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JFJochReceiver: Save information on crystal lattice and spot indexing status to HDF5 file

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This commit is contained in:
leonarski_f
2023-05-18 10:46:46 +02:00
parent e3998a7488
commit bb4cee9b2d
12 changed files with 68 additions and 37 deletions
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17
writer/HDF5DataFile.cpp
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@@ -31,6 +31,7 @@ HDF5DataFile::~HDF5DataFile() {
std::vector<hsize_t> dims = {spot_count.size(), max_spots};
result_group->SaveVector("nPeaks", spot_count);
result_group->SaveVector("indexingResult", indexing_result);
result_group->SaveVector("indexingLattice", indexing_lattice, {max_image_number + 1, 9});
if (!rad_int_bin_to_q.empty())
rad_int_group->SaveVector("bin_to_q", rad_int_bin_to_q);
@@ -74,9 +75,12 @@ void HDF5DataFile::CreateFile() {
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",
data_set_spot_int = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakTotalIntensity",
HDF5DataType(0.0f), data_space_spots, dcpl_spots);
data_set_spot_indexed = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakIndexed",
HDF5DataType(1, false), data_space_spots, dcpl_spots);
spot_count.resize(1);
indexing_result.resize(1);
bunch_id.resize(1);
@@ -84,6 +88,7 @@ void HDF5DataFile::CreateFile() {
timestamp.resize(1);
storage_cell.resize(1);
exptime.resize(1);
indexing_lattice.resize(9);
}
void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
@@ -97,6 +102,7 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
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});
data_set_spot_indexed->SetExtent({max_image_number+1, max_spots});
spot_count.resize(max_image_number + 1);
indexing_result.resize(max_image_number + 1);
@@ -105,6 +111,7 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
timestamp.resize(max_image_number + 1);
exptime.resize(max_image_number + 1);
storage_cell.resize(max_image_number + 1);
indexing_lattice.resize((max_image_number + 1) * 9);
}
nimages++;
@@ -115,14 +122,17 @@ 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);
std::vector<uint8_t> spot_indexed(max_spots);
for (int i = 0; i < cnt; i++) {
spot_x[i] = msg.spots[i].x;
spot_y[i] = msg.spots[i].y;
spot_intensity[i] = msg.spots[i].intensity;
spot_indexed[i] = msg.spots[i].indexed;
}
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});
data_set_spot_indexed->WriteVec(spot_indexed, {image_number, 0}, {1, max_spots});
indexing_result[image_number] = msg.indexing_result;
bunch_id[image_number] = msg.bunch_id;
@@ -131,6 +141,11 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
storage_cell[image_number] = msg.storage_cell;
exptime[image_number] = msg.exptime;
if (msg.indexing_lattice.size() == 9) {
for (int i = 0; i < 9; i++)
indexing_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
}
if (!msg.rad_int_profile.empty() && (msg.rad_int_profile.size() == rad_int_bin_to_q.size()))
rad_int_group->SaveVector("img" + std::to_string(image_number), msg.rad_int_profile);
}