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docs for ClusterFile
This commit is contained in:
froejdh_e
parent
e1cc774d6c
commit
f6d736facd
@ -55,6 +55,19 @@ int32_t frame_number
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uint32_t number_of_clusters
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....
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*/
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/**
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* @brief Class to read and write cluster files
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* Expects data to be laid out as:
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*
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*
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* int32_t frame_number
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* uint32_t number_of_clusters
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* int16_t x, int16_t y, int32_t data[9] x number_of_clusters
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* int32_t frame_number
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* uint32_t number_of_clusters
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* etc.
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*/
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class ClusterFile {
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FILE *fp{};
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uint32_t m_num_left{};
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@ -62,16 +75,52 @@ class ClusterFile {
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const std::string m_mode;
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public:
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/**
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* @brief Construct a new Cluster File object
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* @param fname path to the file
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* @param chunk_size number of clusters to read at a time when iterating
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* over the file
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* @param mode mode to open the file in. "r" for reading, "w" for writing,
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* "a" for appending
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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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~ClusterFile();
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ClusterVector<int32_t> read_clusters(size_t n_clusters);
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ClusterVector<int32_t> read_frame();
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void write_frame(const ClusterVector<int32_t> &clusters);
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std::vector<Cluster3x3>
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read_cluster_with_cut(size_t n_clusters, double *noise_map, int nx, int ny);
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~ClusterFile();
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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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*/
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ClusterVector<int32_t> read_clusters(size_t n_clusters);
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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 file pointer not
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* at the beginning of a frame
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*/
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ClusterVector<int32_t> read_frame();
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void write_frame(const ClusterVector<int32_t> &clusters);
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// Need to be migrated to support NDArray and return a ClusterVector
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// std::vector<Cluster3x3>
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// read_cluster_with_cut(size_t n_clusters, double *noise_map, int nx, int ny);
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/**
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* @brief Return the chunk size
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*/
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size_t chunk_size() const { return m_chunk_size; }
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/**
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* @brief Close the file. If not closed the file will be closed in the destructor
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*/
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void close();
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};
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@ -80,7 +129,6 @@ int analyze_data(int32_t *data, int32_t *t2, int32_t *t3, char *quad,
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int analyze_cluster(Cluster3x3 &cl, int32_t *t2, int32_t *t3, char *quad,
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double *eta2x, double *eta2y, double *eta3x, double *eta3y);
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NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters);
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Eta2 calculate_eta2(Cluster3x3 &cl);
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@ -37,15 +37,15 @@ void define_cluster_file_io_bindings(py::module &m) {
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return v;
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})
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.def("write_frame", &ClusterFile::write_frame)
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.def("read_cluster_with_cut",
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[](ClusterFile &self, size_t n_clusters,
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py::array_t<double> noise_map, int nx, int ny) {
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auto view = make_view_2d(noise_map);
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auto *vec =
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new std::vector<Cluster3x3>(self.read_cluster_with_cut(
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n_clusters, view.data(), nx, ny));
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return return_vector(vec);
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})
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// .def("read_cluster_with_cut",
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// [](ClusterFile &self, size_t n_clusters,
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// py::array_t<double> noise_map, int nx, int ny) {
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// auto view = make_view_2d(noise_map);
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// auto *vec =
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// new std::vector<Cluster3x3>(self.read_cluster_with_cut(
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// n_clusters, view.data(), nx, ny));
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// return return_vector(vec);
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// })
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.def("__enter__", [](ClusterFile &self) { return &self; })
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.def("__exit__",
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[](ClusterFile &self,
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@ -20,6 +20,12 @@ ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
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throw std::runtime_error("Could not open file for writing: " +
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fname.string());
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}
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} else if (mode == "a") {
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fp = fopen(fname.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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fname.string());
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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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@ -35,7 +41,7 @@ void ClusterFile::close() {
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}
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void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
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if (m_mode != "w") {
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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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if (!(clusters.cluster_size_x() == 3) &&
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@ -132,134 +138,135 @@ ClusterVector<int32_t> ClusterFile::read_frame() {
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}
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std::vector<Cluster3x3> ClusterFile::read_cluster_with_cut(size_t n_clusters,
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double *noise_map,
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int nx, int ny) {
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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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std::vector<Cluster3x3> clusters(n_clusters);
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// size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
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// uint32_t *n_left, double *noise_map, int
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// nx, int ny) {
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int iframe = 0;
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// uint32_t nph = *n_left;
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uint32_t nph = m_num_left;
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// uint32_t nn = *n_left;
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uint32_t nn = m_num_left;
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size_t nph_read = 0;
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// std::vector<Cluster3x3> ClusterFile::read_cluster_with_cut(size_t n_clusters,
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// double *noise_map,
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// int nx, int ny) {
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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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// std::vector<Cluster3x3> clusters(n_clusters);
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// // size_t read_clusters_with_cut(FILE *fp, size_t n_clusters, Cluster *buf,
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// // uint32_t *n_left, double *noise_map, int
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// // nx, int ny) {
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// int iframe = 0;
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// // uint32_t nph = *n_left;
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// uint32_t nph = m_num_left;
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// // uint32_t nn = *n_left;
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// uint32_t nn = m_num_left;
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// size_t nph_read = 0;
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int32_t t2max, tot1;
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int32_t tot3;
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// Cluster *ptr = buf;
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Cluster3x3 *ptr = clusters.data();
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int good = 1;
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double noise;
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// read photons left from previous frame
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if (noise_map)
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printf("Using noise map\n");
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// int32_t t2max, tot1;
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// int32_t tot3;
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// // Cluster *ptr = buf;
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// Cluster3x3 *ptr = clusters.data();
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// int good = 1;
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// double noise;
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// // read photons left from previous frame
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// if (noise_map)
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// printf("Using noise map\n");
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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
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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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}
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for (size_t iph = 0; iph < nn; iph++) {
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// read photons 1 by 1
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size_t n_read =
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fread(reinterpret_cast<void *>(ptr), sizeof(Cluster3x3), 1, fp);
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if (n_read != 1) {
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clusters.resize(nph_read);
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return clusters;
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}
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// TODO! error handling on read
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good = 1;
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if (noise_map) {
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if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 && ptr->y < ny) {
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tot1 = ptr->data[4];
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analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL, NULL, NULL,
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NULL);
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noise = noise_map[ptr->y * nx + ptr->x];
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if (tot1 > noise || t2max > 2 * noise || tot3 > 3 * noise) {
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;
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} else {
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good = 0;
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printf("%d %d %f %d %d %d\n", ptr->x, ptr->y, noise,
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tot1, t2max, tot3);
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}
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} else {
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printf("Bad pixel number %d %d\n", ptr->x, ptr->y);
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good = 0;
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}
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}
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if (good) {
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ptr++;
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nph_read++;
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}
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(m_num_left)--;
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if (nph_read >= n_clusters)
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break;
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}
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}
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if (nph_read < n_clusters) {
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// // keep on reading frames and photons until reaching
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// n_clusters
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while (fread(&iframe, sizeof(iframe), 1, fp)) {
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// // printf("%d\n",nph_read);
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if (fread(&nph, sizeof(nph), 1, fp)) {
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// // printf("** %d\n",nph);
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m_num_left = nph;
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for (size_t iph = 0; iph < nph; iph++) {
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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
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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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// }
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// for (size_t iph = 0; iph < nn; iph++) {
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// // read photons 1 by 1
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size_t n_read = fread(reinterpret_cast<void *>(ptr),
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sizeof(Cluster3x3), 1, fp);
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if (n_read != 1) {
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clusters.resize(nph_read);
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return clusters;
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// return nph_read;
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}
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good = 1;
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if (noise_map) {
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if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 &&
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ptr->y < ny) {
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tot1 = ptr->data[4];
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analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL,
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NULL, NULL, NULL);
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// size_t n_read =
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// fread(reinterpret_cast<void *>(ptr), sizeof(Cluster3x3), 1, fp);
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// if (n_read != 1) {
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// clusters.resize(nph_read);
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// return clusters;
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// }
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// // TODO! error handling on read
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// good = 1;
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// if (noise_map) {
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// if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 && ptr->y < ny) {
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// tot1 = ptr->data[4];
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// analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL, NULL, NULL,
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// NULL);
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// noise = noise_map[ptr->y * nx + ptr->x];
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noise = noise_map[ptr->y + ny * ptr->x];
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if (tot1 > noise || t2max > 2 * noise ||
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tot3 > 3 * noise) {
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;
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} else
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good = 0;
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} else {
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printf("Bad pixel number %d %d\n", ptr->x, ptr->y);
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good = 0;
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}
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}
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if (good) {
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ptr++;
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nph_read++;
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}
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(m_num_left)--;
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if (nph_read >= n_clusters)
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break;
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}
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}
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if (nph_read >= n_clusters)
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break;
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}
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}
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// printf("%d\n",nph_read);
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clusters.resize(nph_read);
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return clusters;
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}
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// if (tot1 > noise || t2max > 2 * noise || tot3 > 3 * noise) {
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// ;
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// } else {
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// good = 0;
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// printf("%d %d %f %d %d %d\n", ptr->x, ptr->y, noise,
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// tot1, t2max, tot3);
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// }
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// } else {
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// printf("Bad pixel number %d %d\n", ptr->x, ptr->y);
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// good = 0;
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// }
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// }
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// if (good) {
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// ptr++;
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// nph_read++;
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// }
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// (m_num_left)--;
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// if (nph_read >= n_clusters)
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// break;
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// }
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// }
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// if (nph_read < n_clusters) {
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// // // keep on reading frames and photons until reaching
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// // n_clusters
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// while (fread(&iframe, sizeof(iframe), 1, fp)) {
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// // // printf("%d\n",nph_read);
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// if (fread(&nph, sizeof(nph), 1, fp)) {
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// // // printf("** %d\n",nph);
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// m_num_left = nph;
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// for (size_t iph = 0; iph < nph; iph++) {
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// // // read photons 1 by 1
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// size_t n_read = fread(reinterpret_cast<void *>(ptr),
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// sizeof(Cluster3x3), 1, fp);
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// if (n_read != 1) {
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// clusters.resize(nph_read);
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// return clusters;
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// // return nph_read;
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// }
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// good = 1;
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// if (noise_map) {
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// if (ptr->x >= 0 && ptr->x < nx && ptr->y >= 0 &&
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// ptr->y < ny) {
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// tot1 = ptr->data[4];
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// analyze_cluster(*ptr, &t2max, &tot3, NULL, NULL,
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// NULL, NULL, NULL);
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// // noise = noise_map[ptr->y * nx + ptr->x];
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// noise = noise_map[ptr->y + ny * ptr->x];
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// if (tot1 > noise || t2max > 2 * noise ||
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// tot3 > 3 * noise) {
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// ;
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// } else
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// good = 0;
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// } else {
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// printf("Bad pixel number %d %d\n", ptr->x, ptr->y);
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// good = 0;
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// }
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// }
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// if (good) {
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// ptr++;
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// nph_read++;
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// }
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// (m_num_left)--;
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// if (nph_read >= n_clusters)
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// break;
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// }
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// }
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// if (nph_read >= n_clusters)
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// break;
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// }
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// }
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// // printf("%d\n",nph_read);
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// clusters.resize(nph_read);
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// return clusters;
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// }
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NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
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//TOTO! make work with 2x2 clusters
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NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
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for (size_t i = 0; i < clusters.size(); i++) {
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auto e = calculate_eta2(clusters.at<Cluster3x3>(i));
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