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HDF5DataFile: Save radial integration result

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This commit is contained in:
leonarski_f
2023-05-06 12:13:22 +02:00
parent 116fb8091b
commit 70a10c594c
4 changed files with 69 additions and 13 deletions
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tests/HDF5WritingTest.cpp
+36 -2
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@@ -3,13 +3,13 @@
#include <catch2/catch.hpp>
#include <iostream>
#include <bitshuffle/bitshuffle.h>
#include "../common/DiffractionExperiment.h"
#include "../writer/HDF5Objects.h"
#include "../writer/HDF5Writer.h"
#include "../writer/HDF5NXmx.h"
#include "../compression/JFJochCompressor.h"
#include "../image_analysis/RadialIntegrationProfile.h"
using namespace std::literals::chrono_literals;
@@ -195,6 +195,41 @@ TEST_CASE("HDF5Writer_Spots", "[HDF5][Full]") {
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5Writer_Rad_Int_Profile", "[HDF5][Full]") {
{
RegisterHDF5Filter();
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
x.QSpacingForRadialInt_recipA(0.1).LowQForRadialInt_recipA(0.1).HighQForRadialInt_recipA(4);
RadialIntegrationMapping mapping(x);
RadialIntegrationProfile profile(mapping);
std::vector<float> rad_int_profile(mapping.GetBinNumber(), 4.0);
std::vector<float> rad_int_avg(mapping.GetBinNumber(), 0.33);
x.FilePrefix("test02_1p10_spots").ImagesPerTrigger(5).DataFileCount(2).Compression(JFJochProtoBuf::NO_COMPRESSION);
StartMessage start_message;
x.FillMessage(start_message);
start_message.rad_int_bin_to_q = mapping.GetBinToQ();
HDF5Writer file_set(start_message);
std::vector<uint16_t> image(x.GetPixelsNum());
for (int i = 0; i < x.GetImageNum(); i++) {
DataMessage message{};
message.image.data = (uint8_t *) image.data();
message.image.size = x.GetPixelsNum() * x.GetPixelDepth();
message.rad_int_profile = std::vector<float>(mapping.GetBinNumber(), i);
message.number = i;
REQUIRE_NOTHROW(file_set.Write(message));
}
}
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5Writer_VDS", "[HDF5][Full]") {
DiffractionExperiment x(DetectorGeometry(1));
@@ -345,7 +380,6 @@ TEST_CASE("HDF5Objects_ExtractFilename", "[HDF5]") {
REQUIRE(ExtractFilename("dir1/dir2/filename_data_000001.h5") == "filename_data_000001.h5");
}
TEST_CASE("HDF5DataType", "[HDF5]") {
HDF5DataType type1(1,true);
REQUIRE(type1.GetElemSize() == 1);
writer/HDF5DataFile.cpp
+23 -10
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@@ -5,9 +5,10 @@
#include "../compression/JFJochCompressor.h"
HDF5DataFile::HDF5DataFile(const std::string &in_filename, int64_t width, int64_t height,
int64_t pixel_depth_byte, bool is_signed, CompressionAlgorithm compression,
int64_t pixel_depth_byte, bool is_signed, const std::vector<float>& in_rad_int_bin_to_q,
CompressionAlgorithm compression,
size_t in_max_spots) : data_type(pixel_depth_byte, is_signed),
max_spots(in_max_spots) {
max_spots(in_max_spots), rad_int_bin_to_q(in_rad_int_bin_to_q) {
max_image_number = 0;
nimages = 0;
@@ -27,14 +28,17 @@ HDF5DataFile::~HDF5DataFile() {
data_set.reset();
if (!spot_count.empty()) {
HDF5Group group(*data_file, "/entry/result");
group.NXClass("NXcollection");
std::vector<hsize_t> dims = {spot_count.size(), max_spots};
group.SaveVector("nPeaks", spot_count);
group.SaveVector("peakXPosRaw", spot_x, dims, CompressionAlgorithm::BSHUF_LZ4);
group.SaveVector("peakYPosRaw", spot_y, dims, CompressionAlgorithm::BSHUF_LZ4);
group.SaveVector("peakTotalIntensity", spot_intensity, dims, CompressionAlgorithm::BSHUF_LZ4);
group.SaveVector("indexingResult", indexing_result);
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())
rad_int_group->SaveVector("bin_to_q", rad_int_bin_to_q);
if (!rad_int_file_avg.empty() && (rad_int_file_avg.size() == rad_int_bin_to_q.size()))
rad_int_group->SaveVector("file_avg", rad_int_file_avg);
HDF5Group group_exp(*data_file, "/entry/jungfrau");
group_exp.NXClass("NXcollection");
@@ -42,7 +46,8 @@ HDF5DataFile::~HDF5DataFile() {
group_exp.SaveVector("info", jf_info);
group_exp.SaveVector("timestamp", timestamp);
}
rad_int_group.reset();
result_group.reset();
data_file.reset();
}
@@ -51,6 +56,11 @@ void HDF5DataFile::CreateFile() {
HDF5Group(*data_file, "/entry").NXClass("NXentry");
HDF5Group(*data_file, "/entry/data").NXClass("NXdata");
result_group = std::make_unique<HDF5Group>(*data_file, "/entry/result");
result_group->NXClass("NXcollection");
rad_int_group = std::make_unique<HDF5Group>(*data_file, "/entry/result/rad_int");
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);
@@ -99,6 +109,9 @@ void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
bunch_id[image_number] = msg.bunch_id;
jf_info[image_number] = msg.jf_info;
timestamp[image_number] = msg.timestamp;
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);
}
HDF5DataFileStatistics HDF5DataFile::GetStatistics() const {
writer/HDF5DataFile.h
+9 -1
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@@ -24,6 +24,9 @@ class HDF5DataFile {
std::unique_ptr<HDF5File> data_file = nullptr;
std::unique_ptr<HDF5DataSet> data_set = nullptr;
std::unique_ptr<HDF5Group> result_group = nullptr;
std::unique_ptr<HDF5Group> rad_int_group = nullptr;
size_t xpixel;
size_t ypixel;
size_t max_image_number;
@@ -37,6 +40,9 @@ class HDF5DataFile {
std::vector<uint32_t> jf_info;
std::vector<uint64_t> timestamp;
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;
@@ -48,9 +54,11 @@ class HDF5DataFile {
void CreateFile();
public:
HDF5DataFile(const std::string& name, int64_t width, int64_t height, int64_t pixel_depth_byte,
bool is_signed, CompressionAlgorithm compression = CompressionAlgorithm::BSHUF_LZ4,
bool is_signed, const std::vector<float>& rad_int_bin_to_q,
CompressionAlgorithm compression = CompressionAlgorithm::BSHUF_LZ4,
size_t max_spots = 0);
~HDF5DataFile();
void Write(const DataMessage& msg, uint64_t image_number);
HDF5DataFileStatistics GetStatistics() const;
size_t GetNumImages() const;
writer/HDF5Writer.cpp
+1
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@@ -12,6 +12,7 @@ HDF5Writer::HDF5Writer(const StartMessage &request)
request.image_size_x, request.image_size_y,
request.pixel_bit_depth / 8,
request.pixel_signed,
request.rad_int_bin_to_q,
request.compression_algorithm,
request.max_spot_count);
}