Slicer 5.4
Slicer is a multi-platform, free and open source software package for visualization and medical image computing
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SegmentEditorFillBetweenSlicesEffect.py
Go to the documentation of this file.
1import os
2
3import qt
4import vtk
5
6from SegmentEditorEffects import *
7
8
9class SegmentEditorFillBetweenSlicesEffect(AbstractScriptedSegmentEditorAutoCompleteEffect):
10 """ AutoCompleteEffect is an effect that can create a full segmentation
11 from a partial segmentation (not all slices are segmented or only
12 part of the target structures are painted).
13 """
14
15 def __init__(self, scriptedEffect):
16 AbstractScriptedSegmentEditorAutoCompleteEffect.__init__(self, scriptedEffect)
17 scriptedEffect.name = 'Fill between slices'
18
19 def clone(self):
20 import qSlicerSegmentationsEditorEffectsPythonQt as effects
21 clonedEffect = effects.qSlicerSegmentEditorScriptedEffect(None)
22 clonedEffect.setPythonSource(__file__.replace('\\', '/'))
23 return clonedEffect
24
25 def icon(self):
26 iconPath = os.path.join(os.path.dirname(__file__), 'Resources/Icons/FillBetweenSlices.png')
27 if os.path.exists(iconPath):
28 return qt.QIcon(iconPath)
29 return qt.QIcon()
30
31 def helpText(self):
32 return """<html>Interpolate segmentation between slices<br>. Instructions:
33<p><ul>
34<li>Create complete segmentation on selected slices using any editor effect.
35Segmentation will only expanded if a slice is segmented but none of the direct neighbors are segmented, therefore
36do not use sphere brush with Paint effect and always leave at least one empty slice between segmented slices.</li>
37<li>All visible segments will be interpolated, not just the selected segment.</li>
38<li>The complete segmentation will be created by interpolating segmentations in empty slices.</li>
39</ul><p>
40Masking settings are ignored. If segments overlap, segment higher in the segments table will have priority.
41The effect uses <a href="https://insight-journal.org/browse/publication/977">morphological contour interpolation method</a>.
42<p></html>"""
43
44 def computePreviewLabelmap(self, mergedImage, outputLabelmap):
45 import vtkITK
46 interpolator = vtkITK.vtkITKMorphologicalContourInterpolator()
47 interpolator.SetInputData(mergedImage)
48 interpolator.Update()
49 outputLabelmap.DeepCopy(interpolator.GetOutput())
50 imageToWorld = vtk.vtkMatrix4x4()
51 mergedImage.GetImageToWorldMatrix(imageToWorld)
52 outputLabelmap.SetImageToWorldMatrix(imageToWorld)
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