mirror of
https://github.com/slsdetectorgroup/aare.git
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fixed merge miss
This commit is contained in:
froejdh_e
@ -18,6 +18,8 @@ from .ClusterVector import ClusterVector
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from ._aare import fit_gaus, fit_pol1
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from ._aare import fit_gaus, fit_pol1
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from ._aare import Interpolator
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from ._aare import Interpolator
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from ._aare import calculate_eta2
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from ._aare import calculate_eta2
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from ._aare import apply_custom_weights
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from ._aare import apply_custom_weights
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from .CtbRawFile import CtbRawFile
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from .CtbRawFile import CtbRawFile
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@ -1,402 +0,0 @@
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#include "aare/ClusterFile.hpp"
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#include <algorithm>
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namespace aare {
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ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
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const std::string &mode)
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: m_chunk_size(chunk_size), m_mode(mode) {
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if (mode == "r") {
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fp = fopen(fname.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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fname.string());
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}
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} else if (mode == "w") {
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fp = fopen(fname.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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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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}
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void ClusterFile::set_roi(ROI roi){
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m_roi = roi;
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}
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void ClusterFile::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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void ClusterFile::set_gain_map(const NDView<double, 2> gain_map){
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m_gain_map = NDArray<double, 2>(gain_map);
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// Gain map is passed as ADU/keV to avoid dividing in when applying the gain
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// map we invert it here
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for (auto &item : m_gain_map->view()) {
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item = 1.0 / item;
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}
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}
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ClusterFile::~ClusterFile() { close(); }
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void ClusterFile::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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void ClusterFile::write_frame(const ClusterVector<int32_t> &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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if (!(clusters.cluster_size_x() == 3) &&
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!(clusters.cluster_size_y() == 3)) {
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throw std::runtime_error("Only 3x3 clusters are supported");
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}
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//First write the frame number - 4 bytes
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int32_t frame_number = clusters.frame_number();
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if(fwrite(&frame_number, sizeof(frame_number), 1, fp)!=1){
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throw std::runtime_error(LOCATION + "Could not write frame number");
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}
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//Then write the number of clusters - 4 bytes
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uint32_t n_clusters = clusters.size();
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if(fwrite(&n_clusters, sizeof(n_clusters), 1, fp)!=1){
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throw std::runtime_error(LOCATION + "Could not write number of clusters");
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}
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//Now write the clusters in the frame
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if(fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp)!=clusters.size()){
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throw std::runtime_error(LOCATION + "Could not write clusters");
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}
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}
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ClusterVector<int32_t> ClusterFile::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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ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(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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ClusterVector<int32_t> clusters(3,3, n_clusters);
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int32_t iframe = 0; // frame number needs to be 4 bytes!
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size_t nph_read = 0;
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uint32_t nn = m_num_left;
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uint32_t nph = m_num_left; // number of clusters in frame needs to be 4
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// auto buf = reinterpret_cast<Cluster3x3 *>(clusters.data());
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auto buf = clusters.data();
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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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nn = n_clusters;
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} else {
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nn = nph;
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}
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nph_read += fread((buf + nph_read*clusters.item_size()),
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clusters.item_size(), nn, fp);
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m_num_left = nph - nn; // write back the number of photons left
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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 n_clusters
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while (fread(&iframe, sizeof(iframe), 1, fp)) {
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clusters.set_frame_number(iframe);
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// read number of clusters in frame
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if (fread(&nph, sizeof(nph), 1, fp)) {
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if (nph > (n_clusters - nph_read))
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nn = n_clusters - nph_read;
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else
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nn = nph;
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nph_read += fread((buf + nph_read*clusters.item_size()),
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clusters.item_size(), nn, fp);
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m_num_left = nph - nn;
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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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// Resize the vector to the number of clusters.
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// No new allocation, only change bounds.
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clusters.resize(nph_read);
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if(m_gain_map)
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clusters.apply_gain_map(m_gain_map->view());
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return clusters;
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}
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ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
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ClusterVector<int32_t> clusters(3,3);
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clusters.reserve(n_clusters);
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// if there are photons left from previous frame read them first
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if (m_num_left) {
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while(m_num_left && clusters.size() < n_clusters){
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Cluster3x3 c = read_one_cluster();
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if(is_selected(c)){
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clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
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}
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}
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}
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// we did not have enough clusters left in the previous frame
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// keep on reading frames until reaching n_clusters
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if (clusters.size() < n_clusters) {
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// sanity check
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if (m_num_left) {
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throw std::runtime_error(LOCATION + "Entered second loop with clusters left\n");
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}
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int32_t frame_number = 0; // frame number needs to be 4 bytes!
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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(frame_number); //cluster vector will hold the last frame number
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while(m_num_left && clusters.size() < n_clusters){
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Cluster3x3 c = read_one_cluster();
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if(is_selected(c)){
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clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
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}
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}
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}
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// we have enough clusters, break out of the outer while loop
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if (clusters.size() >= n_clusters)
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break;
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}
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}
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if(m_gain_map)
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clusters.apply_gain_map(m_gain_map->view());
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return clusters;
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}
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Cluster3x3 ClusterFile::read_one_cluster(){
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Cluster3x3 c;
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auto rc = fread(&c, sizeof(c), 1, fp);
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if (rc != 1) {
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throw std::runtime_error(LOCATION + "Could not read cluster");
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}
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--m_num_left;
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return c;
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}
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ClusterVector<int32_t> ClusterFile::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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ClusterVector<int32_t> ClusterFile::read_frame_without_cut() {
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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_num_left) {
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throw std::runtime_error(
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"There are still photons left in the last frame");
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}
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int32_t frame_number;
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if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
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throw std::runtime_error(LOCATION + "Could not read frame number");
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}
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int32_t n_clusters; // Saved as 32bit integer in the cluster file
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if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
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throw std::runtime_error(LOCATION + "Could not read number of clusters");
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}
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ClusterVector<int32_t> clusters(3, 3, n_clusters);
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clusters.set_frame_number(frame_number);
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if (fread(clusters.data(), clusters.item_size(), n_clusters, fp) !=
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static_cast<size_t>(n_clusters)) {
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throw std::runtime_error(LOCATION + "Could not read clusters");
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}
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clusters.resize(n_clusters);
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if (m_gain_map)
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clusters.apply_gain_map(m_gain_map->view());
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return clusters;
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}
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ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
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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_num_left) {
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throw std::runtime_error(
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"There are still photons left in the last frame");
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}
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int32_t frame_number;
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if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
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throw std::runtime_error("Could not read frame number");
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}
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if (fread(&m_num_left, sizeof(m_num_left), 1, fp) != 1) {
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throw std::runtime_error("Could not read number of clusters");
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}
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ClusterVector<int32_t> clusters(3, 3);
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clusters.reserve(m_num_left);
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clusters.set_frame_number(frame_number);
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while(m_num_left){
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Cluster3x3 c = read_one_cluster();
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if(is_selected(c)){
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clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
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}
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}
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if (m_gain_map)
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clusters.apply_gain_map(m_gain_map->view());
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return clusters;
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}
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bool ClusterFile::is_selected(Cluster3x3 &cl) {
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//Should fail fast
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if (m_roi) {
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if (!(m_roi->contains(cl.x, cl.y))) {
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return false;
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}
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}
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if (m_noise_map){
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int32_t sum_1x1 = cl.data[4]; // central pixel
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int32_t sum_2x2 = cl.sum_2x2(); // highest sum of 2x2 subclusters
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int32_t sum_3x3 = cl.sum(); // sum of all pixels
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auto noise = (*m_noise_map)(cl.y, cl.x); //TODO! check if this is correct
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if (sum_1x1 <= noise || sum_2x2 <= 2 * noise || sum_3x3 <= 3 * noise) {
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return false;
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}
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}
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//we passed all checks
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return true;
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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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if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
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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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eta2(i, 0) = e.x;
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eta2(i, 1) = e.y;
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}
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}else if(clusters.cluster_size_x() == 2 || clusters.cluster_size_y() == 2){
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for (size_t i = 0; i < clusters.size(); i++) {
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auto e = calculate_eta2(clusters.at<Cluster2x2>(i));
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eta2(i, 0) = e.x;
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eta2(i, 1) = e.y;
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}
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}else{
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throw std::runtime_error("Only 3x3 and 2x2 clusters are supported");
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}
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return eta2;
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}
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/**
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* @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2 struct
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* containing etay, etax and the corner of the cluster.
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*/
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Eta2 calculate_eta2(Cluster3x3 &cl) {
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Eta2 eta{};
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std::array<int32_t, 4> tot2;
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tot2[0] = cl.data[0] + cl.data[1] + cl.data[3] + cl.data[4];
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tot2[1] = cl.data[1] + cl.data[2] + cl.data[4] + cl.data[5];
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tot2[2] = cl.data[3] + cl.data[4] + cl.data[6] + cl.data[7];
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tot2[3] = cl.data[4] + cl.data[5] + cl.data[7] + cl.data[8];
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auto c = std::max_element(tot2.begin(), tot2.end()) - tot2.begin();
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eta.sum = tot2[c];
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switch (c) {
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case cBottomLeft:
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if ((cl.data[3] + cl.data[4]) != 0)
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eta.x =
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static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
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if ((cl.data[1] + cl.data[4]) != 0)
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eta.y =
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static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
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eta.c = cBottomLeft;
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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
|
|
||||||
@ -62,6 +62,8 @@ TEST_CASE("Read one frame using ROI", "[.files]") {
|
|||||||
std::begin(expected_cluster_data)));
|
std::begin(expected_cluster_data)));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
TEST_CASE("Read clusters from single frame file", "[.files]") {
|
TEST_CASE("Read clusters from single frame file", "[.files]") {
|
||||||
|
|
||||||
// frame_number, num_clusters [135] 97
|
// frame_number, num_clusters [135] 97
|
||||||
|
|||||||
Reference in New Issue
Block a user