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HDF5DataFile: spot information is written as images are coming

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This commit is contained in:
leonarski_f
2023-05-17 20:07:25 +02:00
parent f372c0e697
commit 0febe9856f
4 changed files with 70 additions and 16 deletions
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writer/HDF5DataFile.cpp
+24 -12
View File
@@ -30,9 +30,6 @@ HDF5DataFile::~HDF5DataFile() {
if (!spot_count.empty()) {
std::vector<hsize_t> dims = {spot_count.size(), max_spots};
result_group->SaveVector("nPeaks", spot_count);
result_group->SaveVector("peakXPosRaw", spot_x, dims, CompressionAlgorithm::BSHUF_LZ4);
result_group->SaveVector("peakYPosRaw", spot_y, dims, CompressionAlgorithm::BSHUF_LZ4);
result_group->SaveVector("peakTotalIntensity", spot_intensity, dims, CompressionAlgorithm::BSHUF_LZ4);
result_group->SaveVector("indexingResult", indexing_result);
if (!rad_int_bin_to_q.empty())
@@ -65,10 +62,20 @@ void HDF5DataFile::CreateFile() {
HDF5DataSpace data_space({1, ypixel, xpixel},{H5S_UNLIMITED, ypixel, xpixel});
data_set = std::make_unique<HDF5DataSet>(*data_file, "/entry/data/data", data_type, data_space, dcpl);
HDF5DataSpace data_space_spots({1, max_spots},{H5S_UNLIMITED, max_spots});
HDF5Dcpl dcpl_spots;
dcpl_spots.SetChunking({1, max_spots});
data_set_spot_x = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakXPosRaw",
HDF5DataType(0.0f), data_space_spots, dcpl_spots);
data_set_spot_y = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakYPosRaw",
HDF5DataType(0.0f), data_space_spots, dcpl_spots);
data_set_spot_int = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/TotalIntensity",
HDF5DataType(0.0f), data_space_spots, dcpl_spots);
spot_count.resize(1);
spot_x.resize(max_spots);
spot_y.resize(max_spots);
spot_intensity.resize(max_spots);
indexing_result.resize(1);
bunch_id.resize(1);
jf_info.resize(1);
@@ -84,10 +91,11 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
if (image_number > max_image_number) {
max_image_number = image_number;
data_set->SetExtent({max_image_number+1, ypixel, xpixel});
data_set_spot_x->SetExtent({max_image_number+1, max_spots});
data_set_spot_y->SetExtent({max_image_number+1, max_spots});
data_set_spot_int->SetExtent({max_image_number+1, max_spots});
spot_count.resize(max_image_number + 1);
spot_x.resize(max_spots * (max_image_number + 1));
spot_y.resize(max_spots * (max_image_number + 1));
spot_intensity.resize(max_spots * (max_image_number + 1));
indexing_result.resize(max_image_number + 1);
bunch_id.resize(max_image_number + 1);
jf_info.resize(max_image_number + 1);
@@ -102,11 +110,15 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
spot_count[image_number] = cnt;
std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
for (int i = 0; i < cnt; i++) {
spot_x[max_spots * image_number + i] = msg.spots[i].x;
spot_y[max_spots * image_number + i] = msg.spots[i].y;
spot_intensity[max_spots * image_number + i] = msg.spots[i].intensity;
spot_x[i] = msg.spots[i].x;
spot_y[i] = msg.spots[i].y;
spot_intensity[i] = msg.spots[i].intensity;
}
data_set_spot_x->WriteVec(spot_x, {image_number, 0}, {1, max_spots});
data_set_spot_y->WriteVec(spot_y, {image_number, 0}, {1, max_spots});
data_set_spot_int->WriteVec(spot_intensity, {image_number, 0}, {1, max_spots});
indexing_result[image_number] = msg.indexing_result;
bunch_id[image_number] = msg.bunch_id;
writer/HDF5DataFile.h
+3 -3
View File
@@ -23,6 +23,9 @@ class HDF5DataFile {
std::unique_ptr<HDF5File> data_file = nullptr;
std::unique_ptr<HDF5DataSet> data_set = nullptr;
std::unique_ptr<HDF5DataSet> data_set_spot_x = nullptr;
std::unique_ptr<HDF5DataSet> data_set_spot_y = nullptr;
std::unique_ptr<HDF5DataSet> data_set_spot_int = nullptr;
std::unique_ptr<HDF5Group> result_group = nullptr;
std::unique_ptr<HDF5Group> rad_int_group = nullptr;
@@ -44,9 +47,6 @@ class HDF5DataFile {
std::vector<float> rad_int_bin_to_q;
std::vector<float> rad_int_file_avg;
std::vector<float> spot_x;
std::vector<float> spot_y;
std::vector<float> spot_intensity;
std::vector<uint32_t> spot_count;
const size_t max_spots;
writer/HDF5Objects.cpp
+1 -1
View File
@@ -74,7 +74,7 @@ std::vector<hsize_t> HDF5DataSpace::GetDimensions() const {
void HDF5DataSpace::SelectHyperslab(const std::vector<hsize_t> &start, const std::vector<hsize_t> &size) {
if ((start.size() != ndims) || (size.size() != ndims))
throw JFJochException(JFJochExceptionCategory::HDF5, "Arrays are inconsistent with dataspace dimension number");
throw JFJochException(JFJochExceptionCategory::HDF5, "Arrays are inconsistent with dataspace dimension number " + std::to_string(ndims));
if (H5Sselect_hyperslab(id, H5S_SELECT_SET, start.data(), NULL, size.data(), NULL) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot select hyperslab");
writer/HDF5Objects.h
+42
View File
@@ -115,6 +115,8 @@ public:
std::vector<hsize_t> dim = {}, CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION);
};
#include <iostream>
class HDF5Group : public HDF5Object {
public:
HDF5Group(const HDF5Object& parent, const std::string& name);
@@ -148,6 +150,46 @@ public:
const HDF5DataSpace &data_space);
~HDF5DataSet();
HDF5DataSet& Write(const HDF5DataType &data_type, const void *val);
template <class T>
HDF5DataSet& WriteVec(const std::vector<T> &v,
const std::vector<hsize_t> &start,
const std::vector<hsize_t> &size) {
HDF5DataSpace mem_space({v.size()});
HDF5DataSpace file_space(*this);
std::cout << int32_t(file_space.GetNumOfDimensions()) << std::endl;
std::cout << int32_t(file_space.GetDimensions()[0]) << std::endl;
std::cout << int32_t(mem_space.GetDimensions()[0]) << std::endl;
file_space.SelectHyperslab(start, size);
if (H5Dwrite(id,
HDF5DataType(v[0]).GetID(),
mem_space.GetID(),
file_space.GetID(),
H5P_DEFAULT,
v.data()) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Vector dataset write unsuccessful");
return *this;
}
template <class T>
HDF5DataSet& WriteScalar(const T &val,
const std::vector<hsize_t> &start) {
HDF5DataSpace mem_space({1});
HDF5DataSpace file_space(*this);
std::cout << uint32_t(file_space.GetNumOfDimensions()) << std::endl;
file_space.SelectHyperslab(start, {1});
if (H5Dwrite(id,
HDF5DataType(val).GetID(),
mem_space.GetID(),
file_space.GetID(),
H5P_DEFAULT,
&val) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Vector dataset write unsuccessful");
return *this;
}
HDF5DataSet& WriteDirectChunk(const void *val, hsize_t data_size, const std::vector<hsize_t>& offset);
HDF5DataSet& Flush();