Move read example to an example file

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

tests/examples/test_ecephys_data_read.cpp

@@ -0,0 +1,125 @@
+#include <H5Cpp.h>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_all.hpp>
+
+#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<float> dataBuffer(bufferSize);
+  std::vector<double> timestampsBuffer(bufferSize);
+  std::vector<Types::ChannelVector> mockArrays = getMockChannelArrays();
+  std::string dataPath = "/esdata";
+  BaseDataType dataType = BaseDataType::F32;
+  std::vector<std::vector<float>> mockData =
+      getMockData2D(numSamples, numChannels);
+  std::vector<double> 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<BaseIO> 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<float> dataValues = readDataWrapper->values<float>();
+    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<float> temp;
+      temp.resize(numChannels);
+      for (SizeType c = 0; c < numChannels; c++) {
+        temp[c] = mockData[c][s];
+      }
+      std::vector<float> 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<float> row_s_vector(row_s.begin(), row_s.end());
+
+      // Data for comparison
+      std::vector<float> 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();
+  }
+}

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<float> dataValues = readDataWrapper->values<float>();
-    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<float> temp;
-      temp.resize(numChannels);
-      for (SizeType c = 0; c < numChannels; c++) {
-        temp[c] = mockData[c][s];
-      }
-      std::vector<float> 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<float> row_s_vector(row_s.begin(), row_s.end());
-
-      // Data for comparison
-      std::vector<float> 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