536 lines
20 KiB
C++
536 lines
20 KiB
C++
// Copyright (2019-2023) Paul Scherrer Institute
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#include <catch2/catch_all.hpp>
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#include <iostream>
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#include "../common/DiffractionExperiment.h"
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#include "../writer/HDF5Objects.h"
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#include "../writer/HDF5Writer.h"
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#include "../writer/HDF5NXmx.h"
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#include "../compression/JFJochCompressor.h"
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#include "../image_analysis/AzimuthalIntegrationProfile.h"
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#include <nlohmann/json.hpp>
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using namespace std::literals::chrono_literals;
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TEST_CASE("HDF5DataSet_scalar", "[HDF5][Unit]") {
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uint16_t tmp_scalar = 16788;
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{
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HDF5File file("scratch1.h5");
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file.SaveScalar("scalar", tmp_scalar);
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}
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{
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HDF5ReadOnlyFile file("scratch1.h5");
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HDF5DataSet scalar_dataset(file, "scalar");
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HDF5DataType data_type_scalar(scalar_dataset);
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HDF5DataSpace data_space_scalar(scalar_dataset);
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REQUIRE(data_type_scalar.GetElemSize() == 2);
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REQUIRE(data_space_scalar.GetNumOfDimensions() == 0);
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REQUIRE(scalar_dataset.ReadScalar<uint16_t>() == tmp_scalar);
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REQUIRE(scalar_dataset.ReadScalar<int64_t>() == tmp_scalar);
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std::vector<uint16_t> v;
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REQUIRE_THROWS(scalar_dataset.ReadVector(v));
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}
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remove("scratch1.h5");
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5DataSet_string", "[HDF5][Unit]") {
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std::string tmp_string = "HDF5Content";
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{
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HDF5File file("scratch2.h5");
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file.SaveScalar("str", tmp_string);
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}
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{
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HDF5ReadOnlyFile file("scratch2.h5");
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HDF5DataSet string_dataset(file, "str");
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HDF5DataType data_type_str(string_dataset);
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HDF5DataSpace data_space_str(string_dataset);
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CHECK(data_type_str.GetElemSize() == tmp_string.size() + 1);
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CHECK(data_space_str.GetNumOfDimensions() == 0);
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CHECK(string_dataset.ReadString() == tmp_string);
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}
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remove("scratch2.h5");
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5DataSet_vector", "[HDF5][Unit]") {
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std::vector<double> tmp_vector (16384);
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tmp_vector[0] = 599.88;
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tmp_vector[1000] = 800.12;
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tmp_vector[15000] = 3.1415926;
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{
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RegisterHDF5Filter();
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HDF5File file("scratch3.h5");
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file.SaveVector("vec", tmp_vector);
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}
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{
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HDF5ReadOnlyFile file("scratch3.h5");
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HDF5DataSet vector_dataset(file, "vec");
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HDF5DataType data_type_vec(vector_dataset);
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HDF5DataSpace data_space_vec(vector_dataset);
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CHECK(data_type_vec.GetElemSize() == 8);
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CHECK(data_space_vec.GetNumOfDimensions() == 1);
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CHECK(data_space_vec.GetDimensions()[0] == tmp_vector.size());
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std::vector<double> output;
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REQUIRE_NOTHROW(vector_dataset.ReadVector(output));
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CHECK (output[0] == tmp_vector[0]);
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CHECK (output[1000] == tmp_vector[1000]);
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CHECK (output[15000] == tmp_vector[15000]);
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CHECK (output.size() == tmp_vector.size());
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std::vector<double> output2(10);
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REQUIRE_NOTHROW(vector_dataset.ReadVector(output2, {15000},{10}));
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REQUIRE_THROWS(vector_dataset.ReadVector(output2, {15000},{100}));
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CHECK(output2[0] == tmp_vector[15000]);
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}
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remove("scratch3.h5");
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5DataSet_vector_string", "[HDF5][Unit]") {
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std::string long_string = "ccdcsdcdscsdcsdcs";
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std::vector<std::string> tmp_vector = {"aaaaaaaaa", "b", long_string};
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{
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RegisterHDF5Filter();
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HDF5File file("scratch4.h5");
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REQUIRE_NOTHROW(file.SaveVector("vec", tmp_vector));
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}
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{
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HDF5ReadOnlyFile file("scratch4.h5");
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HDF5DataSet vector_dataset(file, "vec");
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HDF5DataType data_type_vec(vector_dataset);
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HDF5DataSpace data_space_vec(vector_dataset);
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CHECK(data_type_vec.GetElemSize() == long_string.size() + 1);
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CHECK(data_space_vec.GetNumOfDimensions() == 1);
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CHECK(data_space_vec.GetDimensions()[0] == tmp_vector.size());
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}
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remove("scratch4.h5");
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5MasterFile", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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x.FilePrefix("test01").ImagesPerTrigger(950);
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StartMessage start_message;
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x.FillMessage(start_message);
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EndMessage end_message;
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end_message.max_image_number = x.GetImageNum();
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std::unique_ptr<NXmx> master = std::make_unique<NXmx>(start_message);
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master->Finalize(end_message);
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master.reset();
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x.FilePrefix("test02");
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x.FillMessage(start_message);
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master = std::make_unique<NXmx>(start_message);
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master->Finalize(end_message);
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master.reset();
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}
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remove("test01_master.h5");
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remove("test02_master.h5");
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5MasterFile_RadInt", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
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x.QSpacingForAzimInt_recipA(0.1).LowQForAzimInt_recipA(0.1).HighQForAzimInt_recipA(4);
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x.FilePrefix("test01_rad_int").ImagesPerTrigger(950);
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AzimuthalIntegrationMapping mapping(x);
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AzimuthalIntegrationProfile profile(mapping);
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StartMessage start_message;
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x.FillMessage(start_message);
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start_message.az_int_bin_to_q = mapping.GetBinToQ();
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EndMessage end_message;
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end_message.max_image_number = x.GetImageNum();
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end_message.az_int_result["avg1"] = profile.GetResult();
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end_message.az_int_result["avg2"] = profile.GetResult();
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std::unique_ptr<NXmx> master = std::make_unique<NXmx>(start_message);
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master->Finalize(end_message);
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master.reset();
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}
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remove("test01_rad_int_master.h5");
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5Writer", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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std::vector<SpotToSave> spots;
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x.FilePrefix("test02_1p10").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION);
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StartMessage start_message;
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x.FillMessage(start_message);
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HDF5Writer file_set(start_message);
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std::vector<uint16_t> image(x.GetPixelsNum());
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for (int i = 0; i < x.GetImageNum(); i++) {
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DataMessage message{};
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message.image.pixel_depth_bytes = 2;
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message.image.pixel_is_signed = false;
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message.image.algorithm = CompressionAlgorithm::NO_COMPRESSION;
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message.image.xpixel = x.GetXPixelsNum();
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message.image.ypixel = x.GetYPixelsNum();
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message.image.data = (uint8_t *) image.data();
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message.image.size = x.GetPixelsNum() * x.GetByteDepthImage();
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message.spots = spots;
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message.number = i;
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REQUIRE_NOTHROW(file_set.Write(message));
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}
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auto v = file_set.Finalize();
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REQUIRE(v.size() == 3); // 3 files
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REQUIRE(v[0].filename == "test02_1p10_data_000001.h5");
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REQUIRE(v[0].total_images == 2);
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REQUIRE(v[1].filename == "test02_1p10_data_000002.h5");
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REQUIRE(v[1].total_images == 2);
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REQUIRE(v[2].filename == "test02_1p10_data_000003.h5");
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REQUIRE(v[2].total_images == 1);
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REQUIRE(!file_set.GetZMQAddr());
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}
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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remove("test02_1p10_data_000001.h5");
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remove("test02_1p10_data_000002.h5");
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remove("test02_1p10_data_000003.h5");
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}
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TEST_CASE("HDF5Writer_Socket", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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x.FrameTime(std::chrono::microseconds(1000), std::chrono::microseconds(100));
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DatasetSettings d;
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d.FilePrefix("run0345_lysozyme_acq").ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
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.HeaderAppendix(R"({"z":567})"_json).DetectorDistance_mm(155).BeamX_pxl(1606.62).BeamY_pxl(1669.59)
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.PhotonEnergy_keV(12.07).SetUnitCell(UnitCell{.a = 97, .b = 97, .c = 38, .alpha= 90, .beta = 90, .gamma = 90})
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.SpaceGroupNumber(96).RunNumber(345).ExperimentGroup("p12345").SampleName("lysozyme").RunName("run1");
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x.ImportDatasetSettings(d);
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std::vector<SpotToSave> spots;
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StartMessage start_message;
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x.FillMessage(start_message);
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HDF5Writer file_set(start_message);
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file_set.SetupFinalizedFileSocket("ipc://#1");
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std::vector<uint16_t> image(x.GetPixelsNum());
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ZMQSocket s(ZMQSocketType::Sub);
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s.Connect("ipc://#1");
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s.SubscribeAll();
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s.ReceiveTimeout(std::chrono::seconds(5));
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for (int i = 0; i < x.GetImageNum(); i++) {
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DataMessage message{};
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message.image.pixel_depth_bytes = 2;
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message.image.pixel_is_signed = false;
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message.image.algorithm = CompressionAlgorithm::NO_COMPRESSION;
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message.image.xpixel = x.GetXPixelsNum();
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message.image.ypixel = x.GetYPixelsNum();
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message.image.data = (uint8_t *) image.data();
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message.image.size = x.GetPixelsNum() * x.GetByteDepthImage();
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message.spots = spots;
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message.number = i;
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REQUIRE_NOTHROW(file_set.Write(message));
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}
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REQUIRE(file_set.Finalize().size() == 3);
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ZMQMessage msg;
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nlohmann::json j;
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REQUIRE(s.Receive(msg, true));
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j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
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REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000001.h5");
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REQUIRE(j["file_number"] == 1);
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REQUIRE(j["nimages"] == 2);
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REQUIRE(j["incident_energy_eV"] == Catch::Approx(x.GetPhotonEnergy_keV() * 1000.0));
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REQUIRE(j["space_group_number"] == 96);
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REQUIRE(j["experiment_group"] == "p12345");
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REQUIRE(j["run_number"] == 345);
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REQUIRE(j["run_name"] == "run1");
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REQUIRE(j.contains("user_data"));
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REQUIRE(j["user_data"]["z"] == 567);
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std::cout << j.dump(4) << std::endl;
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REQUIRE(s.Receive(msg, true));
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j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
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REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000002.h5");
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REQUIRE(j["file_number"] == 2);
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REQUIRE(j["nimages"] == 2);
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REQUIRE(j.contains("user_data"));
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REQUIRE(j["user_data"]["z"] == 567);
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REQUIRE(s.Receive(msg, true));
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j = nlohmann::json::parse(std::string((char *) msg.data(), msg.size()));
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REQUIRE(j["filename"] == "run0345_lysozyme_acq_data_000003.h5");
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REQUIRE(j["file_number"] == 3);
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REQUIRE(j["nimages"] == 1);
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REQUIRE(j.contains("user_data"));
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REQUIRE(j["user_data"]["z"] == 567);
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}
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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remove("test05_data_000001.h5");
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remove("test05_data_000002.h5");
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remove("test05_data_000003.h5");
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}
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TEST_CASE("HDF5Writer_Spots", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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std::vector<SpotToSave> spots;
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spots.push_back({10,10,7});
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spots.push_back({20,50,12});
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spots.push_back({1000,500,3});
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x.FilePrefix("test02_1p10_spots").ImagesPerTrigger(5).ImagesPerFile(3).Compression(CompressionAlgorithm::NO_COMPRESSION);
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StartMessage start_message;
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x.FillMessage(start_message);
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HDF5Writer file_set(start_message);
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std::vector<uint16_t> image(x.GetPixelsNum());
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for (int i = 0; i < x.GetImageNum(); i++) {
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DataMessage message{};
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message.image.pixel_depth_bytes = 2;
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message.image.pixel_is_signed = false;
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message.image.xpixel = x.GetXPixelsNum();
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message.image.ypixel = x.GetYPixelsNum();
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message.image.algorithm = CompressionAlgorithm::NO_COMPRESSION;
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message.image.data = (uint8_t *) image.data();
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message.image.size = x.GetPixelsNum() * x.GetByteDepthImage();
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message.spots = spots;
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message.number = i;
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REQUIRE_NOTHROW(file_set.Write(message));
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}
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}
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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remove("test02_1p10_spots_data_000001.h5");
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remove("test02_1p10_spots_data_000002.h5");
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}
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TEST_CASE("HDF5Writer_Rad_Int_Profile", "[HDF5][Full]") {
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{
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RegisterHDF5Filter();
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DiffractionExperiment x(DetectorGeometry(8, 2, 8, 36));
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x.DetectorDistance_mm(50).BeamX_pxl(1000).BeamY_pxl(1000);
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x.QSpacingForAzimInt_recipA(0.1).LowQForAzimInt_recipA(0.1).HighQForAzimInt_recipA(4);
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AzimuthalIntegrationMapping mapping(x);
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std::vector<float> rad_int_profile(mapping.GetBinNumber(), 4.0);
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std::vector<float> rad_int_avg(mapping.GetBinNumber(), 0.33);
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x.FilePrefix("test02_1p10_rad_int").ImagesPerTrigger(5).ImagesPerFile(3).Compression(CompressionAlgorithm::NO_COMPRESSION);
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StartMessage start_message;
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x.FillMessage(start_message);
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start_message.az_int_bin_to_q = mapping.GetBinToQ();
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HDF5Writer file_set(start_message);
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std::vector<uint16_t> image(x.GetPixelsNum());
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for (int i = 0; i < x.GetImageNum(); i++) {
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DataMessage message{};
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message.image.pixel_depth_bytes = 2;
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message.image.pixel_is_signed = false;
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message.image.xpixel = x.GetXPixelsNum();
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message.image.ypixel = x.GetYPixelsNum();
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message.image.algorithm = CompressionAlgorithm::NO_COMPRESSION;
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message.image.data = (uint8_t *) image.data();
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message.image.size = x.GetPixelsNum() * x.GetByteDepthImage();
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message.az_int_profile = std::vector<float>(mapping.GetBinNumber(), i);
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message.number = i;
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REQUIRE_NOTHROW(file_set.Write(message));
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}
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}
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// No leftover HDF5 objects
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REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
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}
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TEST_CASE("HDF5NXmx_DataFileName", "[HDF5]") {
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StartMessage message;
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message.file_prefix = "z/x";
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REQUIRE(HDF5Metadata::DataFileName(message, 34) == "z/x_data_000035.h5");
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REQUIRE(HDF5Metadata::DataFileName(message, 0) == "z/x_data_000001.h5");
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REQUIRE_THROWS(HDF5Metadata::DataFileName(message, 1000000));
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REQUIRE_THROWS(HDF5Metadata::DataFileName(message, -1));
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}
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TEST_CASE("HDF5NXmx_DataFileName_SwissFEL", "[HDF5]") {
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StartMessage message;
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message.file_prefix = "acq";
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message.source_name = "SwissFEL";
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message.detector_serial_number = "JF17T16V01";
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REQUIRE(HDF5Metadata::DataFileName(message, 34) == "acq0035.JF17T16V01.h5");
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REQUIRE(HDF5Metadata::DataFileName(message, 0) == "acq0001.JF17T16V01.h5");
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REQUIRE_THROWS(HDF5Metadata::DataFileName(message, 10000));
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REQUIRE_THROWS(HDF5Metadata::DataFileName(message, -1));
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message.detector_serial_number = "";
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REQUIRE(HDF5Metadata::DataFileName(message, 34) == "acq0035.JF.h5");
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}
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TEST_CASE("HDF5Objects_ExtractFilename", "[HDF5]") {
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REQUIRE(ExtractFilename("filename_data_000001.h5") == "filename_data_000001.h5");
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REQUIRE(ExtractFilename("dir1/filename_data_000001.h5") == "filename_data_000001.h5");
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REQUIRE(ExtractFilename("dir1/dir2/filename_data_000001.h5") == "filename_data_000001.h5");
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}
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TEST_CASE("HDF5DataType", "[HDF5]") {
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HDF5DataType type1(1,true);
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REQUIRE(type1.GetElemSize() == 1);
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HDF5DataType type2(2,true);
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REQUIRE(type2.GetElemSize() == 2);
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|
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HDF5DataType type4(4,true);
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REQUIRE(type4.GetElemSize() == 4);
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|
|
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HDF5DataType type8(8,true);
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REQUIRE(type8.GetElemSize() == 8);
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|
|
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REQUIRE_THROWS(HDF5DataType(7,true));
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}
|
|
|
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TEST_CASE("HDF5Writer_Link", "[HDF5][Full]") {
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DiffractionExperiment x(DetectorGeometry(1));
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|
|
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x.ImagesPerTrigger(7).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION).FilePrefix("link");
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|
|
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{
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|
RegisterHDF5Filter();
|
|
|
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StartMessage start_message;
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x.FillMessage(start_message);
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|
|
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EndMessage end_message;
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end_message.max_image_number = x.GetImageNum() - 2;
|
|
|
|
HDF5Writer writer(start_message);
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|
std::vector<uint16_t> image(x.GetPixelsNum());
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|
std::vector<SpotToSave> spots;
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for (int i = 0; i < x.GetImageNum() - 2; i++) {
|
|
for (auto &j: image)
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|
j = i;
|
|
DataMessage message{};
|
|
message.image.pixel_depth_bytes = 2;
|
|
message.image.pixel_is_signed = false;
|
|
message.image.xpixel = x.GetXPixelsNum();
|
|
message.image.ypixel = x.GetYPixelsNum();
|
|
message.image.algorithm = CompressionAlgorithm::NO_COMPRESSION;
|
|
message.image.data = (uint8_t *) image.data();
|
|
message.image.size = x.GetPixelsNum() * x.GetByteDepthImage();
|
|
message.spots = spots;
|
|
message.number = i;
|
|
|
|
REQUIRE_NOTHROW(writer.Write(message));
|
|
}
|
|
|
|
std::unique_ptr<NXmx> master = std::make_unique<NXmx>(start_message);
|
|
master->Finalize(end_message);
|
|
master.reset();
|
|
}
|
|
{
|
|
HDF5ReadOnlyFile file("link_master.h5");
|
|
std::unique_ptr<HDF5DataSet> dataset;
|
|
REQUIRE_NOTHROW(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data_000001"));
|
|
HDF5DataSpace file_space(*dataset);
|
|
REQUIRE(file_space.GetNumOfDimensions() == 3);
|
|
REQUIRE(file_space.GetDimensions()[0] == x.GetImagesPerFile());
|
|
REQUIRE(file_space.GetDimensions()[1] == x.GetYPixelsNum());
|
|
REQUIRE(file_space.GetDimensions()[2] == x.GetXPixelsNum());
|
|
}
|
|
{
|
|
HDF5ReadOnlyFile file("link_master.h5");
|
|
std::unique_ptr<HDF5DataSet> dataset;
|
|
REQUIRE_NOTHROW(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data_000002"));
|
|
HDF5DataSpace file_space(*dataset);
|
|
REQUIRE(file_space.GetNumOfDimensions() == 3);
|
|
REQUIRE(file_space.GetDimensions()[0] == x.GetImagesPerFile());
|
|
REQUIRE(file_space.GetDimensions()[1] == x.GetYPixelsNum());
|
|
REQUIRE(file_space.GetDimensions()[2] == x.GetXPixelsNum());
|
|
}
|
|
{
|
|
HDF5ReadOnlyFile file("link_master.h5");
|
|
std::unique_ptr<HDF5DataSet> dataset;
|
|
REQUIRE_NOTHROW(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data_000003"));
|
|
HDF5DataSpace file_space(*dataset);
|
|
REQUIRE(file_space.GetNumOfDimensions() == 3);
|
|
REQUIRE(file_space.GetDimensions()[0] == 1);
|
|
REQUIRE(file_space.GetDimensions()[1] == x.GetYPixelsNum());
|
|
REQUIRE(file_space.GetDimensions()[2] == x.GetXPixelsNum());
|
|
}
|
|
{
|
|
HDF5ReadOnlyFile file("link_master.h5");
|
|
std::unique_ptr<HDF5DataSet> dataset;
|
|
REQUIRE_THROWS(dataset = std::make_unique<HDF5DataSet>(file,"/entry/data/data_000004"));
|
|
}
|
|
|
|
// No leftover HDF5 objects
|
|
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
|
|
}
|
|
|
|
|
|
TEST_CASE("HDF5Writer_Link_zero_images", "[HDF5][Full]") {
|
|
DiffractionExperiment x(DetectorGeometry(1));
|
|
x.ImagesPerTrigger(5).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION).FilePrefix("link_zero");
|
|
|
|
{
|
|
RegisterHDF5Filter();
|
|
|
|
StartMessage start_message;
|
|
x.FillMessage(start_message);
|
|
|
|
EndMessage end_message;
|
|
end_message.max_image_number = 0;
|
|
|
|
std::unique_ptr<NXmx> master = std::make_unique<NXmx>(start_message);
|
|
master->Finalize(end_message);
|
|
master.reset();
|
|
}
|
|
{
|
|
std::unique_ptr<HDF5ReadOnlyFile> file;
|
|
std::unique_ptr<HDF5DataSet> dataset;
|
|
REQUIRE_NOTHROW(file = std::make_unique<HDF5ReadOnlyFile>("link_zero_master.h5"));
|
|
REQUIRE_THROWS(dataset = std::make_unique<HDF5DataSet>(*file,"/entry/data/data_000001"));
|
|
}
|
|
// No leftover HDF5 objects
|
|
REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
|
|
}
|