m_chunk_size(chunk_size), m_mode(mode) {
+    : m_filename(fname.string()), m_chunk_size(chunk_size), m_mode(mode) {
 
     if (mode == "r") {
-        fp = fopen(fname.c_str(), "rb");
+        fp = fopen(m_filename.c_str(), "rb");
         if (!fp) {
             throw std::runtime_error("Could not open file for reading: " +
-                                     fname.string());
+                                     m_filename);
         }
     } else if (mode == "w") {
-        fp = fopen(fname.c_str(), "wb");
+        fp = fopen(m_filename.c_str(), "wb");
         if (!fp) {
             throw std::runtime_error("Could not open file for writing: " +
-                                     fname.string());
+                                     m_filename);
         }
     } else if (mode == "a") {
-        fp = fopen(fname.c_str(), "ab");
+        fp = fopen(m_filename.c_str(), "ab");
         if (!fp) {
             throw std::runtime_error("Could not open file for appending: " +
-                                     fname.string());
+                                     m_filename);
         }
     } else {
         throw std::runtime_error("Unsupported mode: " + mode);
@@ -165,6 +171,39 @@ void ClusterFile<ClusterType, Enable>::close() {
         fp = nullptr;
     }
 }
+
+template <typename ClusterType, typename Enable>
+void ClusterFile<ClusterType, Enable>::open(const std::string &mode) {
+    if (fp) {
+        close();
+    }
+
+    if (mode == "r") {
+        fp = fopen(m_filename.c_str(), "rb");
+        if (!fp) {
+            throw std::runtime_error("Could not open file for reading: " +
+                                     m_filename);
+        }
+        m_mode = "r";
+    } else if (mode == "w") {
+        fp = fopen(m_filename.c_str(), "wb");
+        if (!fp) {
+            throw std::runtime_error("Could not open file for writing: " +
+                                     m_filename);
+        }
+        m_mode = "w";
+    } else if (mode == "a") {
+        fp = fopen(m_filename.c_str(), "ab");
+        if (!fp) {
+            throw std::runtime_error("Could not open file for appending: " +
+                                     m_filename);
+        }
+        m_mode = "a";
+    } else {
+        throw std::runtime_error("Unsupported mode: " + mode);
+    }
+}
+
 template <typename ClusterType, typename Enable>
 void ClusterFile<ClusterType, Enable>::set_roi(ROI roi) {
     m_roi = roi;
@@ -197,10 +236,7 @@ void ClusterFile<ClusterType, Enable>::write_frame(
     if (m_mode != "w" && m_mode != "a") {
         throw std::runtime_error("File not opened for writing");
     }
-    if (!(clusters.cluster_size_x() == 3) &&
+
-        !(clusters.cluster_size_y() == 3)) {
-        throw std::runtime_error("Only 3x3 clusters are supported");
-    }
     int32_t frame_number = clusters.frame_number();
     fwrite(&frame_number, sizeof(frame_number), 1, fp);
     uint32_t n_clusters = clusters.size();
@@ -270,7 +306,7 @@ ClusterFile<ClusterType, Enable>::read_clusters_without_cut(size_t n_clusters) {
         }
     }
 
-    // Resize the vector to the number of clusters.
+    // Resize the vector to the number o f clusters.
     // No new allocation, only change bounds.
     clusters.resize(nph_read);
     if (m_gain_map)
@@ -375,11 +411,13 @@ ClusterFile<ClusterType, Enable>::read_frame_without_cut() {
     ClusterVector<ClusterType> clusters(n_clusters);
     clusters.set_frame_number(frame_number);
 
+    clusters.resize(n_clusters);
+
     if (fread(clusters.data(), clusters.item_size(), n_clusters, fp) !=
         static_cast<size_t>(n_clusters)) {
         throw std::runtime_error(LOCATION + "Could not read clusters");
     }
-    clusters.resize(n_clusters);
+
     if (m_gain_map)
         m_gain_map->apply_gain_map(clusters);
     return clusters;

include/aare/ClusterFileV2.hpp

@@ -1,154 +0,0 @@
-#pragma once
-#include "aare/core/defs.hpp"
-#include <filesystem>
-#include <fmt/format.h>
-#include <string>
-
-namespace aare {
-struct ClusterHeader {
-    int32_t frame_number;
-    int32_t n_clusters;
-    std::string to_string() const {
-        return "frame_number: " + std::to_string(frame_number) +
-               ", n_clusters: " + std::to_string(n_clusters);
-    }
-};
-
-struct ClusterV2_ {
-    int16_t x;
-    int16_t y;
-    std::array<int32_t, 9> data;
-    std::string to_string(bool detailed = false) const {
-        if (detailed) {
-            std::string data_str = "[";
-            for (auto &d : data) {
-                data_str += std::to_string(d) + ", ";
-            }
-            data_str += "]";
-            return "x: " + std::to_string(x) + ", y: " + std::to_string(y) +
-                   ", data: " + data_str;
-        }
-        return "x: " + std::to_string(x) + ", y: " + std::to_string(y);
-    }
-};
-
-struct ClusterV2 {
-    ClusterV2_ cluster;
-    int32_t frame_number;
-    std::string to_string() const {
-        return "frame_number: " + std::to_string(frame_number) + ", " +
-               cluster.to_string();
-    }
-};
-
-/**
- * @brief
- * important not: fp always points to the clusters header and does not point to
- * individual clusters
- *
- */
-class ClusterFileV2 {
-    std::filesystem::path m_fpath;
-    std::string m_mode;
-    FILE *fp{nullptr};
-
-    void check_open() {
-        if (!fp)
-            throw std::runtime_error(
-                fmt::format("File: {} not open", m_fpath.string()));
-    }
-
-  public:
-    ClusterFileV2(std::filesystem::path const &fpath, std::string const &mode)
-        : m_fpath(fpath), m_mode(mode) {
-        if (m_mode != "r" && m_mode != "w")
-            throw std::invalid_argument("mode must be 'r' or 'w'");
-        if (m_mode == "r" && !std::filesystem::exists(m_fpath))
-            throw std::invalid_argument("File does not exist");
-        if (mode == "r") {
-            fp = fopen(fpath.string().c_str(), "rb");
-        } else if (mode == "w") {
-            if (std::filesystem::exists(fpath)) {
-                fp = fopen(fpath.string().c_str(), "r+b");
-            } else {
-                fp = fopen(fpath.string().c_str(), "wb");
-            }
-        }
-        if (fp == nullptr) {
-            throw std::runtime_error("Failed to open file");
-        }
-    }
-    ~ClusterFileV2() { close(); }
-    std::vector<ClusterV2> read() {
-        check_open();
-
-        ClusterHeader header;
-        fread(&header, sizeof(ClusterHeader), 1, fp);
-        std::vector<ClusterV2_> clusters_(header.n_clusters);
-        fread(clusters_.data(), sizeof(ClusterV2_), header.n_clusters, fp);
-        std::vector<ClusterV2> clusters;
-        for (auto &c : clusters_) {
-            ClusterV2 cluster;
-            cluster.cluster = std::move(c);
-            cluster.frame_number = header.frame_number;
-            clusters.push_back(cluster);
-        }
-
-        return clusters;
-    }
-    std::vector<std::vector<ClusterV2>> read(int n_frames) {
-        std::vector<std::vector<ClusterV2>> clusters;
-        for (int i = 0; i < n_frames; i++) {
-            clusters.push_back(read());
-        }
-        return clusters;
-    }
-
-    size_t write(std::vector<ClusterV2> const &clusters) {
-        check_open();
-        if (m_mode != "w")
-            throw std::runtime_error("File not opened in write mode");
-        if (clusters.empty())
-            return 0;
-
-        ClusterHeader header;
-        header.frame_number = clusters[0].frame_number;
-        header.n_clusters = clusters.size();
-        fwrite(&header, sizeof(ClusterHeader), 1, fp);
-        for (auto &c : clusters) {
-            fwrite(&c.cluster, sizeof(ClusterV2_), 1, fp);
-        }
-        return clusters.size();
-    }
-
-    size_t write(std::vector<std::vector<ClusterV2>> const &clusters) {
-        check_open();
-        if (m_mode != "w")
-            throw std::runtime_error("File not opened in write mode");
-
-        size_t n_clusters = 0;
-        for (auto &c : clusters) {
-            n_clusters += write(c);
-        }
-        return n_clusters;
-    }
-
-    int seek_to_begin() { return fseek(fp, 0, SEEK_SET); }
-    int seek_to_end() { return fseek(fp, 0, SEEK_END); }
-
-    int32_t frame_number() {
-        auto pos = ftell(fp);
-        ClusterHeader header;
-        fread(&header, sizeof(ClusterHeader), 1, fp);
-        fseek(fp, pos, SEEK_SET);
-        return header.frame_number;
-    }
-
-    void close() {
-        if (fp) {
-            fclose(fp);
-            fp = nullptr;
-        }
-    }
-};
-} // namespace aare

include/aare/ClusterVector.hpp

@@ -18,256 +18,6 @@ template <typename ClusterType,
           typename = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterVector; // Forward declaration
 
-/**
- * @brief ClusterVector is a container for clusters of various sizes. It uses a
- * contiguous memory buffer to store the clusters. It is templated on the data
- * type and the coordinate type of the clusters.
- * @note push_back can invalidate pointers to elements in the container
- * @warning ClusterVector is currently move only to catch unintended copies, but
- * this might change since there are probably use cases where copying is needed.
- * @tparam T data type of the pixels in the cluster
- * @tparam CoordType data type of the x and y coordinates of the cluster
- * (normally int16_t)
- */
-#if 0
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType>
-class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
-
-    std::byte *m_data{};
-    size_t m_size{0};
-    size_t m_capacity;
-    uint64_t m_frame_number{0}; // TODO! Check frame number size and type
-    /** 
-    Format string used in the python bindings to create a numpy
-    array from the buffer
-    = - native byte order
-    h - short
-    d - double
-    i - int
-    */
-    constexpr static char m_fmt_base[] = "=h:x:\nh:y:\n({},{}){}:data:";
-
-  public:
-    using value_type = T;
-    using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
-
-    /**
-     * @brief Construct a new ClusterVector object
-     * @param capacity initial capacity of the buffer in number of clusters
-     * @param frame_number frame number of the clusters. Default is 0, which is
-     * also used to indicate that the clusters come from many frames
-     */
-    ClusterVector(size_t capacity = 1024, uint64_t frame_number = 0)
-        : m_capacity(capacity), m_frame_number(frame_number) {
-        allocate_buffer(m_capacity);
-    }
-
-    ~ClusterVector() { delete[] m_data; }
-
-    // Move constructor
-    ClusterVector(ClusterVector &&other) noexcept
-        : m_data(other.m_data), m_size(other.m_size),
-          m_capacity(other.m_capacity), m_frame_number(other.m_frame_number) {
-        other.m_data = nullptr;
-        other.m_size = 0;
-        other.m_capacity = 0;
-    }
-
-    // Move assignment operator
-    ClusterVector &operator=(ClusterVector &&other) noexcept {
-        if (this != &other) {
-            delete[] m_data;
-            m_data = other.m_data;
-            m_size = other.m_size;
-            m_capacity = other.m_capacity;
-            m_frame_number = other.m_frame_number;
-            other.m_data = nullptr;
-            other.m_size = 0;
-            other.m_capacity = 0;
-            other.m_frame_number = 0;
-        }
-        return *this;
-    }
-
-    /**
-     * @brief Reserve space for at least capacity clusters
-     * @param capacity number of clusters to reserve space for
-     * @note If capacity is less than the current capacity, the function does
-     * nothing.
-     */
-    void reserve(size_t capacity) {
-        if (capacity > m_capacity) {
-            allocate_buffer(capacity);
-        }
-    }
-
-    /**
-     * @brief Add a cluster to the vector
-     */
-    void push_back(const ClusterType &cluster) {
-        if (m_size == m_capacity) {
-            allocate_buffer(m_capacity * 2);
-        }
-        std::byte *ptr = element_ptr(m_size);
-        *reinterpret_cast<CoordType *>(ptr) = cluster.x;
-        ptr += sizeof(CoordType);
-        *reinterpret_cast<CoordType *>(ptr) = cluster.y;
-        ptr += sizeof(CoordType);
-
-        std::memcpy(ptr, cluster.data, ClusterSizeX * ClusterSizeY * sizeof(T));
-
-        m_size++;
-    }
-
-    ClusterVector &operator+=(const ClusterVector &other) {
-        if (m_size + other.m_size > m_capacity) {
-            allocate_buffer(m_capacity + other.m_size);
-        }
-        std::copy(other.m_data, other.m_data + other.m_size * item_size(),
-                  m_data + m_size * item_size());
-        m_size += other.m_size;
-        return *this;
-    }
-
-    /**
-     * @brief Sum the pixels in each cluster
-     * @return std::vector<T> vector of sums for each cluster
-     */
-    /*
-    std::vector<T> sum() {
-        std::vector<T> sums(m_size);
-        const size_t stride = item_size();
-        const size_t n_pixels = ClusterSizeX * ClusterSizeY;
-        std::byte *ptr = m_data + 2 * sizeof(CoordType); // skip x and y
-
-        for (size_t i = 0; i < m_size; i++) {
-            sums[i] =
-                std::accumulate(reinterpret_cast<T *>(ptr),
-                                reinterpret_cast<T *>(ptr) + n_pixels, T{});
-            ptr += stride;
-        }
-        return sums;
-    }
-    */
-
-    /**
-     * @brief Sum the pixels in the 2x2 subcluster with the biggest pixel sum in
-     * each cluster
-     * @return std::vector<T> vector of sums for each cluster
-     */ //TODO if underlying container is a vector use std::for_each
-    /*
-    std::vector<T> sum_2x2() {
-        std::vector<T> sums_2x2(m_size);
-
-        for (size_t i = 0; i < m_size; i++) {
-            sums_2x2[i] = at(i).max_sum_2x2;
-        }
-        return sums_2x2;
-    }
-    */
-
-    /**
-     * @brief Return the number of clusters in the vector
-     */
-    size_t size() const { return m_size; }
-
-    uint8_t cluster_size_x() const { return ClusterSizeX; }
-
-    uint8_t cluster_size_y() const { return ClusterSizeY; }
-
-    /**
-     * @brief Return the capacity of the buffer in number of clusters. This is
-     * the number of clusters that can be stored in the current buffer without
-     * reallocation.
-     */
-    size_t capacity() const { return m_capacity; }
-
-    /**
-     * @brief Return the size in bytes of a single cluster
-     */
-    size_t item_size() const {
-        return 2 * sizeof(CoordType) + ClusterSizeX * ClusterSizeY * sizeof(T);
-    }
-
-    /**
-     * @brief Return the offset in bytes for the i-th cluster
-     */
-    size_t element_offset(size_t i) const { return item_size() * i; }
-
-    /**
-     * @brief Return a pointer to the i-th cluster
-     */
-    std::byte *element_ptr(size_t i) { return m_data + element_offset(i); }
-
-    /**
-     * @brief Return a pointer to the i-th cluster
-     */
-    const std::byte *element_ptr(size_t i) const {
-        return m_data + element_offset(i);
-    }
-
-    std::byte *data() { return m_data; }
-    std::byte const *data() const { return m_data; }
-
-    /**
-     * @brief Return a reference to the i-th cluster casted to type V
-     * @tparam V type of the cluster
-     */
-    ClusterType &at(size_t i) {
-        return *reinterpret_cast<ClusterType *>(element_ptr(i));
-    }
-
-    const ClusterType &at(size_t i) const {
-        return *reinterpret_cast<const ClusterType *>(element_ptr(i));
-    }
-
-    template <typename V> const V &at(size_t i) const {
-        return *reinterpret_cast<const V *>(element_ptr(i));
-    }
-
-    const std::string_view fmt_base() const {
-        // TODO! how do we match on coord_t?
-        return m_fmt_base;
-    }
-
-    /** 
-     * @brief Return the frame number of the clusters. 0 is used to indicate
-     * that the clusters come from many frames
-     */
-    uint64_t frame_number() const { return m_frame_number; }
-
-    void set_frame_number(uint64_t frame_number) {
-        m_frame_number = frame_number;
-    }
-
-    /** 
-     * @brief Resize the vector to contain new_size clusters. If new_size is
-     * greater than the current capacity, a new buffer is allocated. If the size
-     * is smaller no memory is freed, size is just updated.
-     * @param new_size new size of the vector
-     * @warning The additional clusters are not initialized
-     */
-    void resize(size_t new_size) {
-        // TODO! Should we initialize the new clusters?
-        if (new_size > m_capacity) {
-            allocate_buffer(new_size);
-        }
-        m_size = new_size;
-    }
-
-  private:
-    void allocate_buffer(size_t new_capacity) {
-        size_t num_bytes = item_size() * new_capacity;
-        std::byte *new_data = new std::byte[num_bytes]{};
-        std::copy(m_data, m_data + item_size() * m_size, new_data);
-        delete[] m_data;
-        m_data = new_data;
-        m_capacity = new_capacity;
-    }
-};
-#endif
-
 /**
  * @brief ClusterVector is a container for clusters of various sizes. It
  * uses a contiguous memory buffer to store the clusters. It is templated on
@@ -285,7 +35,7 @@ template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
 class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
 
     std::vector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> m_data{};
-    uint64_t m_frame_number{0}; // TODO! Check frame number size and type
+    int32_t m_frame_number{0}; // TODO! Check frame number size and type
 
   public:
     using value_type = T;
@@ -319,6 +69,33 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
         return *this;
     }
 
+    /**
+     * @brief Sum the pixels in each cluster
+     * @return std::vector<T> vector of sums for each cluster
+     */
+    std::vector<T> sum() {
+        std::vector<T> sums(m_data.size());
+
+        for (size_t i = 0; i < m_data.size(); i++) {
+            sums[i] = at(i).sum();
+        }
+        return sums;
+    }
+
+    /**
+     * @brief Sum the pixels in the 2x2 subcluster with the biggest pixel sum in
+     * each cluster
+     * @return std::vector<T> vector of sums for each cluster
+     */ //TODO if underlying container is a vector use std::for_each
+    std::vector<T> sum_2x2() {
+        std::vector<T> sums_2x2(m_data.size());
+
+        for (size_t i = 0; i < m_data.size(); i++) {
+            sums_2x2[i] = at(i).max_sum_2x2().first;
+        }
+        return sums_2x2;
+    }
+
     /**
      * @brief Reserve space for at least capacity clusters
      * @param capacity number of clusters to reserve space for
@@ -361,7 +138,8 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
      * @brief Return the size in bytes of a single cluster
      */
     size_t item_size() const {
-        return 2 * sizeof(CoordType) + ClusterSizeX * ClusterSizeY * sizeof(T);
+        return sizeof(ClusterType); // 2 * sizeof(CoordType) + ClusterSizeX *
+                                    // ClusterSizeY * sizeof(T);
     }
 
     ClusterType *data() { return m_data.data(); }
@@ -379,9 +157,9 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
      * @brief Return the frame number of the clusters. 0 is used to indicate
      * that the clusters come from many frames
      */
-    uint64_t frame_number() const { return m_frame_number; }
+    int32_t frame_number() const { return m_frame_number; }
 
-    void set_frame_number(uint64_t frame_number) {
+    void set_frame_number(int32_t frame_number) {
         m_frame_number = frame_number;
     }
 

python/src/cluster.hpp

@@ -66,6 +66,7 @@ void define_cluster(py::module &m, const std::string &typestr) {
 
 
 
+
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType = uint16_t>
 void define_cluster_finder_mt_bindings(py::module &m,

src/Cluster.test.cpp

@@ -26,3 +26,9 @@ TEST_CASE("Correct Instantiation of Cluster and ClusterVector",
     CHECK(not is_cluster_v<int>);
     CHECK(is_cluster_v<Cluster<int, 3, 3>>);
 }
+
+TEST_CASE("Test sum of Cluster", "[.cluster]") {
+    Cluster<int, 2, 2> cluster{0, 0, {1, 2, 3, 4}};
+
+    CHECK(cluster.sum() == 10);
+}

src/ClusterFile.test.cpp

@@ -2,21 +2,29 @@
 #include "test_config.hpp"
 
 #include "aare/defs.hpp"
+#include <algorithm>
 #include <catch2/catch_test_macros.hpp>
 #include <filesystem>
 
 using aare::Cluster;
 using aare::ClusterFile;
+using aare::ClusterVector;
 
-TEST_CASE("Read one frame from a a cluster file", "[.files]") {
+TEST_CASE("Read one frame from a cluster file", "[.files]") {
     // We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
     REQUIRE(std::filesystem::exists(fpath));
 
     ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
     auto clusters = f.read_frame();
-    REQUIRE(clusters.size() == 97);
+    CHECK(clusters.size() == 97);
-    REQUIRE(clusters.frame_number() == 135);
+    CHECK(clusters.frame_number() == 135);
+    CHECK(clusters.at(0).x == 1);
+    CHECK(clusters.at(0).y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters.at(0).data),
+                     std::end(clusters.at(0).data),
+                     std::begin(expected_cluster_data)));
 }
 
 TEST_CASE("Read one frame using ROI", "[.files]") {
@@ -43,6 +51,13 @@ TEST_CASE("Read one frame using ROI", "[.files]") {
         REQUIRE(c.y >= roi.ymin);
         REQUIRE(c.y <= roi.ymax);
     }
+
+    CHECK(clusters.at(0).x == 1);
+    CHECK(clusters.at(0).y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters.at(0).data),
+                     std::end(clusters.at(0).data),
+                     std::begin(expected_cluster_data)));
 }
 
 TEST_CASE("Read clusters from single frame file", "[.files]") {
@@ -154,6 +169,12 @@ TEST_CASE("Read clusters from single frame file", "[.files]") {
         auto clusters = f.read_clusters(50);
         REQUIRE(clusters.size() == 50);
         REQUIRE(clusters.frame_number() == 135);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        REQUIRE(clusters.at(0).x == 1);
+        REQUIRE(clusters.at(0).y == 200);
+        CHECK(std::equal(std::begin(clusters.at(0).data),
+                         std::end(clusters.at(0).data),
+                         std::begin(expected_cluster_data)));
     }
     SECTION("Read more clusters than available") {
         ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
@@ -161,24 +182,169 @@ TEST_CASE("Read clusters from single frame file", "[.files]") {
         auto clusters = f.read_clusters(100);
         REQUIRE(clusters.size() == 97);
         REQUIRE(clusters.frame_number() == 135);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        REQUIRE(clusters.at(0).x == 1);
+        REQUIRE(clusters.at(0).y == 200);
+        CHECK(std::equal(std::begin(clusters.at(0).data),
+                         std::end(clusters.at(0).data),
+                         std::begin(expected_cluster_data)));
     }
     SECTION("Read all clusters") {
         ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
         auto clusters = f.read_clusters(97);
         REQUIRE(clusters.size() == 97);
         REQUIRE(clusters.frame_number() == 135);
-
         REQUIRE(clusters.at(0).x == 1);
         REQUIRE(clusters.at(0).y == 200);
+        int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+        CHECK(std::equal(std::begin(clusters.at(0).data),
+                         std::end(clusters.at(0).data),
+                         std::begin(expected_cluster_data)));
     }
 }
 
-TEST_CASE("Read clusters", "[.files]") {
+TEST_CASE("Read clusters from single frame file with ROI", "[.files]") {
-    // beam_En700eV_-40deg_300V_10us_d0_f0_100.clust
+    auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
-    auto fpath = test_data_path() / "clust" /
-                 "beam_En700eV_-40deg_300V_10us_d0_f0_100.clust";
     REQUIRE(std::filesystem::exists(fpath));
 
     ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
-    auto clusters = f.read_clusters(500);
+
+    aare::ROI roi;
+    roi.xmin = 0;
+    roi.xmax = 50;
+    roi.ymin = 200;
+    roi.ymax = 249;
+    f.set_roi(roi);
+
+    auto clusters = f.read_clusters(10);
+
+    CHECK(clusters.size() == 10);
+    CHECK(clusters.frame_number() == 135);
+    CHECK(clusters.at(0).x == 1);
+    CHECK(clusters.at(0).y == 200);
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    CHECK(std::equal(std::begin(clusters.at(0).data),
+                     std::end(clusters.at(0).data),
+                     std::begin(expected_cluster_data)));
+}
+
+TEST_CASE("Read cluster from multiple frame file", "[.files]") {
+
+    using ClusterType = Cluster<double, 2, 2>;
+
+    auto fpath =
+        test_data_path() / "clust" / "Two_frames_2x2double_test_clusters.clust";
+
+    REQUIRE(std::filesystem::exists(fpath));
+
+    // Two_frames_2x2double_test_clusters.clust
+    //  frame number, num_clusters 0, 4
+    //[10, 20], {0. ,0., 0., 0.}
+    //[11, 30], {1., 1., 1., 1.}
+    //[12, 40], {2., 2., 2., 2.}
+    //[13, 50], {3., 3., 3., 3.}
+    //  1,4
+    //[10, 20], {4., 4., 4., 4.}
+    //[11, 30], {5., 5., 5., 5.}
+    //[12, 40], {6., 6., 6., 6.}
+    //[13, 50], {7., 7., 7., 7.}
+
+    SECTION("Read clusters from both frames") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(2);
+        REQUIRE(clusters.size() == 2);
+        REQUIRE(clusters.frame_number() == 0);
+
+        auto clusters1 = f.read_clusters(3);
+
+        REQUIRE(clusters1.size() == 3);
+        REQUIRE(clusters1.frame_number() == 1);
+    }
+
+    SECTION("Read all clusters") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(8);
+        REQUIRE(clusters.size() == 8);
+        REQUIRE(clusters.frame_number() == 1);
+    }
+
+    SECTION("Read clusters from one frame") {
+        ClusterFile<ClusterType> f(fpath);
+        auto clusters = f.read_clusters(2);
+        REQUIRE(clusters.size() == 2);
+        REQUIRE(clusters.frame_number() == 0);
+
+        auto clusters1 = f.read_clusters(1);
+
+        REQUIRE(clusters1.size() == 1);
+        REQUIRE(clusters1.frame_number() == 0);
+    }
+}
+
+TEST_CASE("Write cluster with potential padding", "[.files][.ClusterFile]") {
+
+    using ClusterType = Cluster<double, 3, 3>;
+
+    REQUIRE(std::filesystem::exists(test_data_path() / "clust"));
+
+    auto fpath = test_data_path() / "clust" / "single_frame_2_clusters.clust";
+
+    ClusterFile<ClusterType> file(fpath, 1000, "w");
+
+    ClusterVector<ClusterType> clustervec(2);
+    int16_t coordinate = 5;
+    clustervec.push_back(ClusterType{
+        coordinate, coordinate, {0., 0., 0., 0., 0., 0., 0., 0., 0.}});
+    clustervec.push_back(ClusterType{
+        coordinate, coordinate, {0., 0., 0., 0., 0., 0., 0., 0., 0.}});
+
+    file.write_frame(clustervec);
+
+    file.close();
+
+    file.open("r");
+
+    auto read_cluster_vector = file.read_frame();
+
+    CHECK(read_cluster_vector.size() == 2);
+    CHECK(read_cluster_vector.frame_number() == 0);
+
+    CHECK(read_cluster_vector.at(0).x == clustervec.at(0).x);
+    CHECK(read_cluster_vector.at(0).y == clustervec.at(0).y);
+    CHECK(std::equal(clustervec.at(0).data, clustervec.at(0).data + 9,
+                     read_cluster_vector.at(0).data, [](double a, double b) {
+                         return std::abs(a - b) <
+                                std::numeric_limits<double>::epsilon();
+                     }));
+
+    CHECK(read_cluster_vector.at(1).x == clustervec.at(1).x);
+    CHECK(read_cluster_vector.at(1).y == clustervec.at(1).y);
+    CHECK(std::equal(clustervec.at(1).data, std::end(clustervec.at(1).data),
+                     read_cluster_vector.at(1).data, [](double a, double b) {
+                         return std::abs(a - b) <
+                                std::numeric_limits<double>::epsilon();
+                     }));
+}
+
+TEST_CASE("Read frame and modify cluster data", "[.files][.ClusterFile]") {
+    auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    ClusterFile<Cluster<int32_t, 3, 3>> f(fpath);
+
+    auto clusters = f.read_frame();
+    CHECK(clusters.size() == 97);
+    CHECK(clusters.frame_number() == 135);
+
+    int32_t expected_cluster_data[] = {0, 1, 2, 3, 4, 5, 6, 7, 8};
+    clusters.push_back(
+        Cluster<int32_t, 3, 3>{0, 0, {0, 1, 2, 3, 4, 5, 6, 7, 8}});
+
+    CHECK(clusters.size() == 98);
+    CHECK(clusters.at(0).x == 1);
+    CHECK(clusters.at(0).y == 200);
+
+    CHECK(std::equal(std::begin(clusters.at(0).data),
+                     std::end(clusters.at(0).data),
+                     std::begin(expected_cluster_data)));
 }

src/ClusterVector.test.cpp

@@ -8,14 +8,13 @@
 using aare::Cluster;
 using aare::ClusterVector;
 
-
+TEST_CASE("item_size return the size of the cluster stored") {
-TEST_CASE("item_size return the size of the cluster stored"){
     using C1 = Cluster<int32_t, 2, 2>;
     ClusterVector<C1> cv(4);
     CHECK(cv.item_size() == sizeof(C1));
 
-    //Sanity check 
+    // Sanity check
-    //2*2*4 = 16 bytes of data for the cluster
+    // 2*2*4 = 16 bytes of data for the cluster
     //  2*2 = 4 bytes for the x and y coordinates
     REQUIRE(cv.item_size() == 20);
 
@@ -30,6 +29,18 @@ TEST_CASE("item_size return the size of the cluster stored"){
     using C4 = Cluster<char, 10, 5>;
     ClusterVector<C4> cv4(4);
     CHECK(cv4.item_size() == sizeof(C4));
+
+    using C5 = Cluster<int32_t, 2, 3>;
+    ClusterVector<C5> cv5(4);
+    CHECK(cv5.item_size() == sizeof(C5));
+
+    using C6 = Cluster<double, 5, 5>;
+    ClusterVector<C6> cv6(4);
+    CHECK(cv6.item_size() == sizeof(C6));
+
+    using C7 = Cluster<double, 3, 3>;
+    ClusterVector<C7> cv7(4);
+    CHECK(cv7.item_size() == sizeof(C7));
 }
 
 TEST_CASE("ClusterVector 2x2 int32_t capacity 4, push back then read",