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moved parts of ClusterFile implementation into declaration
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This commit is contained in:
Mazzoleni Alice Francesca
parent
d4050ec557
commit
acd9d5d487
@ -60,26 +60,81 @@ class ClusterFile {
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* @throws std::runtime_error if the file could not be opened
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*/
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ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000,
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const std::string &mode = "r");
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const std::string &mode = "r")
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~ClusterFile();
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: m_filename(fname.string()), m_chunk_size(chunk_size), m_mode(mode) {
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if (mode == "r") {
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fp = fopen(m_filename.c_str(), "rb");
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if (!fp) {
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throw std::runtime_error("Could not open file for reading: " +
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m_filename);
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}
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} else if (mode == "w") {
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fp = fopen(m_filename.c_str(), "wb");
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if (!fp) {
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throw std::runtime_error("Could not open file for writing: " +
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m_filename);
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}
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} else if (mode == "a") {
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fp = fopen(m_filename.c_str(), "ab");
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if (!fp) {
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throw std::runtime_error("Could not open file for appending: " +
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m_filename);
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}
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} else {
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throw std::runtime_error("Unsupported mode: " + mode);
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}
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}
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~ClusterFile() { close(); }
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/**
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* @brief Read n_clusters clusters from the file discarding frame numbers.
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* If EOF is reached the returned vector will have less than n_clusters
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* clusters
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* @brief Read n_clusters clusters from the file discarding
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* frame numbers. If EOF is reached the returned vector will
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* have less than n_clusters clusters
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*/
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ClusterVector<ClusterType> read_clusters(size_t n_clusters);
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ClusterVector<ClusterType> read_clusters(size_t n_clusters) {
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if (m_mode != "r") {
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throw std::runtime_error("File not opened for reading");
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}
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if (m_noise_map || m_roi) {
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return read_clusters_with_cut(n_clusters);
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} else {
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return read_clusters_without_cut(n_clusters);
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}
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}
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/**
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* @brief Read a single frame from the file and return the clusters. The
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* cluster vector will have the frame number set.
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* @throws std::runtime_error if the file is not opened for reading or the
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* file pointer not at the beginning of a frame
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* @brief Read a single frame from the file and return the
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* clusters. The cluster vector will have the frame number
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* set.
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* @throws std::runtime_error if the file is not opened for
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* reading or the file pointer not at the beginning of a
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* frame
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*/
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ClusterVector<ClusterType> read_frame();
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ClusterVector<ClusterType> read_frame() {
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if (m_mode != "r") {
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throw std::runtime_error(LOCATION + "File not opened for reading");
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}
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if (m_noise_map || m_roi) {
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return read_frame_with_cut();
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} else {
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return read_frame_without_cut();
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}
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}
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void write_frame(const ClusterVector<ClusterType> &clusters);
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void write_frame(const ClusterVector<ClusterType> &clusters) {
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if (m_mode != "w" && m_mode != "a") {
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throw std::runtime_error("File not opened for writing");
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}
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int32_t frame_number = clusters.frame_number();
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fwrite(&frame_number, sizeof(frame_number), 1, fp);
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uint32_t n_clusters = clusters.size();
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fwrite(&n_clusters, sizeof(n_clusters), 1, fp);
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fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp);
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}
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/**
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* @brief Return the chunk size
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@ -87,39 +142,80 @@ class ClusterFile {
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size_t chunk_size() const { return m_chunk_size; }
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/**
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* @brief Set the region of interest to use when reading clusters. If set
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* only clusters within the ROI will be read.
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* @brief Set the region of interest to use when reading
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* clusters. If set only clusters within the ROI will be
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* read.
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*/
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void set_roi(ROI roi);
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void set_roi(ROI roi) { m_roi = roi; }
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/**
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* @brief Set the noise map to use when reading clusters. If set clusters
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* below the noise level will be discarded. Selection criteria one of:
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* Central pixel above noise, highest 2x2 sum above 2 * noise, total sum
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* above 3 * noise.
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* @brief Set the noise map to use when reading clusters. If
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* set clusters below the noise level will be discarded.
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* Selection criteria one of: Central pixel above noise,
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* highest 2x2 sum above 2 * noise, total sum above 3 *
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* noise.
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*/
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void set_noise_map(const NDView<int32_t, 2> noise_map);
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void set_noise_map(const NDView<int32_t, 2> noise_map) {
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m_noise_map = NDArray<int32_t, 2>(noise_map);
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}
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/**
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* @brief Set the gain map to use when reading clusters. If set the gain map
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* will be applied to the clusters that pass ROI and noise_map selection.
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* @brief Set the gain map to use when reading clusters. If
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* set the gain map will be applied to the clusters that
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* pass ROI and noise_map selection.
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*/
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void set_gain_map(const NDView<double, 2> gain_map);
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void set_gain_map(const NDView<double, 2> gain_map) {
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m_gain_map = GainMap(gain_map);
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}
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void set_gain_map(const GainMap &gain_map);
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void set_gain_map(const GainMap &gain_map) { m_gain_map = gain_map; }
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void set_gain_map(const GainMap &&gain_map);
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void set_gain_map(const GainMap &&gain_map) { m_gain_map = gain_map; }
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/**
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* @brief Close the file. If not closed the file will be closed in the
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* destructor
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* @brief Close the file. If not closed the file will be
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* closed in the destructor
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*/
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void close();
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void close() {
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if (fp) {
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fclose(fp);
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fp = nullptr;
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}
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}
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/** @brief Open the file in specific mode
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*
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*/
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void open(const std::string &mode);
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void open(const std::string &mode) {
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if (fp) {
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close();
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}
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if (mode == "r") {
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fp = fopen(m_filename.c_str(), "rb");
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if (!fp) {
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throw std::runtime_error("Could not open file for reading: " +
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m_filename);
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}
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m_mode = "r";
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} else if (mode == "w") {
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fp = fopen(m_filename.c_str(), "wb");
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if (!fp) {
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throw std::runtime_error("Could not open file for writing: " +
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m_filename);
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}
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m_mode = "w";
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} else if (mode == "a") {
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fp = fopen(m_filename.c_str(), "ab");
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if (!fp) {
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throw std::runtime_error("Could not open file for appending: " +
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m_filename);
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}
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m_mode = "a";
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} else {
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throw std::runtime_error("Unsupported mode: " + mode);
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}
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}
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private:
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ClusterVector<ClusterType> read_clusters_with_cut(size_t n_clusters);
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@ -130,133 +226,6 @@ class ClusterFile {
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ClusterType read_one_cluster();
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};
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template <typename ClusterType, typename Enable>
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ClusterFile<ClusterType, Enable>::ClusterFile(
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const std::filesystem::path &fname, size_t chunk_size,
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const std::string &mode)
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: m_filename(fname.string()), m_chunk_size(chunk_size), m_mode(mode) {
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if (mode == "r") {
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fp = fopen(m_filename.c_str(), "rb");
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if (!fp) {
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throw std::runtime_error("Could not open file for reading: " +
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m_filename);
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}
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} else if (mode == "w") {
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fp = fopen(m_filename.c_str(), "wb");
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if (!fp) {
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throw std::runtime_error("Could not open file for writing: " +
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m_filename);
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}
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} else if (mode == "a") {
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fp = fopen(m_filename.c_str(), "ab");
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if (!fp) {
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throw std::runtime_error("Could not open file for appending: " +
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m_filename);
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}
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} else {
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throw std::runtime_error("Unsupported mode: " + mode);
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}
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}
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template <typename ClusterType, typename Enable>
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ClusterFile<ClusterType, Enable>::~ClusterFile() {
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close();
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::close() {
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if (fp) {
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fclose(fp);
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fp = nullptr;
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}
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::open(const std::string &mode) {
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if (fp) {
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close();
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}
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if (mode == "r") {
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fp = fopen(m_filename.c_str(), "rb");
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if (!fp) {
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throw std::runtime_error("Could not open file for reading: " +
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m_filename);
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}
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m_mode = "r";
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} else if (mode == "w") {
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fp = fopen(m_filename.c_str(), "wb");
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if (!fp) {
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throw std::runtime_error("Could not open file for writing: " +
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m_filename);
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}
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m_mode = "w";
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} else if (mode == "a") {
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fp = fopen(m_filename.c_str(), "ab");
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if (!fp) {
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throw std::runtime_error("Could not open file for appending: " +
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m_filename);
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}
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m_mode = "a";
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} else {
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throw std::runtime_error("Unsupported mode: " + mode);
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}
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::set_roi(ROI roi) {
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m_roi = roi;
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::set_noise_map(
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const NDView<int32_t, 2> noise_map) {
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m_noise_map = NDArray<int32_t, 2>(noise_map);
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::set_gain_map(
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const NDView<double, 2> gain_map) {
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m_gain_map = GainMap(gain_map);
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::set_gain_map(const GainMap &gain_map) {
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m_gain_map = gain_map;
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}
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::set_gain_map(const GainMap &&gain_map) {
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m_gain_map = gain_map;
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}
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// TODO generally supported for all clsuter types
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template <typename ClusterType, typename Enable>
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void ClusterFile<ClusterType, Enable>::write_frame(
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const ClusterVector<ClusterType> &clusters) {
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if (m_mode != "w" && m_mode != "a") {
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throw std::runtime_error("File not opened for writing");
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}
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int32_t frame_number = clusters.frame_number();
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fwrite(&frame_number, sizeof(frame_number), 1, fp);
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uint32_t n_clusters = clusters.size();
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fwrite(&n_clusters, sizeof(n_clusters), 1, fp);
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fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp);
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}
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template <typename ClusterType, typename Enable>
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ClusterVector<ClusterType>
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ClusterFile<ClusterType, Enable>::read_clusters(size_t n_clusters) {
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if (m_mode != "r") {
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throw std::runtime_error("File not opened for reading");
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}
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if (m_noise_map || m_roi) {
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return read_clusters_with_cut(n_clusters);
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} else {
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return read_clusters_without_cut(n_clusters);
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}
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}
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template <typename ClusterType, typename Enable>
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ClusterVector<ClusterType>
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ClusterFile<ClusterType, Enable>::read_clusters_without_cut(size_t n_clusters) {
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@ -276,8 +245,8 @@ ClusterFile<ClusterType, Enable>::read_clusters_without_cut(size_t n_clusters) {
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// if there are photons left from previous frame read them first
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if (nph) {
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if (nph > n_clusters) {
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// if we have more photons left in the frame then photons to read we
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// read directly the requested number
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// if we have more photons left in the frame then photons to
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// read we read directly the requested number
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nn = n_clusters;
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} else {
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nn = nph;
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@ -343,8 +312,8 @@ ClusterFile<ClusterType, Enable>::read_clusters_with_cut(size_t n_clusters) {
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while (fread(&frame_number, sizeof(frame_number), 1, fp)) {
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if (fread(&m_num_left, sizeof(m_num_left), 1, fp)) {
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clusters.set_frame_number(
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frame_number); // cluster vector will hold the last frame
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// number
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frame_number); // cluster vector will hold the last
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// frame number
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while (m_num_left && clusters.size() < n_clusters) {
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ClusterType c = read_one_cluster();
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if (is_selected(c)) {
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@ -375,18 +344,6 @@ ClusterType ClusterFile<ClusterType, Enable>::read_one_cluster() {
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return c;
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}
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template <typename ClusterType, typename Enable>
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ClusterVector<ClusterType> ClusterFile<ClusterType, Enable>::read_frame() {
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if (m_mode != "r") {
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throw std::runtime_error(LOCATION + "File not opened for reading");
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}
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if (m_noise_map || m_roi) {
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return read_frame_with_cut();
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} else {
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return read_frame_without_cut();
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}
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}
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template <typename ClusterType, typename Enable>
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ClusterVector<ClusterType>
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ClusterFile<ClusterType, Enable>::read_frame_without_cut() {
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