def onConnectButtonClicked(self):
# Creates a connector Node
if self.connectorNode is None:
if self.connectCheck == 1:
if self.imageNode or self.transformNode is None:
if self.imageNode is None:
print('Please select an US volume')
if self.trandformNode is None:
print('Please select the tip to probe transform')
if self.imageNode is not None and self.transformNode is not None:
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
self.numFid = self.numFid+1
self.numFidLabel.setText(str(self.numFid))
self.manualOutputRegistrationTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.manualOutputRegistrationTransformNode)
self.manualOutputRegistrationTransformNode.SetName('ImageToProbeMan')
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(qt.QCursor(2))
else:
self.connectorNode = slicer.vtkMRMLIGTLConnectorNode()
# Adds this node to the scene, not there is no need for self here as it is its own node
slicer.mrmlScene.AddNode(self.connectorNode)
# Configures the connector
self.connectorNode.SetTypeClient(self.inputIPLineEdit.text, int(self.inputPortLineEdit.text))
self.connectorNode.Start()
else:
if self.connectorNode.GetState() == 2:
# Connected
self.connectorNode.Stop()
self.connectButton.text = "Connect"
self.freezeButton.text = "Unfreeze"
if self.imageSelector.currentNode() or self.TransformSelector.currentNode() is None:
if self.imageNode is None:
print('Please select an US volume')
if self.transformNode is None:
print('Please select the tip to probe transform')
if self.imageNode is not None and self.transformNode is not None:
self.numFid = self.numFid + 1
self.numFidLabel.setText(str(self.numFid))
self.manualOutputRegistrationTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.manualOutputRegistrationTransformNode)
self.manualOutputRegistrationTransformNode.SetName('ImageToProbeMan')
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(qt.QCursor(2))
else:
# This starts the connection
self.connectorNode.Start()
self.connectButton.text = "Disconnect"
self.freezeButton.text = "Freeze"
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
def createReadOnlyLineEdit():
le = qt.QLineEdit()
le.readOnly = True
le.frame = False
le.styleSheet = "QLineEdit { background:transparent; }"
le.cursor = qt.QCursor(qt.Qt.IBeamCursor)
return le
def setBusy(self, flag):
if flag:
qt.QApplication.setOverrideCursor( qt.QCursor(qt.Qt.WaitCursor) )
while qt.QApplication.eventLoop().hasPendingEvents():
qt.QApplication.eventLoop().processEvents(qt.QEventLoop.AllEvents)
else:
qt.QApplication.restoreOverrideCursor()
def __init__(self,
parent=None,
parameterNode=None,
parameter=None,
colorNode=None,
selectCommand=None):
self.colorNode = colorNode
self.parameterNode = parameterNode
self.parameter = parameter
self.selectCommand = selectCommand
self.recents = []
self.label = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setObjectName('EditMRMLWidget')
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.create()
p = qt.QCursor().pos()
self.parent.setGeometry(p.x(), p.y(), 300, 700)
self.parent.show()
self.parent.raise_()
else:
self.parent = parent
self.create()
def processEvent(self, caller=None, event=None):
PointerEffect.CircleEffectTool.processEvent(self, caller, event)
if self.preview and event in [
'LeftButtonDoubleClickEvent', 'LeftButtonReleaseEvent'
]:
# undo pressed opperation. sometimes double click is called before release and viceversa
self.transformArray[self.currentIndex] -= self.smoothContent
self.preview = False
if event == 'LeftButtonDoubleClickEvent':
self.calculateSmoothContent()
self.transformArray[self.currentIndex] += self.smoothContent
self.applyChanges()
elif event == 'LeftButtonReleaseEvent':
self.warpNode.InvokeEvent(
slicer.vtkMRMLGridTransformNode.TransformModifiedEvent)
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.ArrowCursor))
elif event == 'LeftButtonPressEvent':
self.preview = True
self.calculateSmoothContent()
self.transformArray[self.currentIndex] += self.smoothContent
self.warpNode.InvokeEvent(
slicer.vtkMRMLGridTransformNode.TransformModifiedEvent)
def cursorForEffect(self, effectName):
"""Return an instance of QCursor customized for the given effectName.
TODO: this could be moved to the EffectTool class so that effects can manage
per-widget cursors, possibly turning them off or making them dynamic
"""
if not effectName in self.effectCursors:
baseImage = qt.QImage(":/Icons/AnnotationPointWithArrow.png")
effectImage = qt.QImage(self.effectIconFiles[effectName])
width = max(baseImage.width(), effectImage.width())
pad = -9
height = pad + baseImage.height() + effectImage.height()
width = height = max(width, height)
center = int(width / 2)
cursorImage = qt.QImage(width, height, qt.QImage().Format_ARGB32)
painter = qt.QPainter()
cursorImage.fill(0)
painter.begin(cursorImage)
point = qt.QPoint(center - (baseImage.width() / 2), 0)
painter.drawImage(point, baseImage)
point.setX(center - (effectImage.width() / 2))
point.setY(cursorImage.height() - effectImage.height())
painter.drawImage(point, effectImage)
painter.end()
cursorPixmap = qt.QPixmap()
cursorPixmap = cursorPixmap.fromImage(cursorImage)
self.effectCursors[effectName] = qt.QCursor(
cursorPixmap, center, 0)
return self.effectCursors[effectName]
def contentsMouseReleaseEvent(self, e):
"""
"""
if self.__active_item is not None:
if self.__active_item.fullRedraw(): self.canvas().update()
self.setCursor(qt.QCursor(qt.Qt.ArrowCursor))
self.__moving_start = None
self.__moving_scale = 0
def onFiducialButtonClicked(self):
# this line creates the logic for the markup (crosshair) that is being placed
#startPlaceMode(0) means only one markup gets place
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(qt.QCursor(2))
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
def onConnectButtonClicked(self):
if self.connectorNode is None:
if self.connectCheck == 1:
if self.imageNode or self.imageNode2 or self.transformNode is None:
if self.imageNode is None:
print('Please select an US volume')
if self.transformNode is None:
print('Please select the tip to probe transform')
if self.imageNode2 is None:
print('Please select the right volume')
if self.imageNode and self.imageNode2 and self.transformNode is not None:
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
self.numFid = self.numFid +1
self.numFidLabel.setText(str(self.numFid))
slicer.modules.markups.logic().StartPlaceMode(0)
self.redWidget.setCursor(qt.QCursor(2))
self.yellowWidget.setCursor(qt.QCursor(2))
else:
self.connectorNode = slicer.vtkMRMLIGTLConnectorNode()
slicer.mrmlScene.AddNode(self.connectorNode)
self.connectorNode.SetTypeClient('localhost', 18944)
self.connectorNode2 = slicer.vtkMRMLIGTLConnectorNode()
slicer.mrmlScene.AddNode(self.connectorNode2)
self.connectorNode2.SetTypeClient('localhost',18945)
self.connectorNode.Start()
self.connectorNode2.Start()
else:
if self.connectorNode.GetState() == 2:
self.connectorNode.Stop()
self.connectorNode2.Stop()
self.connectButton.text = "Connect"
self.freezeButton.text = "Unfreeze"
self.numFid = self.numFid + 1
self.numFidLabel.setText(str(self.numFid))
slicer.modules.markups.logic().StartPlaceMode(0)
self.redWidget.setCursor(qt.QCursor(2))
self.yellowWidget.setCursor(qt.QCursor(2))
else:
self.connectorNode.Start()
self.connectButton.text = "Disconnect"
self.freezeButton.text = "Freeze"
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
def _addItem(self, parentListItem, item_type, *args):
parent_name = str(parentListItem.text(0))
parent = self.configuration.findContainer(parent_name)
new_item = None
new_list_item = None
try:
qt.qApp.setOverrideCursor(qt.QCursor(qt.Qt.WaitCursor))
if item_type == "window":
new_item = self.configuration.addWindow()
if type(new_item) == types.StringType:
qt.QMessageBox.warning(self, "Cannot add", new_item, qt.QMessageBox.Ok)
else:
new_item["properties"].getProperty("w").setValue(qt.qApp.desktop().width())
new_item["properties"].getProperty("h").setValue(qt.qApp.desktop().height())
new_list_item = self.appendItem(parentListItem, new_item["name"], "window", icon="window_small")
elif item_type == "brick":
brick_type = args[0]
new_item = self.configuration.addBrick(brick_type, parent)
if type(new_item) == types.StringType:
qt.QMessageBox.warning(self, "Cannot add", new_item, qt.QMessageBox.Ok)
else:
brick_name = new_item["name"]
brick = new_item["brick"]
new_list_item = self.appendItem(parentListItem, brick_name, brick_type, icon="brick")
elif item_type == "tab":
new_item = self.configuration.addItem(item_type, parent)
if type(new_item) == types.StringType:
qt.QMessageBox.warning(self, "Cannot add", new_item, qt.QMessageBox.Ok)
else:
item_name = new_item["name"]
new_list_item = self.appendItem(parentListItem, item_name, item_type, icon=item_type)
else:
item_subtype = args[0]
new_item = self.configuration.addItem(item_subtype, parent)
if type(new_item) == types.StringType:
qt.QMessageBox.warning(self, "Cannot add", new_item, qt.QMessageBox.Ok)
else:
item_name = new_item["name"]
new_list_item = self.appendItem(parentListItem, item_name, item_type, icon=item_subtype)
if type(new_item) != types.StringType and new_item is not None:
self.connectItem(parent, new_item, new_list_item)
finally:
qt.qApp.restoreOverrideCursor()
def onFiducialClicked(self):
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
self.numFid = self.numFid + 1
self.numFidLabel.setText(str(self.numFid))
self.OutputRegistrationTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.OutputRegistrationTransformNode)
self.OutputRegistrationTransformNode.SetName('ImageToProbe')
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(qt.QCursor(2))
def TestSection_3_SaveLabelmaps(self):
self.delayDisplay("Save labelmaps to directory\n %s" % (self.outputDir), self.delayMs)
self.assertTrue(len(self.labelmapsToSave) > 0)
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.BusyCursor))
self.logic.SaveLabelmaps(self.labelmapsToSave, self.outputDir)
self.delayDisplay(' Labelmaps saved to %s' % (self.outputDir), self.delayMs)
qt.QApplication.restoreOverrideCursor()
def selectedSlot(self, item, *args, **kw):
#print "package ", item.__package
qt.QApplication.setOverrideCursor(
qt.QCursor(qt.QApplication.WaitCursor))
self.showPackageDescription(item.__package)
self.showPackageCaps(item.__package)
self.showPackageFiles(item.__package)
qt.QApplication.restoreOverrideCursor()
def applyChanges(self):
subjectPath = self.parameterNode.GetParameter("subjectPath")
if not bool(int(self.parameterNode.GetParameter("warpModified"))):
msgBox = qt.QMessageBox()
msgBox.setText('No modifications in warp')
msgBox.setInformativeText('Save subject as approved?')
msgBox.setStandardButtons(qt.QMessageBox().Save | qt.QMessageBox().Discard | qt.QMessageBox().Cancel)
ret = msgBox.exec_()
if ret == qt.QMessageBox().Cancel:
return False
if ret == qt.QMessageBox().Save:
FunctionsUtil.saveApprovedData(subjectPath)
return True
if TransformsUtil.TransformsUtilLogic().getNumberOfLayers(self.parameterNode.GetNodeReference("warpID")) == 1:
msgBox = qt.QMessageBox()
msgBox.setText('Only one layer')
msgBox.setInformativeText('Save changes?')
msgBox.setStandardButtons(qt.QMessageBox().Save | qt.QMessageBox().Discard | qt.QMessageBox().Cancel)
ret = msgBox.exec_()
if ret == qt.QMessageBox().Cancel:
return False
elif ret == qt.QMessageBox().Discard:
return True
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
# harden changes in glanat composite with MNI 0.5 resolution
glanatCompositeNode = self.parameterNode.GetNodeReference("glanatCompositeID")
glanatCompositeNode.HardenTransform()
TransformsUtil.TransformsUtilLogic().flattenTransform(glanatCompositeNode, includeFirstLayer=True, useMNIGrid=True)
# save foreward
slicer.util.saveNode(glanatCompositeNode, os.path.join(subjectPath,'glanatComposite.nii.gz'))
# invert transform
glanatCompositeNode.Inverse()
# get image to set as reference
imageNode = self.getBackgroundNode()
# get inverse
outNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTransformNode')
transformsLogic = slicer.modules.transforms.logic()
transformsLogic.ConvertToGridTransform(glanatCompositeNode, imageNode, outNode)
# save inverse
slicer.util.saveNode(outNode, os.path.join(subjectPath,'glanatInverseComposite.nii.gz'))
# delete aux node
slicer.mrmlScene.RemoveNode(outNode)
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.ArrowCursor))
return True
def cursorOff(self, widget):
"""Turn off and save the current cursor so
the user can see an overlay that tracks the mouse"""
if self.savedWidget == widget:
return
else:
self.cursorOn()
self.savedWidget = widget
self.savedCursor = widget.cursor
qt_BlankCursor = 10
widget.setCursor(qt.QCursor(qt_BlankCursor))
def onFiducialClicked(self):
if self.imageNode or self.imageNode2 or self.transformNode is None:
if self.imageNode is None:
print('Please select an US volume')
if self.transformNode is None:
print('Please select the tip to probe transform')
if self.imageNode2 is None:
print('Please select the right volume')
if self.imageNode and self.imageNode2 and self.transformNode is not None:
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
self.numFid = self.numFid +1
self.numFidLabel.setText(str(self.numFid))
slicer.modules.markups.logic().StartPlaceMode(0)
self.redWidget.setCursor(qt.QCursor(2))
self.yellowWidget.setCursor(qt.QCursor(2))
if self.fidCount == 0:
slicer.modules.markups.logic().StartPlaceMode(0)
self.redWidget.setCursor(qt.QCursor(2))
self.yellowWidget.setCursor(qt.QCursor(2))
def TestSection_2_ConvertStructureSetToLabelmap(self):
self.delayDisplay("Convert loaded structure set to labelmap", self.delayMs)
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.BusyCursor))
try:
self.labelmapsToSave = self.logic.ConvertStructureSetToLabelmap()
self.assertTrue(len(self.labelmapsToSave) > 0)
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e), self.delayMs * 2)
qt.QApplication.restoreOverrideCursor()
def enterFloatingMode(self): self.mainFrame.setParent(None) cursorPosition = qt.QCursor().pos() w = self.mainFrame.width h = self.mainFrame.height self.mainFrame.pos = qt.QPoint(cursorPosition.x() - int(w/2), cursorPosition.y() - int(h/2)) self.mainFrame.show() self.mainFrame.raise_() Key_Space = 0x20 # not in PythonQt self.toggleShortcut = qt.QShortcut(self.mainFrame) self.toggleShortcut.setKey( qt.QKeySequence(Key_Space) ) self.toggleShortcut.connect( 'activated()', self.toggleFloatingMode )
def contentsMousePressEvent(self, e):
"""
"""
point = self.inverseWorldMatrix().map(e.pos())
ilist = self.canvas().collisions(point)
self.__moving_start = None
self.__moving_scale = 0
if not len(ilist) or ilist[0].rtti() not in [PC_RTTI_Rect]:
return
if self.__active_item!=ilist[0]:
if self.__active_item is not None:
self.__active_item.setNormal()
self.__active_item = ilist[0]
self.__active_item.setActive()
zmax = 0
for item in self.canvas().allItems():
zmax = max(zmax, item.z())
self.__active_item.setZ(zmax+1)
self.canvas().update()
rect = self.__active_item.getBoundingRect()
self.__moving_scale = self.__isMovingScale(rect, point)
self.__moving_start = point
if self.__moving_scale ==0: self.setCursor(qt.QCursor(qt.Qt.SizeAllCursor))
elif self.__moving_scale in [11,22]:
self.setCursor(qt.QCursor(qt.Qt.SizeFDiagCursor))
elif self.__moving_scale in [12,21]:
self.setCursor(qt.QCursor(qt.Qt.SizeBDiagCursor))
elif self.__moving_scale in [1,2]:
self.setCursor(qt.QCursor(qt.Qt.SizeHorCursor))
elif self.__moving_scale in [10,20]:
self.setCursor(qt.QCursor(qt.Qt.SizeVerCursor))
def onFiducialClicked(self):
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
if self.imageNode or self.transformNode is None:
if self.imageNode is None:
print('Please select an US volume')
if self.transformNode is None:
print('Please select the tip to probe transform')
if self.imageNode is not None and self.transformNode is not None:
self.numFid = self.numFid+1
self.numFidLabel.setText(str(self.numFid))
self.manualOutputRegistrationTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(self.manualOutputRegistrationTransformNode)
self.manualOutputRegistrationTransformNode.SetName('ImageToProbeMan')
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(qt.QCursor(2))
def applyChanges(subjectPath, inputNode, imageNode):
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
# undo changes to image node
imageNode.SetAndObserveTransformNodeID(None)
# FORWARD
size, origin, spacing = GridNodeHelper.getGridDefinition(inputNode)
# harden changes in input
inputNode.HardenTransform()
# to grid transform
outNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTransformNode')
referenceVolume = GridNodeHelper.emptyVolume(size, origin, spacing)
slicer.modules.transforms.logic().ConvertToGridTransform(inputNode, referenceVolume, outNode)
# set to input and delete aux
inputNode.SetAndObserveTransformFromParent(outNode.GetTransformFromParent())
slicer.mrmlScene.RemoveNode(outNode)
slicer.mrmlScene.RemoveNode(referenceVolume)
# save
slicer.util.saveNode(inputNode, LeadFileManager(subjectPath).getANTSForwardWarp())
# BACKWARD
inputNode.Inverse()
# to grid
outNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTransformNode')
slicer.modules.transforms.logic().ConvertToGridTransform(inputNode, imageNode, outNode)
# save
slicer.util.saveNode(outNode, LeadFileManager(subjectPath).getANTSInverseWarp())
# delete aux node
slicer.mrmlScene.RemoveNode(outNode)
# back to original
inputNode.Inverse()
imageNode.SetAndObserveTransformNodeID(inputNode.GetID())
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.ArrowCursor))
def onConnectButtonClicked(self):
#creates a connector Node
if self.connectorNode is None:
self.connectorNode = slicer.vtkMRMLIGTLConnectorNode()
#Adds this node to the scene, not there is no need for self here as it is its own node
slicer.mrmlScene.AddNode(self.connectorNode)
# Configures the connector
self.connectorNode.SetTypeClient(self.inputIPLineEdit.text,
int(self.inputPortLineEdit.text))
if self.imageSelector.currentNode() is not None:
slicer.app.layoutManager().sliceWidget('Red').sliceLogic(
).GetSliceCompositeNode().SetBackgroundVolumeID(
self.imageSelector.currentNode().GetID())
# Configure volume reslice driver, transverse
self.resliceLogic.SetDriverForSlice(
self.imageSelector.currentNode().GetID(),
slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed'))
self.resliceLogic.SetModeForSlice(
self.resliceLogic.MODE_TRANSVERSE,
slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed'))
slicer.app.layoutManager().sliceWidget(
"Red").sliceController().fitSliceToBackground()
if self.connectorNode.GetState() == 2:
# Connected, disconnect
self.connectorNode.Stop()
self.connectButton.text = "Connect"
# self.freezeButton.text = "Unfreeze"
slicer.modules.markups.logic().StartPlaceMode(0)
slicer.app.layoutManager().sliceWidget('Red').setCursor(
qt.QCursor(2))
else:
# This starts the connection
self.connectorNode.Start()
self.connectButton.text = "Disconnect"
self.freezeButton.text = "Freeze"
if self.fiducialNode is not None:
self.fiducialNode.RemoveAllMarkups()
def addFunction(self):
if not self.parameterNode.GetNodeReferenceID("warpID"):
return
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
# get node
warpNode = self.parameterNode.GetNodeReference("warpID")
# save visibility
vis = warpNode.GetDisplayNode().GetVisibility()
warpNode.GetDisplayNode().SetVisibility(False)
# clone
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
clonedID = slicer.modules.subjecthierarchy.logic(
).CloneSubjectHierarchyItem(shNode, shNode.GetItemByDataNode(warpNode))
shNode.SetItemAttribute(clonedID, 'savedWarp', '1')
# flat new warp
newWarpNode = shNode.GetItemDataNode(clonedID)
newWarpNode.SetName(slicer.mrmlScene.GenerateUniqueName('SavedWarp'))
size, origin, spacing = TransformsUtil.TransformsUtilLogic(
).getGridDefinition(newWarpNode)
outNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTransformNode')
referenceVolume = TransformsUtil.TransformsUtilLogic(
).createEmpyVolume(size, origin, spacing)
transformsLogic = slicer.modules.transforms.logic()
transformsLogic.ConvertToGridTransform(newWarpNode, referenceVolume,
outNode)
newWarpNode.SetAndObserveTransformFromParent(
outNode.GetTransformFromParent())
# remove aux
slicer.mrmlScene.RemoveNode(outNode)
slicer.mrmlScene.RemoveNode(referenceVolume)
# restore visibility
warpNode.GetDisplayNode().SetVisibility(vis)
# simulate double click to change
self.doubleClickFunction(newWarpNode)
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.ArrowCursor))
def saveClicked(self):
try:
qt.qApp.setOverrideCursor(qt.QCursor(qt.Qt.WaitCursor))
if self.filename is not None:
if os.path.exists(self.filename):
should_create_startup_script=False
else:
should_create_startup_script=True
if self.configuration.save(self.filename):
self.setCaption("GUI Builder - %s" % self.filename)
qt.qApp.restoreOverrideCursor()
qt.QMessageBox.information(self, "Success", "Configuration have been saved successfully to\n%s" % self.filename, qt.QMessageBox.Ok)
if should_create_startup_script:
if qt.QMessageBox.question(self, "Launch script",
"Do you want to create a startup script for the new GUI ?",
qt.QMessageBox.Yes, qt.QMessageBox.No) == qt.QMessageBox.Yes:
try:
hwr_server = HardwareRepository.HardwareRepository().serverAddress
except:
hwr_server = ""
else:
pid = subprocess.Popen("newGUI --just-script %s %s" % (self.filename, hwr_server), shell=True).pid
return True
else:
qt.qApp.restoreOverrideCursor()
qt.QMessageBox.warning(self, "Error", "Could not save configuration to file %s !" % self.filename, qt.QMessageBox.Ok)
return False
else:
qt.qApp.restoreOverrideCursor()
self.saveAsClicked()
finally:
qt.qApp.restoreOverrideCursor()
def set_cursor(self, cursor):
if DEBUG: print 'Set cursor', cursor
qt.QApplication.restoreOverrideCursor()
qt.QApplication.setOverrideCursor(qt.QCursor(cursord[cursor]))
def run(self, atlasPath):
"""
Run the actual algorithm
"""
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
folderID = shNode.CreateFolderItem(shNode.GetSceneItemID(),
os.path.split(atlasPath)[-1])
self.createFolderDisplayNode(folderID)
shNode.SetItemAttribute(folderID, 'atlas', '1')
with h5py.File(os.path.join(atlasPath, 'atlas_index.mat'),
'r') as atlasFile:
# get .mat data
fv = atlasFile['atlases']['fv']
colors = atlasFile['atlases']['colors'][()]
try:
colormap = atlasFile['atlases']['colormap'][()].transpose()
except: # colormap not present
colormap = np.array([[0.2422, 0.1504, 0.6603],
[0.2504, 0.1650, 0.7076],
[0.2578, 0.1818, 0.7511],
[0.2647, 0.1978, 0.7952],
[0.2706, 0.2147, 0.8364],
[0.2751, 0.2342, 0.8710],
[0.2783, 0.2559, 0.8991],
[0.2803, 0.2782, 0.9221],
[0.2813, 0.3006, 0.9414],
[0.2810, 0.3228, 0.9579],
[0.2795, 0.3447, 0.9717],
[0.2760, 0.3667, 0.9829],
[0.2699, 0.3892, 0.9906],
[0.2602, 0.4123, 0.9952],
[0.2440, 0.4358, 0.9988],
[0.2206, 0.4603, 0.9973],
[0.1963, 0.4847, 0.9892],
[0.1834, 0.5074, 0.9798],
[0.1786, 0.5289, 0.9682],
[0.1764, 0.5499, 0.9520],
[0.1687, 0.5703, 0.9359],
[0.1540, 0.5902, 0.9218],
[0.1460, 0.6091, 0.9079],
[0.1380, 0.6276, 0.8973],
[0.1248, 0.6459, 0.8883],
[0.1113, 0.6635, 0.8763],
[0.0952, 0.6798, 0.8598],
[0.0689, 0.6948, 0.8394],
[0.0297, 0.7082, 0.8163],
[0.0036, 0.7203, 0.7917],
[0.0067, 0.7312, 0.7660],
[0.0433, 0.7411, 0.7394],
[0.0964, 0.7500, 0.7120],
[0.1408, 0.7584, 0.6842],
[0.1717, 0.7670, 0.6554],
[0.1938, 0.7758, 0.6251],
[0.2161, 0.7843, 0.5923],
[0.2470, 0.7918, 0.5567],
[0.2906, 0.7973, 0.5188],
[0.3406, 0.8008, 0.4789],
[0.3909, 0.8029, 0.4354],
[0.4456, 0.8024, 0.3909],
[0.5044, 0.7993, 0.3480],
[0.5616, 0.7942, 0.3045],
[0.6174, 0.7876, 0.2612],
[0.6720, 0.7793, 0.2227],
[0.7242, 0.7698, 0.1910],
[0.7738, 0.7598, 0.1646],
[0.8203, 0.7498, 0.1535],
[0.8634, 0.7406, 0.1596],
[0.9035, 0.7330, 0.1774],
[0.9393, 0.7288, 0.2100],
[0.9728, 0.7298, 0.2394],
[0.9956, 0.7434, 0.2371],
[0.9970, 0.7659, 0.2199],
[0.9952, 0.7893, 0.2028],
[0.9892, 0.8136, 0.1885],
[0.9786, 0.8386, 0.1766],
[0.9676, 0.8639, 0.1643],
[0.9610, 0.8890, 0.1537],
[0.9597, 0.9135, 0.1423],
[0.9628, 0.9373, 0.1265],
[0.9691, 0.9606, 0.1064],
[0.9769, 0.9839, 0.0805]])
names = self.getAtlasNames(atlasFile)
types = atlasFile['atlases']['types'][()]
try:
showIndexRef = atlasFile['atlases']['presets']['show'][0, 0]
showIndex = atlasFile[showIndexRef][
()].squeeze() - 1 # -1 to fix index base
except:
showIndex = np.array(range(len(names)))
for index in range(len(names)): # for each structure
structureName = os.path.splitext(
os.path.splitext(names[index][0])[0])[0]
structureColor = colormap[int(colors[index]) - 1]
if types[index][0] in [3, 4]:
subName = ['rh', 'lh']
subFolderID = shNode.CreateFolderItem(
folderID, structureName)
self.createFolderDisplayNode(subFolderID, structureColor)
shNode.SetItemDisplayVisibility(subFolderID, index
in showIndex)
shNode.SetItemExpanded(subFolderID, 0)
shNode.SetItemAttribute(subFolderID, 'atlas', '1')
else:
subName = [structureName]
subFolderID = folderID
for sideIndex, sideName in zip(range(len(subName)), subName):
# get faces and vertices data
ref = fv[sideIndex][index]
b = atlasFile[ref]
vertices = b['vertices'][()].transpose()
faces = b['faces'][()].transpose()
# create polydata
structurePolyData = self.createPolyData(vertices, faces)
# add model node
modelNode = self.createModel(structurePolyData, sideName,
structureColor)
modelNode.GetDisplayNode().SetVisibility(
index in showIndex)
# add as child to parent
shNode.SetItemParent(
shNode.GetItemChildWithName(shNode.GetSceneItemID(),
sideName), subFolderID)
shNode.SetItemAttribute(
shNode.GetItemByDataNode(modelNode), 'atlas', '1')
qt.QApplication.setOverrideCursor(qt.QCursor(qt.Qt.ArrowCursor))
return folderID
def onMarkupAdded(self, fiducialNodeCaller, event):
# Set the location and index to zero because its needs to be initialized
centroid=[0,0,0]
# This checks if there is not a display node
if self.fiducialNode.GetDisplayNode() is None:
# then creates one if that is the case
self.fiducialNode.CreateDefaultDisplayNodes()
# This sets a variable as the display node
displayNode = self.fiducialNode.GetDisplayNode()
# This sets the type to be a cross hair
displayNode.SetGlyphType(3)
# This sets the size
displayNode.SetGlyphScale(2.5)
# This says that you dont want text
displayNode.SetTextScale(0)
# This sets the color
displayNode.SetSelectedColor(0, 0, 1)
# This saves the location the markup is place
# Collect the point in image space
self.fiducialNode.GetMarkupPoint(self.fiducialNode.GetNumberOfMarkups()-1, 0, centroid)
tipToProbeTransform = vtk.vtkMatrix4x4()
self.TransformSelector.currentNode().GetMatrixTransformToWorld(tipToProbeTransform)
origin = [tipToProbeTransform.GetElement(0, 3), tipToProbeTransform.GetElement(1,3), tipToProbeTransform.GetElement(2,3)]
dir = [tipToProbeTransform.GetElement(0, 2), tipToProbeTransform.GetElement(1,2), tipToProbeTransform.GetElement(2,2)]
if self.fidCount == 0:
self.logic.AddPointAndLineMan([centroid[0],centroid[1],0], origin, dir)
if self.fidCount == 1:
self.logic.AddPointAndLineMan([0,centroid[1],centroid[2]], origin, dir)
self.ImageToProbe = self.logic.manualRegLogic.CalculateRegistration()
self.transformTable.setItem(0,0, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(0,0))))
self.transformTable.setItem(0,1, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(0,1))))
self.transformTable.setItem(0,2, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(0,2))))
self.transformTable.setItem(0,3, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(0,3))))
self.transformTable.setItem(1,0, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(1,0))))
self.transformTable.setItem(1,1, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(1,1))))
self.transformTable.setItem(1,2, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(1,2))))
self.transformTable.setItem(1,3, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(1,3))))
self.transformTable.setItem(2,0, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(2,0))))
self.transformTable.setItem(2,1, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(2,1))))
self.transformTable.setItem(2,2, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(2,2))))
self.transformTable.setItem(2,3, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(2,3))))
self.transformTable.setItem(3,0, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(3,0))))
self.transformTable.setItem(3,1, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(3,1))))
self.transformTable.setItem(3,2, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(3,2))))
self.transformTable.setItem(3,3, qt.QTableWidgetItem(str(self.ImageToProbe.GetElement(3,3))))
self.transformTable.resizeColumnToContents(0)
self.transformTable.resizeColumnToContents(1)
self.transformTable.resizeColumnToContents(2)
self.transformTable.resizeColumnToContents(3)
self.fiducialNode.RemoveAllMarkups()
self.fiducialNode.RemoveObserver(self.markupAddedObserverTag)
slicer.mrmlScene.RemoveNode(self.fiducialNode)
self.fiducialNode = None
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
if self.fidCount == 0:
slicer.modules.markups.logic().StartPlaceMode(0)
self.redWidget.setCursor(qt.QCursor(2))
self.yellowWidget.setCursor(qt.QCursor(2))
if self.fidCount == 1:
self.connectorNode.Start()
self.connectorNode2.Start()
self.connectButton.text = "Disconnect"
self.freezeButton.text = "Freeze"
def cursorOff(self):
"""Turn off and save the current cursor so
the user can see the background image during editing"""
qt.QApplication.setOverrideCursor(qt.QCursor(10))
def cursorOff(self):
"""Turn off and save the current cursor so
the user can see the background image during editing"""
self.savedCursor = self.sliceWidget.cursor
qt_BlankCursor = 10
self.sliceWidget.setCursor(qt.QCursor(qt_BlankCursor))
def createCursor(self, widget):
# Turn off effect-specific cursor for this effect
#return slicer.util.mainWindow().cursor
return qt.QCursor(qt.Qt.PointingHandCursor)
