def openProject(self, folderName=None):
"""
If no project name is supplied, it will open a file dialog so
that the user can select a project file
or project folder.
:param folderName: Name of a folder with a project
:type folderName: basestring
"""
fileName = ""
if folderName:
fileName = folderName
else:
fileName = QFileDialog.getExistingDirectory(
self, "Open project", "", QFileDialog.ShowDirsOnly)
if len(fileName) > 0:
fullName = fileName + ProjectController.Instance().ProjectFile
if os.path.isfile(fullName):
self.multiDataWidget.transformations.clear()
loaded = ProjectController.Instance().loadProject(fileName)
if loaded:
RegistrationShop.settings.setValue("project/lastProject",
fileName)
else:
print "Couldn't load project:", folderName
else:
print "Warning: Project file does not exist"
RegistrationShop.settings.remove("project/lastProject")
def setRenderWidgets(self, fixed=None, moving=None, multi=None):
self.fixedWidget = fixed
self.movingWidget = moving
self.multiWidget = multi
self.fixedPicker.setWidget(self.fixedWidget)
self.movingPicker.setWidget(self.movingWidget)
self.fixedPicker.pickedLocation.connect(self.pickedFixedLocation)
self.movingPicker.pickedLocation.connect(self.pickedMovingLocation)
# Save the original complete transform
self.originalTransform = self.multiWidget.transformations.completeTransform(
)
self.originalScalingTransform = self.multiWidget.transformations.scalingTransform(
)
# Add a new transform on top of the others
currentProject = ProjectController.Instance().currentProject
transform = Transformation(vtkTransform(), Transformation.TypeLandmark,
currentProject.movingData)
self.multiWidget.transformations.append(transform)
statusWidget = StatusWidget.Instance()
statusWidget.setText(
"Place landmarks in both volumes to create a landmark transform. "
"Available methods for placing landmarks are the surface type and the two-step type."
)
def testSavingAndLoadingProjectsToDisk(self):
projectController = ProjectController.Instance()
# Save the project in the current directory
path = os.path.dirname(os.path.abspath(__file__))
projectPath = path + "/project"
if not os.path.exists(projectPath):
os.makedirs(projectPath)
projectController.currentProject.title = "Unique title"
projectController.currentProject.folder = unicode(projectPath)
projectController.saveProject()
# Reset the project controller
projectController.newProject()
self.assertIsNone(projectController.currentProject.title)
self.assertIsNone(projectController.currentProject.folder)
# Test for existance of a project file in the project folder
self.assertTrue(os.path.exists(projectPath + "/project.yaml"))
self.assertTrue(projectController.loadProject(projectPath))
# Load the project again from disk
projectController.loadProject(projectPath)
self.assertIsNotNone(projectController.currentProject.title)
self.assertIn("Unique", projectController.currentProject.title)
try:
os.remove(projectPath + "/project.yaml")
except Exception:
self.assertTrue(False)
def exportDataAs(self):
"""
Opens a file dialog so that the user can provide a filename
for saving the transformed dataset to.
"""
fileType = FileTypeDialog.getFileType(self,
"Choose file type for export")
if len(fileType) == 0:
return
extension = "(*." + fileType + ")"
fileName, other = QFileDialog.getSaveFileName(
self, "Save registration result to...", "", extension)
if len(fileName) == 0:
return
self.showProgressBar("Exporting data...")
transform = self.multiDataWidget.transformations.completeTransform()
dataReader = DataReader()
imageData = dataReader.GetImageData(
ProjectController.Instance().currentProject.movingData)
transformer = DataTransformer()
outputData = transformer.TransformImageData(imageData, transform)
writer = DataWriter()
writer.WriteToFile(outputData, fileName, fileType)
self.hideProgressBar()
def loadMovingDataSetFile(self):
"""
Open file dialog to search for data files. If valid data is given, it will
pass the data file location on to the slicer and the project controller.
"""
dataReader = DataReader()
extensions = dataReader.GetSupportedExtensionsAsString()
fileName, other = QFileDialog.getOpenFileName(
self,
"Open moving data set",
"",
"Images (" + extensions + ")",
options=QFileDialog.Directory)
if len(fileName) > 0:
# If there was another dataset first, ask if the user if the
# visualizations should be reset
projectController = ProjectController.Instance()
if projectController.currentProject.movingData:
dialog = ResetVisualizationDialog(self)
dialog.setWindowModality(Qt.WindowModal)
dialog.exec_()
if dialog.result is not None:
projectController.loadMovingDataSet(fileName)
if dialog.result:
self.movingRenderController.resetVisualizations()
else:
# Inserting an identity transform
self.multiDataWidget.transformations.append(
Transformation(vtkTransform(), "No transform", fileName))
projectController.loadMovingDataSet(fileName)
def newProject(self):
"""
Create new project by calling the project controller
"""
self.multiDataWidget.transformations.clear()
ProjectController.Instance().newProject()
# Reset the last loaded project in the settings
RegistrationShop.settings.setValue("project/lastProject", "")
def setRenderWidgets(self, fixed=None, moving=None, multi=None):
self.movingWidget = moving
self.renderWidget = multi
currentProject = ProjectController.Instance().currentProject
self.transformBox.setWidget(self.renderWidget)
self.transformBox.setImageData(self.renderWidget.movingImageData)
self.renderWidget.transformations.append(
Transformation(vtkTransform(), Transformation.TypeUser,
currentProject.movingData))
statusWidget = StatusWidget.Instance()
statusWidget.setText(
"Use the box widget to transform the volume. "
"For more specific control of the transformation, use the matrix values to specify the transform."
)
def saveProjectAs(self):
"""
Opens a file dialog so that the user can select a folder
in which to save the project.
"""
# Open file dialog
fileName = QFileDialog.getExistingDirectory(self,
"Select project folder",
"",
QFileDialog.ShowDirsOnly)
if len(fileName) > 0:
# TODO: check for existing project!
# Set filename of project
ProjectController.Instance().currentProject.folder = fileName
# Call save project
self.saveProject()
def __init__(self, args):
"""
Sets app specific properties.
Initializes the UI.
"""
super(RegistrationShop, self).__init__(args)
self.setApplicationPath()
# Instantiate the project controller
ProjectController.Instance()
# Initialize the user interface
self.initUI()
lastProject = RegistrationShop.settings.value("project/lastProject",
None)
if lastProject:
self.openProject(lastProject)
def startComparison(self):
projectController = ProjectController.Instance()
project = projectController.currentProject
if not project or not project.fixedData or not project.movingData:
statusWidget = StatusWidget.Instance()
statusWidget.setText(
"Could not start comparison. Please make a project first"
" and make sure to load two datasets.")
return
if hasattr(self, "compareWidget"):
del self.compareWidget
transform = self.multiDataWidget.transformations.completeTransform()
self.controller = ComparisonController()
self.controller.setInputData(project.fixedData, project.movingData,
transform)
self.compareWidget = CompareWidget(self.controller.widgets)
self.compareWidget.show()
self.controller.initialize()
self.controller.slicerChanged(self.controller.fixedImageWidget)
def saveProject(self):
"""
Save the project to the specified name in the current project. If no name
is specified, then 'save project as' is called.
"""
projCont = ProjectController.Instance()
if projCont.currentProject.folder is not None:
# Save that project
saved = projCont.saveProject()
statusWidget = StatusWidget.Instance()
if saved:
# Save it in the settings that this was the last opened project
RegistrationShop.settings.setValue(
"project/lastProject", projCont.currentProject.folder)
statusWidget.setText(
"The project was succesfully saved to disk.")
else:
statusWidget.setText(
"Something went wrong while saving the project to disk. "
"Please try to save the project again.")
else:
self.saveProjectAs()
def connectElements(self):
"""
All the elements have to be connected because they are dependent
on each other.
There is the project controller, two render controllers and a multi render
controller.
Also there are two render widgets and a multi render widget. Together with some
parameter widgets that show settings and with which the user can interact.
"""
projectController = ProjectController.Instance()
projectController.fixedFileChanged.connect(
self.fixedRenderController.setFile)
projectController.fixedFileChanged.connect(
self.multiRenderController.setFixedFile)
projectController.movingFileChanged.connect(
self.movingRenderController.setFile)
projectController.movingFileChanged.connect(
self.multiRenderController.setMovingFile)
projectController.fixedSettingsChanged.connect(
self.fixedRenderController.setRenderSettings)
projectController.movingSettingsChanged.connect(
self.movingRenderController.setRenderSettings)
projectController.multiSettingsChanged.connect(
self.multiRenderController.setRenderSettings)
self.fixedRenderController.visualizationChanged.connect(
self.multiRenderController.setFixedVisualization)
self.fixedRenderController.visualizationUpdated.connect(
self.multiRenderController.setFixedVisualization)
self.movingRenderController.visualizationChanged.connect(
self.multiRenderController.setMovingVisualization)
self.movingRenderController.visualizationUpdated.connect(
self.multiRenderController.setMovingVisualization)
self.multiDataWidget.transformations.transformationChanged.connect(
self.movingDataWidget.transformationsUpdated)
def applyTransform(self):
"""
* Show progress bar dialog
* Define folder for output (projectFolder/data/result-<id>/.)
* Write parameter file to output folder
* Call elastix to process the data
* Load the new data into the moving widget / project
"""
statusWidget = StatusWidget.Instance()
statusWidget.setText(
"Please grab a cup of coffee while Elastix " +
"performs the registration: this might take a while...")
self.startedElastix.emit("Transforming data...")
projectController = ProjectController.Instance()
currentProject = projectController.currentProject
path = currentProject.folder
if not path:
statusWidget.setText(
"Please create and save a project first so "
"that the results of the registration can be saved to disk.")
return
# Determine filename + folder for new dataset (projectFolder/data/result-<id>/.)
dataFolder = os.path.join(path, "data")
filenames = os.listdir(dataFolder) if os.path.isdir(dataFolder) else []
resultId = 0
for filename in filenames:
if os.path.isdir(os.path.join(dataFolder,
filename)) and "result" in filename:
resultId += 1
outputFolder = os.path.join(dataFolder, "result-" + str(resultId))
parameterFilePath = os.path.join(outputFolder, "Parameters.txt")
initialTransformPath = os.path.join(outputFolder,
"InitialTransformation.txt")
# Iterate over the parameters to ensure that some parameters are adjusted
# according to the data from the project
for i in range(len(self.transformation)):
param = self.transformation[i]
if param.key() == "DefaultPixelValue":
# Set the default pixel value to minimum scalar value
scalarRange = self.movingWidget.imageData.GetScalarRange()
param.setValue(scalarRange[0])
if param.key() == "ResultImagePixelType":
# Set the resulting image pixel type to the type of the input data
pixelType = self.movingWidget.imageData.GetScalarTypeAsString()
param.setValue(pixelType)
self.transformation.saveToFile(parameterFilePath)
transform = self.multiWidget.transformations.completeTransform()
dataset = ProjectController.Instance().currentProject.movingData
initialTransform = TransformixTransformation(
dataset, transform).transformation()
if initialTransform:
initialTransform.saveToFile(initialTransformPath)
else:
initialTransformPath = None
command = ElastixCommand(fixedData=currentProject.fixedData,
movingData=currentProject.movingData,
outputFolder=outputFolder,
transformation=parameterFilePath,
initialTransformation=initialTransformPath)
self.operator = Operator()
self.operator.addCommand(command)
self.operator.queue.join()
self.endedElastix.emit()
# Assume that there is only one resulting dataset: result.0.mhd
outputData = os.path.join(outputFolder, "result.0.mhd")
if os.path.exists(outputData):
statusWidget.setText(
"Thanks for your patience. The " +
"transformed data will now be loaded. It can be found in the project folder."
)
transformation = Transformation(vtkTransform(),
Transformation.TypeDeformable,
outputData)
self.multiWidget.transformations.append(transformation)
projectController.loadMovingDataSet(outputData)
else:
statusWidget.setText(
"Something went wrong. Please see the project folder for the "
+ "elastix log to see what went wrong.")
from subprocess import call
call(["open", outputFolder])
def testProjectController(self):
projectController = ProjectController.Instance()
self.assertIsNotNone(projectController.currentProject)
projectController.newProject()
self.assertIsNone(projectController.currentProject.title)
def createElements(self):
"""
Creates the widgets and docks of which the
main window is composed.
"""
self.mainWindow = QMainWindow()
projectController = ProjectController.Instance()
self.transformTool = None
# Render widgets
self.fixedDataWidget = RenderWidget()
self.movingDataWidget = RenderWidget()
self.multiDataWidget = MultiRenderWidget()
self.fixedRenderController = RenderController(self.fixedDataWidget,
"fixed")
self.movingRenderController = RenderController(self.movingDataWidget,
"moving")
self.multiRenderController = MultiRenderController(
self.multiDataWidget)
# Give references of the render controllers to the project controller
projectController.fixedRenderController = self.fixedRenderController
projectController.movingRenderController = self.movingRenderController
projectController.multiRenderController = self.multiRenderController
# Render properties widgets
sizePolicy = QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(1)
self.fixedPropWidget = RenderPropWidget(self.fixedRenderController,
parent=self)
self.fixedPropWidget.setSizePolicy(sizePolicy)
self.fixedPropWidget.setFileChangedSignal(
projectController.fixedFileChanged)
self.fixedPropWidget.setLoadDataSlot(self.loadFixedDataSetFile)
self.movingPropWidget = RenderPropWidget(self.movingRenderController,
parent=self)
self.movingPropWidget.setSizePolicy(sizePolicy)
self.movingPropWidget.setFileChangedSignal(
projectController.movingFileChanged)
self.movingPropWidget.setLoadDataSlot(self.loadMovingDataSetFile)
self.multiPropWidget = MultiRenderPropWidget(
self.multiRenderController, parent=self)
self.multiPropWidget.setSizePolicy(sizePolicy)
self.verticalSplitter = QSplitter()
self.verticalSplitter.setOrientation(Qt.Vertical)
# Create the layouts
fixedDataTitleWidget = TitleWidget("Fixed volume")
multiDataTitleWidget = TitleWidget("Fixed + Moving")
movingDataTitleWidget = TitleWidget("Moving volume")
fixedLayout = QGridLayout()
fixedLayout.setSpacing(0)
fixedLayout.setContentsMargins(0, 0, 0, 0)
fixedLayout.addWidget(fixedDataTitleWidget)
fixedLayout.addWidget(self.fixedDataWidget)
fixedWidget = QWidget()
fixedWidget.setLayout(fixedLayout)
multiLayout = QGridLayout()
multiLayout.setSpacing(0)
multiLayout.setContentsMargins(0, 0, 0, 0)
multiLayout.addWidget(multiDataTitleWidget)
multiLayout.addWidget(self.multiDataWidget)
multiWidget = QWidget()
multiWidget.setLayout(multiLayout)
movingLayout = QGridLayout()
movingLayout.setSpacing(0)
movingLayout.setContentsMargins(0, 0, 0, 0)
movingLayout.addWidget(movingDataTitleWidget)
movingLayout.addWidget(self.movingDataWidget)
movingWidget = QWidget()
movingWidget.setLayout(movingLayout)
horizontalSplitter = QSplitter()
horizontalSplitter.setOrientation(Qt.Horizontal)
horizontalSplitter.addWidget(fixedWidget)
horizontalSplitter.addWidget(multiWidget)
horizontalSplitter.addWidget(movingWidget)
propsLayout = QHBoxLayout()
propsLayout.setSpacing(1)
propsLayout.setContentsMargins(0, 0, 0, 0)
propsLayout.addWidget(self.fixedPropWidget)
propsLayout.addWidget(self.multiPropWidget)
propsLayout.addWidget(self.movingPropWidget)
propsWidget = QWidget()
propsWidget.setMinimumHeight(245)
propsWidget.setMaximumHeight(350)
propsWidget.setLayout(propsLayout)
self.verticalSplitter.addWidget(horizontalSplitter)
self.verticalSplitter.addWidget(propsWidget)
self.verticalSplitter.setStretchFactor(0, 2)
self.verticalSplitter.setStretchFactor(1, 1)
self.setCentralWidget(self.verticalSplitter)