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formatted main branch

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mazzol_a
2025-06-10 16:09:06 +02:00
parent efd2338f54
commit f9751902a2
87 changed files with 1710 additions and 1639 deletions
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161
src/ClusterFile.cpp
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@@ -31,17 +31,15 @@ ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
}
}
void ClusterFile::set_roi(ROI roi){
m_roi = roi;
}
void ClusterFile::set_roi(ROI roi) { m_roi = roi; }
void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map){
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){
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()) {
@@ -66,42 +64,44 @@ void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
!(clusters.cluster_size_y() == 3)) {
throw std::runtime_error("Only 3x3 clusters are supported");
}
//First write the frame number - 4 bytes
// First write the frame number - 4 bytes
int32_t frame_number = clusters.frame_number();
if(fwrite(&frame_number, sizeof(frame_number), 1, fp)!=1){
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
// 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");
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()){
// 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){
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){
if (m_noise_map || m_roi) {
return read_clusters_with_cut(n_clusters);
}else{
} else {
return read_clusters_without_cut(n_clusters);
}
}
ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t 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);
ClusterVector<int32_t> clusters(3, 3, n_clusters);
int32_t iframe = 0; // frame number needs to be 4 bytes!
size_t nph_read = 0;
@@ -119,7 +119,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
} else {
nn = nph;
}
nph_read += fread((buf + nph_read*clusters.item_size()),
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
}
@@ -135,7 +135,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
else
nn = nph;
nph_read += fread((buf + nph_read*clusters.item_size()),
nph_read += fread((buf + nph_read * clusters.item_size()),
clusters.item_size(), nn, fp);
m_num_left = nph - nn;
}
@@ -147,22 +147,22 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
// Resize the vector to the number of clusters.
// No new allocation, only change bounds.
clusters.resize(nph_read);
if(m_gain_map)
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);
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){
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));
if (is_selected(c)) {
clusters.push_back(c.x, c.y,
reinterpret_cast<std::byte *>(c.data));
}
}
}
@@ -172,17 +172,21 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t 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");
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){
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));
if (is_selected(c)) {
clusters.push_back(
c.x, c.y, reinterpret_cast<std::byte *>(c.data));
}
}
}
@@ -191,15 +195,14 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
if (clusters.size() >= n_clusters)
break;
}
}
if(m_gain_map)
if (m_gain_map)
clusters.apply_gain_map(m_gain_map->view());
return clusters;
}
Cluster3x3 ClusterFile::read_one_cluster(){
Cluster3x3 ClusterFile::read_one_cluster() {
Cluster3x3 c;
auto rc = fread(&c, sizeof(c), 1, fp);
if (rc != 1) {
@@ -209,13 +212,13 @@ Cluster3x3 ClusterFile::read_one_cluster(){
return c;
}
ClusterVector<int32_t> ClusterFile::read_frame(){
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){
if (m_noise_map || m_roi) {
return read_frame_with_cut();
}else{
} else {
return read_frame_without_cut();
}
}
@@ -235,7 +238,8 @@ ClusterVector<int32_t> ClusterFile::read_frame_without_cut() {
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");
throw std::runtime_error(LOCATION +
"Could not read number of clusters");
}
ClusterVector<int32_t> clusters(3, 3, n_clusters);
@@ -264,18 +268,17 @@ ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
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){
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 (is_selected(c)) {
clusters.push_back(c.x, c.y, reinterpret_cast<std::byte *>(c.data));
}
}
if (m_gain_map)
@@ -283,56 +286,56 @@ ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
return clusters;
}
bool ClusterFile::is_selected(Cluster3x3 &cl) {
//Should fail fast
// 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
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
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
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
// we passed all checks
return true;
}
NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
//TOTO! make work with 2x2 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){
} 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{
} 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.
*/
/**
* @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{};
@@ -347,56 +350,46 @@ Eta2 calculate_eta2(Cluster3x3 &cl) {
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]);
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.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]);
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.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]);
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.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]);
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.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
// 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
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