ENH: image and transform baselines and experiment notebook testing

.cursor/rules/project-standards.mdc

@@ -100,3 +100,7 @@ The user prefers to review and stage changes manually.
 - Make atomic commits with clear messages
 - Don't commit large binary files (add to `.gitignore`)
 - Use `git status` to verify changes before committing
+
+**Code and documentation versions:**
+- Refer to code and documentation in the folder reference_code to get examples and documentation of the APIs and best practices for the advanced libraries used in this project:
+    - ITK, VTK, PyVista, Omniverse, PhysicsNeMo, Simpleware, MONAI, and OpenUSD

.gitattributes

@@ -0,0 +1,2 @@
+*.hdf filter=lfs diff=lfs merge=lfs -text
+*.mha filter=lfs diff=lfs merge=lfs -text

.github/workflows/ci.yml

@@ -35,6 +35,8 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        lfs: true
 
     - name: Free up disk space on Ubuntu
       if: matrix.os == 'ubuntu-latest'
@@ -134,6 +136,8 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        lfs: true
 
     - name: Free up disk space
       run: |
@@ -264,6 +268,8 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        lfs: true
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -341,6 +347,8 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        lfs: true
 
     - name: Set up Python 3.10
       uses: actions/setup-python@v5

.github/workflows/test-slow.yml

@@ -17,6 +17,8 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
+      with:
+        lfs: true
 
     - name: Set up Python 3.10
       uses: actions/setup-python@v5

.gitignore

@@ -24,7 +24,6 @@ network_weights
 # Data files
 *.gz
 *.mat
-*.mha
 *.mhd
 *.zip
 *.nii

README.md

@@ -29,6 +29,7 @@ PhysioMotion4D is a comprehensive medical imaging package that converts 4D CT sc
 - NVIDIA GPU with CUDA 12.6+ (for AI models and registration)
 - 16GB+ RAM (32GB+ recommended for large datasets)
 - NVIDIA Omniverse (for USD visualization)
+- **Git LFS** (required for running tests: baseline files in `tests/baselines/` are stored with Git LFS; install from [git-lfs.github.com](https://git-lfs.github.com), then run `git lfs install` and `git lfs pull` after cloning)
 
 ### Installation from PyPI
 
@@ -43,10 +44,12 @@ pip install physiomotion4d[nim]
 
 ### Installation from Source
 
-1. **Clone the repository**:
+1. **Clone the repository** (Git LFS is required for tests; install it first from [git-lfs.github.com](https://git-lfs.github.com)):
    ```bash
    git clone <repository-url>
    cd PhysioMotion4D
+   git lfs install   # if not already done
+   git lfs pull     # fetch .hdf and .mha baselines in tests/baselines/
    ```
 
 2. **Create virtual environment**:

data/KCL-Heart-Model/.gitignore

@@ -1,3 +1,4 @@
 training_cases*
 pca*
 surfaces*
+labelmap*

data/Slicer-Heart-CT/.gitignore

@@ -0,0 +1 @@
+*.mha

experiments/Colormap-VTK_To_USD/colormap_vtk_to_usd.ipynb

@@ -34,10 +34,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.026051Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.025056Z"
+     "iopub.execute_input": "2026-02-09T03:48:28.123883Z",
+     "iopub.status.busy": "2026-02-09T03:48:28.123883Z",
+     "iopub.status.idle": "2026-02-09T03:48:43.826000Z",
+     "shell.execute_reply": "2026-02-09T03:48:43.825409Z"
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    "outputs": [],
@@ -72,10 +72,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.056057Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.055050Z"
+     "iopub.execute_input": "2026-02-09T03:48:43.846529Z",
+     "iopub.status.busy": "2026-02-09T03:48:43.846034Z",
+     "iopub.status.idle": "2026-02-09T03:48:43.857215Z",
+     "shell.execute_reply": "2026-02-09T03:48:43.856121Z"
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@@ -130,10 +130,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.220731Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.219708Z"
+     "iopub.execute_input": "2026-02-09T03:48:43.858745Z",
+     "iopub.status.busy": "2026-02-09T03:48:43.858745Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.022573Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.021580Z"
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    "outputs": [],
@@ -182,10 +182,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.355566Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.354562Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.024575Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.024575Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.158618Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.157624Z"
     }
    },
    "outputs": [],
@@ -224,10 +224,10 @@
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-     "iopub.status.busy": "2026-02-04T01:32:33.356562Z",
-     "iopub.status.idle": "2026-02-04T01:32:33.492011Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.490997Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.159626Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.159626Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.293616Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.292622Z"
     }
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    "outputs": [],
@@ -266,10 +266,10 @@
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-     "iopub.status.busy": "2026-02-04T01:32:33.494019Z",
-     "iopub.status.idle": "2026-02-04T01:32:33.627873Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.626854Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.295616Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.295616Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.428154Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.428154Z"
     }
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    "outputs": [],
@@ -308,10 +308,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.764342Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.763320Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.430154Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.430154Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.563163Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.563163Z"
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    "outputs": [],
@@ -348,10 +348,10 @@
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-     "iopub.status.idle": "2026-02-04T01:32:33.900294Z",
-     "shell.execute_reply": "2026-02-04T01:32:33.899437Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.565157Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.565157Z",
+     "iopub.status.idle": "2026-02-09T03:48:44.699684Z",
+     "shell.execute_reply": "2026-02-09T03:48:44.698691Z"
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    "outputs": [],
@@ -394,10 +394,10 @@
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-     "shell.execute_reply": "2026-02-04T01:32:34.034169Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.701683Z",
+     "iopub.status.busy": "2026-02-09T03:48:44.701683Z",
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+     "shell.execute_reply": "2026-02-09T03:48:44.833694Z"
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@@ -458,10 +458,10 @@
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-     "shell.execute_reply": "2026-02-04T01:32:34.049224Z"
+     "iopub.execute_input": "2026-02-09T03:48:44.836684Z",
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+     "shell.execute_reply": "2026-02-09T03:48:44.848691Z"
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    "outputs": [],