Rename ApplyPointwise -> TransformVolumeData

src/Visualization/Python/CMakeLists.txt

@@ -7,7 +7,6 @@ spectre_python_add_module(
   Visualization
   PYTHON_FILES
   __init__.py
-  ApplyPointwise.py
   GenerateXdmf.py
   InterpolateToCoords.py
   InterpolateToMesh.py
@@ -16,4 +15,5 @@ spectre_python_add_module(
   plots.mplstyle
   ReadH5.py
   Render1D.py
+  TransformVolumeData.py
 )

src/Visualization/Python/ApplyPointwise.py → src/Visualization/Python/TransformVolumeData.py

@@ -220,7 +220,7 @@ def one_index_constraint(
                 f"Unknown argument type '{arg.annotation}' for argument "
                 f"'{arg.name}'. It must be either a Tensor or one of "
                 "the supported structural types listed in "
-                "'ApplyPointwise.parse_kernel_arg'.")
+                "'TransformVolumeData.parse_kernel_arg'.")
         return TensorArg(tensor_type=arg.annotation,
                          dataset_name=map_input_names.get(
                              arg.name, snake_case_to_camel_case(arg.name)))
@@ -232,7 +232,7 @@ def __init__(self,
                  map_input_names: Dict[str, str] = {},
                  output_name: Optional[str] = None,
                  elementwise: Optional[bool] = None):
-        """Specifies input and output tensor names for a pointwise function
+        """Transforms volume data with a Python function
 
         Arguments:
           callable: A Python function that takes and returns tensors
@@ -277,7 +277,7 @@ def __init__(self,
                 raise ValueError(
                     f"The function '{callable.__name__}' has no overload "
                     "with supported arguments. See "
-                    "'ApplyPointwise.parse_kernel_arg' for a list of "
+                    "'TransformVolumeData.parse_kernel_arg' for a list of "
                     "supported arguments. The overloads are: " +
                     rich.pretty.pretty_repr(overloads))
         # If any argument is not a Tensor then we have to call the kernel
@@ -309,19 +309,19 @@ def __call__(self, all_tensor_data: Dict[str, Tensor],
         return output
 
 
-def apply_pointwise(
+def transform_volume_data(
         volfiles: Union[spectre_h5.H5Vol, Iterable[spectre_h5.H5Vol]],
         kernels: Sequence[Kernel],
         integrate: bool = False) -> Union[None, Dict[str, Sequence[float]]]:
-    """Apply pointwise functions to data in the 'volfiles'
+    """Transforms data in the 'volfiles' with a sequence of 'kernels'
 
     Arguments:
       volfiles: Iterable of open H5 volume files, or a single H5 volume file.
         Must be opened in writable mode, e.g. in mode "a". The transformed
         data will be written back into these files. All observations in these
         files will be transformed.
-      kernels: List of pointwise transformations to apply to the volume data
-        in the form of 'Kernel' objects.
+      kernels: List of transformations to apply to the volume data in the form
+        of 'Kernel' objects.
       integrate: Compute the volume integral over the kernels instead of
         writing them back into the volume files. The integral is computed in
         inertial coordinates for every tensor component of all kernels and over
@@ -519,12 +519,12 @@ def parse_kernels(kernels, exec_files, map_input_names):
 @click.option("--output-subfile",
               help=("Subfile name in the '--output' / '-o' file, if it is "
                     "an H5 file."))
-def apply_pointwise_command(h5files, subfile_name, kernels, exec_files,
-                            map_input_names, integrate, output, output_subfile,
-                            **kwargs):
-    """Apply pointwise functions to volume data
+def transform_volume_data_command(h5files, subfile_name, kernels, exec_files,
+                                  map_input_names, integrate, output,
+                                  output_subfile, **kwargs):
+    """Transform volume data with Python functions
 
-    Run pointwise functions (kernels) over all volume data in the 'H5FILES' and
+    Run Python functions (kernels) over all volume data in the 'H5FILES' and
     write the output data back into the same files. You can use any Python
     function as kernel that takes tensors as input arguments and returns a
     tensor (from 'spectre.DataStructures.Tensor'). The function must be
@@ -607,10 +607,10 @@ def shift_magnitude(
     task_id = progress.add_task("Applying to files")
     volfiles_progress = progress.track(volfiles, task_id=task_id)
     with progress:
-        integrals = apply_pointwise(volfiles_progress,
-                                    kernels=kernels,
-                                    integrate=integrate,
-                                    **kwargs)
+        integrals = transform_volume_data(volfiles_progress,
+                                          kernels=kernels,
+                                          integrate=integrate,
+                                          **kwargs)
         progress.update(task_id, completed=len(volfiles))
 
     # Write integrals to output file or print to terminal
@@ -644,4 +644,4 @@ def shift_magnitude(
 
 
 if __name__ == "__main__":
-    apply_pointwise_command(help_option_names=["-h", "--help"])
+    transform_volume_data_command(help_option_names=["-h", "--help"])

support/Python/__main__.py

@@ -17,7 +17,6 @@
 class Cli(click.MultiCommand):
     def list_commands(self, ctx):
         return [
-            "apply-pointwise",
             "clean-output",
             "extract-dat",
             "extract-input",
@@ -28,14 +27,11 @@ def list_commands(self, ctx):
             "plot-power-monitors",
             "render-1d",
             "simplify-traces",
+            "transform-volume-data",
         ]
 
     def get_command(self, ctx, name):
-        if name == "apply-pointwise":
-            from spectre.Visualization.ApplyPointwise import (
-                apply_pointwise_command)
-            return apply_pointwise_command
-        elif name == "clean-output":
+        if name == "clean-output":
             from spectre.tools.CleanOutput import clean_output_command
             return clean_output_command
         elif name == "delete-subfiles":
@@ -74,6 +70,10 @@ def get_command(self, ctx, name):
             from spectre.tools.CharmSimplifyTraces import (
                 simplify_traces_command)
             return simplify_traces_command
+        elif name in ["transform-volume-data", "transform-vol"]:
+            from spectre.Visualization.TransformVolumeData import (
+                transform_volume_data_command)
+            return transform_volume_data_command
         raise NotImplementedError(f"The command '{name}' is not implemented.")
 
 

tests/Unit/Visualization/Python/CMakeLists.txt

@@ -1,12 +1,6 @@
 # Distributed under the MIT License.
 # See LICENSE.txt for details.
 
-spectre_add_python_bindings_test(
-  "Unit.Visualization.Python.ApplyPointwise"
-  Test_ApplyPointwise.py
-  "unit;visualization;python"
-  None)
-
 spectre_add_python_bindings_test(
   "Unit.Visualization.Python.GenerateXdmf"
   Test_GenerateXdmf.py
@@ -63,3 +57,9 @@ spectre_add_python_bindings_test(
   Test_InterpolateToMesh.py
   "unit;visualization;python"
   None)
+
+spectre_add_python_bindings_test(
+  "Unit.Visualization.Python.TransformVolumeData"
+  Test_TransformVolumeData.py
+  "unit;visualization;python"
+  None)

tests/Unit/Visualization/Python/Test_ApplyPointwise.py → tests/Unit/Visualization/Python/Test_TransformVolumeData.py

@@ -1,10 +1,9 @@
 # Distributed under the MIT License.
 # See LICENSE.txt for details.
 
-from spectre.Visualization.ApplyPointwise import (snake_case_to_camel_case,
-                                                  parse_pybind11_signatures,
-                                                  Kernel, apply_pointwise,
-                                                  apply_pointwise_command)
+from spectre.Visualization.TransformVolumeData import (
+    snake_case_to_camel_case, parse_pybind11_signatures, Kernel,
+    transform_volume_data, transform_volume_data_command)
 
 import inspect
 import numpy as np
@@ -57,10 +56,10 @@ def square_component(component: DataVector) -> Scalar[DataVector]:
     return Scalar[DataVector]([component**2])
 
 
-class TestApplyPointwise(unittest.TestCase):
+class TestTransformVolumeData(unittest.TestCase):
     def setUp(self):
         self.test_dir = os.path.join(unit_test_build_path(),
-                                     'Visualization/ApplyPointwise')
+                                     'Visualization/TransformVolumeData')
         self.h5_filename = os.path.join(self.test_dir, "Test.h5")
         os.makedirs(self.test_dir, exist_ok=True)
         shutil.copyfile(
@@ -78,7 +77,7 @@ def test_parse_pybind11_signatures(self):
     def test_snake_case_to_camel_case(self):
         self.assertEqual(snake_case_to_camel_case("hello_world"), "HelloWorld")
 
-    def test_apply_pointwise(self):
+    def test_transform_volume_data(self):
         open_h5_files = [spectre_h5.H5File(self.h5_filename, "a")]
         open_volfiles = [
             h5file.get_vol("/element_data") for h5file in open_h5_files
@@ -95,7 +94,7 @@ def test_apply_pointwise(self):
                    map_input_names={"component": "InertialCoordinates_x"}),
         ]
 
-        apply_pointwise(volfiles=open_volfiles, kernels=kernels)
+        transform_volume_data(volfiles=open_volfiles, kernels=kernels)
 
         obs_id = open_volfiles[0].list_observation_ids()[0]
         result_psisq = open_volfiles[0].get_tensor_component(
@@ -136,9 +135,9 @@ def test_integrate(self):
             Kernel(sinusoid),
         ]
 
-        integrals = apply_pointwise(volfiles=open_volfiles,
-                                    kernels=kernels,
-                                    integrate=True)
+        integrals = transform_volume_data(volfiles=open_volfiles,
+                                          kernels=kernels,
+                                          integrate=True)
 
         npt.assert_allclose(integrals["Volume"], (2 * np.pi)**3)
         # The domain has pretty low resolution so the integral is not
@@ -154,7 +153,7 @@ def test_cli(self):
             "-e",
             __file__,
         ]
-        result = runner.invoke(apply_pointwise_command,
+        result = runner.invoke(transform_volume_data_command,
                                cli_flags + [
                                    "-k",
                                    "psi_squared",
@@ -182,7 +181,7 @@ def test_cli(self):
             npt.assert_allclose(np.array(result_radius), radius)
 
         # Test integrals
-        result = runner.invoke(apply_pointwise_command,
+        result = runner.invoke(transform_volume_data_command,
                                cli_flags + [
                                    "-k",
                                    "sinusoid",
@@ -193,7 +192,7 @@ def test_cli(self):
         self.assertIn("63.88", result.output)
 
         output_filename = os.path.join(self.test_dir, "integrals.h5")
-        result = runner.invoke(apply_pointwise_command,
+        result = runner.invoke(transform_volume_data_command,
                                cli_flags + [
                                    "-k",
                                    "sinusoid",