Merge pull request PetroleumCyberneticsGroup#50 from PetroleumCyberne…

…ticsGroup/feature/get-cellnum-from-H5-reader

Feature/get cellnum from h5 reader

FieldOpt/Hdf5SummaryReader/hdf5_summary_reader.cpp

@@ -4,13 +4,47 @@
 
 using namespace H5;
 Hdf5SummaryReader::Hdf5SummaryReader(const std::string file_path)
-: GROUP_NAME_RESTART(("RESTART")), DATASET_NAME_TIMES("TIMES"),
-  GROUP_NAME_FLOW_TRANSPORT("FLOW_TRANSPORT"), DATASET_NAME_WELL_STATES("WELL_STATES")
+: GROUP_NAME_RESTART("RESTART"),
+  DATASET_NAME_TIMES("TIMES"),
+  GROUP_NAME_FLOW_TRANSPORT("FLOW_TRANSPORT"),
+  DATASET_NAME_ACTIVE_CELLS("ACTIVE_CELLS"),
+  DATASET_NAME_WELL_STATES("WELL_STATES")
 {
     readTimeVector(file_path);
+    readActiveCells(file_path);
     readWellStates(file_path);
 }
 
+void Hdf5SummaryReader::readActiveCells(std::string file_path) {
+    // Read the file
+    H5File file(file_path, H5F_ACC_RDONLY);
+    Group group = Group(file.openGroup(GROUP_NAME_FLOW_TRANSPORT));
+    DataSet dataset = DataSet(group.openDataSet(DATASET_NAME_ACTIVE_CELLS));
+
+    DataSpace dataspace = dataset.getSpace();
+    hsize_t dims[2];
+
+    auto rank = dataspace.getSimpleExtentDims(dims, NULL);
+    // Uncomment to debug:
+    // std::cout << "dataset rank = " << rank << ", dimensions "
+    //     << (unsigned long)(dims[0]) << " x "
+    //     << (unsigned long)(dims[1]) << std::endl;
+
+    // Define hyperslab
+    hsize_t  count[2] = { dims[0], 1 };
+    hsize_t offset[2] = { 0, 0 };
+    dataspace.selectHyperslab( H5S_SELECT_SET, count, offset );
+
+    // Size of selected colum + define memory space
+    hsize_t col_sz[1] = { dims[0] };
+    DataSpace mspace( 1, col_sz );
+
+    std::vector<int> vector;
+    vector.resize(dims[0]);
+    dataset.read(vector.data(), PredType::NATIVE_INT, mspace, dataspace);
+    active_cells_ = vector;
+}
+
 void Hdf5SummaryReader::readTimeVector(std::string file_path) {
     // Read the file
     H5File file(file_path, H5F_ACC_RDONLY);

FieldOpt/Hdf5SummaryReader/hdf5_summary_reader.h

@@ -38,6 +38,11 @@ class Hdf5SummaryReader {
      */
     const std::vector<double> &times_steps() const { return times_; }
 
+    /*!
+     * Get the vector containing defining active cells.
+     */
+    const std::vector<int> &active_cells() const { return active_cells_; }
+
     /*!
      * Get the number of wells found in the summary.
      */
@@ -185,6 +190,7 @@ class Hdf5SummaryReader {
     const H5std_string DATASET_NAME_TIMES; //!< The name of the dataset containing the time step vector in the HDF5 file.
     const H5std_string GROUP_NAME_FLOW_TRANSPORT; //!< The name of the flow transport group in the HDF5 file.
     const H5std_string DATASET_NAME_WELL_STATES; //!< The name of the dataset containing the well states in the HDF5 file.
+    const H5std_string DATASET_NAME_ACTIVE_CELLS; //!< The name of the dataset containing active cells vector.
 
     /*!
      * The wstype_t datatype represents the datatype in which well states are stored in the HDF5 file. Each element
@@ -243,13 +249,15 @@ class Hdf5SummaryReader {
     };
 
     void readTimeVector(std::string file_path); //!< Read the time vector from the HDF5 summary file.
+    void readActiveCells(std::string file_path); //!< Read vector defining which cells are active from the HDF5 summary file.
     void readWellStates(std::string file_path); //!< Read all well state information from the HDF5 summary file.
     void parseWsVector(std::vector<wstype_t> &wsvec); //!< Populate well_states_ by creating well_data and perforation_data objects from the wstype_t vector.
     well_data parseWellState(std::vector<wstype_t> &ws, int wnr); //!< Parse the states for a single well and create a well_data object.
 
     int nwells_; //!< Number of wells in summary.
     int ntimes_; //!< Number of time steps in the summary.
     int nphases_; //!< Number of phases in the model
+    std::vector<int> active_cells_; //!< Vector defining active cells (size equal to total number of cells) .
     std::vector<double> times_; //!< Vector containing all time steps.
 
     /*!

FieldOpt/Hdf5SummaryReader/tests/test_hdf5_summary_reader.cpp

@@ -33,6 +33,16 @@ namespace {
         }
     }
 
+    TEST_F(Hdf5SummaryReaderTest, ActiveCellVector) {
+        auto reader = Hdf5SummaryReader(file_path);
+        std::vector<int> active_cells = reader.active_cells();
+
+        for (int i = 0; i < active_cells.size(); ++i) {
+            // std::cout << active_cells[i] << std::endl;
+            EXPECT_EQ(active_cells[i], i);
+        }
+    }
+
     TEST_F(Hdf5SummaryReaderTest, IntegerData) {
         auto reader = Hdf5SummaryReader(file_path);
         int expected_types[5] = {1, -1, -1, -1, -1};