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File writer and spot finding improvements

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This commit is contained in:
leonarski_f
2024-04-08 11:18:50 +02:00
parent 15d99c6162
commit c6d2b5eedf
72 changed files with 690 additions and 893 deletions
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103
writer/HDF5DataFilePluginMX.cpp
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@@ -2,7 +2,9 @@
#include "HDF5DataFilePluginMX.h"
void HDF5DataFilePluginMX::SetupSWMRFile(HDF5File &data_file, const DataMessage &msg) {
HDF5DataFilePluginMX::HDF5DataFilePluginMX(size_t in_max_spots) : max_spots(in_max_spots) {}
void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) {
if (max_spots == 0)
return;
@@ -11,45 +13,14 @@ void HDF5DataFilePluginMX::SetupSWMRFile(HDF5File &data_file, const DataMessage
HDF5DataSpace data_space_spots({1, max_spots}, {H5S_UNLIMITED, max_spots});
HDF5Dcpl dcpl_spots;
dcpl_spots.SetChunking({1, max_spots});
HDF5DataSet(data_file, "/entry/MX/peakXPosRaw", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
HDF5DataSet(data_file, "/entry/MX/peakYPosRaw", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
HDF5DataSet(data_file, "/entry/MX/peakTotalIntensity", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
HDF5DataSet(data_file, "/entry/MX/peakIndexed", HDF5DataType(1, false), data_space_spots, dcpl_spots);
HDF5DataSpace data_space_linear({2}, {H5S_UNLIMITED});
HDF5Dcpl dcpl_linear;
dcpl_linear.SetChunking({1});
HDF5DataSet(data_file, "/entry/MX/nPeaks", HDF5DataType(4, false), data_space_linear, dcpl_linear).SetExtent({1});
HDF5DataSet(data_file, "/entry/MX/strongPixels", HDF5DataType(4, false), data_space_linear, dcpl_linear).SetExtent({1});
HDF5DataSet(data_file, "/entry/MX/imageIndexed", HDF5DataType(1, false), data_space_linear, dcpl_linear).SetExtent({1});
if (msg.resolution_estimation) {
res_estimation = true;
HDF5DataSet(data_file, "/entry/MX/resolutionEstimation", HDF5DataType(0.0f), data_space_linear,
dcpl_linear).SetExtent({1});
}
HDF5DataSpace data_space_lattice({1, 9}, {H5S_UNLIMITED, 9});
HDF5Dcpl dcpl_lattice;
dcpl_lattice.SetChunking({1, 9});
HDF5DataSet(data_file, "/entry/MX/latticeIndexed", HDF5DataType(0.0f), data_space_lattice, dcpl_lattice);
}
void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) {
if (max_spots == 0)
return;
data_set_spot_x = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakXPosRaw");
data_set_spot_y = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakYPosRaw");
data_set_spot_int = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakTotalIntensity");
data_set_spot_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakIndexed");
data_set_spot_npeaks = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/nPeaks");
data_set_strong_pixel_count = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/strongPixels");
data_set_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/imageIndexed");
data_set_indexed_lattice = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/latticeIndexed");
if (res_estimation)
data_set_resolution_estimation = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/resolutionEstimation");
data_set_spot_x = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakXPosRaw", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_y = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakYPosRaw", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_int = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakTotalIntensity", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakIndexed", HDF5DataType(1, false),
data_space_spots, dcpl_spots);
}
void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
@@ -64,13 +35,11 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
data_set_spot_y->SetExtent({max_image_number+1, max_spots});
data_set_spot_int->SetExtent({max_image_number+1, max_spots});
data_set_spot_indexed->SetExtent({max_image_number+1, max_spots});
data_set_spot_npeaks->SetExtent({max_image_number+1});
data_set_strong_pixel_count->SetExtent({max_image_number + 1});
data_set_indexed->SetExtent({max_image_number + 1});
data_set_indexed_lattice->SetExtent({max_image_number + 1, 9});
if (res_estimation)
data_set_resolution_estimation->SetExtent({max_image_number + 1});
npeaks.resize(max_image_number + 1);
strong_pixel_count.resize(max_image_number + 1);
indexed.resize(max_image_number + 1);
indexed_lattice.resize((max_image_number + 1) * 9);
}
std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
@@ -88,33 +57,23 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
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});
data_set_spot_indexed->WriteVec(spot_indexed, {image_number, 0}, {1, max_spots});
data_set_spot_npeaks->WriteScalar(spot_cnt, {image_number});
data_set_strong_pixel_count->WriteScalar(static_cast<uint32_t>(msg.strong_pixel_count), {image_number});
data_set_indexed->WriteScalar((uint8_t) msg.indexing_result, {image_number});
if (msg.indexing_lattice.size() == 9)
data_set_indexed_lattice->WriteVec(msg.indexing_lattice, {image_number, 0}, {1, 9});
if (res_estimation)
data_set_resolution_estimation->WriteScalar(msg.resolution_estimation.value(), {image_number});
npeaks[image_number] = spot_cnt;
strong_pixel_count[image_number] = msg.strong_pixel_count;
indexed[image_number] = msg.indexing_result;
if (msg.indexing_lattice.size() == 9) {
for (int i = 0; i < 9; i++)
indexed_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
}
}
void HDF5DataFilePluginMX::Flush() {
if (max_spots == 0)
return;
data_set_spot_x->Flush();
data_set_spot_y->Flush();
data_set_spot_int->Flush();
data_set_spot_indexed->Flush();
data_set_spot_npeaks->Flush();
data_set_strong_pixel_count->Flush();
data_set_indexed->Flush();
data_set_indexed_lattice->Flush();
if (res_estimation)
data_set_resolution_estimation->Flush();
}
HDF5DataFilePluginMX::HDF5DataFilePluginMX(size_t in_max_spots) : max_spots(in_max_spots) {
void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
if (!npeaks.empty())
data_file.SaveVector("/entry/MX/nPeaks", npeaks);
if (!strong_pixel_count.empty())
data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count);
if (!indexed.empty())
data_file.SaveVector("/entry/MX/imageIndexed", indexed);
if (!indexed_lattice.empty())
data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9});
}