Added CombineH5 Pybindings and related test

src/IO/H5/CombineH5.cpp

@@ -46,7 +46,7 @@ size_t get_number_of_elements(const std::vector<std::string>& input_filenames,
   }
   return total_elements;
 }
-}  // namespace
+}
 namespace h5 {
 
 void combine_h5(const std::string& file_prefix, const std::string& subfile_name,

src/IO/H5/CombineH5.hpp

@@ -21,6 +21,8 @@
 #include "Utilities/StdHelpers.hpp"
 
 namespace h5 {
+
 void combine_h5(const std::string& file_prefix, const std::string& subfile_name,
                 const std::string& output);
+
 }  // namespace h5

src/IO/H5/Python/Bindings.cpp

@@ -3,6 +3,7 @@
 
 #include <pybind11/pybind11.h>
 
+#include "IO/H5/Python/CombineH5.hpp"
 #include "IO/H5/Python/Dat.hpp"
 #include "IO/H5/Python/File.hpp"
 #include "IO/H5/Python/TensorData.hpp"
@@ -19,4 +20,5 @@ PYBIND11_MODULE(_Pybindings, m) {  // NOLINT
   py_bindings::bind_h5dat(m);
   py_bindings::bind_h5vol(m);
   py_bindings::bind_tensordata(m);
+  py_bindings::bind_h5combine(m);
 }

src/IO/H5/Python/CMakeLists.txt

@@ -15,6 +15,7 @@ spectre_python_add_module(
   VolumeData.cpp
   PYTHON_FILES
   __init__.py
+  CombineH5.py
   DeleteSubfiles.py
   ExtendConnectivityData.py
   ExtractDatFromH5.py

src/IO/H5/Python/CombineH5.cpp

@@ -0,0 +1,20 @@
+// Distributed under the MIT License.
+// See LICENSE.txt for details.
+
+#include "IO/H5/Python/CombineH5.hpp"
+
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <string>
+
+#include "IO/H5/CombineH5.hpp"
+
+namespace py = pybind11;
+
+namespace py_bindings {
+void bind_h5combine(py::module& m) {
+  // Wrapper for combining h5 files
+  m.def("combine_h5", &h5::combine_h5, py::arg("file_prefix"),
+        py::arg("subfile_name"), py::arg("output"));
+}
+}  // namespace py_bindings

src/IO/H5/Python/CombineH5.hpp

@@ -0,0 +1,11 @@
+// Distributed under the MIT License.
+// See LICENSE.txt for details.
+
+#pragma once
+
+#include <pybind11/pybind11.h>
+
+namespace py_bindings {
+// NOLINTNEXTLINE(google-runtime-references)
+void bind_h5combine(pybind11::module& m);
+}  // namespace py_bindings

tests/Unit/IO/H5/CMakeLists.txt

@@ -34,6 +34,23 @@ target_link_libraries(
   Utilities
   )
 
+spectre_add_python_bindings_test(
+  "Unit.IO.H5.CombineH5.Python"
+  "Test_CombineH5.py"
+  "unit;IO;H5;Python"
+  PyH5
+  )
+
+if(${BUILD_PYTHON_BINDINGS})
+  # Test is a bit slow because it writes a bunch of plot files to verify
+  # the argument handling works.
+  set_tests_properties(
+    "Unit.IO.H5.CombineH5.Python"
+    PROPERTIES
+    TIMEOUT 80
+    )
+endif()
+
 spectre_add_python_bindings_test(
   "Unit.IO.H5.Python"
   "Test_H5.py"

tests/Unit/IO/H5/Test_CombineH5.py

@@ -0,0 +1,159 @@
+# Distributed under the MIT License.
+# See LICENSE.txt for details.
+
+import os
+import unittest
+
+import numpy as np
+
+import spectre.IO.H5 as spectre_h5
+from spectre import Informer
+from spectre.DataStructures import DataVector
+from spectre.IO.H5 import ElementVolumeData, TensorComponent, combine_h5
+from spectre.Spectral import Basis, Quadrature
+
+
+class TestCombineH5(unittest.TestCase):
+    # Test Fixtures
+    def setUp(self):
+        # The tests in this class combine 2 HDF5 files to generate one,
+        # using the Combine_H5 functionality.
+        self.file_name1 = os.path.join(
+            Informer.unit_test_build_path(), "IO/TestVolumeData0.h5"
+        )
+        self.file_name2 = os.path.join(
+            Informer.unit_test_build_path(), "IO/TestVolumeData1.h5"
+        )
+
+        self.output_file = os.path.join(
+            Informer.unit_test_build_path(), "IO/TestOutput"
+        )
+
+        if os.path.isfile(self.file_name1):
+            os.remove(self.file_name1)
+        if os.path.isfile(self.file_name2):
+            os.remove(self.file_name2)
+        if os.path.isfile(self.output_file + "0.h5"):
+            os.remove(self.output_file + "0.h5")
+
+        # Initializing attributes
+        grid_names1 = ["[B0(L0I0,L0I0,L1I0)]"]
+        grid_names2 = ["[B0(L1I0,L0I0,L0I0)]"]
+        observation_values = {0: 7.0, 1: 1.3}
+        basis = Basis.Legendre
+        quad = Quadrature.Gauss
+        self.observation_ids = [0, 1]
+
+        # Writing ElementVolume data and TensorComponent Data to first file
+        self.h5_file1 = spectre_h5.H5File(file_name=self.file_name1, mode="a")
+        self.tensor_component_data1 = np.array([[0.0], [0.3], [0.6]])
+        self.h5_file1.insert_vol("/element_data", version=0)
+        self.h5_file1.close_current_object()
+        self.vol_file1 = self.h5_file1.get_vol(path="/element_data")
+
+        self.element_vol_data_file_1 = [
+            ElementVolumeData(
+                element_name=grid_names1[0],
+                components=[
+                    TensorComponent(
+                        "field_1", DataVector(self.tensor_component_data1[i])
+                    ),
+                    TensorComponent(
+                        "field_2",
+                        DataVector(self.tensor_component_data1[i + 1]),
+                    ),
+                ],
+                extents=3 * [2],
+                basis=3 * [basis],
+                quadrature=3 * [quad],
+            )
+            for i, observation_id in enumerate(self.observation_ids)
+        ]
+
+        # Write extents and tensor volume data to the volfile
+        for i, observation_id in enumerate(self.observation_ids):
+            self.vol_file1.write_volume_data(
+                observation_id,
+                observation_values[observation_id],
+                [
+                    self.element_vol_data_file_1[i],
+                ],
+            )
+
+        # Store initial connectivity data
+        self.initial_h5_connectivity = self.vol_file1.get_tensor_component(
+            self.observation_ids[0], "connectivity"
+        ).data
+
+        self.h5_file1.close()
+
+        # Writing ElementVolume data and TensorComponent Data to second file
+        self.h5_file2 = spectre_h5.H5File(file_name=self.file_name2, mode="a")
+        self.tensor_component_data2 = np.array([[1.0], [0.13], [0.16]])
+        self.h5_file2.insert_vol("/element_data", version=0)
+        self.h5_file2.close_current_object()
+        self.vol_file2 = self.h5_file2.get_vol(path="/element_data")
+
+        self.element_vol_data_file_2 = [
+            ElementVolumeData(
+                element_name=grid_names2[0],
+                components=[
+                    TensorComponent(
+                        "field_1", DataVector(self.tensor_component_data2[i])
+                    ),
+                    TensorComponent(
+                        "field_2",
+                        DataVector(self.tensor_component_data2[i + 1]),
+                    ),
+                ],
+                extents=3 * [2],
+                basis=3 * [basis],
+                quadrature=3 * [quad],
+            )
+            for i, observation_id in enumerate(self.observation_ids)
+        ]
+
+        # Write extents and tensor volume data to the volfile
+        for i, observation_id in enumerate(self.observation_ids):
+            self.vol_file2.write_volume_data(
+                observation_id,
+                observation_values[observation_id],
+                [
+                    self.element_vol_data_file_2[i],
+                ],
+            )
+        self.h5_file2.close()
+
+    def tearDown(self):
+        self.h5_file1.close()
+        self.h5_file2.close()
+        if os.path.isfile(self.file_name1):
+            os.remove(self.file_name1)
+        if os.path.isfile(self.file_name2):
+            os.remove(self.file_name2)
+        if os.path.isfile(self.output_file + "0.h5"):
+            os.remove(self.output_file + "0.h5")
+
+    def test_combine_h5(self):
+        # Run the combine_h5 command and check if any feature (for eg.
+        # connectivity length has increased due to combining two files)
+
+        combine_h5(self.file_name1[:-4], "element_data", self.output_file)
+        h5_output = spectre_h5.H5File(
+            file_name=self.output_file + "0.h5", mode="a"
+        )
+        output_vol = h5_output.get_vol(path="/element_data")
+
+        # Extracts the connectivity data from the volume file
+        # If length of final connectivity is more, combine_h5
+        # has successfully merged the two HDF5 files.
+
+        final_h5_connectivity = output_vol.get_tensor_component(
+            self.observation_ids[0], "connectivity"
+        ).data
+
+        assert len(self.initial_h5_connectivity) < len(final_h5_connectivity)
+
+
+if __name__ == "__main__":
+    unittest.main(verbosity=2)