ENH: Add lut trait

Author: thewtex

itkwidgets/lut.py

@@ -0,0 +1,10 @@
+# Some aliases similar to matplotlib.cm
+glasbey = "glasbey"
+glasbey_light = "glasbey_light"
+glasbey_warm = "glasbey_warm"
+modulate = "modulate"
+
+glasbey_bw = "glasbey_bw"
+glasbey_dark = "glasbey_dark"
+glasbey_cool = "glasbey_cool"
+modulate_dark = "modulate_dark"

itkwidgets/trait_types.py

@@ -680,3 +680,38 @@ def validate(self, obj, value):
                 'Custom'):
             raise self.error('Invalid colormap')
         return super(Colormap, self).validate(obj, value)
+
+class LookupTable(traitlets.Unicode):
+    """A trait type holding a lookup table."""
+
+    info_text = 'A lookup table, either a itk-vtk-viewer categorical colormap preset, todo: np.ndarray of RGB points, or matplotlib ListedColormap.'
+
+    _lookup_table_presets = ('glasbey',
+                             'glasbey_light',
+                             'glasbey_warm',
+                             'modulate',
+                             'glasbey_bw',
+                             'glasbey_dark',
+                             'glasbey_cool',
+                             'modulate_dark',
+                             )
+
+    def validate(self, obj, value):
+        if value is None:
+            return None
+        # elif isinstance(value, np.ndarray):
+            # custom_cmap = value.astype(np.float32)
+            # custom_cmap = custom_cmap[:, :3]
+            # obj._custom_cmap = custom_cmap
+            # timestamp = str(datetime.timestamp(datetime.now()))
+            # return 'Custom NumPy ' + timestamp
+        # elif isinstance(value, matplotlib.colors.ListedColormap):
+            # custom_cmap = value(np.linspace(0.0, 1.0, 64)).astype(np.float32)
+            # custom_cmap = custom_cmap[:, :3]
+            # obj._custom_cmap = custom_cmap
+            # timestamp = str(datetime.timestamp(datetime.now()))
+            # return 'Custom matplotlib ' + timestamp
+        if value not in self._lookup_table_presets and not value.startswith(
+                'Custom'):
+            raise self.error('Invalid lookup table')
+        return super(LookupTable, self).validate(obj, value)

itkwidgets/widget_viewer.py

@@ -5,7 +5,6 @@
 In the future, will add optional segmentation mesh overlay.
 """
 
-from . import cm
 import colorcet
 import matplotlib
 import collections
@@ -17,7 +16,7 @@
 import ipywidgets as widgets
 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
+from .trait_types import ITKImage, ImagePointTrait, ImagePoint, PointSetList, PolyDataList, itkimage_serialization, image_point_serialization, polydata_list_serialization, Colormap, LookupTable
 
 try:
     import ipywebrtc
@@ -167,6 +166,12 @@ class Viewer(ViewerParent):
                            help="RGB triples from 0.0 to 1.0 that define a custom linear, sequential colormap")\
         .tag(sync=True, **array_serialization)\
         .valid(shape_constraints(None, 3))
+    lut = LookupTable('glasbey',
+        help='Lookup table for the label map.').tag(sync=True)
+    _custom_cmap = NDArray(dtype=np.float32, default_value=None, allow_none=True,
+                           help="RGB triples from 0.0 to 1.0 that define a custom linear, sequential colormap")\
+        .tag(sync=True, **array_serialization)\
+        .valid(shape_constraints(None, 3))
     shadow = CBool(
         default_value=True,
         help="Use shadowing in the volume rendering.").tag(sync=True)
@@ -752,6 +757,7 @@ def view(image=None,  # noqa: C901
          label_map_weights=None,  # noqa: C901
          label_map_blend=0.5,
          cmap=None,
+         lut='glasbey',
          select_roi=False,
          interpolation=True,
          gradient_opacity=0.22, opacity_gaussians=None, channels=None,
@@ -843,12 +849,20 @@ def view(image=None,  # noqa: C901
         Value that maps to the minimum of image colormap.  A single value can
         be provided or a list for multi-component images.
 
-    cmap: list of strings
+    cmap: list of colormaps
             default:
                 - single component: 'viridis', 'grayscale' with a label map,
                 - two components: 'BkCy', 'BkMa'
                 - three components: 'BkRd', 'BkGn', 'BkBu'
-        Colormap for each image component. Some valid values available at itkwidgets.cm.*
+        Colormap for each image component. Some valid values available at
+        itkwidgets.cm.*
+        Colormaps can also be Nx3 float NumPy arrays from 0.0 to 1.0 for the
+        red, green, blue points on the map or a
+        matplotlib.colors.LinearSegmentedColormap.
+
+    lut: lookup table, default: 'glasbey'
+        Lookup table for the label map. Some valid values available at
+        itkwidgets.lut.*
 
     select_roi: bool, default: False
         Enable an interactive region of interest widget for the image.
@@ -1017,6 +1031,7 @@ def view(image=None,  # noqa: C901
                     label_map_names=label_map_names,
                     label_map_weights=label_map_weights,
                     cmap=cmap,
+                    lut=lut,
                     select_roi=select_roi,
                     interpolation=interpolation,
                     gradient_opacity=gradient_opacity, slicing_planes=slicing_planes,

js/lib/viewer.js

@@ -746,6 +746,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
       this.label_map_names_changed()
       this.label_map_weights_changed()
       this.label_map_blend_changed()
+      this.lut_changed()
     }
 
     const onUserInterfaceCollapsedToggle = (collapsed) => {
@@ -796,6 +797,17 @@ const ViewerView = widgets.DOMWidgetView.extend({
     }
     this.model.itkVtkViewer.on('selectColorMap', onSelectColorMap)
 
+    const onSelectLookupTable = (lookupTable) => {
+      let lut = this.model.get('lut')
+      if (
+        lut !== null && lookupTable !== lut
+      ) {
+        this.model.set('lut', lookupTable)
+        this.model.save_changes()
+      }
+    }
+    this.model.itkVtkViewer.on('selectLookupTable', onSelectLookupTable)
+
     const onChangeColorRange = (component, colorRange) => {
       const vmin = this.model.get('vmin')
       if (vmin === null) {
@@ -1076,6 +1088,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
       this
     )
     this.model.on('change:cmap', this.cmap_changed, this)
+    this.model.on('change:lut', this.lut_changed, this)
     this.model.on('change:vmin', this.vmin_changed, this)
     this.model.on('change:vmax', this.vmax_changed, this)
     this.model.on('change:shadow', this.shadow_changed, this)
@@ -1519,6 +1532,30 @@ const ViewerView = widgets.DOMWidgetView.extend({
     }
   },
 
+  lut_changed: function () {
+    const lut = this.model.get('lut')
+    if (lut !== null && this.model.hasOwnProperty('itkVtkViewer')) {
+      //if (lut.startsWith('Custom')) {
+      // -> from cmap, to be updated for lookup table
+        //const lutProxies = this.model.itkVtkViewer.getLookupTableProxies()
+        //const lutProxy = lutProxies[index]
+        //const customCmap = this.model.get('_custom_cmap')
+        //const numPoints = customCmap.shape[0]
+        //const rgbPoints = new Array(numPoints)
+        //const cmapArray = customCmap.array
+        //const step = 1.0 / (numPoints - 1)
+        //let xx = 0.0
+        //for (let pointIndex = 0; pointIndex < numPoints; pointIndex++) {
+          //const rgb = cmapArray.slice(pointIndex * 3, (pointIndex + 1) * 3)
+          //rgbPoints[pointIndex] = [xx, rgb[0], rgb[1], rgb[2]]
+          //xx += step
+        //}
+        //lutProxy.setRGBPoints(rgbPoints)
+      //}
+      this.model.itkVtkViewer.setLookupTable(lut)
+    }
+  },
+
   vmin_changed: function () {
     const vmin = this.model.get('vmin')
     if (vmin !== null && this.model.hasOwnProperty('itkVtkViewer')) {