ClusterFile

class ClusterFile

Class to read and write cluster files Expects data to be laid out as:

  int32_t frame_number
  uint32_t number_of_clusters
  int16_t x, int16_t y, int32_t data[9] * number_of_clusters
  int32_t frame_number
  uint32_t number_of_clusters
  etc.

Public Functions

ClusterFile(const std::filesystem::path &fname, size_t chunk_size = 1000, const std::string &mode = "r")

Construct a new Cluster File object.

Parameters:

• fname – path to the file

• chunk_size – number of clusters to read at a time when iterating over the file

• mode – mode to open the file in. “r” for reading, “w” for writing, “a” for appending

Throws:

std::runtime_error – if the file could not be opened

~ClusterFile()

ClusterVector<int32_t> read_clusters(size_t n_clusters)

Read n_clusters clusters from the file discarding frame numbers. If EOF is reached the returned vector will have less than n_clusters clusters.

ClusterVector<int32_t> read_clusters(size_t n_clusters, ROI roi)

ClusterVector<int32_t> read_frame()

Read a single frame from the file and return the clusters. The cluster vector will have the frame number set.

Throws:

std::runtime_error – if the file is not opened for reading or the file pointer not at the beginning of a frame

void write_frame(const ClusterVector<int32_t> &clusters)

inline size_t chunk_size() const

Return the chunk size.

void set_roi(ROI roi)

Set the region of interest to use when reading clusters. If set only clusters within the ROI will be read.

void set_noise_map(const NDView<int32_t, 2> noise_map)

Set the noise map to use when reading clusters. If set clusters below the noise level will be discarded. Selection criteria one of: Central pixel above noise, highest 2x2 sum above 2 * noise, total sum above 3 * noise.

void set_gain_map(const NDView<double, 2> gain_map)

Set the gain map to use when reading clusters. If set the gain map will be applied to the clusters that pass ROI and noise_map selection.

void close()

Close the file. If not closed the file will be closed in the destructor.

Private Functions

ClusterVector<int32_t> read_clusters_with_cut(size_t n_clusters)

ClusterVector<int32_t> read_clusters_without_cut(size_t n_clusters)

ClusterVector<int32_t> read_frame_with_cut()

ClusterVector<int32_t> read_frame_without_cut()

bool is_selected(Cluster3x3 &cl)

Cluster3x3 read_one_cluster()

Private Members

FILE *fp = {}

uint32_t m_num_left = {}

size_t m_chunk_size = {}

const std::string m_mode

std::optional<ROI> m_roi

std::optional<NDArray<int32_t, 2>> m_noise_map

std::optional<NDArray<double, 2>> m_gain_map