Add baseline comparison tests for time-series image registration

- TestTools: compare_result_to_baseline_transform and compare_result_to_baseline_image
- TestRegisterTimeSeriesImages: baseline .hdf transforms and .mha images
- pytest --create-baselines support; CI and test docs updated

Author: aylward

.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/Heart-GatedCT_To_USD/0-download_and_convert_4d_to_3d.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2026-02-09T04:51:59.431418Z",
@@ -22,7 +22,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2026-02-09T04:52:14.024235Z",
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2026-02-09T04:52:14.039220Z",
@@ -65,7 +65,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {
     "execution": {
      "iopub.execute_input": "2026-02-09T04:52:14.055215Z",
@@ -74,18 +74,7 @@
      "shell.execute_reply": "2026-02-09T04:52:57.153872Z"
     }
    },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'./results//slice_fixed.mha'"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "conv = ConvertNRRD4DTo3D()\n",
     "conv.load_nrrd_4d(f\"{data_dir}/TruncalValve_4DCT.seq.nrrd\")\n",