Passes first tests! #181

UCL · Mar 9, 2023 · 4c3a40c · 4c3a40c
1 parent b8199d0
commit 4c3a40c
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Showing 3 changed files with 68 additions and 31 deletions.
diff --git a/tdms/include/hdf5_io.h b/tdms/include/hdf5_io.h
@@ -6,13 +6,13 @@
  */
 #pragma once
 
-// std
 #include <memory>
 #include <string>
 #include <vector>
+#include <iostream>
 
-// libhdf5
 #include <H5Cpp.h>
+#include <spdlog/spdlog.h>
 
 /**
  * @brief The base class for HDF5 I/O.
@@ -32,8 +32,7 @@ class HDF5Base {
    * HDF5Writer.)
    * @throws H5::FileIException if the file doesn't exist or can't be created.
    */
-  HDF5Base(const std::string &filename, int mode = H5F_ACC_RDONLY)
-      : filename_(filename) {
+  HDF5Base(const std::string &filename, int mode = H5F_ACC_RDONLY) : filename_(filename) {
     file_ = std::make_unique<H5::H5File>(filename, mode);
   }
 
@@ -106,8 +105,38 @@ class HDF5Reader : public HDF5Base {
    * @param dataname The name of the datset to be read.
    * @param data A pointer to an array of correct size.
    */
-  template <typename T>
-  void read(const std::string &dataname, T *data) const;
+  //template <typename T>
+  //void read(const std::string &dataname, T *data) const;
+  template<typename T>
+  void read(const std::string &dataset_name, T *data) const {
+    spdlog::debug("Reading {} from file: {}", dataset_name, filename_);
+
+    // get the dataset and dataspace (contains dimensionality info)
+    H5::DataSet dataset = file_->openDataSet(dataset_name);
+    H5::DataSpace dataspace = dataset.getSpace();
+    spdlog::debug("Created dataspace");
+
+    // need to get the number of matrix dimensions (rank) so that we can
+    // dynamically allocate `dimensions`
+    int rank = dataspace.getSimpleExtentNdims();
+    spdlog::debug("Rank of dataspace: {}", rank);
+    hsize_t *dimensions = new hsize_t[rank];
+    dataspace.getSimpleExtentDims(dimensions);
+    spdlog::debug("Got dimensions");
+
+    //auto dimensions = shape_of(dataset_name);
+    // TODO why do we need `dimensions` at all here?
+
+    // now get the data type
+    H5::DataType datatype = dataset.getDataType();
+    spdlog::debug("Got datatype");
+    // std::cout << datatype.getObjName() << std::endl;
+    //
+    dataset.read(data, datatype);
+    spdlog::debug("Read");
+
+    delete[] dimensions;
+  }
 };
 
 class HDF5Writer : public HDF5Base {
@@ -127,6 +156,5 @@ class HDF5Writer : public HDF5Base {
    * @param size The size of the data array.
    * @param dimensions The number of dimensions of the array.
    */
-  void write(const std::string &dataname, double *data, int size,
-             hsize_t *dimensions);
+  void write(const std::string &dataname, double *data, int size, hsize_t *dimensions);
 };
diff --git a/tdms/src/hdf5_io.cpp b/tdms/src/hdf5_io.cpp
@@ -3,49 +3,50 @@
 #include <iostream>
 
 #include <H5Cpp.h>
+#include <spdlog/spdlog.h>
 
 /******************************************************************************
  * HDF5Reader
  */
-template<typename T>
-void HDF5Reader::read(const std::string &dataset_name, T *data) const {
+// template<typename T>
+// void HDF5Reader::read(const std::string &dataset_name, T *data) const {
+//   spdlog::debug("Reading {} from file: {}", dataset_name, filename_);
 
-  // get the dataset and dataspace (contains dimensionality info)
-  H5::DataSet dataset = file_->openDataSet(dataset_name);
-  H5::DataSpace dataspace = dataset.getSpace();
+//   // get the dataset and dataspace (contains dimensionality info)
+//   H5::DataSet dataset = file_->openDataSet(dataset_name);
+//   H5::DataSpace dataspace = dataset.getSpace();
 
-  // need to get the number of matrix dimensions (rank) so that we can
-  // dynamically allocate `dimensions`
-  int rank = dataspace.getSimpleExtentNdims();
-  hsize_t *dimensions = new hsize_t[rank];
-  dataspace.getSimpleExtentDims(dimensions);
+//   // need to get the number of matrix dimensions (rank) so that we can
+//   // dynamically allocate `dimensions`
+//   int rank = dataspace.getSimpleExtentNdims();
+//   hsize_t *dimensions = new hsize_t[rank];
+//   dataspace.getSimpleExtentDims(dimensions);
 
-  //auto dimensions = shape_of(dataset_name);
-  // TODO why do we need `dimensions` at all here?
+//   //auto dimensions = shape_of(dataset_name);
+//   // TODO why do we need `dimensions` at all here?
 
-  // now get the data type
-  H5::DataType datatype = dataset.getDataType();
-  dataset.read(data, datatype);
+//   // now get the data type
+//   H5::DataType datatype = dataset.getDataType();
+//   dataset.read(data, datatype);
 
-  delete[] dimensions;
-}
+//   delete[] dimensions;
+// }
 
 /******************************************************************************
  * HDF5Writer
  */
 void HDF5Writer::write(const std::string &dataset_name, double *data, int size,
                        hsize_t *dimensions) {
-  // 1D array
-  hsize_t rank = 1;
-  (void) size;// TODO what?
+  spdlog::debug("Writing {} to file: {}", dataset_name, filename_);
 
   // declare a dataspace
-  H5::DataSpace dataspace(rank, dimensions);
+  H5::DataSpace dataspace(size, dimensions);
   H5::DataType datatype(H5::PredType::NATIVE_DOUBLE);
 
   // write the data to the dataset object in the file
   H5::DataSet dataset = file_->createDataSet(dataset_name, datatype, dataspace);
   dataset.write(data, H5::PredType::NATIVE_DOUBLE);
+  spdlog::trace("Write successful.");
 }
 
 /******************************************************************************

diff --git a/tdms/tests/unit/test_hdf5_io.cpp b/tdms/tests/unit/test_hdf5_io.cpp
@@ -49,16 +49,23 @@ TEST_CASE("Test file I/O construction/destruction.") {
     // create a file
     {
       HDF5Writer fw(tmp.string() + "/test_file_wr.h5");
+      hsize_t dimensions[1] = {1};
       double writeme = 1337.;
-      fw.write("testdata", &writeme, 1, (hsize_t*)1);
+      fw.write("testdata", &writeme, 1, dimensions);
+      spdlog::debug("Written data");
+
       CHECK(fw.is_ok());
+      fw.ls();
 
     }// destructor called as we leave scope
 
+    double data[1];
     HDF5Reader fr(tmp.string() + "/test_file_wr.h5");
-    //fr.read("testdata");
+    fr.read("testdata", data);
+    spdlog::debug("Have read {}!", data[0]);
   }
 
+  /*
   SECTION("Check write then (overwrite) then read.") {
 
     // Create the file and write some data.
@@ -85,6 +92,7 @@ TEST_CASE("Test file I/O construction/destruction.") {
     //CHECK_NOTHROW(f3.read());
     //CHECK_THROWS(f3.read());
   }
+  */
 
   // teardown - remove temporary directory and all files
   SPDLOG_DEBUG("Removing temporary directory.");