ENH: Add point_set_sizes trait

Author: thewtex

itkwidgets/widget_viewer.py

@@ -272,6 +272,10 @@ class Viewer(ViewerParent):
                                   help="Opacities for the points sets")\
         .tag(sync=True, **array_serialization)\
         .valid(shape_constraints(None,))
+    point_set_sizes = NDArray(dtype=np.uint8, default_value=np.zeros((0,), dtype=np.uint8),
+                              help="Sizes for the points sets")\
+        .tag(sync=True, **array_serialization)\
+        .valid(shape_constraints(None,))
     point_set_representations = List(
         trait=Unicode(),
         default_value=[],
@@ -332,6 +336,10 @@ def __init__(self, **kwargs):  # noqa: C901
             proposal = {'value': kwargs['point_set_opacities']}
             opacities_array = self._validate_point_set_opacities(proposal)
             kwargs['point_set_opacities'] = opacities_array
+        if 'point_set_sizes' in kwargs:
+            proposal = {'value': kwargs['point_set_sizes']}
+            sizes_array = self._validate_point_set_sizes(proposal)
+            kwargs['point_set_sizes'] = sizes_array
         if 'point_set_representations' in kwargs:
             proposal = {'value': kwargs['point_set_representations']}
             representations_list = self._validate_point_set_representations(
@@ -650,6 +658,21 @@ def _validate_point_set_opacities(self, proposal):
         result[:n_values] = value
         return result
 
+    @validate('point_set_sizes')
+    def _validate_point_set_sizes(self, proposal):
+        value = proposal['value']
+        n_values = 0
+        if isinstance(value, float):
+            n_values = 1
+        else:
+            n_values = len(value)
+        n_sizes = n_values
+        if self.point_sets:
+            n_sizes = len(self.point_sets)
+        result = 3 * np.ones((n_sizes,), dtype=np.uint8)
+        result[:n_values] = value
+        return result
+
     @validate('point_set_representations')
     def _validate_point_set_representations(self, proposal):
         value = proposal['value']
@@ -672,6 +695,9 @@ def _on_point_sets_changed(self, change=None):
         # Make sure we have a sufficient number of opacities
         old_opacities = self.point_set_opacities
         self.point_set_opacities = old_opacities[:len(self.point_sets)]
+        # Make sure we have a sufficient number of sizes
+        old_sizes = self.point_set_sizes
+        self.point_set_sizes = old_sizes[:len(self.point_sets)]
         # Make sure we have a sufficient number of representations
         old_representations = self.point_set_representations
         self.point_set_representations = old_representations[:len(
@@ -763,8 +789,8 @@ def view(image=None,  # noqa: C901
          gradient_opacity=0.22, opacity_gaussians=None, channels=None,
          slicing_planes=False, shadow=True, blend_mode='composite',
          point_sets=[],
-         point_set_colors=[], point_set_opacities=[], point_set_representations=[],
-         # point_set_sizes=[],
+         point_set_colors=[], point_set_opacities=[],
+         point_set_representations=[], point_set_sizes=[],
          geometries=[],
          geometry_colors=[], geometry_opacities=[],
          ui_collapsed=False, rotate=False, annotations=True, mode='v',
@@ -907,13 +933,16 @@ def view(image=None,  # noqa: C901
     point_sets: point set, or sequence of point sets
         The point sets to visualize.
 
-    point_set_colors: list of RGB colors
-        Colors for the N geometries. See help(matplotlib.colors) for
+    point_set_colors: list of (r, g, b) colors
+        Colors for the N points. See help(matplotlib.colors) for
         specification. Defaults to the Glasbey series of categorical colors.
 
-    point_set_opacities: list of floats, default: [0.5,]*n
+    point_set_opacities: array of floats, default: [0.5,]*n
         Opacity for the point sets, in the range (0.0, 1.0].
 
+    point_set_sizes: array of unsigned integers, default: [3,]*n
+        Sizes for the point sets, in pixel size units.
+
     point_set_representations: list of strings, default: ['points',]*n
         How to represent the point set. One of 'hidden', 'points', or 'spheres'.
 

js/lib/viewer.js

@@ -122,7 +122,8 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
         _rendering_image: false,
         interpolation: true,
         cmap: null,
-        _custom_cmap: new Float32Array([0, 0, 0]),
+        lut: 'glasbey',
+        _custom_cmap: { array: new Float32Array([0, 0, 0]), shape: [1,3] },
         vmin: null,
         vmax: null,
         shadow: true,
@@ -142,8 +143,9 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
         _scale_factors: new Uint8Array([1, 1, 1]),
         units: '',
         point_sets: null,
-        point_set_colors: new Float32Array([0, 0, 0]),
-        point_set_opacities: new Float32Array([1.0]),
+        point_set_colors: { array: new Float32Array([0, 0, 0]), shape: [1,3] },
+        point_set_opacities: { array: new Float32Array([1.0]), shape: [1] },
+        point_set_sizes: { array: new Uint8Array([3]), shape: [1] },
         point_set_representations: new Array(),
         geometries: null,
         geometry_colors: new Float32Array([0, 0, 0]),
@@ -188,6 +190,7 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
         camera: fixed_shape_serialization([3, 3]),
         point_set_colors: simplearray_serialization,
         point_set_opacities: simplearray_serialization,
+        point_set_sizes: simplearray_serialization,
         geometry_colors: simplearray_serialization,
         geometry_opacities: simplearray_serialization
       },
@@ -447,6 +450,7 @@ function replacePointSets (domWidgetView, pointSets) {
   domWidgetView.model.itkVtkViewer.setPointSets(vtkPointSets)
   domWidgetView.point_set_colors_changed()
   domWidgetView.point_set_opacities_changed()
+  domWidgetView.point_set_sizes_changed()
   domWidgetView.point_set_representations_changed()
   domWidgetView.model.itkVtkViewer.renderLater()
 }
@@ -838,14 +842,15 @@ const ViewerView = widgets.DOMWidgetView.extend({
         this.model.skipOnCroppingPlanesChanged = true
         this.model.set(
           'roi',
-          new Float64Array([
-            bboxCorners[0][0],
-            bboxCorners[0][1],
-            bboxCorners[0][2],
-            bboxCorners[7][0],
-            bboxCorners[7][1],
-            bboxCorners[7][2]
-          ])
+          { array: new Float64Array([
+              bboxCorners[0][0],
+              bboxCorners[0][1],
+              bboxCorners[0][2],
+              bboxCorners[7][0],
+              bboxCorners[7][1],
+              bboxCorners[7][2]
+          ]),
+          shape: [2,3] }
         )
         this.model.save_changes()
       } else {
@@ -1068,8 +1073,65 @@ const ViewerView = widgets.DOMWidgetView.extend({
     if (point_sets) {
       this.point_set_colors_changed()
       this.point_set_opacities_changed()
+      this.point_set_sizes_changed()
       this.point_set_representations_changed()
     }
+
+    const onPointSetColorChanged = (index, color) => {
+      const modelColors = this.model.get('point_set_colors')
+      const modelColor = modelColors.array[index]
+      if (color !== modelColor) {
+        const newColors = modelColors.array.slice()
+        newColors[index] = color
+        this.model.set('point_set_colors', { array: newColors, shape: modelColors.shape })
+        this.model.save_changes()
+      }
+    }
+    this.model.itkVtkViewer.on('pointSetColorChanged',
+      onPointSetColorChanged
+    )
+
+    const onPointSetOpacityChanged = (index, opacity) => {
+      const modelOpacities = this.model.get('point_set_opacities')
+      const modelOpacity = modelOpacities.array[index]
+      if (opacity !== modelOpacity) {
+        const newOpacities = modelOpacities.array.slice()
+        newOpacities[index] = opacity
+        this.model.set('point_set_opacities', { array: newOpacities, shape: modelOpacities.shape })
+        this.model.save_changes()
+      }
+    }
+    this.model.itkVtkViewer.on('pointSetOpacityChanged',
+      onPointSetOpacityChanged
+    )
+
+    const onPointSetRepresentationChanged = (index, representation) => {
+      const modelRepresentations = this.model.get('point_set_representations')
+      const modelRepresentation = modelRepresentations[index]
+      if (representation !== modelRepresentation) {
+        modelRepresentations[index] = representation
+        this.model.set('point_set_representations', modelRepresentation)
+        this.model.save_changes()
+      }
+    }
+    this.model.itkVtkViewer.on('pointSetRepresentationChanged',
+      onPointSetRepresentationChanged
+    )
+
+    const onPointSetSizeChanged = (index, size) => {
+      const modelSizes = this.model.get('point_set_sizes')
+      const modelSize = modelSizes.array[index]
+      if (size !== modelSize) {
+        const newSize = modelSizes.array.slice()
+        newSize[index] = size
+        this.model.set('point_set_sizes', { array: newSize, shape: modelSizes.shape })
+        this.model.save_changes()
+      }
+    }
+    this.model.itkVtkViewer.on('pointSetSizeChanged',
+      onPointSetSizeChanged
+    )
+
     const geometries = this.model.get('geometries')
     if (geometries) {
       this.geometry_colors_changed()
@@ -1115,6 +1177,11 @@ const ViewerView = widgets.DOMWidgetView.extend({
       this.point_set_opacities_changed,
       this
     )
+    this.model.on(
+      'change:point_set_sizes',
+      this.point_set_sizes_changed,
+      this
+    )
     this.model.on(
       'change:point_set_representations',
       this.point_set_representations_changed,
@@ -1308,27 +1375,42 @@ const ViewerView = widgets.DOMWidgetView.extend({
   },
 
   point_set_colors_changed: function () {
-    const point_setColors = this.model.get('point_set_colors').array
     if (this.model.hasOwnProperty('itkVtkViewer')) {
+      const point_set_colors = this.model.get('point_set_colors').array
       const point_sets = this.model.get('point_sets')
       if (point_sets && !!point_sets.length) {
         point_sets.forEach((point_set, index) => {
-          const color = point_setColors.slice(index * 3, (index + 1) * 3)
+          const color = point_set_colors.slice(index * 3, (index + 1) * 3)
           this.model.itkVtkViewer.setPointSetColor(index, color)
         })
       }
     }
   },
 
   point_set_opacities_changed: function () {
-    const point_setOpacities = this.model.get('point_set_opacities').array
     if (this.model.hasOwnProperty('itkVtkViewer')) {
+      const point_set_opacities = this.model.get('point_set_opacities').array
       const point_sets = this.model.get('point_sets')
       if (point_sets && !!point_sets.length) {
         point_sets.forEach((point_set, index) => {
           this.model.itkVtkViewer.setPointSetOpacity(
             index,
-            point_setOpacities[index]
+            point_set_opacities[index]
+          )
+        })
+      }
+    }
+  },
+
+  point_set_sizes_changed: function () {
+    if (this.model.hasOwnProperty('itkVtkViewer')) {
+      const point_set_sizes = this.model.get('point_set_sizes').array
+      const point_sets = this.model.get('point_sets')
+      if (point_sets && !!point_sets.length) {
+        point_sets.forEach((point_set, index) => {
+          this.model.itkVtkViewer.setPointSetSize(
+            index,
+            point_set_sizes[index]
           )
         })
       }
@@ -1342,6 +1424,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
     if (this.model.hasOwnProperty('itkVtkViewer')) {
       const point_sets = this.model.get('point_sets')
       if (point_sets && !!point_sets.length) {
+        console.log(point_set_representations)
         point_set_representations.forEach((representation, index) => {
           switch (representation.toLowerCase()) {
             case 'hidden':