Merge pull request sxs-collaboration#5924 from nilsvu/normalize_subfi…

…le_path

Normalize subfile path in H5 lib

src/IO/Exporter/Exporter.cpp

@@ -151,7 +151,7 @@ template <size_t Dim>
 std::vector<std::vector<double>> interpolate_to_points(
     const std::variant<std::vector<std::string>, std::string>&
         volume_files_or_glob,
-    std::string subfile_name,
+    const std::string& subfile_name,
     const std::variant<ObservationId, ObservationStep>& observation,
     const std::vector<std::string>& tensor_components,
     const std::array<std::vector<double>, Dim>& target_points,
@@ -173,15 +173,6 @@ std::vector<std::vector<double>> interpolate_to_points(
     ERROR_NO_TRACE("No volume files found. Specify at least one volume file.");
   }
 
-  // Normalize subfile name
-  if (subfile_name.size() > 4 &&
-      subfile_name.substr(subfile_name.size() - 4) == ".vol") {
-    subfile_name = subfile_name.substr(0, subfile_name.size() - 4);
-  }
-  if (subfile_name.front() != '/') {
-    subfile_name = '/' + subfile_name;
-  }
-
   // Retrieve info from the first volume file
   const h5::H5File<h5::AccessType::ReadOnly> first_h5file(filenames.front());
   const auto& first_volfile = first_h5file.get<h5::VolumeData>(subfile_name);
@@ -278,7 +269,7 @@ std::vector<std::vector<double>> interpolate_to_points(
   template std::vector<std::vector<double>> interpolate_to_points<DIM(data)>( \
       const std::variant<std::vector<std::string>, std::string>&              \
           volume_files_or_glob,                                               \
-      std::string subfile_name,                                               \
+      const std::string& subfile_name,                                        \
       const std::variant<ObservationId, ObservationStep>& observation,        \
       const std::vector<std::string>& tensor_components,                      \
       const std::array<std::vector<double>, DIM(data)>& target_points,        \

src/IO/Exporter/Exporter.hpp

@@ -58,7 +58,7 @@ template <size_t Dim>
 std::vector<std::vector<double>> interpolate_to_points(
     const std::variant<std::vector<std::string>, std::string>&
         volume_files_or_glob,
-    std::string subfile_name,
+    const std::string& subfile_name,
     const std::variant<ObservationId, ObservationStep>& observation,
     const std::vector<std::string>& tensor_components,
     const std::array<std::vector<double>, Dim>& target_points,

src/IO/H5/File.hpp

@@ -209,7 +209,7 @@ class H5File {
 
   template <typename ObjectType>
   std::tuple<bool, detail::OpenGroup, std::string> check_if_object_exists(
-      const std::string& path) const;
+      std::string path) const;
 
   std::string file_name_;
   // NOLINTNEXTLINE(spectre-mutable)
@@ -392,7 +392,16 @@ const ObjectType& H5File<Access_t>::convert_to_derived(
 template <AccessType Access_t>
 template <typename ObjectType>
 std::tuple<bool, detail::OpenGroup, std::string>
-H5File<Access_t>::check_if_object_exists(const std::string& path) const {
+H5File<Access_t>::check_if_object_exists(std::string path) const {
+  // Normalize path to have a leading slash and the correct extension
+  if (path.front() != '/') {
+    path = '/' + path;
+  }
+  const size_t extension_length = ObjectType::extension().size();
+  if (path.size() > extension_length and
+      path.substr(path.size() - extension_length) == ObjectType::extension()) {
+    path = path.substr(0, path.size() - extension_length);
+  }
   std::string name_only = "/";
   if (path != "/") {
     name_only = file_system::get_file_name(path);

src/IO/H5/Python/CombineH5.py

@@ -78,11 +78,6 @@ def combine_h5_vol_command(h5files, subfile_name, output, check_src):
         rich.print(rich.columns.Columns(spectre_file.all_vol_files()))
         return
 
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-
     if not output.endswith(".h5"):
         output += ".h5"
 

src/IO/H5/Python/ExtendConnectivityData.py

@@ -40,11 +40,6 @@ def extend_connectivity_data_command(filename, subfile_name):
     files, the combine-h5 executable must be run first. The extend-connectivity
     command can then be run on the newly generated HDF5 file.
     """
-    # Ensure that the format of the subfile is correct
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if subfile_name[0] != "/":
-        subfile_name = "/" + subfile_name
     # Read the h5 file and extract the volume file from it
     h5_file = spectre_h5.H5File(filename, "r+")
     vol_file = h5_file.get_vol(subfile_name)

src/Visualization/Python/OpenVolfiles.py

@@ -168,12 +168,6 @@ def command(
                     rich.print(rich.columns.Columns(available_subfiles))
                     return
 
-            # Normalize subfile name
-            if subfile_name.endswith(".vol"):
-                subfile_name = subfile_name[:-4]
-            if not subfile_name.startswith("/"):
-                subfile_name = "/" + subfile_name
-
             # Print available observations/times and exit
             if list_times:
                 import rich.columns

src/Visualization/Python/Render1D.py

@@ -310,11 +310,6 @@ def render_1d_command(
         rich.print(rich.columns.Columns(open_h5_files[0].all_vol_files()))
         return
 
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-
     volfiles = [h5file.get_vol(subfile_name) for h5file in open_h5_files]
     dim = volfiles[0].get_dimension()
     assert (

src/Visualization/Python/TransformVolumeData.py

@@ -800,11 +800,6 @@ def shift_magnitude(
             rich.print(rich.columns.Columns())
             return
 
-    if subfile_name.endswith(".vol"):
-        subfile_name = subfile_name[:-4]
-    if not subfile_name.startswith("/"):
-        subfile_name = "/" + subfile_name
-
     volfiles = [h5file.get_vol(subfile_name) for h5file in open_h5_files]
 
     # Load kernels

tests/Unit/IO/H5/Test_Dat.cpp

@@ -321,7 +321,9 @@ void test_dat_read() {
     error_file.append(std::vector<double>{0.33, 0.66, 0.77, 0.90});
   }
   h5::H5File<h5::AccessType::ReadOnly> my_file(h5_file_name);
-  const auto& error_file = my_file.get<h5::Dat>("/L2_errors");
+  // No leading slash should also find the subfile, and a ".dat" extension as
+  // well
+  const auto& error_file = my_file.get<h5::Dat>("L2_errors.dat");
   CHECK(error_file.subfile_path() == "/L2_errors");
 
   // Check version info is correctly retrieved from Dat file

tests/Unit/IO/H5/Test_VolumeData.cpp

@@ -264,9 +264,10 @@ void test() {
     my_file.close_current_object();
   }
   // Open the read volume file and check that the observation id and values are
-  // correct.
+  // correct. No leading slash should also find the subfile, and a ".vol"
+  // extension as well.
   const auto& volume_file =
-      my_file.get<h5::VolumeData>("/element_data", version_number);
+      my_file.get<h5::VolumeData>("element_data.vol", version_number);
   CHECK(volume_file.subfile_path() == "/element_data");
   const auto read_observation_ids = volume_file.list_observation_ids();
   // The observation IDs should be sorted by their observation value