refactor: Remove '4d' naming convention across codebase (#22)

Remove '4d' suffix from module names, function names, and references throughout the codebase.
Update documentation, examples, and notebooks to reflect simplified naming convention.
The temporal dimension is implicit in the physiomotion4d package name,
and most methods work on 3D as well as 4D data.

Author: aylward

.github/workflows/ci.yml

@@ -221,7 +221,7 @@ jobs:
 
     - name: Run USD conversion tests
       run: |
-        pytest tests/test_convert_vtk_4d_to_usd_polymesh.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
+        pytest tests/test_convert_vtk_to_usd_polymesh.py -v -m "not slow" --cov=physiomotion4d --cov-append --cov-report=xml
       continue-on-error: true
 
     - name: Run USD utility tests

docs/api/index.rst

@@ -100,7 +100,7 @@ By Category
 **USD Tools**
    * :mod:`~physiomotion4d.usd_tools` - USD file utilities
    * :mod:`~physiomotion4d.usd_anatomy_tools` - Anatomical structure tools
-   * :class:`~physiomotion4d.ConvertVTK4DToUSD` - VTK to USD conversion
+   * :class:`~physiomotion4d.ConvertVTKToUSD` - VTK to USD conversion
 
 Module Index
 ============

docs/api/usd/index.rst

@@ -47,9 +47,9 @@ Convert VTK to USD
 
 .. code-block:: python
 
-   from physiomotion4d import ConvertVTK4DToUSD
+   from physiomotion4d import ConvertVTKToUSD
    
-   converter = ConvertVTK4DToUSD(
+   converter = ConvertVTKToUSD(
        output_file="animated_heart.usd",
        colormap="rainbow",
        verbose=True

docs/api/usd/polymesh.rst

@@ -9,7 +9,7 @@ Surface mesh (polygon mesh) representation in USD.
 Class Reference
 ===============
 
-.. autoclass:: ConvertVTK4DToUSDPolyMesh
+.. autoclass:: ConvertVTKToUSDPolyMesh
    :members:
    :undoc-members:
    :show-inheritance:

docs/api/usd/tetmesh.rst

@@ -9,7 +9,7 @@ Tetrahedral mesh representation in USD for volumetric models.
 Class Reference
 ===============
 
-.. autoclass:: ConvertVTK4DToUSDTetMesh
+.. autoclass:: ConvertVTKToUSDTetMesh
    :members:
    :undoc-members:
    :show-inheritance:

docs/api/usd/vtk_conversion.rst

@@ -9,7 +9,7 @@ Convert VTK mesh files to USD format with animation support.
 Class Reference
 ===============
 
-.. autoclass:: ConvertVTK4DToUSD
+.. autoclass:: ConvertVTKToUSD
    :members:
    :undoc-members:
    :show-inheritance:

docs/architecture.rst

@@ -46,7 +46,7 @@ Core Components
 
 5. **USD Export Module**
 
-   * :class:`ConvertVTK4DToUSD`: VTK to USD conversion
+   * :class:`ConvertVTKToUSD`: VTK to USD conversion
    * :class:`USDTools`: USD manipulation
    * :class:`USDAnatomyTools`: Material application
 

docs/developer/architecture.rst

@@ -69,10 +69,10 @@ The package is organized into functional modules:
    │       └── register_models_pca.py             PCA-based
    │
    ├── USD Generation
-   │   ├── convert_vtk_4d_to_usd_base.py          Base converter
-   │   ├── convert_vtk_4d_to_usd_polymesh.py      Polygon meshes
-   │   ├── convert_vtk_4d_to_usd_tetmesh.py       Tetrahedral meshes
-   │   └── convert_vtk_4d_to_usd.py               Main converter
+   │   ├── convert_vtk_to_usd_base.py          Base converter
+   │   ├── convert_vtk_to_usd_polymesh.py      Polygon meshes
+   │   ├── convert_vtk_to_usd_tetmesh.py       Tetrahedral meshes
+   │   └── convert_vtk_to_usd.py               Main converter
    │
    └── Utilities
        ├── image_tools.py                          Image manipulation
@@ -107,9 +107,9 @@ Most PhysioMotion4D classes inherit from :class:`PhysioMotion4DBase`:
    │   │   └── RegisterImagesICON
    │   └── (Model registration classes)
    └── Conversion Classes
-       └── ConvertVTK4DToUSDBase
-           ├── ConvertVTK4DToUSDPolyMesh
-           └── ConvertVTK4DToUSDTetMesh
+       └── ConvertVTKToUSDBase
+           ├── ConvertVTKToUSDPolyMesh
+           └── ConvertVTKToUSDTetMesh
 
 The base class provides:
 

docs/developer/extending.rst

@@ -54,7 +54,7 @@ Start with this template for new workflows:
    from physiomotion4d import PhysioMotion4DBase
    from physiomotion4d import SegmentChestTotalSegmentator
    from physiomotion4d import RegisterImagesICON
-   from physiomotion4d import ConvertVTK4DToUSDPolyMesh
+   from physiomotion4d import ConvertVTKToUSDPolyMesh
 
    class MyCustomWorkflow(PhysioMotion4DBase):
        """
@@ -95,7 +95,7 @@ Start with this template for new workflows:
            """Initialize processing components."""
            self.segmentator = SegmentChestTotalSegmentator(verbose=self.verbose)
            self.registrator = RegisterImagesICON(device="cuda:0")
-           self.usd_converter = ConvertVTK4DToUSDPolyMesh(verbose=self.verbose)
+           self.usd_converter = ConvertVTKToUSDPolyMesh(verbose=self.verbose)
 
        def process(self):
            """Execute complete workflow."""
@@ -146,7 +146,7 @@ Complete example of a custom workflow:
    from physiomotion4d import PhysioMotion4DBase
    from physiomotion4d.image_tools import read_image, write_image
    from physiomotion4d.contour_tools import extract_surface_mesh
-   from physiomotion4d import ConvertVTK4DToUSD
+   from physiomotion4d import ConvertVTKToUSD
    import SimpleITK as sitk
 
    class BrainVesselWorkflow(PhysioMotion4DBase):
@@ -189,7 +189,7 @@ Complete example of a custom workflow:
 
            # Convert to USD
            usd_file = f"{self.output_directory}/brain_vessels.usd"
-           converter = ConvertVTK4DToUSD()
+           converter = ConvertVTKToUSD()
            converter.convert(
                vtk_file=vessel_mesh,
                usd_file=usd_file,

docs/developer/usd_generation.rst

@@ -22,17 +22,17 @@ PhysioMotion4D provides comprehensive USD conversion capabilities:
 * **Anatomical Materials**: Organ-specific material painting
 * **Time-Varying Geometry**: 4D animation support
 
-All converters inherit from :class:`ConvertVTK4DToUSDBase`.
+All converters inherit from :class:`ConvertVTKToUSDBase`.
 
 Base Converter Class
 ====================
 
-ConvertVTK4DToUSDBase
+ConvertVTKToUSDBase
 ---------------------
 
 Abstract base class for USD conversion.
 
-.. autoclass:: physiomotion4d.ConvertVTK4DToUSDBase
+.. autoclass:: physiomotion4d.ConvertVTKToUSDBase
    :members:
    :undoc-members:
    :show-inheritance:
@@ -51,7 +51,7 @@ Polygon Mesh Converter
 
 Convert surface meshes (VTK PolyData) to USD.
 
-.. autoclass:: physiomotion4d.ConvertVTK4DToUSDPolyMesh
+.. autoclass:: physiomotion4d.ConvertVTKToUSDPolyMesh
    :members:
    :undoc-members:
    :show-inheritance:
@@ -66,10 +66,10 @@ Convert surface meshes (VTK PolyData) to USD.
 
 .. code-block:: python
 
-   from physiomotion4d import ConvertVTK4DToUSDPolyMesh
+   from physiomotion4d import ConvertVTKToUSDPolyMesh
    
    # Initialize converter
-   converter = ConvertVTK4DToUSDPolyMesh(
+   converter = ConvertVTKToUSDPolyMesh(
        start_time=0,
        end_time=1.0,
        fps=30,
@@ -137,7 +137,7 @@ Tetrahedral Mesh Converter
 
 Convert volumetric meshes (VTK UnstructuredGrid) to USD.
 
-.. autoclass:: physiomotion4d.ConvertVTK4DToUSDTetMesh
+.. autoclass:: physiomotion4d.ConvertVTKToUSDTetMesh
    :members:
    :undoc-members:
    :show-inheritance:
@@ -152,10 +152,10 @@ Convert volumetric meshes (VTK UnstructuredGrid) to USD.
 
 .. code-block:: python
 
-   from physiomotion4d import ConvertVTK4DToUSDTetMesh
+   from physiomotion4d import ConvertVTKToUSDTetMesh
    
    # Initialize for tetrahedral meshes
-   converter = ConvertVTK4DToUSDTetMesh(verbose=True)
+   converter = ConvertVTKToUSDTetMesh(verbose=True)
    
    # Convert volumetric mesh
    converter.convert(
@@ -263,10 +263,10 @@ Create animated USD files from 4D VTK sequences:
 
 .. code-block:: python
 
-   from physiomotion4d import ConvertVTK4DToUSD
+   from physiomotion4d import ConvertVTKToUSD
    
    # Initialize with timing
-   converter = ConvertVTK4DToUSD(
+   converter = ConvertVTKToUSD(
        start_time=0.0,
        end_time=2.0,    # 2 second animation
        fps=30,          # 30 frames per second
@@ -290,7 +290,7 @@ Control temporal resolution:
 .. code-block:: python
 
    # High temporal resolution
-   converter = ConvertVTK4DToUSD(
+   converter = ConvertVTKToUSD(
        start_time=0,
        end_time=1.0,
        fps=60  # Smooth animation
@@ -300,7 +300,7 @@ Control temporal resolution:
    num_frames = len(vtk_files)
    cycle_duration = 1.0  # 1 second cardiac cycle
    
-   converter = ConvertVTK4DToUSD(
+   converter = ConvertVTKToUSD(
        start_time=0,
        end_time=cycle_duration,
        fps=num_frames / cycle_duration
@@ -316,9 +316,9 @@ Visualize scalar data on meshes:
 
 .. code-block:: python
 
-   from physiomotion4d import ConvertVTK4DToUSDPolyMesh
+   from physiomotion4d import ConvertVTKToUSDPolyMesh
    
-   converter = ConvertVTK4DToUSDPolyMesh()
+   converter = ConvertVTKToUSDPolyMesh()
    
    # Available colormaps
    colormaps = [
@@ -423,7 +423,7 @@ Create multi-resolution meshes:
 
 .. code-block:: python
 
-   class LODConverter(ConvertVTK4DToUSDPolyMesh):
+   class LODConverter(ConvertVTKToUSDPolyMesh):
        """Converter with LOD support."""
        
        def create_lod_mesh(self, vtk_file, usd_file, lod_levels):
@@ -508,7 +508,7 @@ Convert multiple files efficiently:
    
    def batch_convert_to_usd(vtk_dir, usd_dir, num_workers=4):
        """Convert multiple VTK files to USD in parallel."""
-       converter = ConvertVTK4DToUSDPolyMesh()
+       converter = ConvertVTKToUSDPolyMesh()
        
        vtk_files = list(Path(vtk_dir).glob("*.vtk"))