def closeCase(self, save_loaded_masks=False, save_new_masks=False, reader_name=None):
# Save the results (label maps reviewed or created)
if reader_name == '':
reader_name = None
loaded_masks = {node.GetName(): node for node in self.mask_nodes.values()}
new_masks = {node.GetName(): node for node in slicer.util.getNodesByClass('vtkMRMLLabelMapVolumeNode')
if node.GetName() not in loaded_masks.keys()}
# If enabled, save label maps
if save_loaded_masks:
if len(loaded_masks) == 0:
self.logger.debug('No loaded masks to save...')
else:
self.logger.info('Saving %d loaded masks...', len(loaded_masks))
self._saveMasks(loaded_masks, self.image_root, reader_name)
if save_new_masks:
if len(new_masks) == 0:
self.logger.debug('No new masks to save...')
else:
self.logger.info('Saving %d new masks...', len(new_masks))
self._saveMasks(new_masks, self.image_root, reader_name)
# Close the scene and start a fresh one
if slicer.util.selectedModule() == 'Editor':
slicer.modules.EditorWidget.exit()
slicer.mrmlScene.Clear(0)
node = slicer.vtkMRMLViewNode()
slicer.mrmlScene.AddNode(node)
def onLayoutSelectButton(self):
layoutManager = slicer.app.layoutManager()
currentLayout = layoutManager.layout
# place skeleton model in first 3d view
skeleton_volume = slicer.util.getFirstNodeByName("SkeletonModel")
viewNode = layoutManager.threeDWidget(0).mrmlViewNode()
if skeleton_volume is not None:
displayNode = skeleton_volume.GetDisplayNode()
displayNode.SetViewNodeIDs([viewNode.GetID()])
# place reconstructed volume in second 3d view
# hacky but necessary way to ensure that we grab the correct browser node
i = 1
found = False
browser = slicer.util.getFirstNodeByClassByName(
'vtkMRMLSequenceBrowserNode', 'LandmarkingScan')
while not found and i < 6:
if browser == None:
browser = slicer.util.getFirstNodeByClassByName(
'vtkMRMLSequenceBrowserNode',
'LandmarkingScan_{}'.format(str(i)))
if browser != None:
found = True
else:
found = True
i += 1
if browser is not None:
spine_volume = slicer.util.getFirstNodeByName(
browser.GetName() + 'ReconstructionResults')
if layoutManager.threeDWidget(1) is not None:
viewNode = layoutManager.threeDWidget(1).mrmlViewNode()
else:
newView = slicer.vtkMRMLViewNode()
newView = slicer.mrmlScene.AddNode(newView)
newWidget = slicer.qMRMLThreeDWidget()
newWidget.setMRMLScene(slicer.mrmlScene)
newWidget.setMRMLViewNode(newView)
if spine_volume is not None:
displayNode = slicer.modules.volumerendering.logic(
).GetFirstVolumeRenderingDisplayNode(spine_volume)
displayNode.SetViewNodeIDs([viewNode.GetID()])
spine_volume.SetDisplayVisibility(1)
if currentLayout == 501:
layoutManager.setLayout(
502) # switch to dual 3d + red slice layout
elif currentLayout == 502:
layoutManager.setLayout(6) # switch to red slice only layout
else:
layoutManager.setLayout(
501) # switch to custom layout with 3d viewer
def TestSection_InitializeTest(self):
#
# Define variables
#
# A certain model to test that is both in the brain and the midbrain folders
self.testModelNodeName = 'Model_79_left_red_nucleus'
self.testModelNode = None
self.overrideColor = [255, 255, 0]
# Get subject hierarchy node
self.shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
self.assertIsNotNone(self.shNode)
# Get folder plugin
pluginHandler = slicer.qSlicerSubjectHierarchyPluginHandler().instance(
)
self.assertIsNotNone(pluginHandler)
self.folderPlugin = pluginHandler.pluginByName('Folder')
self.assertIsNotNone(self.folderPlugin)
#
# Initialize test
#
# Create 3D view
self.layoutName = "Test3DView"
# ownerNode manages this view instead of the layout manager (it can be any node in the scene)
self.viewOwnerNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLScriptedModuleNode")
self.viewNode = slicer.vtkMRMLViewNode()
self.viewNode.SetName(self.layoutName)
self.viewNode.SetLayoutName(self.layoutName)
self.viewNode.SetLayoutColor(1, 1, 0)
self.viewNode.SetAndObserveParentLayoutNodeID(
self.viewOwnerNode.GetID())
self.viewNode = slicer.mrmlScene.AddNode(self.viewNode)
self.viewWidget = slicer.qMRMLThreeDWidget()
self.viewWidget.setMRMLScene(slicer.mrmlScene)
self.viewWidget.setMRMLViewNode(self.viewNode)
self.viewWidget.show()
# Get model displayable manager for the 3D view
self.modelDisplayableManager = self.getModelDisplayableManager()
self.assertIsNotNone(self.modelDisplayableManager)
def _closeCase(self):
_, mask, _, additionalMasks = self.currentCase
if self.saveLoaded:
if mask is not None:
self.iterator.saveMask(mask, self.reader)
for ma in additionalMasks:
self.iterator.saveMask(ma, self.reader)
if self.saveNew:
nodes = [n for n in slicer.util.getNodesByClass('vtkMRMLSegmentationNode')
if n not in additionalMasks and n != mask]
for n in nodes:
self.iterator.saveMask(n, self.reader)
# Remove reference to current case, signalling it is closed
self.currentCase = None
# Close the scene and start a fresh one
slicer.mrmlScene.Clear(0)
if slicer.util.selectedModule() == 'SegmentEditor':
slicer.modules.SegmentEditorWidget.exit()
node = slicer.vtkMRMLViewNode()
slicer.mrmlScene.AddNode(node)
# \version 0.1
# */
# //==============================================================================
import slicer
# Load the scene first
slicer.util.loadScene(
'/home/adnan/NewWorkingHamlynDemo/AnatomicalMRIRegisteredToDTI.mrml')
# Create a Widget for Right Window
#
#
layout_name_right = "Right_Window"
layout_label = "T3"
# Create MRML node
view_node_right = slicer.vtkMRMLViewNode()
view_node_right.SetName(layout_name_right)
view_node_right.SetLayoutName(layout_name_right)
view_node_right.SetLayoutLabel(layout_label)
view_node_right = slicer.mrmlScene.AddNode(view_node_right)
view_node_right.SetName(layout_name_right)
# Create widget
view_widget_right = slicer.qMRMLThreeDWidget()
view_widget_right.setMRMLScene(slicer.mrmlScene)
view_widget_right.setMRMLViewNode(view_node_right)
view_widget_right.setWindowTitle(
layout_name_right) # Make sure to name the window
view_widget_right.show()
# Create a Widget for Right Window