ENH: Add support for itk.PointBasedSpatialObject's

Based on:

  https://github.com/KitwareMedical/ITKTubeTK/blob/7dbad677ed989cc7ec91748158c064088dc315f8/examples/ITKSpatialObjects-SimpleExample.ipynb

.gitignore

@@ -26,6 +26,7 @@ examples/cow.vtk
 examples/Bunny.vtp
 examples/uGridEx.vtk
 examples/input.tiff
+examples/Normal071-VascularNetwork.tre
 
 js/lib/ZstdDecompress/web-build/
 .pytest_cache/

README.rst

@@ -56,6 +56,7 @@ Interactive Jupyter_ widgets to visualize images, point sets, and meshes.
 
   - NumPy array point sets
   - `itk.PointSet <https://itk.org/Doxygen/html/classitk_1_1PointSet.html>`_
+  - `itk.PointBasedSpatialObject <https://itk.org/Doxygen/html/classitk_1_1PointBasedSpatialObject.html>`_
   - `vtk.vtkPolyData <https://vtk.org/doc/nightly/html/classvtkPolyData.html>`_ point sets
   - `pyvista.PolyData <https://docs.pyvista.org/core/points.html>`_ point sets
 
@@ -114,6 +115,7 @@ Data types:
 - `Binder: NumPy array for image with anisotropic spacing <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/ImageWithAnisotropicPixelSpacing.ipynb>`_
 - `Binder: NumPy array point sets <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/NumPyArrayPointSet.ipynb>`_
 - `Binder: ITK Mesh <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/Mesh.ipynb>`_
+- `Binder: ITK PointBasedSpatialObject <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/PointBasedSpatialObject.ipynb>`_
 - `Binder: skan segmentation skeleton <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SegmentationSkeleton.ipynb>`_
 
 Tasks:
@@ -250,6 +252,7 @@ After installation, try the following examples that demonstrate how to visualize
 - `pyvista UniformGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.UniformGrid.ipynb>`_
 - `NumPy array point sets <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/NumPyArrayPointSet.ipynb>`_
 - `ITK Mesh <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/Mesh.ipynb>`_
+- `ITK PointBasedSpatialObject <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/PointBasedSpatialObject.ipynb>`_
 - `VTK vtkPolyData <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vtkPolyData.ipynb>`_
 - `VTK vtkUnstructuredGrid <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/vtkUnstructuredGrid.ipynb>`_
 - `pyvista PolyData <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/pyvista.PolyData.ipynb>`_

examples/PointBasedSpatialObject.ipynb

@@ -0,0 +1,113 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Install dependencies for this example\n",
+    "# Note: This does not include itkwidgets, itself\n",
+    "import sys\n",
+    "!{sys.executable} -m pip install itk-io"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from urllib.request import urlretrieve\n",
+    "import os\n",
+    "\n",
+    "import itk\n",
+    "\n",
+    "from itkwidgets import view"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Example data from ITKTubeTK: https://github.com/KitwareMedical/ITKTubeTK\n",
+    "\n",
+    "tubes_file = \"Normal071-VascularNetwork.tre\"\n",
+    "if not os.path.exists(tubes_file):\n",
+    "    url = 'https://data.kitware.com/api/v1/item/5e1b3727af2e2eed35f5c48a/download'\n",
+    "    urlretrieve(url, tubes_file)\n",
+    "    \n",
+    "mra_file = \"Normal071-MRA.mha\"\n",
+    "if not os.path.exists(mra_file):\n",
+    "    url = 'https://data.kitware.com/api/v1/item/5e1b3721af2e2eed35f5c482/download'\n",
+    "    urlretrieve(url, mra_file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "PixelType = itk.F\n",
+    "Dimension = 3\n",
+    "    \n",
+    "# Read tre file\n",
+    "tubesReader = itk.SpatialObjectReader[Dimension].New()\n",
+    "tubesReader.SetFileName(tubes_file)\n",
+    "tubesReader.Update()\n",
+    "tubes = tubesReader.GetGroup()\n",
+    "\n",
+    "# Read mra image\n",
+    "mra = itk.imread(mra_file, PixelType)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "0f0c8f7c10aa406e9a1f19a63a6f21ce",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Viewer(geometries=[], gradient_opacity=0.22, point_set_colors=array([[0.8392157, 0.       , 0.       ]], dtype…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "view(point_sets=tubes)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.6.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

itkwidgets/_transform_types.py

@@ -131,6 +131,33 @@ def _vtk_data_attributes_to_vtkjs(attributes):
     vtkjs_attributes["arrays"] = arrays
     return vtkjs_attributes
 
+def _numpy_array_to_point_set(point_set_like):
+    point_values = np.asarray(point_set_like).astype(np.float32)
+    if len(
+            point_values.shape) > 1 and point_values.shape[1] == 2 or point_values.shape[1] == 3:
+        if point_values.shape[1] == 2:
+            point_values = np.hstack(
+                (point_values, -5.0e-6 * np.ones((point_values.shape[0], 1)))).astype(np.float32)
+        point_set = {'vtkClass': 'vtkPolyData'}
+        points = {'vtkClass': 'vtkPoints',
+                  'name': '_points',
+                  'numberOfComponents': 3,
+                  'dataType': 'Float32Array',
+                  'size': point_values.size,
+                  'values': point_values}
+        point_set['points'] = points
+        vert_values = np.ones((point_values.size * 2,), dtype=np.uint32)
+        vert_values[1::2] = np.arange(point_values.size)
+        verts = {'vtkClass': 'vtkCellArray',
+                 'name': '_verts',
+                 'numberOfComponents': 1,
+                 'dataType': 'Uint32Array',
+                 'size': vert_values.size,
+                 'values': vert_values}
+        point_set['verts'] = verts
+        return point_set
+    else:
+        return None
 
 def to_itk_image(image_like):
     if is_arraylike(image_like):
@@ -226,33 +253,25 @@ def to_point_set(point_set_like):  # noqa: C901
             point_set['pointData'] = point_data
 
         return point_set
+    elif isinstance(point_set_like, itk.GroupSpatialObject):
+        children = point_set_like.GetChildren()
+
+        point_set = {'vtkClass': 'vtkPolyData'}
+
+        points_list = []
+        for ii in range(len(children)):
+            child = children[ii]
+            down_casted = itk.down_cast(child)
+            if isinstance(down_casted, itk.PointBasedSpatialObject):
+                n_points = down_casted.GetNumberOfPoints()
+                for ii in range(n_points):
+                    point = down_casted.GetPoint(ii)
+                    point.SetSpatialObject(down_casted)
+                    position = point.GetPositionInWorldSpace()
+                    points_list.append(list(position))
+        return _numpy_array_to_point_set(points_list)
     elif is_arraylike(point_set_like):
-        point_values = np.asarray(point_set_like).astype(np.float32)
-        if len(
-                point_values.shape) > 1 and point_values.shape[1] == 2 or point_values.shape[1] == 3:
-            if point_values.shape[1] == 2:
-                point_values = np.hstack(
-                    (point_values, -5.0e-6 * np.ones((point_values.shape[0], 1)))).astype(np.float32)
-            point_set = {'vtkClass': 'vtkPolyData'}
-            points = {'vtkClass': 'vtkPoints',
-                      'name': '_points',
-                      'numberOfComponents': 3,
-                      'dataType': 'Float32Array',
-                      'size': point_values.size,
-                      'values': point_values}
-            point_set['points'] = points
-            vert_values = np.ones((point_values.size * 2,), dtype=np.uint32)
-            vert_values[1::2] = np.arange(point_values.size)
-            verts = {'vtkClass': 'vtkCellArray',
-                     'name': '_verts',
-                     'numberOfComponents': 1,
-                     'dataType': 'Uint32Array',
-                     'size': vert_values.size,
-                     'values': vert_values}
-            point_set['verts'] = verts
-            return point_set
-        else:
-            return None
+        return _numpy_array_to_point_set(point_set_like)
     elif have_vtk and isinstance(point_set_like, vtk.vtkPolyData):
         from vtk.util.numpy_support import vtk_to_numpy
         point_set = {'vtkClass': 'vtkPolyData'}

js/lib/viewer.js

@@ -1003,7 +1003,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
         const viewProxy = this.model.itkVtkViewer.getViewProxy()
         const representation = viewProxy.getRepresentations()[0];
         const shadow = this.model.get('shadow')
-        representation.setUseShadow(shadow);
+        !!representation && representation.setUseShadow(shadow);
         break
       default:
         throw new Error('Unknown view mode')