code stringlengths 3 6.57k |
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logging.debug("Slice Index: {}".format(sliceIndex) |
logging.debug("Foreground: {}".format(foreground) |
logging.debug("Background: {}".format(background) |
logging.debug("Current point: {}".format(current_point) |
params.update(self.getParamsFromConfig("infer", model) |
print(f"Request Params for Deepgrow/Deepedit: {params}") |
self.logic.infer(model, image_file, params, session_id=self.getSessionId() |
print(f"Result Params for Deepgrow/Deepedit: {params}") |
params.get("label_names") |
params.get("label_names") |
get("labels") |
isinstance(labels, dict) |
sorted(labels.items() |
self.updateSegmentationMask(result_file, labels, None if deepgrow_3d else sliceIndex, freeze=freeze) |
logging.exception("Unknown Exception") |
slicer.util.errorDisplay(operationDescription + " - unexpected error.", detailedText=traceback.format_exc() |
qt.QApplication.restoreOverrideCursor() |
self.updateGUIFromParameterNode() |
logging.info("Time consumed by Deepgrow: {0:3.1f}".format(time.time() |
createCursor(self, widget) |
slicer.util.mainWindow() |
createSegmentNode(self) |
self._volumeNode.GetName() |
slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") |
self._segmentNode.SetReferenceImageGeometryParameterFromVolumeNode(self._volumeNode) |
self._segmentNode.SetName(name) |
getLabelColor(self, name) |
GenericAnatomyColors.get(name.lower() |
updateSegmentationMask(self, in_file, labels, sliceIndex=None, freeze=None) |
Node (for Bounding Box if provided in the result) |
time.time() |
logging.debug("Update Segmentation Mask from: {}".format(in_file) |
os.path.exists(in_file) |
segmentationNode.GetSegmentation() |
segmentation.GetSegmentIdBySegmentName(label) |
segmentation.AddEmptySegment(label, label, self.getLabelColor(label) |
print(f"Update Segmentation Mask using Labels: {labels}") |
self.currentSegment() |
sitk.ReadImage(in_file) |
sitkUtils.PushVolumeToSlicer(labelImage, None, className="vtkMRMLLabelMapVolumeNode") |
segmentation.GetSegmentIdBySegmentName(label) |
isinstance(freeze, str) |
print(f"Import only Freezed label: {freeze}") |
segmentation.GetNumberOfSegments() |
slicer.modules.segmentations.logic() |
ImportLabelmapToSegmentationNode(labelmapVolumeNode, segmentationNode) |
slicer.mrmlScene.RemoveNode(labelmapVolumeNode) |
segmentation.GetNumberOfSegments() |
logging.debug("Adding {} segments".format(numberOfAddedSegments) |
segmentation.GetNthSegmentID(numberOfExistingSegments + i) |
range(numberOfAddedSegments) |
enumerate(addedSegmentIds) |
segmentation.GetSegment(segmentId) |
print("Setting new segmentation with id: {} => {}".format(segmentId, segment.GetName() |
len(labels) |
format(i) |
segment.SetName(label) |
segment.SetColor(self.getLabelColor(label) |
print(f"Discard label update for: {label}") |
slicer.modules.segmenteditor.widgetRepresentation() |
self() |
segmentEditorWidget.setSegmentationNode(segmentationNode) |
segmentEditorWidget.setMasterVolumeNode(self._volumeNode) |
segmentEditorWidget.setCurrentSegmentID(existing_label_ids[label]) |
segmentEditorWidget.effectByName("Logical operators") |
slicer.vtkOrientedImageData() |
segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap) |
effect.selectedSegmentLabelmap() |
selectedSegmentLabelmap.GetDimensions() |
range(dims[0]) |
range(dims[1]) |
selectedSegmentLabelmap.GetScalarComponentAsDouble(x, y, sliceIndex, 0) |
selectedSegmentLabelmap.SetScalarComponentFromDouble(x, y, sliceIndex, 0, 0) |
logging.debug("Total Non Zero: {}".format(count) |
segmentationNode.RemoveSegment(segmentId) |
self.showSegmentationsIn3D() |
logging.info("Time consumed by updateSegmentationMask: {0:3.1f}".format(time.time() |
showSegmentationsIn3D(self) |
self._segmentNode.CreateClosedSurfaceRepresentation() |
slicer.app.layoutManager() |
threeDWidget(0) |
threeDView() |
view.resetFocalPoint() |
updateServerUrlGUIFromSettings(self) |
qt.QSettings() |
settings.value("MONAILabel/serverUrlHistory") |
self.ui.serverComboBox.blockSignals(True) |
self.ui.serverComboBox.clear() |
self.ui.serverComboBox.addItems(serverUrlHistory.split(";") |
self.ui.serverComboBox.setCurrentText(settings.value("MONAILabel/serverUrl") |
self.ui.serverComboBox.blockSignals(wasBlocked) |
createFiducialNode(self, name, onMarkupNodeModified, color) |
slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsDisplayNode") |
displayNode.SetTextScale(0) |
displayNode.SetSelectedColor(color) |
slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode") |
fiducialNode.SetName(name) |
fiducialNode.SetAndObserveDisplayNodeID(displayNode.GetID() |
self.addFiducialNodeObserver(fiducialNode, onMarkupNodeModified) |
removeFiducialNodeObservers(self, fiducialNode, fiducialNodeObservers) |
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