updated release notes

CMakeLists.txt

@@ -369,22 +369,22 @@ set(PUBLICHEADERS
 
 set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/FilePtr.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Fit.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/PixelMap.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
 )

RELEASE.md

@@ -10,6 +10,7 @@ Features:
 
 Bugfixes:
 - Fixed reading RawFiles with ROI fully excluding some sub files. 
+- Removed unused file: ClusterFile.cpp 
 
 ### 2025.05.22
 

src/ClusterFile.cpp

@@ -1,395 +0,0 @@
-#include "aare/ClusterFile.hpp"
-
-#include <algorithm>
-
-namespace aare {
-
-ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
-                         const std::string &mode)
-    : m_chunk_size(chunk_size), m_mode(mode) {
-
-    if (mode == "r") {
-        fp = fopen(fname.c_str(), "rb");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for reading: " +
-                                     fname.string());
-        }
-    } else if (mode == "w") {
-        fp = fopen(fname.c_str(), "wb");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for writing: " +
-                                     fname.string());
-        }
-    } else if (mode == "a") {
-        fp = fopen(fname.c_str(), "ab");
-        if (!fp) {
-            throw std::runtime_error("Could not open file for appending: " +
-                                     fname.string());
-        }
-    } else {
-        throw std::runtime_error("Unsupported mode: " + mode);
-    }
-}
-
-void ClusterFile::set_roi(ROI roi) { m_roi = roi; }
-
-void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map) {
-    m_noise_map = NDArray<int32_t, 2>(noise_map);
-}
-
-void ClusterFile::set_gain_map(const NDView<double, 2> gain_map) {
-    m_gain_map = NDArray<double, 2>(gain_map);
-
-    // Gain map is passed as ADU/keV to avoid dividing in when applying the gain
-    // map we invert it here
-    for (auto &item : m_gain_map->view()) {
-        item = 1.0 / item;
-    }
-}
-
-ClusterFile::~ClusterFile() { close(); }
-
-void ClusterFile::close() {
-    if (fp) {
-        fclose(fp);
-        fp = nullptr;
-    }
-}
-
-void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
-    if (m_mode != "w" && m_mode != "a") {
-        throw std::runtime_error("File not opened for writing");
-    }
-    if (!(clusters.cluster_size_x() == 3) &&
-        !(clusters.cluster_size_y() == 3)) {
-        throw std::runtime_error("Only 3x3 clusters are supported");
-    }
-    // First write the frame number - 4 bytes
-    int32_t frame_number = clusters.frame_number();
-    if (fwrite(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not write frame number");
-    }
-
-    // Then write the number of clusters - 4 bytes
-    uint32_t n_clusters = clusters.size();
-    if (fwrite(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION +
-                                 "Could not write number of clusters");
-    }
-
-    // Now write the clusters in the frame
-    if (fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp) !=
-        clusters.size()) {
-        throw std::runtime_error(LOCATION + "Could not write clusters");
-    }
-}
-
-ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters) {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_noise_map || m_roi) {
-        return read_clusters_with_cut(n_clusters);
-    } else {
-        return read_clusters_without_cut(n_clusters);
-    }
-}
-
-ClusterVector<int32_t>
-ClusterFile::read_clusters_without_cut(size_t n_clusters) {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-
-    ClusterVector<int32_t> clusters(3, 3, n_clusters);
-
-    int32_t iframe = 0; // frame number needs to be 4 bytes!
-    size_t nph_read = 0;
-    uint32_t nn = m_num_left;
-    uint32_t nph = m_num_left; // number of clusters in frame needs to be 4
-
-    // auto buf = reinterpret_cast<Cluster3x3 *>(clusters.data());
-    auto buf = clusters.data();
-    // if there are photons left from previous frame read them first
-    if (nph) {
-        if (nph > n_clusters) {
-            // if we have more photons left in the frame then photons to read we
-            // read directly the requested number
-            nn = n_clusters;
-        } else {
-            nn = nph;
-        }
-        nph_read += fread((buf + nph_read * clusters.item_size()),
-                          clusters.item_size(), nn, fp);
-        m_num_left = nph - nn; // write back the number of photons left
-    }
-
-    if (nph_read < n_clusters) {
-        // keep on reading frames and photons until reaching n_clusters
-        while (fread(&iframe, sizeof(iframe), 1, fp)) {
-            clusters.set_frame_number(iframe);
-            // read number of clusters in frame
-            if (fread(&nph, sizeof(nph), 1, fp)) {
-                if (nph > (n_clusters - nph_read))
-                    nn = n_clusters - nph_read;
-                else
-                    nn = nph;
-
-                nph_read += fread((buf + nph_read * clusters.item_size()),
-                                  clusters.item_size(), nn, fp);
-                m_num_left = nph - nn;
-            }
-            if (nph_read >= n_clusters)
-                break;
-        }
-    }
-
-    // Resize the vector to the number of clusters.
-    // No new allocation, only change bounds.
-    clusters.resize(nph_read);
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
-    ClusterVector<int32_t> clusters(3, 3);
-    clusters.reserve(n_clusters);
-
-    // if there are photons left from previous frame read them first
-    if (m_num_left) {
-        while (m_num_left && clusters.size() < n_clusters) {
-            Cluster3x3 c = read_one_cluster();
-            if (is_selected(c)) {
-                clusters.push_back(c.x, c.y,
-                                   reinterpret_cast<std::byte *>(c.data));
-            }
-        }
-    }
-
-    // we did not have enough clusters left in the previous frame
-    // keep on reading frames until reaching n_clusters
-    if (clusters.size() < n_clusters) {
-        // sanity check
-        if (m_num_left) {
-            throw std::runtime_error(
-                LOCATION + "Entered second loop with clusters left\n");
-        }
-
-        int32_t frame_number = 0; // frame number needs to be 4 bytes!
-        while (fread(&frame_number, sizeof(frame_number), 1, fp)) {
-            if (fread(&m_num_left, sizeof(m_num_left), 1, fp)) {
-                clusters.set_frame_number(
-                    frame_number); // cluster vector will hold the last frame
-                                   // number
-                while (m_num_left && clusters.size() < n_clusters) {
-                    Cluster3x3 c = read_one_cluster();
-                    if (is_selected(c)) {
-                        clusters.push_back(
-                            c.x, c.y, reinterpret_cast<std::byte *>(c.data));
-                    }
-                }
-            }
-
-            // we have enough clusters, break out of the outer while loop
-            if (clusters.size() >= n_clusters)
-                break;
-        }
-    }
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-
-    return clusters;
-}
-
-Cluster3x3 ClusterFile::read_one_cluster() {
-    Cluster3x3 c;
-    auto rc = fread(&c, sizeof(c), 1, fp);
-    if (rc != 1) {
-        throw std::runtime_error(LOCATION + "Could not read cluster");
-    }
-    --m_num_left;
-    return c;
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame() {
-    if (m_mode != "r") {
-        throw std::runtime_error(LOCATION + "File not opened for reading");
-    }
-    if (m_noise_map || m_roi) {
-        return read_frame_with_cut();
-    } else {
-        return read_frame_without_cut();
-    }
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame_without_cut() {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_num_left) {
-        throw std::runtime_error(
-            "There are still photons left in the last frame");
-    }
-    int32_t frame_number;
-    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not read frame number");
-    }
-
-    int32_t n_clusters; // Saved as 32bit integer in the cluster file
-    if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION +
-                                 "Could not read number of clusters");
-    }
-
-    ClusterVector<int32_t> clusters(3, 3, n_clusters);
-    clusters.set_frame_number(frame_number);
-
-    if (fread(clusters.data(), clusters.item_size(), n_clusters, fp) !=
-        static_cast<size_t>(n_clusters)) {
-        throw std::runtime_error(LOCATION + "Could not read clusters");
-    }
-    clusters.resize(n_clusters);
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
-    if (m_mode != "r") {
-        throw std::runtime_error("File not opened for reading");
-    }
-    if (m_num_left) {
-        throw std::runtime_error(
-            "There are still photons left in the last frame");
-    }
-    int32_t frame_number;
-    if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        throw std::runtime_error("Could not read frame number");
-    }
-
-    if (fread(&m_num_left, sizeof(m_num_left), 1, fp) != 1) {
-        throw std::runtime_error("Could not read number of clusters");
-    }
-
-    ClusterVector<int32_t> clusters(3, 3);
-    clusters.reserve(m_num_left);
-    clusters.set_frame_number(frame_number);
-    while (m_num_left) {
-        Cluster3x3 c = read_one_cluster();
-        if (is_selected(c)) {
-            clusters.push_back(c.x, c.y, reinterpret_cast<std::byte *>(c.data));
-        }
-    }
-    if (m_gain_map)
-        clusters.apply_gain_map(m_gain_map->view());
-    return clusters;
-}
-
-bool ClusterFile::is_selected(Cluster3x3 &cl) {
-    // Should fail fast
-    if (m_roi) {
-        if (!(m_roi->contains(cl.x, cl.y))) {
-            return false;
-        }
-    }
-    if (m_noise_map) {
-        int32_t sum_1x1 = cl.data[4];   // central pixel
-        int32_t sum_2x2 = cl.sum_2x2(); // highest sum of 2x2 subclusters
-        int32_t sum_3x3 = cl.sum();     // sum of all pixels
-
-        auto noise =
-            (*m_noise_map)(cl.y, cl.x); // TODO! check if this is correct
-        if (sum_1x1 <= noise || sum_2x2 <= 2 * noise || sum_3x3 <= 3 * noise) {
-            return false;
-        }
-    }
-    // we passed all checks
-    return true;
-}
-
-NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
-    // TOTO! make work with 2x2 clusters
-    NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
-
-    if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
-        for (size_t i = 0; i < clusters.size(); i++) {
-            auto e = calculate_eta2(clusters.at<Cluster3x3>(i));
-            eta2(i, 0) = e.x;
-            eta2(i, 1) = e.y;
-        }
-    } else if (clusters.cluster_size_x() == 2 ||
-               clusters.cluster_size_y() == 2) {
-        for (size_t i = 0; i < clusters.size(); i++) {
-            auto e = calculate_eta2(clusters.at<Cluster2x2>(i));
-            eta2(i, 0) = e.x;
-            eta2(i, 1) = e.y;
-        }
-    } else {
-        throw std::runtime_error("Only 3x3 and 2x2 clusters are supported");
-    }
-
-    return eta2;
-}
-
-/**
- * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2
- * struct containing etay, etax and the corner of the cluster.
- */
-Eta2 calculate_eta2(Cluster3x3 &cl) {
-    Eta2 eta{};
-
-    std::array<int32_t, 4> tot2;
-    tot2[0] = cl.data[0] + cl.data[1] + cl.data[3] + cl.data[4];
-    tot2[1] = cl.data[1] + cl.data[2] + cl.data[4] + cl.data[5];
-    tot2[2] = cl.data[3] + cl.data[4] + cl.data[6] + cl.data[7];
-    tot2[3] = cl.data[4] + cl.data[5] + cl.data[7] + cl.data[8];
-
-    auto c = std::max_element(tot2.begin(), tot2.end()) - tot2.begin();
-    eta.sum = tot2[c];
-    switch (c) {
-    case cBottomLeft:
-        if ((cl.data[3] + cl.data[4]) != 0)
-            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-        if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y = static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-        eta.c = cBottomLeft;
-        break;
-    case cBottomRight:
-        if ((cl.data[2] + cl.data[5]) != 0)
-            eta.x = static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
-        if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y = static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-        eta.c = cBottomRight;
-        break;
-    case cTopLeft:
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y = static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-        eta.c = cTopLeft;
-        break;
-    case cTopRight:
-        if ((cl.data[5] + cl.data[4]) != 0)
-            eta.x = static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
-        if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y = static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-        eta.c = cTopRight;
-        break;
-        // no default to allow compiler to warn about missing cases
-    }
-    return eta;
-}
-
-Eta2 calculate_eta2(Cluster2x2 &cl) {
-    Eta2 eta{};
-    if ((cl.data[0] + cl.data[1]) != 0)
-        eta.x = static_cast<double>(cl.data[1]) / (cl.data[0] + cl.data[1]);
-    if ((cl.data[0] + cl.data[2]) != 0)
-        eta.y = static_cast<double>(cl.data[2]) / (cl.data[0] + cl.data[2]);
-    eta.sum = cl.data[0] + cl.data[1] + cl.data[2] + cl.data[3];
-    eta.c = cBottomLeft; // TODO! This is not correct, but need to put something
-    return eta;
-}
-
-} // namespace aare