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Jungfraujoch/tests/HDF5WritingTest.cpp

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// Copyright (2019-2022) Paul Scherrer Institute
// SPDX-License-Identifier: GPL-3.0-or-later
#include <catch2/catch.hpp>
#include <iostream>
#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;
TEST_CASE("HDF5DataSet_scalar", "[HDF5][Unit]") {
uint16_t tmp_scalar = 16788;
{
HDF5File file("scratch1.h5", true, true, false);
file.SaveScalar("scalar", tmp_scalar);
}
{
HDF5ReadOnlyFile file("scratch1.h5");
HDF5DataSet scalar_dataset(file, "scalar");
HDF5DataType data_type_scalar(scalar_dataset);
HDF5DataSpace data_space_scalar(scalar_dataset);
REQUIRE(data_type_scalar.GetElemSize() == 2);
REQUIRE(data_space_scalar.GetNumOfDimensions() == 0);
REQUIRE(scalar_dataset.ReadScalar<uint16_t>() == tmp_scalar);
REQUIRE(scalar_dataset.ReadScalar<int64_t>() == tmp_scalar);
std::vector<uint16_t> v;
REQUIRE_THROWS(scalar_dataset.ReadVector(v));
}
remove("scratch1.h5");
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5DataSet_string", "[HDF5][Unit]") {
std::string tmp_string = "HDF5Content";
{
HDF5File file("scratch2.h5", true, true, false);
file.SaveScalar("str", tmp_string);
}
{
HDF5ReadOnlyFile file("scratch2.h5");
HDF5DataSet string_dataset(file, "str");
HDF5DataType data_type_str(string_dataset);
HDF5DataSpace data_space_str(string_dataset);
CHECK(data_type_str.GetElemSize() == tmp_string.size() + 1);
CHECK(data_space_str.GetNumOfDimensions() == 0);
CHECK(string_dataset.ReadString() == tmp_string);
}
remove("scratch2.h5");
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5DataSet_vector", "[HDF5][Unit]") {
std::vector<double> tmp_vector (16384);
tmp_vector[0] = 599.88;
tmp_vector[1000] = 800.12;
tmp_vector[15000] = 3.1415926;
{
RegisterHDF5Filter();
HDF5File file("scratch3.h5", true, true, false);
file.SaveVector("vec", tmp_vector);
}
{
HDF5ReadOnlyFile file("scratch3.h5");
HDF5DataSet vector_dataset(file, "vec");
HDF5DataType data_type_vec(vector_dataset);
HDF5DataSpace data_space_vec(vector_dataset);
CHECK(data_type_vec.GetElemSize() == 8);
CHECK(data_space_vec.GetNumOfDimensions() == 1);
CHECK(data_space_vec.GetDimensions()[0] == tmp_vector.size());
std::vector<double> output;
REQUIRE_NOTHROW(vector_dataset.ReadVector(output));
CHECK (output[0] == tmp_vector[0]);
CHECK (output[1000] == tmp_vector[1000]);
CHECK (output[15000] == tmp_vector[15000]);
CHECK (output.size() == tmp_vector.size());
std::vector<double> output2(10);
REQUIRE_NOTHROW(vector_dataset.ReadVector(output2, {15000},{10}));
REQUIRE_THROWS(vector_dataset.ReadVector(output2, {15000},{100}));
CHECK(output2[0] == tmp_vector[15000]);
}
remove("scratch3.h5");
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5File_Delete", "[HDF5][Unit]") {
uint16_t tmp_scalar = 16788;
{
HDF5File file("scratch1.h5", true, true, false);
file.SaveScalar("scalar", tmp_scalar);
}
{
HDF5File file("scratch1.h5", false, true, false);
std::unique_ptr<HDF5DataSet> scalar_dataset;
REQUIRE_NOTHROW(scalar_dataset = std::make_unique<HDF5DataSet>(file, "scalar"));
file.Delete("/scalar");
}
{
HDF5File file("scratch1.h5", false, true, false);
std::unique_ptr<HDF5DataSet> scalar_dataset;
REQUIRE_THROWS(scalar_dataset = std::make_unique<HDF5DataSet>(file, "scalar"));
}
remove("scratch1.h5");
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5MasterFile", "[HDF5][Full]") {
{
RegisterHDF5Filter();
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
x.FilePrefix("test01").ImagesPerTrigger(950);
StartMessage start_message;
x.FillMessage(start_message);
EndMessage end_message;
end_message.number_of_images = x.GetImageNum();
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
x.FilePrefix("test02");
x.FillMessage(start_message);
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
}
remove("test01_master.h5");
remove("test02_master.h5");
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5MasterFile_RadInt", "[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);
x.FilePrefix("test01_rad_int").ImagesPerTrigger(950);
RadialIntegrationMapping mapping(x);
RadialIntegrationProfile profile(mapping);
StartMessage start_message;
x.FillMessage(start_message);
start_message.rad_int_bin_to_q = mapping.GetBinToQ();
EndMessage end_message;
end_message.number_of_images = x.GetImageNum();
end_message.rad_int_result["avg1"] = profile.GetResult(x);
end_message.rad_int_result["avg2"] = profile.GetResult(x);
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
}
remove("test01_rad_int_master.h5");
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5Writer", "[HDF5][Full]") {
{
RegisterHDF5Filter();
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
std::vector<SpotToSave> spots;
x.FilePrefix("test02_1p10").ImagesPerTrigger(5).DataFileCount(2).Compression(JFJochProtoBuf::NO_COMPRESSION);
StartMessage start_message;
x.FillMessage(start_message);
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.spots = spots;
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_Spots", "[HDF5][Full]") {
{
RegisterHDF5Filter();
DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
std::vector<SpotToSave> spots;
spots.push_back({10,10,7});
spots.push_back({20,50,12});
spots.push_back({1000,500,3});
x.FilePrefix("test02_1p10_spots").ImagesPerTrigger(5).DataFileCount(2).Compression(JFJochProtoBuf::NO_COMPRESSION);
StartMessage start_message;
x.FillMessage(start_message);
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.spots = spots;
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_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_rad_int").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));
x.ImagesPerTrigger(5).DataFileCount(5)
.Compression(JFJochProtoBuf::NO_COMPRESSION).FilePrefix("vds");
{
RegisterHDF5Filter();
StartMessage start_message;
x.FillMessage(start_message);
EndMessage end_message;
end_message.number_of_images = x.GetImageNum();
HDF5Writer writer(start_message);
std::vector<uint16_t> image(x.GetPixelsNum());
std::vector<SpotToSave> spots;
for (int i = 0; i < x.GetImageNum(); i++) {
for (auto &j: image)
j = i;
DataMessage message{};
message.image.data = (uint8_t *) image.data();
message.image.size = x.GetPixelsNum() * x.GetPixelDepth();
message.spots = spots;
message.number = i;
REQUIRE_NOTHROW(writer.Write(message));
}
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
}
{
HDF5File file("vds_master.h5", false, true, false);
std::unique_ptr<HDF5DataSet> dataset;
REQUIRE_NOTHROW(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data"));
HDF5DataSpace file_space(*dataset);
REQUIRE(file_space.GetNumOfDimensions() == 3);
REQUIRE(file_space.GetDimensions()[0] == x.GetImageNum());
REQUIRE(file_space.GetDimensions()[1] == x.GetYPixelsNum());
REQUIRE(file_space.GetDimensions()[2] == x.GetXPixelsNum());
std::vector<int16_t> v(x.GetImageNum() * x.GetYPixelsNum() * x.GetXPixelsNum());
std::vector<hsize_t> start = {0, 0, 0};
dataset->ReadVector(v, start, file_space.GetDimensions());
REQUIRE(v[0] == 0);
REQUIRE(v[x.GetYPixelsNum() * x.GetXPixelsNum()] == 1);
REQUIRE(v[2 * x.GetYPixelsNum() * x.GetXPixelsNum()] == 2);
REQUIRE(v[3 * x.GetYPixelsNum() * x.GetXPixelsNum()] == 3);
REQUIRE(v[4 * x.GetYPixelsNum() * x.GetXPixelsNum()] == 4);
}
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5Writer_VDS_missing", "[HDF5][Full]") {
DiffractionExperiment x(DetectorGeometry(1));
x.ImagesPerTrigger(5).DataFileCount(5).Compression(JFJochProtoBuf::NO_COMPRESSION).FilePrefix("vds_missing");
{
RegisterHDF5Filter();
StartMessage start_message;
x.FillMessage(start_message);
EndMessage end_message;
end_message.number_of_images = x.GetImageNum() - 1;
HDF5Writer writer(start_message);
std::vector<uint16_t> image(x.GetPixelsNum());
std::vector<SpotToSave> spots;
for (int i = 0; i < x.GetImageNum() - 1; i++) {
for (auto &j: image)
j = i;
DataMessage message{};
message.image.data = (uint8_t *) image.data();
message.image.size = x.GetPixelsNum() * x.GetPixelDepth();
message.spots = spots;
message.number = i;
REQUIRE_NOTHROW(writer.Write(message));
}
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
}
{
HDF5File file("vds_missing_master.h5", false, true, false);
std::unique_ptr<HDF5DataSet> dataset;
REQUIRE_NOTHROW(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data"));
HDF5DataSpace file_space(*dataset);
REQUIRE(file_space.GetNumOfDimensions() == 3);
REQUIRE(file_space.GetDimensions()[0] == x.GetImageNum()-1);
REQUIRE(file_space.GetDimensions()[1] == x.GetYPixelsNum());
REQUIRE(file_space.GetDimensions()[2] == x.GetXPixelsNum());
std::vector<int16_t> v((x.GetImageNum() - 1) * x.GetYPixelsNum() * x.GetXPixelsNum());
std::vector<hsize_t> start = {0, 0, 0};
dataset->ReadVector(v, start, file_space.GetDimensions());
REQUIRE(v[0] == 0);
REQUIRE(v[x.GetYPixelsNum() * x.GetXPixelsNum()] == 1);
REQUIRE(v[2 * x.GetYPixelsNum() * x.GetXPixelsNum()] == 2);
REQUIRE(v[3 * x.GetYPixelsNum() * x.GetXPixelsNum()] == 3);
}
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5Writer_VDS_zero_images", "[HDF5][Full]") {
DiffractionExperiment x(DetectorGeometry(1));
x.ImagesPerTrigger(5).DataFileCount(5).Compression(JFJochProtoBuf::NO_COMPRESSION).FilePrefix("vds_zero");
{
RegisterHDF5Filter();
StartMessage start_message;
x.FillMessage(start_message);
EndMessage end_message;
end_message.number_of_images = 0;
REQUIRE_NOTHROW(HDF5Metadata::NXmx(start_message, end_message));
}
{
std::unique_ptr<HDF5ReadOnlyFile> file;
std::unique_ptr<HDF5DataSet> dataset;
REQUIRE_NOTHROW(file = std::make_unique<HDF5ReadOnlyFile>("vds_zero_master.h5"));
REQUIRE_THROWS(dataset = std::make_unique<HDF5DataSet>(*file,"/entry/data/data"));
}
// No leftover HDF5 objects
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("HDF5NXmx_DataFileName", "[HDF5]") {
REQUIRE(HDF5Metadata::DataFileName("z/x", 34) == "z/x_data_034.h5");
REQUIRE(HDF5Metadata::DataFileName("z/x", 0) == "z/x_data_000.h5");
REQUIRE_THROWS(HDF5Metadata::DataFileName("z/x", 1000));
REQUIRE_THROWS(HDF5Metadata::DataFileName("z/x", -1));
}
TEST_CASE("HDF5Objects_ExtractFilename", "[HDF5]") {
REQUIRE(ExtractFilename("filename_data_000001.h5") == "filename_data_000001.h5");
REQUIRE(ExtractFilename("dir1/filename_data_000001.h5") == "filename_data_000001.h5");
REQUIRE(ExtractFilename("dir1/dir2/filename_data_000001.h5") == "filename_data_000001.h5");
}
TEST_CASE("HDF5DataType", "[HDF5]") {
HDF5DataType type1(1,true);
REQUIRE(type1.GetElemSize() == 1);
HDF5DataType type2(2,true);
REQUIRE(type2.GetElemSize() == 2);
HDF5DataType type4(4,true);
REQUIRE(type4.GetElemSize() == 4);
HDF5DataType type8(8,true);
REQUIRE(type8.GetElemSize() == 8);
REQUIRE_THROWS(HDF5DataType(7,true));
}
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