ENH: Support label_map_names

InsightSoftwareConsortium · Jun 3, 2020 · 4401035 · 4401035
1 parent b3a0702
commit 4401035
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Showing 5 changed files with 72 additions and 23 deletions.
diff --git a/examples/LabelMap.ipynb b/examples/LabelMap.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,27 +65,53 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
+   "execution_count": 21,
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7416595a86114b29b9cdd40676af0e84",
+       "model_id": "37dcf1f9c89b4f9c8e7ab039d3f38dde",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(cmap='Grayscale', geometries=[], gradient_opacity=0.8, interpolation=False, point_sets=[], rendered_ima…"
+       "Viewer(cmap='Grayscale', geometries=[], gradient_opacity=0.5, interpolation=False, label_map_names=[(0, 'Backg…"
       ]
      },
      "metadata": {},
      "output_type": "display_data"
     }
    ],
    "source": [
-    "view(image, label_map=label_map, rotate=True, gradient_opacity=0.8)"
+    "names = [(0, 'Background'), (1, 'First cell'), (2, 'Second cell')]\n",
+    "viewer = view(image,\n",
+    "              label_map=label_map,\n",
+    "              label_map_names=names,\n",
+    "              rotate=True,\n",
+    "              gradient_opacity=0.5,\n",
+    "              slicing_planes=True)\n",
+    "viewer"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "names = [(0, 'Background'), (1, 'First cell'), (2, 'Second cell')]\n",
+    "viewer.label_map_names = names"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/itkwidgets/widget_viewer.py b/itkwidgets/widget_viewer.py
@@ -15,7 +15,7 @@
 import itk
 import numpy as np
 import ipywidgets as widgets
-from traitlets import CBool, CFloat, CInt, Unicode, CaselessStrEnum, List, validate
+from traitlets import CBool, CFloat, CInt, Unicode, CaselessStrEnum, List, validate, TraitError, Tuple
 from ipydatawidgets import NDArray, array_serialization, shape_constraints
 from .trait_types import ITKImage, ImagePointTrait, ImagePoint, PointSetList, PolyDataList, itkimage_serialization, image_point_serialization, polydata_list_serialization, Colormap
 
@@ -143,6 +143,12 @@ class Viewer(ViewerParent):
         allow_none=True).tag(
         sync=True,
         **itkimage_serialization)
+    label_map_names = List(
+        trait=Tuple(),
+        allow_none=True,
+        default_value=None,
+        help="Names for labels in the label map.").tag(
+        sync=True)
     interpolation = CBool(
         default_value=True,
         help="Use linear interpolation in slicing planes.").tag(sync=True)
@@ -649,6 +655,7 @@ def roi_slice(self):
 
 def view(image=None,  # noqa: C901
          label_map=None,  # noqa: C901
+         label_map_names=None,  # noqa: C901
          cmap=None,
          select_roi=False,
          interpolation=True,
@@ -720,6 +727,9 @@ def view(image=None,  # noqa: C901
         The 2D or 3D label map to visualize. If an image is also provided, the
         label map must have the same size.
 
+    label_map_names : OrderedDict of (label_value, label_name)
+        String names associated with the integer label values.
+
     vmin: float, optional, default: None
         Value that maps to the minimum of image colormap. Defaults to minimum of
         the image pixel buffer.
@@ -886,6 +896,7 @@ def view(image=None,  # noqa: C901
 
     viewer = Viewer(image=image,
                     label_map=label_map,
+                    label_map_names=label_map_names,
                     cmap=cmap,
                     select_roi=select_roi,
                     interpolation=interpolation,

diff --git a/js/lib/viewer.js b/js/lib/viewer.js
@@ -16,11 +16,11 @@ import macro from 'vtk.js/Sources/macro'
 const widgets = require('@jupyter-widgets/base')
 
 const ANNOTATION_DEFAULT =
-  '<table style="margin-left: 0;"><tr><td style="margin-left: auto; margin-right: 0;">Index:</td><td>${iIndex},</td><td>${jIndex},</td><td>${kIndex}</td></tr><tr><td style="margin-left: auto; margin-right: 0;">Position:</td><td>${xPosition},</td><td>${yPosition},</td><td>${zPosition}</td></tr><tr><td style="margin-left: auto; margin-right: 0;"">Value:</td><td>${value}</td></tr></table>'
+  '<table style="margin-left: 0;"><tr><td style="margin-left: auto; margin-right: 0;">Index:</td><td>${iIndex},</td><td>${jIndex},</td><td>${kIndex}</td></tr><tr><td style="margin-left: auto; margin-right: 0;">Position:</td><td>${xPosition},</td><td>${yPosition},</td><td>${zPosition}</td></tr><tr><td style="margin-left: auto; margin-right: 0;"">Value:</td><td style="text-align:center;" colspan="3">${value}</td></tr><tr ${annotationLabelStyle}><td style="margin-left: auto; margin-right: 0;">Label:</td><td style="text-align:center;" colspan="3">${annotation}</td></tr></table>'
 const ANNOTATION_CUSTOM_PREFIX =
   '<table style="margin-left: 0;"><tr><td style="margin-left: auto; margin-right: 0;">Scale/Index:</td>'
 const ANNOTATION_CUSTOM_POSTFIX =
-  '</tr><tr><td style="margin-left: auto; margin-right: 0;">Position:</td><td>${xPosition},</td><td>${yPosition},</td><td>${zPosition}</td></tr><tr><td style="margin-left: auto; margin-right: 0;"">Value:</td><td>${value}</td></tr></table>'
+  '</tr><tr><td style="margin-left: auto; margin-right: 0;">Position:</td><td>${xPosition},</td><td>${yPosition},</td><td>${zPosition}</td></tr><tr><td style="margin-left: auto; margin-right: 0;"">Value:</td><td style="text-align:center;" colspan="3">${value}</td></tr><tr ${annotationLabelStyle}><td style="margin-left: auto; margin-right: 0;">Label:</td><td style="text-align:center;" colspan="3">${annotation}</td></tr></table>'
 
 const cores = navigator.hardwareConcurrency ? navigator.hardwareConcurrency : 4
 const numberOfWorkers = cores + Math.floor(Math.sqrt(cores))
@@ -116,6 +116,7 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
         _view_module_version: '0.27.5',
         rendered_image: null,
         rendered_label_map: null,
+        label_map_names: null,
         _rendering_image: false,
         interpolation: true,
         cmap: 'Viridis (matplotlib)',
@@ -719,6 +720,9 @@ const ViewerView = widgets.DOMWidgetView.extend({
       this.select_roi_changed()
       this.scale_factors_changed()
     }
+    if (rendered_label_map) {
+      this.label_map_names_changed()
+    }
 
     const onUserInterfaceCollapsedToggle = (collapsed) => {
       if (collapsed !== this.model.get('ui_collapsed')) {
@@ -1044,6 +1048,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
     this.model.on('change:mode', this.mode_changed, this)
     this.model.on('change:units', this.units_changed, this)
     this.model.on('change:camera', this.camera_changed, this)
+    this.model.on('change:label_map_names', this.label_map_names_changed, this)
 
     let toDecompress = []
     const rendered_image = this.model.get('rendered_image')
@@ -1161,6 +1166,14 @@ const ViewerView = widgets.DOMWidgetView.extend({
     return Promise.resolve(null)
   },
 
+  label_map_names_changed: function () {
+    const label_map_names = this.model.get('label_map_names')
+    if (label_map_names && this.model.hasOwnProperty('itkVtkViewer')) {
+      const labelMapNames = new Map(label_map_names)
+      this.model.itkVtkViewer.setLabelMapNames(labelMapNames)
+    }
+  },
+
   point_sets_changed: function () {
     const point_sets = this.model.get('point_sets')
     if (point_sets && !!point_sets.length) {
@@ -1524,7 +1537,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
         scaleFactors[1] === 1 &&
         scaleFactors[2] === 1
       ) {
-        viewProxy.setCornerAnnotation('se', `${ANNOTATION_DEFAULT}`)
+        viewProxy.setSeCornerAnnotation(`${ANNOTATION_DEFAULT}`)
       } else {
         let scaleIndex = ''
         if (scaleFactors[0] === 1) {
@@ -1542,8 +1555,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
         } else {
           scaleIndex = `${scaleIndex}<td>${scaleFactors[2]}X</td>`
         }
-        viewProxy.setCornerAnnotation(
-          'se',
+        viewProxy.setSeCornerAnnotation(
           `${ANNOTATION_CUSTOM_PREFIX}${scaleIndex}${ANNOTATION_CUSTOM_POSTFIX}`
         )
       }

diff --git a/js/package-lock.json b/js/package-lock.json
diff --git a/js/package.json b/js/package.json
@@ -63,11 +63,11 @@
     "copy-webpack-plugin": "^5.1.1",
     "css-element-queries": "^1.2.3",
     "itk": "^13.1.0",
-    "itk-vtk-viewer": "^10.0.0",
+    "itk-vtk-viewer": "^10.1.0",
     "jupyter-dataserializers": "^2.2.0",
     "mobx": "^5.15.4",
     "regenerator-runtime": "^0.13.5",
-    "vtk.js": "^14.1.2"
+    "vtk.js": "^14.3.2"
   },
   "jupyterlab": {
     "extension": "dist/labextension"