Merge pull request #779 from dave3d/SimpleITKImageSupport

ENH:  Added support for SimpleITK Image loading

Author: thewtex

.github/workflows/notebook-test.yml

@@ -31,6 +31,7 @@ jobs:
           python3 -m pip install pyimagej urllib3
           python3 -c "import imagej; ij = imagej.init('2.5.0'); print(ij.getVersion())"
           python3 -m pip install "itk>=5.3.0"
+          python3 -m pip install "simpleitk>=2.5.3"
 
       - name: Test notebooks
         run: |

examples/integrations/SimpleITK/SimpleITKImage.ipynb

@@ -0,0 +1,117 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6d0d7f82",
+   "metadata": {
+    "jupyter": {
+     "source_hidden": true
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Install SimpleITK if needed\n",
+    "# %pip install SimpleITK"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e212530d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import SimpleITK as sitk\n",
+    "import numpy as np\n",
+    "from itkwidgets import view"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "555d9dd2",
+   "metadata": {},
+   "source": [
+    "## Create a Simple 3D Image\n",
+    "\n",
+    "Let's create a synthetic 3D image with SimpleITK:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "03397401",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create a 3D image using SimpleITK's GaussianSource\n",
+    "size = [64, 64, 64]\n",
+    "image = sitk.GaussianSource(\n",
+    "    sitk.sitkFloat32,\n",
+    "    size,\n",
+    "    sigma=[10.0, 10.0, 10.0],\n",
+    "    mean=[32.0, 32.0, 32.0],\n",
+    "    scale=255.0,\n",
+    "    normalized=False\n",
+    ")\n",
+    "\n",
+    "# Set spacing and origin\n",
+    "image.SetSpacing([1.0, 1.0, 2.0])  # Anisotropic spacing\n",
+    "image.SetOrigin([0.0, 0.0, 0.0])\n",
+    "\n",
+    "print(f\"Image size: {image.GetSize()}\")\n",
+    "print(f\"Image spacing: {image.GetSpacing()}\")\n",
+    "print(f\"Image origin: {image.GetOrigin()}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "03ec254a",
+   "metadata": {},
+   "source": [
+    "## Visualize the SimpleITK Image\n",
+    "\n",
+    "Now we can directly pass the SimpleITK image to itkwidgets:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1ad1a724",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view(image)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b44dd52-f7a4-4b84-842d-5fee9bc72232",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "widgets",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

itkwidgets/integrations/__init__.py

@@ -7,6 +7,7 @@
 from .itk import HAVE_ITK
 from .pytorch import HAVE_TORCH
 from .monai import HAVE_MONAI
+from .simpleitk import HAVE_SIMPLEITK, simpleitk_image_to_ngff_image
 from .vtk import HAVE_VTK, vtk_image_to_ngff_image, vtk_polydata_to_vtkjs
 from .xarray import HAVE_XARRAY, HAVE_MULTISCALE_SPATIAL_IMAGE, xarray_data_array_to_numpy, xarray_data_set_to_numpy
 from ..render_types import RenderType
@@ -99,6 +100,14 @@ def _get_viewer_image(image, label=False):
             to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
             return store
 
+    if HAVE_SIMPLEITK:
+        import SimpleITK as sitk
+        if isinstance(image, sitk.Image):
+            ngff_image = simpleitk_image_to_ngff_image(image)
+            multiscales = to_multiscales(ngff_image, method=method)
+            to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
+            return store
+
     if isinstance(image, dask.array.core.Array):
         ngff_image = to_ngff_image(image)
         multiscales = to_multiscales(ngff_image, method=method)
@@ -228,6 +237,10 @@ def _detect_render_type(data, input_type) -> RenderType:
             return RenderType.IMAGE
         elif isinstance(data, vtk.vtkPolyData):
             return RenderType.POINT_SET
+    if HAVE_SIMPLEITK:
+        import SimpleITK as sitk
+        if isinstance(data, sitk.Image):
+            return RenderType.IMAGE
     if isinstance(data, dask.array.core.Array):
         if data.ndim ==2 and data.shape[1] < 4:
             return RenderType.POINT_SET

itkwidgets/integrations/simpleitk.py

@@ -0,0 +1,55 @@
+import importlib_metadata
+
+HAVE_SIMPLEITK = False
+try:
+    importlib_metadata.metadata("SimpleITK")
+    HAVE_SIMPLEITK = True
+except importlib_metadata.PackageNotFoundError:
+    pass
+
+from ngff_zarr import to_ngff_image
+
+
+def simpleitk_image_to_ngff_image(image):
+    """Convert a SimpleITK image to an NGFF image.
+    
+    Parameters
+    ----------
+    image : sitk.Image
+        The SimpleITK image to convert
+        
+    Returns
+    -------
+    NgffImage
+        The converted NGFF image with proper spacing and origin
+    """
+    import SimpleITK as sitk
+    
+    # Get the numpy array from SimpleITK image
+    # Note: SimpleITK has XYZ ordering, numpy has ZYX ordering
+    array = sitk.GetArrayFromImage(image)
+    
+    # Get origin
+    origin = image.GetOrigin()
+    translation = {}
+    if len(origin) >= 1:
+        translation['x'] = origin[0]
+    if len(origin) >= 2:
+        translation['y'] = origin[1]
+    if len(origin) >= 3:
+        translation['z'] = origin[2]
+    
+    # Get spacing
+    spacing = image.GetSpacing()
+    scale = {}
+    if len(spacing) >= 1:
+        scale['x'] = spacing[0]
+    if len(spacing) >= 2:
+        scale['y'] = spacing[1]
+    if len(spacing) >= 3:
+        scale['z'] = spacing[2]
+    
+    # Create NGFF image with metadata
+    ngff_image = to_ngff_image(array, scale=scale, translation=translation)
+    
+    return ngff_image