ENH: Remove '4d' naming convention across codebase

[aylward]

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.

[Copilot]

Pull request overview

This PR systematically removes the '4d' suffix from module names, function names, and references throughout the codebase. The rationale is that the temporal dimension is already implicit in the package name (physiomotion4d), and the methods work on both 3D and 4D data.

Changes:

• Renamed all convert_vtk_4d_to_usd* modules and classes to convert_vtk_to_usd*
• Updated imports and references in test files, source code, and workflows
• Updated documentation files including API docs, guides, and examples

Reviewed changes

Copilot reviewed 45 out of 45 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_convert_vtk_to_usd_polymesh.py	Renamed test file, updated all class imports from ConvertVTK4DToUSDPolyMesh to ConvertVTKToUSDPolyMesh
tests/TESTING_GUIDE.md	Updated test file reference in dependency diagram
tests/README.md	Updated test file reference in documentation
tests/GITHUB_WORKFLOWS.md	Updated pytest command to reference new test file name
statistics.md	Updated module names in statistics table
src/physiomotion4d/workflow_convert_heart_gated_ct_to_usd.py	Updated import from convert_vtk_4d_to_usd to convert_vtk_to_usd
src/physiomotion4d/convert_vtk_to_usd_tetmesh.py	Updated imports and class name from ConvertVTK4DToUSDTetMesh to ConvertVTKToUSDTetMesh
src/physiomotion4d/convert_vtk_to_usd_polymesh.py	Updated imports and class name from ConvertVTK4DToUSDPolyMesh to ConvertVTKToUSDPolyMesh
src/physiomotion4d/convert_vtk_to_usd_base.py	Updated class name from ConvertVTK4DToUSDBase to ConvertVTKToUSDBase
src/physiomotion4d/convert_vtk_to_usd.py	Updated all class names and references, including error messages
src/physiomotion4d/init.py	Updated all exports to use new class names
experiments/*/notebooks	Updated imports throughout all experiment notebooks
docs/**/*.rst	Updated all API documentation and examples with new class names
.github/workflows/ci.yml	Updated pytest command in CI workflow

Comments suppressed due to low confidence (1)

experiments/Heart-GatedCT_To_USD/4-merge_dynamic_and_static_usd.ipynb:77

• This notebook now includes execution outputs and changes the execution_count from null to integer values (1, 2), and also changes file paths to include "results/" prefix. While adding execution outputs can be helpful for documentation, these changes are unrelated to the stated purpose of the PR (removing '4d' naming convention). Consider whether these changes should be in a separate commit or documented in the PR description.

   "execution_count": 1,
   "id": "3ce61753-11ad-4ade-9afe-6ad1bc748e25",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-01-26T17:16:51.961127Z",
     "iopub.status.busy": "2026-01-26T17:16:51.960134Z",
     "iopub.status.idle": "2026-01-26T17:17:25.063841Z",
     "shell.execute_reply": "2026-01-26T17:17:25.062413Z"
    }
   },
   "outputs": [],
   "source": [
    "import os\n",
    "\n",
    "from physiomotion4d.usd_tools import USDTools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "4c0ece8e",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2026-01-26T17:17:25.068335Z",
     "iopub.status.busy": "2026-01-26T17:17:25.067236Z",
     "iopub.status.idle": "2026-01-26T17:18:11.504444Z",
     "shell.execute_reply": "2026-01-26T17:18:11.503440Z"
    }
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2026-01-28 13:47:29 INFO USDTools Copying /World to /World\n",
      "2026-01-28 13:47:31 INFO USDTools Copying /World to /World\n",
      "2026-01-28 13:47:31 INFO USDTools Set stage time range: 0.0 to 20.0\n",
      "2026-01-28 13:47:31 INFO USDTools Time codes per second: 1.0, Frames per second: 24.0\n",
      "2026-01-28 13:47:45 INFO USDTools Referencing files: 1/2 (50.0%)\n",
      "2026-01-28 13:47:45 INFO USDTools Referencing files: 2/2 (100.0%)\n",
      "2026-01-28 13:47:45 INFO USDTools Time range: 0.0 to 20.0\n",
      "2026-01-28 13:47:45 INFO USDTools Time codes per second: 1.0, Frames per second: 24.0\n",
      "2026-01-28 13:47:45 INFO USDTools Flattening composed stage...\n",
      "2026-01-28 13:47:46 INFO USDTools Set output TimeCodesPerSecond: 1.0\n",
      "2026-01-28 13:47:46 INFO USDTools Set output FramesPerSecond: 24.0\n",
      "2026-01-28 13:47:46 INFO USDTools Exporting to results/Slicer_CardiacGatedCT.flattened_merged_painted.usd\n"
     ]
    }
   ],
   "source": [
    "usd_tools = USDTools()\n",
    "\n",
    "if os.path.exists(\"results/Slicer_CardiacGatedCT.merged_painted.usd\"):\n",
    "    os.remove(\"results/Slicer_CardiacGatedCT.merged_painted.usd\")\n",
    "\n",
    "usd_tools.merge_usd_files(\n",
    "    \"results/Slicer_CardiacGatedCT.merged_painted.usd\",\n",
    "    [\n",
    "        \"results/Slicer_CardiacGatedCT.dynamic_anatomy_painted.usd\",\n",
    "        \"results/Slicer_CardiacGatedCT.static_anatomy_painted.usd\",\n",
    "    ],\n",
    ")\n",
    "\n",
    "if os.path.exists(\"results/Slicer_CardiacGatedCT.flattened_merged_painted.usd\"):\n",
    "    os.remove(\"results/Slicer_CardiacGatedCT.flattened_merged_painted.usd\")\n",
    "\n",
    "usd_tools.merge_usd_files_flattened(\n",
    "    \"results/Slicer_CardiacGatedCT.flattened_merged_painted.usd\",\n",
    "    [\n",
    "        \"results/Slicer_CardiacGatedCT.dynamic_anatomy_painted.usd\",\n",
    "        \"results/Slicer_CardiacGatedCT.static_anatomy_painted.usd\",\n",
    "    ],\n",
    ")"

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[Copilot]

This PR changes the loop range from range(1, 21) to range(4, 21, 4) to process every 4th slice for faster testing. While this may be useful for development, this change is unrelated to the stated purpose of the PR (removing '4d' naming convention) and changes the behavior of the notebook. Consider reverting this change or documenting it separately in the PR description.

[Copilot]

The configuration flag re_run_image_max is changed from False to True. This behavioral change is unrelated to the stated purpose of the PR (removing '4d' naming convention) and should either be reverted or documented in the PR description.

[Copilot]

This PR changes the loop range from range(21) to range(0, 21, 4) to process every 4th slice. This behavioral change is unrelated to the stated purpose of the PR (removing '4d' naming convention) and changes how the notebook executes. Consider reverting this change or documenting it separately in the PR description.