Fix spelling and complete merge

NeurodataWithoutBorders · Dec 22, 2024 · 54d55da · 54d55da
1 parent ddb8f50
commit 54d55da
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Showing 3 changed files with 19 additions and 39 deletions.
diff --git a/src/io/hdf5/HDF5RecordingData.cpp b/src/io/hdf5/HDF5RecordingData.cpp
@@ -19,20 +19,19 @@ HDF5RecordingData::HDF5RecordingData(std::unique_ptr<H5::DataSet> data)
   DataSpace dSpace = data->getSpace();
   DSetCreatPropList prop = data->getCreatePlist();
 
-  int nDimensions = dSpace.getSimpleExtentNdims();
-  std::vector<hsize_t> dims(nDimensions), chunk(nDimensions);
+  this->nDimensions = static_cast<SizeType>(dSpace.getSimpleExtentNdims());
+  std::vector<hsize_t> dims(this->nDimensions), chunk(this->nDimensions);
 
-  nDimensions = dSpace.getSimpleExtentDims(
-      dims.data());  // TODO -redefine here or use original?
-  prop.getChunk(static_cast<int>(nDimensions), chunk.data());
+  this->nDimensions =
+      static_cast<SizeType>(dSpace.getSimpleExtentDims(dims.data()));
+  prop.getChunk(static_cast<int>(this->nDimensions), chunk.data());
 
-  this->size = std::vector<SizeType>(nDimensions);
-  for (int i = 0; i < nDimensions; ++i) {
-    this->size[i] = dims[i];
+  this->size = std::vector<SizeType>(this->nDimensions);
+  for (SizeType i = 0; i < this->nDimensions; ++i) {
+    this->size[i] = static_cast<SizeType>(dims[i]);
   }
-  this->nDimensions = nDimensions;
   this->position = std::vector<SizeType>(
-      nDimensions, 0);  // Initialize position with 0 for each dimension
+      this->nDimensions, 0);  // Initialize position with 0 for each dimension
   m_dataset = std::make_unique<H5::DataSet>(*data);
 }
 
@@ -58,7 +57,7 @@ Status HDF5RecordingData::writeDataBlock(
 
     // Ensure that we have enough space to accommodate new data
     std::vector<hsize_t> dSetDims(nDimensions), offset(nDimensions);
-    for (int i = 0; i < nDimensions; ++i) {
+    for (SizeType i = 0; i < nDimensions; ++i) {
       offset[i] = static_cast<hsize_t>(positionOffset[i]);
 
       if (dataShape[i] + offset[i] > size[i])  // TODO - do I need offset here
@@ -73,14 +72,14 @@ Status HDF5RecordingData::writeDataBlock(
     // Set size to new size based on updated dimensionality
     DataSpace fSpace = m_dataset->getSpace();
     fSpace.getSimpleExtentDims(dSetDims.data());
-    for (int i = 0; i < nDimensions; ++i) {
+    for (SizeType i = 0; i < nDimensions; ++i) {
       size[i] = dSetDims[i];
     }
 
     // Create memory space with the shape of the data
     // DataSpace mSpace(dimension, dSetDim.data());
     std::vector<hsize_t> dataDims(nDimensions);
-    for (int i = 0; i < nDimensions; ++i) {
+    for (SizeType i = 0; i < nDimensions; ++i) {
       if (dataShape[i] == 0) {
         dataDims[i] = 1;
       } else {
@@ -97,7 +96,7 @@ Status HDF5RecordingData::writeDataBlock(
     m_dataset->write(data, nativeType, mSpace, fSpace);
 
     // Update position for simple extension
-    for (int i = 0; i < dataShape.size(); ++i) {
+    for (SizeType i = 0; i < dataShape.size(); ++i) {
       position[i] += dataShape[i];
     }
   } catch (DataSetIException error) {

diff --git a/src/nwb/file/ElectrodeTable.cpp b/src/nwb/file/ElectrodeTable.cpp
@@ -26,8 +26,8 @@ ElectrodeTable::ElectrodeTable(std::shared_ptr<IO::BaseIO> io)
 ElectrodeTable::ElectrodeTable(const std::string& path,
                                std::shared_ptr<IO::BaseIO> io)
     : DynamicTable(
-        electrodeTablePath,  // use the electrodeTablePath
-        io)  // TODO May need to initialize the colNames in DynamicTable
+          electrodeTablePath,  // use the electrodeTablePath
+          io)  // TODO May need to initialize the colNames in DynamicTable
     , m_electrodeDataset(std::make_unique<ElementIdentifiers>(
           AQNWB::mergePaths(electrodeTablePath, "id"), io))
     , m_groupNamesDataset(std::make_unique<VectorData>(
@@ -69,20 +69,12 @@ void ElectrodeTable::initialize(const std::string& description)
 void ElectrodeTable::addElectrodes(std::vector<Channel> channelsInput)
 {
   // create datasets
-<<<<<<< HEAD
-  for (const auto& ch : channels) {
+  for (const auto& ch : channelsInput) {
     m_groupReferences.push_back(
         AQNWB::mergePaths(m_groupPathBase, ch.getGroupName()));
     m_groupNames.push_back(ch.getGroupName());
-    m_electrodeNumbers.push_back(ch.getGlobalIndex());
+    m_electrodeNumbers.push_back(static_cast<int>(ch.getGlobalIndex()));
     m_locationNames.push_back("unknown");
-=======
-  for (const auto& ch : channelsInput) {
-    groupReferences.push_back(groupPathBase + ch.getGroupName());
-    groupNames.push_back(ch.getGroupName());
-    electrodeNumbers.push_back(static_cast<int>(ch.getGlobalIndex()));
-    locationNames.push_back("unknown");
->>>>>>> main
   }
 }
 

diff --git a/tests/testHDF5IO.cpp b/tests/testHDF5IO.cpp
@@ -318,14 +318,9 @@ TEST_CASE("SWMRmode", "[hdf5io]")
   SECTION("useSWMRMODE")
   {
     // create and open file
-<<<<<<< HEAD
-    std::string path = getTestFilePath("testSWMRmode.h5");
+    std::string path = getTestFilePath("testSWMRmodeEnable.h5");
     std::unique_ptr<IO::HDF5::HDF5IO> hdf5io =
         std::make_unique<IO::HDF5::HDF5IO>(path);
-=======
-    std::string path = getTestFilePath("testSWMRmodeEnable.h5");
-    std::unique_ptr<HDF5::HDF5IO> hdf5io = std::make_unique<HDF5::HDF5IO>(path);
->>>>>>> main
     hdf5io->open();
 
     // add a dataset
@@ -403,15 +398,9 @@ TEST_CASE("SWMRmode", "[hdf5io]")
   SECTION("disableSWMRMode")
   {
     // create and open file with SWMR mode disabled
-<<<<<<< HEAD
-    std::string path = getTestFilePath("testSWMRmode.h5");
+    std::string path = getTestFilePath("testSWMRmodeDisable.h5");
     std::unique_ptr<IO::HDF5::HDF5IO> hdf5io =
         std::make_unique<IO::HDF5::HDF5IO>(path, true);
-=======
-    std::string path = getTestFilePath("testSWMRmodeDisable.h5");
-    std::unique_ptr<HDF5::HDF5IO> hdf5io =
-        std::make_unique<HDF5::HDF5IO>(path, true);
->>>>>>> main
     hdf5io->open();
 
     // add a dataset