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ENH: Add label_map_weights traitlet
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@thewtex
thewtex committed Jun 3, 2020
1 parent 4401035 commit 8a6c13e
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Showing 2 changed files with 72 additions and 28 deletions.
77 changes: 49 additions & 28 deletions itkwidgets/widget_viewer.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,10 @@ class Viewer(ViewerParent):
default_value=None,
help="Names for labels in the label map.").tag(
sync=True)
label_map_weights = NDArray(dtype=np.float32, default_value=None, allow_none=True,
help="Weights, from 0.0 to 1.0, for every label in the label map.")\
.tag(sync=True, **array_serialization)\
.valid(shape_constraints(None,))
interpolation = CBool(
default_value=True,
help="Use linear interpolation in slicing planes.").tag(sync=True)
Expand Down Expand Up @@ -374,6 +378,7 @@ def __init__(self, **kwargs): # noqa: C901

self.observe(self._on_reset_crop_requested, ['_reset_crop_requested'])
self.observe(self.update_rendered_image, ['image', 'label_map'])
self.observe(self.update_rendered_image, ['image', 'label_map'])

def _on_roi_changed(self, change=None):
if self._downsampling:
Expand Down Expand Up @@ -512,6 +517,17 @@ def f():
if self.label_map:
self.rendered_label_map = self.image

@validate('label_map_weights')
def _validate_label_map_weights(self, proposal):
"""Check the number of weights equals the number of labels."""
value = proposal['value']
value = np.array(value, dtype=np.float32)
if self.rendered_label_map:
labels = len(np.unique(itk.array_view_from_image(self.rendered_label_map)))
if labels != len(value):
raise TraitError('Number of labels, {0}, does not equal number of label weights, {1}'.format(labels, len(value)))
return value

@validate('gradient_opacity')
def _validate_gradient_opacity(self, proposal):
"""Enforce 0 < value <= 1.0."""
Expand Down Expand Up @@ -656,6 +672,7 @@ def roi_slice(self):
def view(image=None, # noqa: C901
label_map=None, # noqa: C901
label_map_names=None, # noqa: C901
label_map_weights=None, # noqa: C901
cmap=None,
select_roi=False,
interpolation=True,
Expand Down Expand Up @@ -691,26 +708,26 @@ def view(image=None, # noqa: C901
General Interface
^^^^^^^^^^^^^^^^^
ui_collapsed : bool, optional, default: False
ui_collapsed : bool, default: False
Collapse the native widget user interface.
rotate : bool, optional, default: False
rotate : bool, default: False
Continuously rotate the camera around the scene in volume rendering
mode.
annotations : bool, optional, default: True
annotations : bool, default: True
Display annotations describing orientation and the value of a
mouse-position-based data probe.
mode: 'x', 'y', 'z', or 'v', optional, default: 'v'
mode: 'x', 'y', 'z', or 'v', default: 'v'
Only relevant for 3D scenes.
Viewing mode:
'x': x-plane
'y': y-plane
'z': z-plane
'v': volume rendering
camera: 3x3 numpy float32 array, optional
camera: 3x3 numpy float32 array
Camera parameters:
[[position_x, position_y, position_z],
[focal_point_x, focal_point_y, focal_point_z],
Expand All @@ -730,89 +747,92 @@ def view(image=None, # noqa: C901
label_map_names : OrderedDict of (label_value, label_name)
String names associated with the integer label values.
vmin: float, optional, default: None
label_map_weights : 1D numpy float32 array, default: None
Rendering weights, from 0.0 to 1.0, associated labels in the label map.
vmin: float, default: None
Value that maps to the minimum of image colormap. Defaults to minimum of
the image pixel buffer.
vmax: float, optional, default: None
vmax: float, default: None
Value that maps to the minimum of image colormap. Defaults to maximum of
the image pixel buffer.
cmap: string, optional, default: viridis, grayscale with a label map
cmap: string, default: viridis, grayscale with a label map
Colormap. Some valid values available at itkwidgets.cm.*
select_roi: bool, optional, default: False
select_roi: bool, default: False
Enable an interactive region of interest widget for the image.
slicing_planes: bool, optional, default: False
slicing_planes: bool, default: False
Enable slicing planes on the volume rendering.
x_slice: float, optional, default: None
x_slice: float, default: None
World-space position of the X slicing plane.
y_slice: float, optional, default: None
y_slice: float, default: None
World-space position of the Y slicing plane.
z_slice: float, optional, default: None
z_slice: float, default: None
World-space position of the Z slicing plane.
interpolation: bool, optional, default: True
interpolation: bool, default: True
Linear as opposed to nearest neighbor interpolation for image slices.
Note: Interpolation is not currently supported with label maps.
gradient_opacity: float, optional, default: 0.22
gradient_opacity: float, default: 0.22
Gradient opacity for composite volume rendering, in the range (0.0, 1.0].
shadow: bool, optional, default: True
shadow: bool, default: True
Use shadowing with composite volume rendering.
blend: 'composite', 'max', 'min', or 'average', optional, default: 'composite'
blend: 'composite', 'max', 'min', or 'average', default: 'composite'
Volume rendering blend mode.
Point Sets
^^^^^^^^^^
point_sets: point set, or sequence of point sets, optional
point_sets: point set, or sequence of point sets
The point sets to visualize.
point_set_colors: list of RGB colors, optional
point_set_colors: list of RGB colors
Colors for the N geometries. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
point_set_opacities: list of floats, optional, default: [0.5,]*n
point_set_opacities: list of floats, default: [0.5,]*n
Opacity for the point sets, in the range (0.0, 1.0].
point_set_representations: list of strings, optional, default: ['points',]*n
point_set_representations: list of strings, default: ['points',]*n
How to represent the point set. One of 'hidden', 'points', or 'spheres'.
Geometries
^^^^^^^^^^
geometries: geometries, or sequence of geometries, optional
geometries: geometries, or sequence of geometries
The geometries to visualize.
geometry_colors: list of RGB colors, optional
geometry_colors: list of RGB colors
Colors for the N geometries. See help(matplotlib.colors) for
specification. Defaults to the Glasbey series of categorical colors.
geometry_opacities: list of floats, optional, default: [1.0,]*n
geometry_opacities: list of floats, default: [1.0,]*n
Opacity for the point sets, in the range (0.0, 1.0].
Other Parameters
----------------
units: string, optional, default: ''
units: string, default: ''
Units to display in the scale bar.
actors: vtkActor, vtkAssembly, vtkVolume, optional, default: None
actors: vtkActor, vtkAssembly, vtkVolume, default: None
List of standard vtk objects, colors are extracted from their properties
size_limit_2d: 2x1 numpy int64 array, optional, default: [1024, 1024]
size_limit_2d: 2x1 numpy int64 array, default: [1024, 1024]
Size limit for 2D image visualization. If the roi is larger than this
size, it will be downsampled for visualization
size_limit_3d: 3x1 numpy int64 array, optional, default: [192, 192, 192]
size_limit_3d: 3x1 numpy int64 array, default: [192, 192, 192]
Size limit for 3D image visualization. If the roi is larger than this
size, it will be downsampled for visualization.
Expand Down Expand Up @@ -897,6 +917,7 @@ def view(image=None, # noqa: C901
viewer = Viewer(image=image,
label_map=label_map,
label_map_names=label_map_names,
label_map_weights=label_map_weights,
cmap=cmap,
select_roi=select_roi,
interpolation=interpolation,
Expand Down
23 changes: 23 additions & 0 deletions js/lib/viewer.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,7 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
rendered_image: null,
rendered_label_map: null,
label_map_names: null,
label_map_weights: null,
_rendering_image: false,
interpolation: true,
cmap: 'Viridis (matplotlib)',
Expand Down Expand Up @@ -163,6 +164,7 @@ const ViewerModel = widgets.DOMWidgetModel.extend(
serialize: serialize_itkimage,
deserialize: deserialize_itkimage
},
label_map_weights: simplearray_serialization,
clicked_slice_point: {
serialize: serialize_image_point,
deserialize: deserialize_image_point
Expand Down Expand Up @@ -722,6 +724,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
}
if (rendered_label_map) {
this.label_map_names_changed()
this.label_map_weights_changed()
}

const onUserInterfaceCollapsedToggle = (collapsed) => {
Expand Down Expand Up @@ -825,6 +828,17 @@ const ViewerView = widgets.DOMWidgetView.extend({
onToggleCroppingPlanes
)

const onLabelMapWeightsChanged = ({ weights }) => {
const typedWeights = new Float32Array(weights)
this.model.set('label_map_weights', { shape: [weights.length],
array: typedWeights
})
this.model.save_changes()
}
this.model.itkVtkViewer.on('labelMapWeightsChanged',
onLabelMapWeightsChanged
)

if (!this.model.use2D) {
const onBlendModeChanged = (blend) => {
let pythonMode = null
Expand Down Expand Up @@ -1049,6 +1063,7 @@ const ViewerView = widgets.DOMWidgetView.extend({
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)
this.model.on('change:label_map_weights', this.label_map_weights_changed, this)

let toDecompress = []
const rendered_image = this.model.get('rendered_image')
Expand Down Expand Up @@ -1174,6 +1189,14 @@ const ViewerView = widgets.DOMWidgetView.extend({
}
},

label_map_weights_changed: function () {
const label_map_weights = this.model.get('label_map_weights')
if (label_map_weights && this.model.hasOwnProperty('itkVtkViewer')) {
const labelMapWeights = !!label_map_weights.array ? Array.from(label_map_weights.array) : Array.from(label_map_weights)
this.model.itkVtkViewer.setLabelMapWeights(labelMapWeights)
}
},

point_sets_changed: function () {
const point_sets = this.model.get('point_sets')
if (point_sets && !!point_sets.length) {
Expand Down

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