From 3d86aff955e668b9fd69c1533d94afb178ab61eb Mon Sep 17 00:00:00 2001 From: Oliver Ruebel Date: Sun, 1 Sep 2024 00:21:38 -0700 Subject: [PATCH] Move read example to an example file --- tests/CMakeLists.txt | 1 + tests/examples/test_ecephys_data_read.cpp | 125 ++++++++++++++++++++++ tests/testEcephys.cpp | 61 ----------- 3 files changed, 126 insertions(+), 61 deletions(-) create mode 100644 tests/examples/test_ecephys_data_read.cpp diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt index b830774f..4d25d641 100644 --- a/tests/CMakeLists.txt +++ b/tests/CMakeLists.txt @@ -20,6 +20,7 @@ add_executable(aqnwb_test testNWBRecording.cpp examples/test_HDF5IO_examples.cpp examples/test_example.cpp + examples/test_ecephys_data_read.cpp ) # Ensure the aqnwb_test target can include headers from the current directory diff --git a/tests/examples/test_ecephys_data_read.cpp b/tests/examples/test_ecephys_data_read.cpp new file mode 100644 index 00000000..c0421165 --- /dev/null +++ b/tests/examples/test_ecephys_data_read.cpp @@ -0,0 +1,125 @@ +#include +#include +#include + +#include "BaseIO.hpp" +#include "Channel.hpp" +#include "Types.hpp" +#include "Utils.hpp" +#include "hdf5/HDF5IO.hpp" +#include "nwb/device/Device.hpp" +#include "nwb/ecephys/ElectricalSeries.hpp" +#include "nwb/file/ElectrodeGroup.hpp" +#include "nwb/file/ElectrodeTable.hpp" +#include "testUtils.hpp" + +using namespace AQNWB; + +TEST_CASE("ElectricalSeriesReadExample", "[ecephys]") +{ + // setup recording info + SizeType numSamples = 100; + SizeType numChannels = 2; + SizeType bufferSize = numSamples / 5; + std::vector dataBuffer(bufferSize); + std::vector timestampsBuffer(bufferSize); + std::vector mockArrays = getMockChannelArrays(); + std::string dataPath = "/esdata"; + BaseDataType dataType = BaseDataType::F32; + std::vector> mockData = + getMockData2D(numSamples, numChannels); + std::vector mockTimestamps = getMockTimestamps(numSamples, 1); + std::string devicePath = "/device"; + std::string electrodePath = "/elecgroup/"; + + SECTION("ecephys data read example") + { + // setup io object + std::string path = getTestFilePath("ElectricalSeriesReadExample.h5"); + std::shared_ptr io = createIO("HDF5", path); + io->open(); + io->createGroup("/general"); + io->createGroup("/general/extracellular_ephys"); + + // setup electrode table, device, and electrode group + NWB::ElectrodeTable elecTable = NWB::ElectrodeTable(io); + elecTable.initialize(); + + // setup electrical series + NWB::ElectricalSeries es = NWB::ElectricalSeries(dataPath, io); + es.initialize(dataType, + mockArrays[0], + "no description", + SizeArray {0, mockArrays[0].size()}, + SizeArray {1, 1}); + + // write channel data + for (SizeType ch = 0; ch < numChannels; ++ch) { + es.writeChannel( + ch, numSamples, mockData[ch].data(), mockTimestamps.data()); + } + + io->flush(); + + // TODO START Move this check to a proper test and expand on it + std::string esdataPath = es.dataPath(); + std::string expectedDataPath = dataPath + "/data"; + REQUIRE(esdataPath == expectedDataPath); + + auto readDataWrapper = es.dataLazy(); + DataBlock dataValues = readDataWrapper->values(); + REQUIRE(dataValues.data.size() == (numSamples * numChannels)); + REQUIRE(dataValues.shape[0] == numSamples); + REQUIRE(dataValues.shape[1] == numChannels); + for (SizeType s = 0; s < numSamples; s++) { + std::vector temp; + temp.resize(numChannels); + for (SizeType c = 0; c < numChannels; c++) { + temp[c] = mockData[c][s]; + } + std::vector selectedRange( + dataValues.data.begin() + (s * numChannels), + dataValues.data.begin() + ((s + 1) * numChannels)); + REQUIRE_THAT(selectedRange, Catch::Matchers::Approx(temp).margin(1)); + } + // Check the boost multi-array feature + auto boostMulitArray = dataValues.as_multi_array<2>(); + for (SizeType s = 0; s < numSamples; s++) { + // Get timestamp s (i.e., the values from all channels at time index s) + // Accessing [a, :] + auto row_s = boostMulitArray[s]; // This returns a 1D array representing + // the first row + // Convert the row from boost to a std:vector + std::vector row_s_vector(row_s.begin(), row_s.end()); + + // Data for comparison + std::vector temp; + temp.resize(numChannels); + for (SizeType c = 0; c < numChannels; c++) { + temp[c] = mockData[c][s]; + } + REQUIRE_THAT(row_s_vector, Catch::Matchers::Approx(temp).margin(1)); + } + + // std::cout<<"Data shape:" << dataValues.shape.size() << std::endl; + + // + // REQUIRE_THAT(readDataValues, Catch::Matchers::Approx(data).margin(1)); + + // TODO Add an attribute getter and test that it works as well + // auto dataLazyWrapper = es.dataLazy(); + // auto dataValueGeneric = dataLazyWrapper->valuesGeneric(); + // TODO Check why this causes Assertion failed: + // (this->file->attrExists(dataPath)), function readAttribute, file + // HDF5IO.cpp, line 161. + // the attribute does not seem to exists so either the path is wrong or + // something is bad with the write? + // REQUIRE(unitValueGeneric.shape.size() == 0); + + // std::string esUnit = es.unit(); + // REQUIRE(esUnit == std::string("volts")); + // TODO END Move this code + + io->close(); + } +} diff --git a/tests/testEcephys.cpp b/tests/testEcephys.cpp index aeb0106c..f36870bf 100644 --- a/tests/testEcephys.cpp +++ b/tests/testEcephys.cpp @@ -68,68 +68,7 @@ TEST_CASE("ElectricalSeries", "[ecephys]") es.writeChannel( ch, numSamples, mockData[ch].data(), mockTimestamps.data()); } - io->flush(); - - // TODO START Move this check to a proper test and expand on it - std::string esdataPath = es.dataPath(); - std::string expectedDataPath = dataPath + "/data"; - REQUIRE(esdataPath == expectedDataPath); - - auto readDataWrapper = es.dataLazy(); - DataBlock dataValues = readDataWrapper->values(); - REQUIRE(dataValues.data.size() == (numSamples * numChannels)); - REQUIRE(dataValues.shape[0] == numSamples); - REQUIRE(dataValues.shape[1] == numChannels); - for (SizeType s = 0; s < numSamples; s++) { - std::vector temp; - temp.resize(numChannels); - for (SizeType c = 0; c < numChannels; c++) { - temp[c] = mockData[c][s]; - } - std::vector selectedRange( - dataValues.data.begin() + (s * numChannels), - dataValues.data.begin() + ((s + 1) * numChannels)); - REQUIRE_THAT(selectedRange, Catch::Matchers::Approx(temp).margin(1)); - } - // Check the boost multi-array feature - auto boostMulitArray = dataValues.as_multi_array<2>(); - for (SizeType s = 0; s < numSamples; s++) { - // Get timestamp s (i.e., the values from all channels at time index s) - // Accessing [a, :] - auto row_s = boostMulitArray[s]; // This returns a 1D array representing - // the first row - // Convert the row from boost to a std:vector - std::vector row_s_vector(row_s.begin(), row_s.end()); - - // Data for comparison - std::vector temp; - temp.resize(numChannels); - for (SizeType c = 0; c < numChannels; c++) { - temp[c] = mockData[c][s]; - } - REQUIRE_THAT(row_s_vector, Catch::Matchers::Approx(temp).margin(1)); - } - - // std::cout<<"Data shape:" << dataValues.shape.size() << std::endl; - - // - // REQUIRE_THAT(readDataValues, Catch::Matchers::Approx(data).margin(1)); - - // TODO Add an attribute getter and test that it works as well - // auto dataLazyWrapper = es.dataLazy(); - // auto dataValueGeneric = dataLazyWrapper->valuesGeneric(); - // TODO Check why this causes Assertion failed: - // (this->file->attrExists(dataPath)), function readAttribute, file - // HDF5IO.cpp, line 161. - // the attribute does not seem to exists so either the path is wrong or - // something is bad with the write? - // REQUIRE(unitValueGeneric.shape.size() == 0); - - // std::string esUnit = es.unit(); - // REQUIRE(esUnit == std::string("volts")); - // TODO END Move this code - io->close(); // Read data back from file