class MainWindow(qtw.QMainWindow):
def __init__(self, input_file, gaussian, radius, isosurface, window_size,
*args, **kwargs):
"""MainWindow constructor"""
super().__init__(*args, **kwargs)
# Window setup
self.resize(window_size[0], window_size[1])
self.title = "Basic Qt Viewer for MDSC 689.03"
self.statusBar().showMessage("Welcome.", 8000)
# Capture defaults
self.gaussian = gaussian
self.radius = radius
self.isosurface = isosurface
# Initialize the window
self.initUI()
# Set up some VTK pipeline classes
self.reader = None
self.gauss = vtk.vtkImageGaussianSmooth()
self.marchingCubes = vtk.vtkImageMarchingCubes()
self.mapper = vtk.vtkPolyDataMapper()
self.actor = vtk.vtkActor()
# Take inputs from command line. Only use these if there is an input file specified
if (input_file != None):
if (not os.path.exists(input_file)):
qtw.QMessageBox.warning(self, "Error", "Invalid input file.")
return
#_,ext = os.path.splitext(input_file)
#if not (self.validExtension(ext.lower())):
# qtw.QMessageBox.warning(self, "Error", "Invalid file type.")
# return
self.createPipeline(input_file)
self.statusBar().showMessage("Loading file " + input_file, 4000)
self.changeSigma(gaussian)
self.changeRadius(radius)
self.changeIsosurface(isosurface)
def initUI(self):
########################################
# Create Widgets
########################################
self.loadPushButton = qtw.QPushButton(
"Load Image",
self,
objectName="loadPushButton",
shortcut=qtg.QKeySequence("Ctrl+f"))
self.sigmaSpinBox = qtw.QDoubleSpinBox(self,
objectName="sigmaSpinBox",
value=self.gaussian,
decimals=1,
maximum=20.0,
minimum=0.1,
singleStep=0.1,
keyboardTracking=False)
self.radiusSpinBox = qtw.QSpinBox(self,
objectName="radiusSpinBox",
value=self.radius,
maximum=20,
minimum=1,
singleStep=1,
keyboardTracking=False)
self.isosurfaceSpinBox = qtw.QSpinBox(self,
objectName="isosurfaceSpinBox",
value=self.isosurface,
maximum=32768,
minimum=0,
singleStep=1,
keyboardTracking=False)
# Create the menu options --------------------------------------------------------------------
menubar = qtw.QMenuBar()
self.setMenuBar(menubar)
menubar.setNativeMenuBar(False)
file_menu = menubar.addMenu("File")
open_action = file_menu.addAction("Open Image")
file_menu.addSeparator()
about_action = file_menu.addAction("About")
quit_action = file_menu.addAction("Quit")
# Lay out the GUI ----------------------------------------------------------------------------
self.mainGroupBox = qtw.QGroupBox("Image Controls")
self.mainGroupBox.setLayout(qtw.QHBoxLayout())
self.isosurfaceGroupBox = qtw.QGroupBox("Isosurface controls")
self.isosurfaceGroupBox.setLayout(qtw.QVBoxLayout())
self.isosurfaceFormLayout = qtw.QFormLayout()
self.isosurfaceFormLayout.addRow("Sigma", self.sigmaSpinBox)
self.isosurfaceFormLayout.addRow("Radius", self.radiusSpinBox)
self.isosurfaceFormLayout.addRow("Isosurface", self.isosurfaceSpinBox)
self.isosurfaceGroupBox.layout().addLayout(self.isosurfaceFormLayout)
self.mainGroupBox.layout().addWidget(self.loadPushButton)
self.mainGroupBox.layout().addWidget(self.isosurfaceGroupBox)
# Assemble the side control panel and put it in a QPanel widget ------------------------------
self.panel = qtw.QVBoxLayout()
self.panel.addWidget(self.mainGroupBox)
self.panelWidget = qtw.QFrame()
self.panelWidget.setLayout(self.panel)
# Create the VTK rendering window ------------------------------------------------------------
self.vtkWidget = QVTKRenderWindowInteractor()
self.vtkWidget.AddObserver("ExitEvent", lambda o, e, a=self: a.quit())
self.vtkWidget.AddObserver("KeyReleaseEvent", self.keyEventDetected)
self.vtkWidget.AddObserver("LeftButtonPressEvent",
self.mouseEventDetected)
# Create main layout and add VTK window and control panel
self.mainLayout = qtw.QHBoxLayout()
self.mainLayout.addWidget(self.vtkWidget, 4)
self.mainLayout.addWidget(self.panelWidget, 1)
self.frame = qtw.QFrame()
self.frame.setLayout(self.mainLayout)
self.setCentralWidget(self.frame)
self.setWindowTitle(self.title)
self.centreWindow()
# Set size policies --------------------------------------------------------------------------
self.sigmaSpinBox.setMinimumSize(70, 20)
self.radiusSpinBox.setMinimumSize(70, 20)
self.isosurfaceSpinBox.setMinimumSize(70, 20)
self.mainGroupBox.setMaximumSize(1000, 200)
self.vtkWidget.setSizePolicy(qtw.QSizePolicy.MinimumExpanding,
qtw.QSizePolicy.MinimumExpanding)
self.mainGroupBox.setSizePolicy(qtw.QSizePolicy.Maximum,
qtw.QSizePolicy.Maximum)
# Connect signals and slots ------------------------------------------------------------------
self.loadPushButton.clicked.connect(self.openFile)
self.sigmaSpinBox.valueChanged.connect(lambda s: self.changeSigma(s))
self.radiusSpinBox.valueChanged.connect(lambda s: self.changeRadius(s))
self.isosurfaceSpinBox.valueChanged.connect(
lambda s: self.changeIsosurface(s))
self.initRenderWindow()
# Menu actions
open_action.triggered.connect(self.openFile)
about_action.triggered.connect(self.about)
quit_action.triggered.connect(self.quit)
self.pipe = None
# End main UI code
self.show()
########################################
# Define methods for controlling GUI
########################################
def centreWindow(self):
qr = self.frameGeometry()
cp = qtw.QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def initRenderWindow(self):
# Create renderer
self.renderer = vtk.vtkRenderer()
self.renderer.SetBackground(
(0.000, 0.000, 204.0 / 255.0)) # Scanco blue
# Create interactor
self.renWin = self.vtkWidget.GetRenderWindow()
self.renWin.AddRenderer(self.renderer)
self.iren = self.renWin.GetInteractor()
self.iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
# Initialize
self.iren.Initialize()
self.iren.Start()
def createPipeline(self, _filename):
# Read in the file
if _filename.lower().endswith('.nii'):
self.reader = vtk.vtkNIFTIImageReader()
self.reader.SetFileName(_filename)
elif _filename.lower().endswith('.nii.gz'):
self.reader = vtk.vtkNIFTIImageReader()
self.reader.SetFileName(_filename)
elif _filename.lower().endswith('.dcm'):
self.reader = vtk.vtkDICOMImageReader()
self.reader.SetDirectoryName(os.path.dirname(_filename))
elif os.path.isdir(_filename):
self.reader = vtk.vtkDICOMImageReader()
self.reader.SetDirectoryName(_filename)
if self.reader is None:
os.sys.exit("[ERROR] Cannot find reader for file \"{}\"".format(
self.filename))
self.reader.Update()
# Gaussian smoothing
self.gauss.SetStandardDeviation(self.gaussian, self.gaussian,
self.gaussian)
self.gauss.SetRadiusFactors(self.radius, self.radius, self.radius)
self.gauss.SetInputConnection(self.reader.GetOutputPort())
# Marching Cubes
self.marchingCubes.SetInputConnection(self.gauss.GetOutputPort())
self.marchingCubes.ComputeGradientsOn()
self.marchingCubes.ComputeNormalsOn()
self.marchingCubes.ComputeScalarsOff()
self.marchingCubes.SetNumberOfContours(1)
self.marchingCubes.SetValue(0, self.isosurface)
# Set mapper for image data
self.mapper.SetInputConnection(self.marchingCubes.GetOutputPort())
# Actor
self.actor.SetMapper(self.mapper)
self.actor.GetProperty().SetColor((0.890, 0.855, 0.788))
self.renderer.AddActor(self.actor)
self.refreshRenderWindow()
return
def changeSigma(self, _value):
self.gauss.SetStandardDeviation(_value, _value, _value)
self.statusBar().showMessage(
f"Changing standard deviation to {_value}", 4000)
self.refreshRenderWindow()
return
def changeRadius(self, _value):
self.gauss.SetRadiusFactors(_value, _value, _value)
self.statusBar().showMessage(f"Changing radius to {_value}", 4000)
self.refreshRenderWindow()
return
def changeIsosurface(self, _value):
self.marchingCubes.SetValue(0, _value)
self.statusBar().showMessage(f"Changing isosurface to {_value}", 4000)
self.refreshRenderWindow()
return
def keyEventDetected(self, obj, event):
key = self.vtkWidget.GetKeySym()
print("key press – clicked " + key + "!")
return
def mouseEventDetected(self, obj, event):
print("mouse press – click!")
return
def validExtension(self, extension):
if (extension == ".nii" or \
extension == ".dcm"):
return True
else:
return False
def openFile(self):
self.statusBar().showMessage("Load image types (.nii, .dcm)", 4000)
filename, _ = qtw.QFileDialog.getOpenFileName(
self, "Select a 3D image file to open…", qtc.QDir.homePath(),
"Nifti Files (*.nii) ;;DICOM Files (*.dcm) ;;All Files (*)",
"All Files (*)", qtw.QFileDialog.DontUseNativeDialog
| qtw.QFileDialog.DontResolveSymlinks)
if filename:
_, ext = os.path.splitext(filename)
if not (self.validExtension(ext.lower())):
qtw.QMessageBox.warning(self, "Error", "Invalid file type.")
return
self.createPipeline(filename)
self.statusBar().showMessage("Loading file " + filename, 4000)
return
def quit(self):
reply = qtw.QMessageBox.question(
self, "Message", "Are you sure you want to quit?",
qtw.QMessageBox.Yes | qtw.QMessageBox.No, qtw.QMessageBox.Yes)
if reply == qtw.QMessageBox.Yes:
exit(0)
def about(self):
about = qtw.QMessageBox(self)
about.setText("blQtBasic 1.0")
about.setInformativeText(
"Copyright (C) 2021\nBone Imaging Laboratory\nAll rights reserved.\[email protected]"
)
about.setStandardButtons(qtw.QMessageBox.Ok | qtw.QMessageBox.Cancel)
about.exec_()
class MainWindow(qtw.QMainWindow):
def __init__(self, input_file, gaussian, radius, isosurface, window_size,
*args, **kwargs):
"""MainWindow constructor"""
super().__init__(*args, **kwargs)
# Window setup
self.resize(window_size[0], window_size[1])
self.title = "Bone Imaging Laboratory – Viewer"
self.iconPath = os.path.join(os.getcwd(), "qtviewer")
self.iconPath = os.path.abspath(os.path.join(self.iconPath,
"icon.png"))
self.statusBar().showMessage("Welcome.", 8000)
# Initialize the window
self.initUI()
# Take inputs from command line. Only use these if there is an input file specified
if (input_file != None):
if (not os.path.exists(input_file)):
qtw.QMessageBox.warning(self, "Error", "Invalid input file.")
return
_, ext = os.path.splitext(input_file)
if not (self.validExtension(ext.lower())):
qtw.QMessageBox.warning(self, "Error", "Invalid file type.")
return
self.createPipeline(input_file, "in1")
self.statusBar().showMessage("Loading file " + input_file, 4000)
self.changeSigma(gaussian, "in1")
self.changeRadius(radius, "in1")
self.changeIsosurface(isosurface, "in1")
self.updateGUI()
def initUI(self):
########################################
# Create Widgets
########################################
# Fixed image (in1)
self.in1_loadPushButton = qtw.QPushButton(
"Load Image 1",
self,
objectName="in1_loadPushButton",
shortcut=qtg.QKeySequence("Ctrl+f"))
self.in1_pickableCheckBox = qtw.QCheckBox(
"Pickable",
self,
objectName="in1_pickableCheckBox",
checkable=True,
checked=True)
self.in1_visibilityCheckBox = qtw.QCheckBox(
"Visibility",
self,
objectName="in1_visibilityCheckBox",
checkable=True,
checked=True)
self.in1_filenameLabel = qtw.QLabel("", self)
self.in1_sigmaSpinBox = qtw.QDoubleSpinBox(
self,
objectName="in1_sigmaSpinBox",
value=1.2,
decimals=1,
maximum=20.0,
minimum=0.1,
singleStep=0.1,
keyboardTracking=False)
self.in1_radiusSpinBox = qtw.QSpinBox(self,
objectName="in1_radiusSpinBox",
value=2,
maximum=20,
minimum=1,
singleStep=1,
keyboardTracking=False)
self.in1_isosurfaceSpinBox = qtw.QSpinBox(
self,
objectName="in1_isosurfaceSpinBox",
value=0,
maximum=32768,
minimum=0,
singleStep=1,
keyboardTracking=False)
# Moving image (in2)
self.in2_loadPushButton = qtw.QPushButton(
"Load Image 2",
self,
objectName="in2_loadPushButton",
shortcut=qtg.QKeySequence("Ctrl+m"))
self.in2_pickableCheckBox = qtw.QCheckBox(
"Pickable",
self,
objectName="in2_pickableCheckBox",
checkable=True,
checked=False)
self.in2_visibilityCheckBox = qtw.QCheckBox(
"Visibility",
self,
objectName="in2_visibilityCheckBox",
checkable=True,
checked=True)
self.in2_filenameLabel = qtw.QLabel("", self)
self.in2_sigmaSpinBox = qtw.QDoubleSpinBox(
self,
objectName="in2_sigmaSpinBox",
value=1.2,
decimals=1,
maximum=20.0,
minimum=0.1,
singleStep=0.1,
keyboardTracking=False)
self.in2_radiusSpinBox = qtw.QSpinBox(self,
objectName="in2_radiusSpinBox",
value=2,
maximum=20,
minimum=1,
singleStep=1,
keyboardTracking=False)
self.in2_isosurfaceSpinBox = qtw.QSpinBox(
self,
objectName="in2_isosurfaceSpinBox",
value=0,
maximum=32768,
minimum=0,
singleStep=1,
keyboardTracking=False)
# Camera controls
self.rollCameraPushButton = qtw.QPushButton(
"Roll", self, objectName="rollCameraPushButton")
self.elevationCameraPushButton = qtw.QPushButton(
"Elevation", self, objectName="elevationCameraPushButton")
self.azimuthCameraPushButton = qtw.QPushButton(
"Azimuth", self, objectName="azimuthCameraPushButton")
self.incrementCameraSpinBox = qtw.QSpinBox(
self,
objectName="incrementCameraSpinBox",
value=90,
maximum=90,
minimum=-90,
singleStep=10)
# Landmark transform
self.landmarkTransformPushButton = qtw.QPushButton(
"Landmark",
self,
objectName="Landmark Transform",
enabled=False,
shortcut=qtg.QKeySequence("Ctrl+l"))
# ICP transform
self.icpTransformPushButton = qtw.QPushButton(
"ICP",
self,
objectName="ICP Transform",
enabled=True,
shortcut=qtg.QKeySequence("Ctrl+i"))
# Reset transform
self.resetTransformPushButton = qtw.QPushButton(
"Reset",
self,
objectName="Reset Transform",
enabled=True,
shortcut=qtg.QKeySequence("Ctrl+r"))
self.viewTransformCheckBox = qtw.QCheckBox("Toggle View",
self,
objectName="View Transform",
checkable=True,
checked=True)
self.in1_points_count_label = qtw.QLabel("in1_points_label",
self,
text="Points")
self.in2_points_count_label = qtw.QLabel("in2_points_label",
self,
text="Points")
self.in1_points_count = qtw.QLCDNumber(
self, intValue=0, segmentStyle=qtw.QLCDNumber.Flat)
self.in2_points_count = qtw.QLCDNumber(
self, intValue=0, segmentStyle=qtw.QLCDNumber.Flat)
# Vectors
self.rot1 = qtw.QLabel("rot1", self, text=" 0.000")
self.rot2 = qtw.QLabel("rot2", self, text=" 0.000")
self.rot3 = qtw.QLabel("rot3", self, text=" 0.000")
self.trans1 = qtw.QLabel("trans1", self, text=" 0.000")
self.trans2 = qtw.QLabel("trans2", self, text=" 0.000")
self.trans3 = qtw.QLabel("trans3", self, text=" 0.000")
self.rotLabel = qtw.QLabel("R:", self)
self.transLabel = qtw.QLabel("T:", self)
# 4x4 matrix
self.mat11 = qtw.QLabel("mat11", self, text=" 0.000")
self.mat12 = qtw.QLabel("mat12", self, text=" 0.000")
self.mat13 = qtw.QLabel("mat13", self, text=" 0.000")
self.mat14 = qtw.QLabel("mat14", self, text=" 0.000")
self.mat21 = qtw.QLabel("mat21", self, text=" 0.000")
self.mat22 = qtw.QLabel("mat22", self, text=" 0.000")
self.mat23 = qtw.QLabel("mat23", self, text=" 0.000")
self.mat24 = qtw.QLabel("mat24", self, text=" 0.000")
self.mat31 = qtw.QLabel("mat31", self, text=" 0.000")
self.mat32 = qtw.QLabel("mat32", self, text=" 0.000")
self.mat33 = qtw.QLabel("mat33", self, text=" 0.000")
self.mat34 = qtw.QLabel("mat34", self, text=" 0.000")
self.mat41 = qtw.QLabel("mat41", self, text=" 0.000")
self.mat42 = qtw.QLabel("mat42", self, text=" 0.000")
self.mat43 = qtw.QLabel("mat43", self, text=" 0.000")
self.mat44 = qtw.QLabel("mat44", self, text=" 0.000")
self.updateMatrixGUI(vtk.vtkMatrix4x4())
# Log window
self.log_window = qtw.QTextEdit(self,
objectName="log_window",
acceptRichText=False,
lineWrapMode=qtw.QTextEdit.NoWrap,
lineWrapColumnOrWidth=80,
placeholderText="Ready...")
# Create the menu options --------------------------------------------------------------------
menubar = qtw.QMenuBar()
self.setMenuBar(menubar)
menubar.setNativeMenuBar(False)
file_menu = menubar.addMenu("File")
open_in1_action = file_menu.addAction("Open Image1")
open_in2_action = file_menu.addAction("Open Image2")
file_menu.addSeparator()
about_action = file_menu.addAction("About")
quit_action = file_menu.addAction("Quit")
save_menu = menubar.addMenu("Save")
save_log_action = save_menu.addAction("Log Window")
save_menu.addSeparator()
save_points_action = save_menu.addAction("Points")
save_transform_matrix_action = save_menu.addAction("Transform Matrix")
save_transform_vector_action = save_menu.addAction("Transform Vector")
save_menu.addSeparator()
save_extrusion_action = save_menu.addAction("Extruded Shape")
########################################
# Layouts
########################################
# Fixed Image (in1) --------------------------------------------------------------------------
self.in1_mainGroupBox = qtw.QGroupBox("Fixed Image (in1)")
self.in1_mainGroupBox.setLayout(qtw.QHBoxLayout())
self.in1_pointWidget = qtw.QFrame()
self.in1_pointWidget.setLayout(qtw.QHBoxLayout())
self.in1_pointWidget.layout().addWidget(self.in1_points_count_label)
self.in1_pointWidget.layout().addWidget(self.in1_points_count)
self.in1_loadGridLayout = qtw.QGridLayout()
self.in1_loadGridLayout.addWidget(self.in1_loadPushButton, 0, 0, 1, 1)
self.in1_loadGridLayout.addWidget(self.in1_pickableCheckBox, 0, 1, 1,
1)
self.in1_loadGridLayout.addWidget(self.in1_pointWidget, 1, 0, 1, 1)
self.in1_loadGridLayout.addWidget(self.in1_visibilityCheckBox, 1, 1, 1,
1)
self.in1_loadGridLayout.addWidget(self.in1_filenameLabel, 2, 0, 1, 4)
self.in1_isosurfaceGroupBox = qtw.QGroupBox("Isosurface controls")
self.in1_isosurfaceGroupBox.setLayout(qtw.QVBoxLayout())
self.in1_isosurfaceFormLayout = qtw.QFormLayout()
self.in1_isosurfaceFormLayout.addRow("Sigma", self.in1_sigmaSpinBox)
self.in1_isosurfaceFormLayout.addRow("Radius", self.in1_radiusSpinBox)
self.in1_isosurfaceFormLayout.addRow("Isosurface",
self.in1_isosurfaceSpinBox)
self.in1_isosurfaceGroupBox.layout().addLayout(
self.in1_isosurfaceFormLayout)
self.in1_mainGroupBox.layout().addLayout(self.in1_loadGridLayout)
self.in1_mainGroupBox.layout().addWidget(self.in1_isosurfaceGroupBox)
# Moving Image (in2) -------------------------------------------------------------------------
self.in2_mainGroupBox = qtw.QGroupBox("Moving Image (in2)")
self.in2_mainGroupBox.setLayout(qtw.QHBoxLayout())
self.in2_pointWidget = qtw.QFrame()
self.in2_pointWidget.setLayout(qtw.QHBoxLayout())
self.in2_pointWidget.layout().addWidget(self.in2_points_count_label)
self.in2_pointWidget.layout().addWidget(self.in2_points_count)
self.in2_loadGridLayout = qtw.QGridLayout()
self.in2_loadGridLayout.addWidget(self.in2_loadPushButton, 0, 0, 1, 1)
self.in2_loadGridLayout.addWidget(self.in2_pickableCheckBox, 0, 1, 1,
1)
self.in2_loadGridLayout.addWidget(self.in2_pointWidget, 1, 0, 1, 1)
self.in2_loadGridLayout.addWidget(self.in2_visibilityCheckBox, 1, 1, 1,
1)
self.in2_loadGridLayout.addWidget(self.in2_filenameLabel, 2, 0, 1, 4)
self.in2_isosurfaceGroupBox = qtw.QGroupBox("Isosurface controls")
self.in2_isosurfaceGroupBox.setLayout(qtw.QVBoxLayout())
self.in2_isosurfaceFormLayout = qtw.QFormLayout()
self.in2_isosurfaceFormLayout.addRow("Sigma", self.in2_sigmaSpinBox)
self.in2_isosurfaceFormLayout.addRow("Radius", self.in2_radiusSpinBox)
self.in2_isosurfaceFormLayout.addRow("Isosurface",
self.in2_isosurfaceSpinBox)
self.in2_isosurfaceGroupBox.layout().addLayout(
self.in2_isosurfaceFormLayout)
self.in2_mainGroupBox.layout().addLayout(self.in2_loadGridLayout)
self.in2_mainGroupBox.layout().addWidget(self.in2_isosurfaceGroupBox)
# Camera controls panel ----------------------------------------------------------------------
self.cameraControlsGroupBox = qtw.QGroupBox("Camera")
self.cameraControlsGroupBox.setLayout(qtw.QHBoxLayout())
self.cameraControlsGroupBox.layout().addWidget(
self.rollCameraPushButton)
self.cameraControlsGroupBox.layout().addWidget(
self.elevationCameraPushButton)
self.cameraControlsGroupBox.layout().addWidget(
self.azimuthCameraPushButton)
self.incrementCameraFormLayout = qtw.QFormLayout()
self.incrementCameraFormLayout.addRow("Increment",
self.incrementCameraSpinBox)
self.cameraControlsGroupBox.layout().addLayout(
self.incrementCameraFormLayout)
# Transform panel ----------------------------------------------------------------------------
self.transformPanelGroupBox = qtw.QGroupBox("Transform")
self.transformPanelGroupBox.setLayout(qtw.QHBoxLayout())
# Transform actions
self.transformLayout = qtw.QGridLayout()
self.transformLayout.addWidget(self.landmarkTransformPushButton, 0, 0,
1, 1)
self.transformLayout.addWidget(self.icpTransformPushButton, 0, 1, 1, 1)
self.transformLayout.addWidget(self.resetTransformPushButton, 1, 0, 1,
1)
self.transformLayout.addWidget(self.viewTransformCheckBox, 1, 1, 1, 1)
# Vectors display
self.vectorsLayout = qtw.QGridLayout()
self.vectorsLayout.addWidget(self.rotLabel, 0, 0, 1, 1)
self.vectorsLayout.addWidget(self.rot1, 0, 1, 1, 1)
self.vectorsLayout.addWidget(self.rot2, 0, 2, 1, 1)
self.vectorsLayout.addWidget(self.rot3, 0, 3, 1, 1)
self.vectorsLayout.addWidget(self.transLabel, 1, 0, 1, 1)
self.vectorsLayout.addWidget(self.trans1, 1, 1, 1, 1)
self.vectorsLayout.addWidget(self.trans2, 1, 2, 1, 1)
self.vectorsLayout.addWidget(self.trans3, 1, 3, 1, 1)
self.vectorsGroupBox = qtw.QGroupBox()
self.vectorsGroupBox.setLayout(self.vectorsLayout)
self.transformLayout.addWidget(self.vectorsGroupBox, 2, 0, 2, 2)
# Matrix display
self.matrixLayout = qtw.QGridLayout()
self.matrixLayout.addWidget(self.mat11, 0, 0, 1, 1)
self.matrixLayout.addWidget(self.mat12, 0, 1, 1, 1)
self.matrixLayout.addWidget(self.mat13, 0, 2, 1, 1)
self.matrixLayout.addWidget(self.mat14, 0, 3, 1, 1)
self.matrixLayout.addWidget(self.mat21, 1, 0, 1, 1)
self.matrixLayout.addWidget(self.mat22, 1, 1, 1, 1)
self.matrixLayout.addWidget(self.mat23, 1, 2, 1, 1)
self.matrixLayout.addWidget(self.mat24, 1, 3, 1, 1)
self.matrixLayout.addWidget(self.mat31, 2, 0, 1, 1)
self.matrixLayout.addWidget(self.mat32, 2, 1, 1, 1)
self.matrixLayout.addWidget(self.mat33, 2, 2, 1, 1)
self.matrixLayout.addWidget(self.mat34, 2, 3, 1, 1)
self.matrixLayout.addWidget(self.mat41, 3, 0, 1, 1)
self.matrixLayout.addWidget(self.mat42, 3, 1, 1, 1)
self.matrixLayout.addWidget(self.mat43, 3, 2, 1, 1)
self.matrixLayout.addWidget(self.mat44, 3, 3, 1, 1)
self.matrixGroupBox = qtw.QGroupBox("Matrix4x4 (in2)")
self.matrixGroupBox.setLayout(self.matrixLayout)
self.transformPanelGroupBox.layout().addLayout(self.transformLayout)
self.transformPanelGroupBox.layout().addWidget(self.matrixGroupBox)
# Set up the log window ----------------------------------------------------------------------
font = qtg.QFont("Courier")
font.setStyleHint(qtg.QFont.TypeWriter)
font.setWeight(25)
self.log_window.setTextColor(qtg.QColor("blue"))
self.log_window.setCurrentFont(font)
# Add logo -----------------------------------------------------------------------------------
logo = qtg.QPixmap(':/bonelab/icon.png')
self.logoLabel = qtw.QLabel("", self)
self.logoLabel.setPixmap(logo)
# Assemble the side control panel and put it in a QPanel widget ------------------------------
self.panel = qtw.QVBoxLayout()
self.panel.addWidget(self.in1_mainGroupBox)
self.panel.addWidget(self.in2_mainGroupBox)
self.panel.addWidget(self.cameraControlsGroupBox)
self.panel.addWidget(self.transformPanelGroupBox)
self.panel.addWidget(self.log_window)
self.panel.addWidget(self.logoLabel, alignment=qtc.Qt.AlignRight)
self.panelWidget = qtw.QFrame()
self.panelWidget.setLayout(self.panel)
# Create the VTK rendering window ------------------------------------------------------------
self.vtkWidget = QVTKRenderWindowInteractor()
self.vtkWidget.AddObserver("ExitEvent", lambda o, e, a=self: a.quit())
#self.vtkWidget.AddObserver("KeyReleaseEvent", self.keyEventDetected)
self.vtkWidget.AddObserver("LeftButtonReleaseEvent",
self.mouseEventDetected)
# Create main layout and add VTK window and control panel
self.mainLayout = qtw.QHBoxLayout()
self.mainLayout.addWidget(self.vtkWidget, 4)
self.mainLayout.addWidget(self.panelWidget, 2)
self.frame = qtw.QFrame()
self.frame.setLayout(self.mainLayout)
self.setCentralWidget(self.frame)
self.setWindowTitle(self.title)
self.centreWindow()
#print(self.iconPath)
self.setWindowIcon(qtg.QIcon(self.iconPath))
self.cp = ColourPalette()
# Set size policies --------------------------------------------------------------------------
self.in1_sigmaSpinBox.setMinimumSize(70, 20)
self.in1_radiusSpinBox.setMinimumSize(70, 20)
self.in1_isosurfaceSpinBox.setMinimumSize(70, 20)
self.in2_sigmaSpinBox.setMinimumSize(70, 20)
self.in2_radiusSpinBox.setMinimumSize(70, 20)
self.in2_isosurfaceSpinBox.setMinimumSize(70, 20)
self.in1_mainGroupBox.setMaximumSize(1000, 1000)
self.in2_mainGroupBox.setMaximumSize(1000, 1000)
self.transformPanelGroupBox.setMaximumSize(1000, 1000)
self.rotLabel.setMaximumSize(15, 20)
self.transLabel.setMaximumSize(15, 20)
self.vtkWidget.setSizePolicy(qtw.QSizePolicy.MinimumExpanding,
qtw.QSizePolicy.MinimumExpanding)
self.in1_points_count.setMaximumSize(50, 30)
self.in2_points_count.setMaximumSize(50, 30)
self.in1_mainGroupBox.setSizePolicy(qtw.QSizePolicy.Maximum,
qtw.QSizePolicy.Maximum)
self.in2_mainGroupBox.setSizePolicy(qtw.QSizePolicy.Maximum,
qtw.QSizePolicy.Maximum)
self.transformPanelGroupBox.setSizePolicy(qtw.QSizePolicy.Maximum,
qtw.QSizePolicy.Maximum)
self.log_window.setSizePolicy(qtw.QSizePolicy.MinimumExpanding,
qtw.QSizePolicy.MinimumExpanding)
# Connect signals and slots ------------------------------------------------------------------
# The use of the lambda function is so that the same slot can be used for either pipeline
self.in1_loadPushButton.clicked.connect(lambda: self.openFile("in1"))
self.in1_pickableCheckBox.stateChanged.connect(
lambda s: self.togglePickable(s, "in1"))
self.in1_visibilityCheckBox.stateChanged.connect(
lambda s: self.toggleVisibility(s, "in1"))
self.in1_sigmaSpinBox.valueChanged.connect(
lambda s: self.changeSigma(s, "in1"))
self.in1_radiusSpinBox.valueChanged.connect(
lambda s: self.changeRadius(s, "in1"))
self.in1_isosurfaceSpinBox.valueChanged.connect(
lambda s: self.changeIsosurface(s, "in1"))
self.in2_loadPushButton.clicked.connect(lambda: self.openFile("in2"))
self.in2_pickableCheckBox.stateChanged.connect(
lambda s: self.togglePickable(s, "in2"))
self.in2_visibilityCheckBox.stateChanged.connect(
lambda s: self.toggleVisibility(s, "in2"))
self.in2_sigmaSpinBox.valueChanged.connect(
lambda s: self.changeSigma(s, "in2"))
self.in2_radiusSpinBox.valueChanged.connect(
lambda s: self.changeRadius(s, "in2"))
self.in2_isosurfaceSpinBox.valueChanged.connect(
lambda s: self.changeIsosurface(s, "in2"))
self.initRenderWindow()
self.in2_mainGroupBox.setEnabled(
False) # Force user to load in1 before in2
# Camera
self.rollCameraPushButton.clicked.connect(
lambda: self.updateCamera("roll"))
self.elevationCameraPushButton.clicked.connect(
lambda: self.updateCamera("elevation"))
self.azimuthCameraPushButton.clicked.connect(
lambda: self.updateCamera("azimuth"))
# Transform
self.landmarkTransformPushButton.clicked.connect(
self.applyLandmarkTransform)
self.icpTransformPushButton.clicked.connect(self.applyICPTransform)
self.resetTransformPushButton.clicked.connect(self.resetTransform)
self.viewTransformCheckBox.stateChanged.connect(
self.toggleTransformApplied)
# Menu actions
open_in1_action.triggered.connect(lambda: self.openFile("in1"))
open_in2_action.triggered.connect(lambda: self.openFile("in2"))
about_action.triggered.connect(self.about)
quit_action.triggered.connect(self.quit)
save_log_action.triggered.connect(self.saveLogFile)
save_points_action.triggered.connect(self.savePointsFile)
save_transform_matrix_action.triggered.connect(
lambda: self.saveTransformFile("matrix"))
save_transform_vector_action.triggered.connect(
lambda: self.saveTransformFile("vector"))
save_extrusion_action.triggered.connect(self.extrudeFromPoints)
# Variables for managing the VTK pipelines
self.in1_pipe = None
self.in2_pipe = None
# End main UI code
self.show()
def centreWindow(self):
qr = self.frameGeometry()
cp = qtw.QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def initRenderWindow(self):
# Create renderer
self.renderer = vtk.vtkRenderer()
self.renderer.SetBackground(self.cp.getColour("background2"))
# Create interactor
self.renWin = self.vtkWidget.GetRenderWindow()
self.renWin.AddRenderer(self.renderer)
self.iren = self.renWin.GetInteractor()
self.pickerstyle = MyInteractorStyle()
self.pickerstyle.AddObserver("UpdateEvent", self.keyEventDetected)
#self.pickerstyle.SetCurrentStyleToTrackballCamera()
self.iren.SetInteractorStyle(self.pickerstyle)
#print(self.iren.GetInteractorStyle().GetClassName())
# Initialize
self.iren.Initialize()
self.iren.Start()
def refreshRenderWindow(self):
self.renWin.Render()
self.renderer.ResetCamera()
self.iren.Render()
def setPipelineAttributesFromGUI(self, pipeline):
if (pipeline == "in1"):
if self.in1_pickableCheckBox.isChecked():
self.in1_pipe.setActorPickable(1)
else:
self.in1_pipe.setActorPickable(0)
if self.in1_visibilityCheckBox.isChecked():
self.in1_pipe.setActorVisibility(1)
else:
self.in1_pipe.setActorVisibility(0)
self.in1_pipe.setGaussStandardDeviation(
self.in1_sigmaSpinBox.value())
self.in1_pipe.setGaussRadius(self.in1_radiusSpinBox.value())
self.in1_pipe.setIsosurface(self.in1_isosurfaceSpinBox.value())
elif (pipeline == "in2"):
if self.in2_pickableCheckBox.isChecked():
self.in2_pipe.setActorPickable(1)
else:
self.in2_pipe.setActorPickable(0)
if self.in2_visibilityCheckBox.isChecked():
self.in2_pipe.setActorVisibility(1)
else:
self.in2_pipe.setActorVisibility(0)
self.in2_pipe.setGaussStandardDeviation(
self.in2_sigmaSpinBox.value())
self.in2_pipe.setGaussRadius(self.in2_radiusSpinBox.value())
self.in2_pipe.setIsosurface(self.in2_isosurfaceSpinBox.value())
else:
return
def createPipeline(self, _filename, pipeline):
# Remove any existing pipelines before creating a new one
if (pipeline == "in1"):
if (self.in1_pipe != None):
self.renderer.RemoveActor(self.in1_pipe.getActor())
self.pickerstyle.removePoints("in1_pipeline")
del self.in1_pipe
self.in1_pipe = None
self.in1_pipe = Pipeline()
self.in1_pipe.setActorColor(self.cp.getColour("bone1"))
self.in1_filenameLabel.setText(os.path.basename(_filename))
self.in1_filenameLabel.setToolTip(_filename)
ptr = self.in1_pipe
elif (pipeline == "in2"):
if (self.in2_pipe != None):
self.renderer.RemoveActor(self.in2_pipe.getActor())
self.pickerstyle.removePoints("in2_pipeline")
del self.in2_pipe
self.in2_pipe = None
self.in2_pipe = Pipeline()
self.in2_pipe.setActorColor(self.cp.getColour("bone2"))
self.in2_filenameLabel.setText(os.path.basename(_filename))
self.in2_filenameLabel.setToolTip(_filename)
ptr = self.in2_pipe
else:
return
self.setPipelineAttributesFromGUI(pipeline)
ptr.constructPipeline(_filename)
ptr.addActor(self.renderer)
self.pickerstyle.setMainActor(ptr.getActor(), (pipeline + "_pipeline"))
self.log_window.append(ptr.getProcessingLog())
self.log_window.append(ptr.getImageInfoLog())
self.refreshRenderWindow()
self.updateGUI()
return
def togglePickable(self, _state, pipeline):
if (pipeline == "in1"):
if (self.in1_pipe != None):
ptr = self.in1_pipe
else:
return
elif (pipeline == "in2"):
if (self.in2_pipe != None):
ptr = self.in2_pipe
else:
return
# Only two states are possible
if (qtc.Qt.Checked == _state):
ptr.setActorPickable(1)
self.statusBar().showMessage("Toggling actor pickability ON", 4000)
self.refreshRenderWindow()
else:
ptr.setActorPickable(0)
self.statusBar().showMessage("Toggling actor pickability OFF",
4000)
self.refreshRenderWindow()
return
def toggleVisibility(self, _state, pipeline):
if (pipeline == "in1"):
if (self.in1_pipe != None):
name = "in1_pipeline"
ptr = self.in1_pipe
else:
return
elif (pipeline == "in2"):
if (self.in2_pipe != None):
name = "in2_pipeline"
ptr = self.in2_pipe
else:
return
# Only two states are possible
if (qtc.Qt.Checked == _state):
ptr.setActorVisibility(1)
self.pickerstyle.setVisibilityOfPoints(name, 1)
self.statusBar().showMessage("Toggling actor visibility ON", 4000)
self.refreshRenderWindow()
else:
ptr.setActorVisibility(0)
self.pickerstyle.setVisibilityOfPoints(name, 0)
self.statusBar().showMessage("Toggling actor visibility OFF", 4000)
self.refreshRenderWindow()
return
def changeSigma(self, _value, pipeline):
if (pipeline == "in1"):
if (self.in1_pipe != None):
self.in1_pipe.setGaussStandardDeviation(_value)
self.statusBar().showMessage(
f"Changing standard deviation to {_value}", 4000)
self.refreshRenderWindow()
elif (pipeline == "in2"):
if (self.in2_pipe != None):
self.in2_pipe.setGaussStandardDeviation(_value)
self.statusBar().showMessage(
f"Changing standard deviation to {_value}", 4000)
self.refreshRenderWindow()
else:
return
return
def changeRadius(self, _value, pipeline):
if (pipeline == "in1"):
if (self.in1_pipe != None):
self.in1_pipe.setGaussRadius(_value)
self.statusBar().showMessage(f"Changing radius to {_value}",
4000)
self.refreshRenderWindow()
elif (pipeline == "in2"):
if (self.in2_pipe != None):
self.in2_pipe.setGaussRadius(_value)
self.statusBar().showMessage(f"Changing radius to {_value}",
4000)
self.refreshRenderWindow()
else:
return
return
def changeIsosurface(self, _value, pipeline):
if (pipeline == "in1"):
if (self.in1_pipe != None):
self.in1_pipe.setIsosurface(_value)
self.statusBar().showMessage(
f"Changing isosurface to {_value}", 4000)
self.refreshRenderWindow()
elif (pipeline == "in2"):
if (self.in2_pipe != None):
self.in2_pipe.setIsosurface(_value)
self.statusBar().showMessage(
f"Changing isosurface to {_value}", 4000)
self.refreshRenderWindow()
else:
return
return
def updateCamera(self, type):
camera = self.renderer.GetActiveCamera()
inc = self.incrementCameraSpinBox.value()
if (type == "roll"):
camera.Roll(inc)
if (type == "elevation"):
camera.Elevation(inc)
if (type == "azimuth"):
camera.Azimuth(inc)
camera.OrthogonalizeViewUp()
self.refreshRenderWindow()
return
def applyLandmarkTransform(self):
if (self.in2_pipe != None):
in1_pts = self.pickerstyle.getNumberOfPoints("in1_pipeline")
in2_pts = self.pickerstyle.getNumberOfPoints("in2_pipeline")
if (in1_pts == in2_pts and in1_pts >= 3):
lm = vtk.vtkLandmarkTransform()
lm.SetTargetLandmarks(
self.pickerstyle.getPoints("in1_pipeline"))
lm.SetSourceLandmarks(
self.pickerstyle.getPoints("in2_pipeline"))
lm.SetModeToRigidBody()
lm.Update()
mat = lm.GetMatrix()
self.in2_pipe.setRigidBodyTransformConcatenateMatrix(mat)
self.pickerstyle.removePoints("in1_pipeline")
self.pickerstyle.removePoints("in2_pipeline")
self.refreshRenderWindow()
self.updateGUI()
self.statusBar().showMessage(
f"Landmark transform complete based on {in1_pts}", 4000)
else:
self.statusBar().showMessage(
"ERROR: Landmark transform could not be executed", 4000)
def applyICPTransform(self):
if (self.in2_pipe != None):
icp = vtk.vtkIterativeClosestPointTransform()
icp.SetTarget(self.in1_pipe.getPolyData())
icp.SetSource(self.in2_pipe.getPolyData())
icp.SetMaximumNumberOfIterations(10)
icp.StartByMatchingCentroidsOn()
icp.GetInverse()
icp.Update()
# Concatenate the transform
mat = icp.GetMatrix()
self.in2_pipe.setRigidBodyTransformConcatenateMatrix(mat)
# Clean up
self.pickerstyle.removePoints("in1_pipeline")
self.pickerstyle.removePoints("in2_pipeline")
self.refreshRenderWindow()
self.updateGUI()
self.statusBar().clearMessage()
self.statusBar().showMessage("ICP transform complete", 4000)
def resetTransform(self):
if (self.in2_pipe != None):
reply = qtw.QMessageBox.question(
self, "Message",
"Are you sure you want to reset the transform?",
qtw.QMessageBox.Yes | qtw.QMessageBox.No, qtw.QMessageBox.Yes)
if reply == qtw.QMessageBox.Yes:
self.in2_pipe.setRigidBodyTransformToIdentity()
self.pickerstyle.removePoints("in1_pipeline")
self.pickerstyle.removePoints("in2_pipeline")
self.refreshRenderWindow()
self.updateGUI()
self.statusBar().showMessage("Reset transform complete", 4000)
def toggleTransformApplied(self, _state):
if (self.in2_pipe != None):
if (qtc.Qt.Checked == _state):
self.in2_pipe.useTransform(True)
self.statusBar().showMessage(
"Toggling transform visibility ON", 4000)
else:
self.in2_pipe.useTransform(False)
self.statusBar().showMessage(
"Toggling transform visibility OFF", 4000)
self.refreshRenderWindow()
def updateMatrixGUI(self, _mat):
precision = 3
formatter = "{{:6.{}f}}".format(precision)
self.mat11.setText(formatter.format(float(_mat.GetElement(0, 0))))
self.mat12.setText(formatter.format(float(_mat.GetElement(0, 1))))
self.mat13.setText(formatter.format(float(_mat.GetElement(0, 2))))
self.mat14.setText(formatter.format(float(_mat.GetElement(0, 3))))
self.mat21.setText(formatter.format(float(_mat.GetElement(1, 0))))
self.mat22.setText(formatter.format(float(_mat.GetElement(1, 1))))
self.mat23.setText(formatter.format(float(_mat.GetElement(1, 2))))
self.mat24.setText(formatter.format(float(_mat.GetElement(1, 3))))
self.mat31.setText(formatter.format(float(_mat.GetElement(2, 0))))
self.mat32.setText(formatter.format(float(_mat.GetElement(2, 1))))
self.mat33.setText(formatter.format(float(_mat.GetElement(2, 2))))
self.mat34.setText(formatter.format(float(_mat.GetElement(2, 3))))
self.mat41.setText(formatter.format(float(_mat.GetElement(3, 0))))
self.mat42.setText(formatter.format(float(_mat.GetElement(3, 1))))
self.mat43.setText(formatter.format(float(_mat.GetElement(3, 2))))
self.mat44.setText(formatter.format(float(_mat.GetElement(3, 3))))
return
def updateVectorsGUI(self):
if (self.in2_pipe == None):
return
converter = ScancoMatrixConverter()
mat = self.in2_pipe.getMatrix()
converter.setDimImage1(self.in1_pipe.getDimensions())
converter.setDimImage2(self.in2_pipe.getDimensions())
converter.setPosImage1(self.in1_pipe.getPosition())
converter.setPosImage2(self.in2_pipe.getPosition())
converter.setElSizeMMImage1(self.in1_pipe.getElementSize())
converter.setElSizeMMImage2(self.in2_pipe.getElementSize())
converter.setTransform(mat)
converter.calculateVectors()
rot = converter.getRotationVector()
trans = converter.getTranslationVector()
precision = 3
formatter = "{{:6.{}f}}".format(precision)
self.rot1.setText(formatter.format(float(rot[0])))
self.rot2.setText(formatter.format(float(rot[1])))
self.rot3.setText(formatter.format(float(rot[2])))
self.trans1.setText(formatter.format(float(trans[0])))
self.trans2.setText(formatter.format(float(trans[1])))
self.trans3.setText(formatter.format(float(trans[2])))
return
def updateGUI(self):
in1_pts = self.pickerstyle.getNumberOfPoints("in1_pipeline")
in2_pts = self.pickerstyle.getNumberOfPoints("in2_pipeline")
#print("There are " + str(in1_pts) + " in1 points.")
#print("There are " + str(in2_pts) + " in2 points.")
self.in1_points_count.display(in1_pts)
self.in2_points_count.display(in2_pts)
if (in1_pts == in2_pts and in1_pts >= 3):
self.landmarkTransformPushButton.setEnabled(True)
else:
self.landmarkTransformPushButton.setEnabled(False)
if (self.in1_pipe != None):
self.in2_mainGroupBox.setEnabled(
True) # activate GUI for in2_pipeline
self.in1_sigmaSpinBox.setValue(
self.in1_pipe.getGaussStandardDeviation())
self.in1_radiusSpinBox.setValue(self.in1_pipe.getGaussRadius())
self.in1_isosurfaceSpinBox.setValue(self.in1_pipe.getIsosurface())
if (self.in2_pipe != None):
self.updateMatrixGUI(self.in2_pipe.getMatrix())
self.updateVectorsGUI()
self.in2_sigmaSpinBox.setValue(
self.in2_pipe.getGaussStandardDeviation())
self.in2_radiusSpinBox.setValue(self.in2_pipe.getGaussRadius())
self.in2_isosurfaceSpinBox.setValue(self.in2_pipe.getIsosurface())
return
def keyEventDetected(self, obj, event):
self.updateGUI()
key = self.vtkWidget.GetKeySym()
if (key in 'p') or (key in 'd'): # pick or delete points
self.log_window.append(self.pickerstyle.getPointActionString())
# print("keypress – clicked "+key)
return
def mouseEventDetected(self, obj, event):
print("mouserelease – click!")
return
def validExtension(self, extension):
if (extension == ".aim" or \
extension == ".nii" or \
extension == ".dcm" or \
extension == ".stl"):
return True
else:
return False
def openFile(self, pipeline_name):
if (pipeline_name == "in2" and self.in1_pipe == None):
qtw.QMessageBox.warning(
self, "Warning", "Image 2 cannot be loaded before image 1.")
return
self.statusBar().showMessage("Load image types (.aim, .nii, .dcm)",
4000)
filename, _ = qtw.QFileDialog.getOpenFileName(
self, "Select a 3D image file to open…", qtc.QDir.homePath(),
"Aim Files (*.aim) ;;Nifti Files (*.nii) ;;DICOM Files (*.dcm) ;;STL Files (*.stl) ;;All Files (*)",
"All Files (*)", qtw.QFileDialog.DontUseNativeDialog
| qtw.QFileDialog.DontResolveSymlinks)
if filename:
_, ext = os.path.splitext(filename)
if not (self.validExtension(ext.lower())):
qtw.QMessageBox.warning(self, "Error", "Invalid file type.")
return
self.createPipeline(filename, pipeline_name)
self.statusBar().showMessage("Loading file " + filename, 4000)
return
def saveLogFile(self):
filename, _ = qtw.QFileDialog.getSaveFileName(
self, "Select the file to save to…", qtc.QDir.homePath(),
"Text Files (*.txt) ")
if filename:
try:
with open(filename, 'w') as fh:
fh.write(self.log_window.toPlainText())
except Exception as e:
qtw.QMessageBox.critical(self, f"Could not save file: {e}")
def savePointsFile(self):
filename, _ = qtw.QFileDialog.getSaveFileName(
self, "Select the file to save to…", qtc.QDir.homePath(),
"Text Files (*.txt) ;;Python Files (*.py) ;;All Files (*)")
if filename:
try:
with open(filename, 'w') as fh:
fh.write(self.pickerstyle.getAllPointsAsString())
except Exception as e:
qtw.QMessageBox.critical(self, f"Could not save file: {e}")
def saveTransformFile(self, type):
converter = ScancoMatrixConverter()
if (self.in2_pipe == None):
mat = vtk.vtkMatrix4x4()
converter.setDimImage1(self.in1_pipe.getDimensions())
converter.setPosImage1(self.in1_pipe.getPosition())
converter.setElSizeMMImage1(self.in1_pipe.getElementSize())
converter.setTransform(mat)
converter.calculateVectors()
else:
mat = self.in2_pipe.getMatrix()
converter.setDimImage1(self.in1_pipe.getDimensions())
converter.setDimImage2(self.in2_pipe.getDimensions())
converter.setPosImage1(self.in1_pipe.getPosition())
converter.setPosImage2(self.in2_pipe.getPosition())
converter.setElSizeMMImage1(self.in1_pipe.getElementSize())
converter.setElSizeMMImage2(self.in2_pipe.getElementSize())
converter.setTransform(mat)
converter.calculateVectors()
filename, _ = qtw.QFileDialog.getSaveFileName(
self, "Select the file to save to…", qtc.QDir.homePath(),
"Text Files (*.txt) ;;Python Files (*.py) ;;All Files (*)")
if filename:
try:
with open(filename, 'w') as fh:
s = ""
if (type == "matrix"):
s += converter.getTransformAsString()
if (type == "vector"):
s += converter.getVectorsAsString()
fh.write(s)
except Exception as e:
qtw.QMessageBox.critical(self, f"Could not save file: {e}")
def quit(self):
reply = qtw.QMessageBox.question(
self, "Message", "Are you sure you want to quit?",
qtw.QMessageBox.Yes | qtw.QMessageBox.No, qtw.QMessageBox.Yes)
if reply == qtw.QMessageBox.Yes:
exit(0)
def about(self):
about = qtw.QMessageBox(self)
about.setWindowIcon(qtg.QIcon('/bonelab/gui/src/icon.png'))
about.setIcon(qtw.QMessageBox.Information)
about.setText("blQtViewer 1.0")
about.setInformativeText(
"Copyright (C) 2020\nBone Imaging Laboratory\nAll rights reserved.\[email protected]"
)
about.setStandardButtons(qtw.QMessageBox.Ok | qtw.QMessageBox.Cancel)
about.exec_()
def extrudeFromPoints(self):
pts = self.pickerstyle.getPoints("in1_pipeline")
if (pts.GetNumberOfPoints() < 3):
qtw.QMessageBox.warning(
self, "Warning",
"At least 3 points must be defined on image 1 to create extrusion."
)
return
if (not self.in1_pipe.getIsValidForExtrusion()):
qtw.QMessageBox.warning(
self, "Warning",
"Extrusion may not work properly when input file is not of type AIM."
)
# Spline
spline = vtk.vtkParametricSpline()
spline.SetPoints(pts)
spline.ClosedOn()
parametricFunction = vtk.vtkParametricFunctionSource()
parametricFunction.SetParametricFunction(spline)
parametricFunction.Update()
# Extrude
extrusionFactor = 100.0 # mm above and below surface
# A large number will cause the extrusion to fill the extent of the input image
positiveExtruder = vtk.vtkLinearExtrusionFilter()
positiveExtruder.SetInputConnection(parametricFunction.GetOutputPort())
positiveExtruder.SetExtrusionTypeToNormalExtrusion()
positiveExtruder.SetVector(0, 0, 1)
positiveExtruder.CappingOn()
positiveExtruder.SetScaleFactor(extrusionFactor)
posTriFilter = vtk.vtkTriangleFilter()
posTriFilter.SetInputConnection(positiveExtruder.GetOutputPort())
negativeExtruder = vtk.vtkLinearExtrusionFilter()
negativeExtruder.SetInputConnection(parametricFunction.GetOutputPort())
negativeExtruder.SetExtrusionTypeToNormalExtrusion()
negativeExtruder.SetVector(0, 0, -1)
negativeExtruder.CappingOn()
negativeExtruder.SetScaleFactor(extrusionFactor)
negTriFilter = vtk.vtkTriangleFilter()
negTriFilter.SetInputConnection(negativeExtruder.GetOutputPort())
# Combine data
combiner = vtk.vtkAppendPolyData()
combiner.AddInputConnection(posTriFilter.GetOutputPort())
combiner.AddInputConnection(negTriFilter.GetOutputPort())
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(combiner.GetOutputPort())
cleaner.Update()
el_size_mm = self.in1_pipe.getElementSize()
dim = self.in1_pipe.getDimensions()
extent = self.in1_pipe.getExtent()
origin = self.in1_pipe.getOrigin()
foregroundValue = 127
backgroundValue = 0
# Stencil
whiteImage = vtk.vtkImageData()
whiteImage.SetSpacing(el_size_mm)
whiteImage.SetDimensions(dim)
whiteImage.SetExtent(extent)
whiteImage.SetOrigin(origin)
whiteImage.AllocateScalars(vtk.VTK_CHAR, 1)
whiteImage.GetPointData().GetScalars().Fill(foregroundValue)
# Use our extruded polydata to stencil the solid image
poly2sten = vtk.vtkPolyDataToImageStencil()
poly2sten.SetTolerance(0)
#poly2sten.SetInputConnection(clipper.GetOutputPort())
poly2sten.SetInputConnection(cleaner.GetOutputPort())
poly2sten.SetOutputOrigin(origin)
poly2sten.SetOutputSpacing(el_size_mm)
poly2sten.SetOutputWholeExtent(whiteImage.GetExtent())
stencil = vtk.vtkImageStencil()
stencil.SetInputData(whiteImage)
stencil.SetStencilConnection(poly2sten.GetOutputPort())
#stencil.ReverseStencilOff()
stencil.SetBackgroundValue(backgroundValue)
stencil.Update()
# Write image
filename, _ = qtw.QFileDialog.getSaveFileName(
self, "Select the file to save to…", qtc.QDir.homePath(),
"AIM File (*.aim)")
if (filename):
writer = vtkbone.vtkboneAIMWriter()
writer.SetInputConnection(stencil.GetOutputPort())
writer.SetFileName(filename)
writer.SetProcessingLog(
'!-------------------------------------------------------------------------------\n'
+ 'Written by blQtViewer.')
writer.Update()
self.statusBar().showMessage("File " + filename + " written.",
4000)
