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fiducialNode.RemoveObserver(observer) |
addFiducialNodeObserver(self, fiducialNode, onMarkupNodeModified) |
fiducialNodeObservers.append(fiducialNode.AddObserver(eventId, onMarkupNodeModified) |
scribblesLayersPresent(self) |
segmentationNode.GetSegmentation() |
segmentation.GetNumberOfSegments() |
segmentation.GetNthSegmentID(i) |
range(numSegments) |
sum([int("scribbles" in sid) |
onStartScribbling(self) |
logging.debug("Scribbles start event") |
if (not self.scribblesLayersPresent() |
and (self._scribblesEditorWidget is None) |
self._segmentNode.GetSegmentation() |
self._segmentNode.GetSegmentation() |
self._segmentNode.GetDisplayNode() |
segmentationDisplayNode.SetSegmentOpacity2DFill("background_scribbles", opacity) |
segmentationDisplayNode.SetSegmentOpacity2DOutline("background_scribbles", opacity) |
segmentationDisplayNode.SetSegmentOpacity2DFill("foreground_scribbles", opacity) |
segmentationDisplayNode.SetSegmentOpacity2DOutline("foreground_scribbles", opacity) |
slicer.qMRMLSegmentEditorWidget() |
self._scribblesEditorWidget.setMRMLScene(slicer.mrmlScene) |
slicer.vtkMRMLSegmentEditorNode() |
segmentEditorNode.SetOverwriteMode(slicer.vtkMRMLSegmentEditorNode.OverwriteNone) |
slicer.mrmlScene.AddNode(segmentEditorNode) |
self._scribblesEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode) |
self._scribblesEditorWidget.setSegmentationNode(self._segmentNode) |
self._scribblesEditorWidget.setMasterVolumeNode(self._volumeNode) |
onUpdateScribbles(self) |
logging.info("Scribbles update event") |
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor) |
slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode") |
slicer.modules.segmentations.logic() |
tempfile.NamedTemporaryFile(suffix=self.file_ext, dir=self.tmpdir) |
self.reportProgress(5) |
slicer.util.saveNode(labelmapVolumeNode, scribbles_in) |
self.reportProgress(30) |
self.updateServerSettings() |
self.reportProgress(60) |
slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLAnnotationROINode") |
slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLMarkupsROINode") |
self.getROIPointsXYZ(roiNode) |
self.getParamsFromConfig("infer", scribblesMethod) |
params.update({"roi": selected_roi}) |
self.getSessionId() |
self.reportProgress(90) |
self.currentSegment() |
segment.GetName() |
self.updateSegmentationMask(result_file, [label]) |
format(scribblesMethod) |
traceback.format_exc() |
qt.QApplication.restoreOverrideCursor() |
self.reportProgress(100) |
os.path.exists(scribbles_in) |
os.unlink(scribbles_in) |
os.path.exists(result_file) |
os.unlink(result_file) |
getROIPointsXYZ(self, roiNode) |
vtk.vtkMatrix4x4() |
v.GetRASToIJKMatrix(RasToIjkMatrix) |
print(roiNode.__class__.__name__) |
roiNode.GetCenter(center) |
zip(center, roiNode.GetSize() |
vtkMRMLAnnotationROINode (old method) |
print(roiNode.__class__.__name__) |
roiNode.GetBounds(roi_points_ras) |
RasToIjkMatrix.MultiplyDoublePoint(min_points_ras) |
RasToIjkMatrix.MultiplyDoublePoint(max_points_ras) |
round(i) |
round(i) |
zip(min_points_ijk[0:3], max_points_ijk[0:3]) |
logging.debug("RAS: {}; IJK: {}".format(roi_points_ras, roi_points_ijk) |
print("RAS: {}; IJK: {}".format(roi_points_ras, roi_points_ijk) |
onClearScribblesSegmentNodes(self) |
segmentation.GetSegmentation() |
GetNumberOfSegments() |
range(num_segments) |
segmentation.GetSegmentation() |
GetNthSegmentID(i) |
logging.info("clearning {}".format(segmentId) |
slicer.vtkOrientedImageData() |
segmentation.GetBinaryLabelmapRepresentation(segmentId, labelMapRep) |
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(labelMapRep, 0, labelMapRep.GetExtent() |
onClearScribbles(self) |
self.onClearScribblesSegmentNodes() |
self.ui.paintScribblesButton.setChecked(False) |
self.ui.eraseScribblesButton.setChecked(False) |
self.ui.scribblesLabelSelector.setCurrentIndex(0) |
checkAndInitialiseScribbles(self) |
self.onStartScribbling() |
self.changeScribblesMode(tool="Paint", layer="foreground_scribbles") |
self.updateScribToolLayerFromMode() |
updateScribToolLayerFromMode(self) |
logging.info("Scribbles mode {} ".format(self.scribblesMode) |
self.checkAndInitialiseScribbles() |
self.getToolAndLayerFromScribblesMode() |
self._scribblesEditorWidget.setActiveEffectByName(tool) |
self._scribblesEditorWidget.setCurrentSegmentID(layer) |
in ("Paint", "Erase") |
self.ui.brush3dCheckbox.checkState() |
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