def __init__(self):
#os.system("pwd")
if os.path.exists(self.gladeFile):
theFile = self.gladeFile
elif os.path.exists("gui/"+self.gladeFile):
theFile = "gui/"+self.gladeFile
else:
theFile = os.path.join(
distutils.sysconfig.PREFIX,
'share', 'pbrain', self.gladeFile)
self.widgets = gtk.glade.XML (theFile)
self.widgets.signal_autoconnect(GladeHandlers.__dict__)
#self['entryDir'].set_text('/home/jdhunter/python/examples/vtk/images/')
self.outDim = 256, 256
self.viewer = vtk.vtkImageViewer()
self.preview = GtkGLExtVTKRenderWindow()
self.preview.set_size_request(self.outDim[0], self.outDim[1])
self.preview.show()
self.renderer = self.viewer.GetRenderer()
self.preview.GetRenderWindow().AddRenderer(self.renderer)
self['vboxPreview'].pack_start(self.preview, False, False)
self['vboxPreview'].reorder_child(self.preview, 1)
def main():
file_name = get_program_parameters()
reader = vtk.vtkHDRReader()
# Check the image can be read
if not reader.CanReadFile(file_name):
print('CanReadFile failed for ', file_name)
return
reader.SetFileName(file_name)
reader.UpdateInformation()
# Whole extent
we = reader.GetDataExtent()
extents = [we[0], we[1], we[2], we[3], 0, 0]
reader.UpdateExtent(extents)
# Visualize
image_viewer = vtk.vtkImageViewer()
image_viewer.SetInputData(reader.GetOutput())
image_viewer.SetColorWindow(1)
image_viewer.SetColorLevel(1)
image_viewer.SetPosition(0, 100)
iren = vtk.vtkRenderWindowInteractor()
image_viewer.SetupInteractor(iren)
image_viewer.GetRenderWindow().SetWindowName('HDRReader')
image_viewer.Render()
iren.AddObserver('EndInteractionEvent', ColorCallback(image_viewer))
iren.Start()
def __init__(self):
#os.system("pwd")
if os.path.exists(self.gladeFile):
theFile = self.gladeFile
elif os.path.exists("gui/"+self.gladeFile):
theFile = "gui/"+self.gladeFile
else:
theFile = os.path.join(
distutils.sysconfig.PREFIX,
'share', 'pbrain', self.gladeFile)
self.widgets = gtk.glade.XML (theFile)
self.widgets.signal_autoconnect(GladeHandlers.__dict__)
#self['entryDir'].set_text('/home/jdhunter/python/examples/vtk/images/')
self.outDim = 256, 256
self.viewer = vtk.vtkImageViewer()
self.preview = GtkGLExtVTKRenderWindow()
self.preview.set_size_request(self.outDim[0], self.outDim[1])
self.preview.show()
self.renderer = self.viewer.GetRenderer()
self.preview.GetRenderWindow().AddRenderer(self.renderer)
self['vboxPreview'].pack_start(self.preview, False, False)
self['vboxPreview'].reorder_child(self.preview, 1)
def viewVtk(mat):
import vtk
imageData = vtk.vtkImageData()
imageData.SetDimensions(mat.shape[0], mat.shape[1], 1)
imageData.SetScalarTypeToUnsignedShort()
imageData.SetNumberOfScalarComponents(1)
imageData.AllocateScalars()
viewer = vtk.vtkImageViewer()
viewer.SetInput(imageData)
viewer.SetZSlice(0)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(viewer.GetRenderWindow())
iren.Initialize()
iren.Start()
imageData = vtk.vtkImageSinusoidSource()
imageData.SetWholeExtent(0, 300, 0, 300, 0, 10)
imageData.SetAmplitude(63)
imageData.SetDirection(1, 1, 0)
imageData.SetPeriod(25)
viewer = vtk.vtkImageViewer()
viewer.SetInput(imageData.GetOutput())
viewer.SetColorWindow(126)
viewer.SetColorLevel(0)
viewer.SetZSlice(0)
def hamschti(obj, event):
print 'Haam:'
print obj
print event
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(viewer.GetRenderWindow())
iren.Initialize()
interactor = vtk.vtkInteractorStyleImage()
##interactor.AddObserver('LeftButtonPressEvent', hamschti)
iren.SetInteractorStyle(interactor)
iren.Start()
def viewVtk(mat):
import vtk
imageData = vtk.vtkImageData()
imageData.SetDimensions(mat.shape[0], mat.shape[1], 1)
imageData.SetScalarTypeToUnsignedShort()
imageData.SetNumberOfScalarComponents(1)
imageData.AllocateScalars()
viewer = vtk.vtkImageViewer()
viewer.SetInput(imageData)
viewer.SetZSlice(0)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(viewer.GetRenderWindow())
iren.Initialize()
iren.Start()
imageData = vtk.vtkImageSinusoidSource()
imageData.SetWholeExtent(0, 300, 0, 300, 0, 10)
imageData.SetAmplitude(63)
imageData.SetDirection(1, 1, 0)
imageData.SetPeriod(25)
viewer = vtk.vtkImageViewer()
viewer.SetInput(imageData.GetOutput())
viewer.SetColorWindow(126)
viewer.SetColorLevel(0)
viewer.SetZSlice(0)
def hamschti(obj, event):
print "Haam:"
print obj
print event
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(viewer.GetRenderWindow())
iren.Initialize()
interactor = vtk.vtkInteractorStyleImage()
##interactor.AddObserver('LeftButtonPressEvent', hamschti)
iren.SetInteractorStyle(interactor)
iren.Start()
def __getattr__(self, attr):
# because the tk part of vtkTkImageViewerWidget must have
# the only remaining reference to the ImageViewer when
# it is destroyed, we can't actually store the ImageViewer
# as an attribute but instead have to get it from the tk-side
if attr == "_ImageViewer":
addr = self.tk.call(self._w, "GetImageViewer")[5:]
return vtk.vtkImageViewer("_%s_vtkImageViewer_p" % addr)
raise AttributeError, self.__class__.__name__ + " has no attribute named " + attr
def View(imagedata):
viewer = vtk.vtkImageViewer()
viewer.SetInput(imagedata)
viewer.SetColorWindow(200)
viewer.SetColorLevel(100)
viewer.Render()
import time
time.sleep(10)
def View(imagedata):
viewer = vtk.vtkImageViewer()
viewer.SetInput(imagedata)
viewer.SetColorWindow(200)
viewer.SetColorLevel(100)
viewer.Render()
import time
time.sleep(10)
def __getattr__(self, attr):
# because the tk part of vtkTkImageViewerWidget must have
# the only remaining reference to the ImageViewer when
# it is destroyed, we can't actually store the ImageViewer
# as an attribute but instead have to get it from the tk-side
if attr == '_ImageViewer':
addr = self.tk.call(self._w, 'GetImageViewer')[5:]
return vtk.vtkImageViewer('_%s_vtkImageViewer_p' % addr)
raise AttributeError, self.__class__.__name__ + \
" has no attribute named " + attr
def displayOneSlice(image, slice=30, window=255, level=127):
viewer = vtk.vtkImageViewer()
viewer.SetInput(image)
viewer.SetZSlice(slice)
viewer.SetColorWindow(window)
viewer.SetColorLevel(level)
viewer.Render()
interact = vtk.vtkRenderWindowInteractor()
viewer.SetupInteractor(interact)
interact.Initialize()
interact.Start()
def slotShowDICOMImage(self, item):
reader = vtkgdcm.vtkGDCMImageReader()
dicom_file = unicode(item.data(QtCore.Qt.UserRole).toString())
reader.SetFileName(dicom_file)
reader.Update()
imageViewer = vtk.vtkImageViewer()
imageViewer.SetInputConnection(reader.GetOutputPort())
self.qvtkWidget.SetRenderWindow(imageViewer.GetRenderWindow())
imageViewer.SetupInteractor(self.qvtkWidget.GetRenderWindow().GetInteractor())
#imageViewer.SetColorLevel(128)
#imageViewer.SetColorWindow(256)
imageViewer.SetSize(self.qvtkWidget.geometry().width(), self.qvtkWidget.geometry().height())
def __init__(self, master, cnf={}, **kw):
"""
Constructor.
Keyword arguments:
iv -- Use passed image viewer instead of creating a new one.
double -- If True, generate a double-buffered viewer.
Defaults to False.
focus_on_enter -- If True, use a focus-follows-mouse mode.
Defaults to False where the widget will use a click-to-focus
mode.
"""
# load the necessary extensions into tk
vtkLoadPythonTkWidgets(master.tk)
try: # use specified vtkImageViewer
imageViewer = kw['iv']
except KeyError: # or create one if none specified
imageViewer = vtk.vtkImageViewer()
doubleBuffer = 0
try:
if kw['double']:
doubleBuffer = 1
del kw['double']
except:
pass
# check if focus should follow mouse
if kw.get('focus_on_enter'):
self._FocusOnEnter = 1
del kw['focus_on_enter']
else:
self._FocusOnEnter = 0
kw['iv'] = imageViewer.GetAddressAsString("vtkImageViewer")
Tkinter.Widget.__init__(self, master, 'vtkTkImageViewerWidget',
cnf, kw)
if doubleBuffer:
imageViewer.GetRenderWindow().DoubleBufferOn()
self.BindTkImageViewer()
def __init__(self, master, cnf={}, **kw):
"""
Constructor.
Keyword arguments:
iv -- Use passed image viewer instead of creating a new one.
double -- If True, generate a double-buffered viewer.
Defaults to False.
focus_on_enter -- If True, use a focus-follows-mouse mode.
Defaults to False where the widget will use a click-to-focus
mode.
"""
# load the necessary extensions into tk
vtkLoadPythonTkWidgets(master.tk)
try: # use specified vtkImageViewer
imageViewer = kw['iv']
except KeyError: # or create one if none specified
imageViewer = vtk.vtkImageViewer()
doubleBuffer = 0
try:
if kw['double']:
doubleBuffer = 1
del kw['double']
except:
pass
# check if focus should follow mouse
if kw.get('focus_on_enter'):
self._FocusOnEnter = 1
del kw['focus_on_enter']
else:
self._FocusOnEnter = 0
kw['iv'] = imageViewer.GetAddressAsString("vtkImageViewer")
Tkinter.Widget.__init__(self, master, 'vtkTkImageViewerWidget', cnf,
kw)
if doubleBuffer:
imageViewer.GetRenderWindow().DoubleBufferOn()
self.BindTkImageViewer()
def setupUi(self, ReadDICOMSeriesQt):
ReadDICOMSeriesQt.setObjectName(_fromUtf8("ReadDICOMSeriesQt"))
ReadDICOMSeriesQt.resize(541, 531)
self.centralWidget = QtGui.QWidget(ReadDICOMSeriesQt)
self.centralWidget.setObjectName(_fromUtf8("centralWidget"))
self.buttonOpenFolder = QtGui.QPushButton(self.centralWidget)
self.buttonOpenFolder.setGeometry(QtCore.QRect(10, 430, 121, 24))
self.buttonOpenFolder.setObjectName(_fromUtf8("buttonOpenFolder"))
self.sliderSlices = QtGui.QSlider(self.centralWidget)
self.sliderSlices.setGeometry(QtCore.QRect(140, 430, 381, 23))
self.sliderSlices.setOrientation(QtCore.Qt.Horizontal)
self.sliderSlices.setObjectName(_fromUtf8("sliderSlices"))
self.labelFolderName = QtGui.QLabel(self.centralWidget)
self.labelFolderName.setGeometry(QtCore.QRect(140, 470, 381, 15))
self.labelFolderName.setObjectName(_fromUtf8("labelFolderName"))
self.labelSlicesNumber = QtGui.QLabel(self.centralWidget)
self.labelSlicesNumber.setGeometry(QtCore.QRect(140, 500, 381, 15))
self.labelSlicesNumber.setObjectName(_fromUtf8("labelSlicesNumber"))
self.labelSlicesNumberTitle = QtGui.QLabel(self.centralWidget)
self.labelSlicesNumberTitle.setGeometry(QtCore.QRect(20, 500, 59, 15))
self.labelSlicesNumberTitle.setObjectName(
_fromUtf8("labelSlicesNumberTitle"))
self.labelFolderNameTitle = QtGui.QLabel(self.centralWidget)
self.labelFolderNameTitle.setGeometry(QtCore.QRect(20, 470, 59, 15))
self.labelFolderNameTitle.setObjectName(
_fromUtf8("labelFolderNameTitle"))
self.qvtkWidget = QVTKRenderWindowInteractor(self.centralWidget)
self.qvtkWidget.setGeometry(QtCore.QRect(10, 10, 521, 411))
self.qvtkWidget.setObjectName(_fromUtf8("qvtkWidget"))
ReadDICOMSeriesQt.setCentralWidget(self.centralWidget)
self.reader = vtk.vtkDICOMImageReader()
self.imageViewer = vtk.vtkImageViewer()
self.interactor = vtk.vtkInteractorStyleImage()
self.renderWindowInteractor = vtk.vtkRenderWindowInteractor()
self.minSlice = 0
self.maxSlice = 0
self.fname = ""
self.dicomfiles = []
self.retranslateUi(ReadDICOMSeriesQt)
QtCore.QMetaObject.connectSlotsByName(ReadDICOMSeriesQt)
def ImageActor(img):
reader = vtkImageImportFromArray()
reader.SetArray(img)
ImageDataGeometryFilter = vtk.vtkImageDataGeometryFilter()
ImageDataGeometryFilter.SetInputConnection(reader.GetOutputPort())
ImageDataGeometryFilter.Update()
# textureCoordinates = vtk.vtkFloatArray()
# textureCoordinates.SetNumberOfComponents(2)
# textureCoordinates.InsertNextTuple2(0.0, 1.0)
# textureCoordinates.InsertNextTuple2(1.0, 1.0)
# textureCoordinates.InsertNextTuple2(1.0, 0.0)
# textureCoordinates.InsertNextTuple2(0.0, 0.0)
mag = vtk.vtkImageMagnify()
mag.SetMagnificationFactors(512, 512, 1)
mag.InterpolateOff()
mag.SetInputConnection(reader.GetOutputPort())
mapper = vtk.vtkImageMapper()
# mapper.SetInputConnection(reader.GetOutputPort())
# mapper.SetColorWindow(4)
# mapper.SetColorLevel(255)
# mapper.SetZSlice(0)
mapper.SetInputConnection(mag.GetOutputPort())
# mapper.SetColorlevel(1000)
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(reader.GetOutputPort())
viewer.SetColorWindow(4)
viewer.SetColorLevel(255)
# viewer.SetZSlice(0)
viewer.Render()
actor = vtk.vtkActor2D()
actor.SetMapper(mapper.GetOutputPort())
# actor=vtk.vtkImageActor()
# actor.SetMapper(mapper)
# actor.SetInputData(reader.GetOutput())
return actor, viewer
def initGUI(self):
QtGui.QMainWindow.__init__(self)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.setWindowTitle("Simple Dicom Viewer")
#self.dicomReader = vtk.vtkDICOMImageReader()
#self.dicomReader = vtkgdcm.vtkGDCMImageReader()
self.show()
self.figure = plt.figure()
self.canvas = FigureCanvas(self.figure)
self.toolbar = NavigationToolbar(self.canvas, self)
self.ui.numpyLayout.addWidget(self.toolbar)
self.ui.numpyLayout.addWidget(self.canvas)
self.vtkWidget = QVTKRenderWindowInteractor(self.ui.imageFrame)
self.vtkWidget.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
#self.ui.imageLayout.removeWidget(self.ui.dicomSlider)
self.ui.imageLayout.addWidget(self.vtkWidget)
#self.ui.imageLayout.addWidget(self.ui.dicomSlider)
self.disableSlider()
self.viewer= vtk.vtkImageViewer()
#self.viewer.SetupInteractor(MyInteractor())
self.vtkWidget.GetRenderWindow().AddRenderer(self.viewer.GetRenderer())
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
#self.iren.SetRenderWindow(self.vtkWidget.GetRenderWindow())
self.drag = False
self.measuring = False
self.iren.AddObserver("LeftButtonPressEvent", self.leftClick)
self.iren.AddObserver("LeftButtonReleaseEvent", self.leftRelease)
self.iren.AddObserver("EnterEvent", self.mouseEntered)
self.iren.AddObserver("LeaveEvent", self.mouseLeft)
self.iren.AddObserver("MouseMoveEvent", self.mouseMoved)
def SetUp(self):
'''
Set up cursor3D
'''
def OnClosing():
self.root.quit()
def ViewerDown(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() - 1)
def ViewerUp(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() + 1)
def ViewerSetZSlice(tkvw, z):
viewer = tkvw.GetImageViewer()
viewer.SetZSlice(z)
txt = 'slice: ' + str(z)
sliceLabel.configure(text=txt)
tkvw.Render()
def SetCursorFromViewer(event):
x = int(event.x)
y = int(event.y)
# We have to flip y axis because tk uses upper right origin.
self.root.update_idletasks()
height = int(self.tkvw.configure()['height'][4])
y = height - y
z = self.tkvw.GetImageViewer().GetZSlice()
SetCursor(x / IMAGE_MAG_X, y / IMAGE_MAG_Y, z / IMAGE_MAG_Z)
def SetCursor(x, y, z):
CURSOR_X = x
CURSOR_Y = y
CURSOR_Z = z
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
self.viewer.Render()
self.tkrw.Render()
# Pipeline stuff.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/neghip.slc")
# Cursor stuff
magnify = vtk.vtkImageMagnify()
magnify.SetInputConnection(reader.GetOutputPort())
magnify.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
imageCursor = vtk.vtkImageCursor3D()
imageCursor.SetInputConnection(magnify.GetOutputPort())
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
imageCursor.SetCursorValue(255)
imageCursor.SetCursorRadius(50 * IMAGE_MAG_X)
axes = vtk.vtkAxes()
axes.SymmetricOn()
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
axes.SetScaleFactor(50.0)
axes_mapper = vtk.vtkPolyDataMapper()
axes_mapper.SetInputConnection(axes.GetOutputPort())
axesActor = vtk.vtkActor()
axesActor.SetMapper(axes_mapper)
axesActor.GetProperty().SetAmbient(0.5)
# Image viewer stuff.
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageCursor.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(256)
viewer.SetColorLevel(128)
# Create transfer functions for opacity and color.
opacity_transfer_function = vtk.vtkPiecewiseFunction()
opacity_transfer_function.AddPoint(20, 0.0)
opacity_transfer_function.AddPoint(255, 0.2)
color_transfer_function = vtk.vtkColorTransferFunction()
color_transfer_function.AddRGBPoint(0, 0, 0, 0)
color_transfer_function.AddRGBPoint(64, 1, 0, 0)
color_transfer_function.AddRGBPoint(128, 0, 0, 1)
color_transfer_function.AddRGBPoint(192, 0, 1, 0)
color_transfer_function.AddRGBPoint(255, 0, .2, 0)
# Create properties, mappers, volume actors, and ray cast function.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_transfer_function)
# volume_property.SetColor(color_transfer_function[0],
# color_transfer_function[1],
# color_transfer_function[2])
volume_property.SetScalarOpacity(opacity_transfer_function)
volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volume_property)
# Create outline.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outline_mapper)
outlineActor.GetProperty().SetColor(1, 1, 1)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.AddActor(axesActor)
ren.AddVolume(volume)
ren.SetBackground(0.1, 0.2, 0.4)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(256, 256)
# Create the GUI: two renderer widgets and a quit button.
self.root = tkinter.Tk()
self.root.title("cursor3D")
# Define what to do when the user explicitly closes a window.
self.root.protocol("WM_DELETE_WINDOW", OnClosing)
# Help label, frame and quit button
helpLabel = tkinter.Label(
self.root,
text=
"MiddleMouse (or shift-LeftMouse) in image viewer to place cursor")
displayFrame = tkinter.Frame(self.root)
quitButton = tkinter.Button(self.root, text="Quit", command=OnClosing)
# Pack the GUI.
helpLabel.pack()
displayFrame.pack(fill=BOTH, expand=TRUE)
quitButton.pack(fill=X)
# Create the viewer widget.
viewerFrame = tkinter.Frame(displayFrame)
viewerFrame.pack(padx=3,
pady=3,
side=LEFT,
anchor=N,
fill=BOTH,
expand=FALSE)
self.tkvw = vtkTkImageViewerWidget(viewerFrame,
iv=viewer,
width=264,
height=264)
viewerControls = tkinter.Frame(viewerFrame)
viewerControls.pack(side=BOTTOM, anchor=S, fill=BOTH, expand=TRUE)
self.tkvw.pack(side=TOP, anchor=N, fill=BOTH, expand=FALSE)
downButton = tkinter.Button(viewerControls,
text="Down",
command=[ViewerDown, self.tkvw])
upButton = tkinter.Button(viewerControls,
text="Up",
command=[ViewerUp, self.tkvw])
sliceLabel = tkinter.Label(viewerControls,
text="slice: " +
str(CURSOR_Z * IMAGE_MAG_Z))
downButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
upButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
sliceLabel.pack(side=LEFT, expand=TRUE, fill=BOTH)
# Create the render widget
renderFrame = tkinter.Frame(displayFrame)
renderFrame.pack(padx=3,
pady=3,
side=LEFT,
anchor=N,
fill=BOTH,
expand=TRUE)
self.tkrw = vtkTkRenderWidget(renderFrame,
rw=renWin,
width=264,
height=264)
self.tkrw.pack(side=TOP, anchor=N, fill=BOTH, expand=TRUE)
# Bindings
self.tkvw.BindTkImageViewer()
self.tkrw.BindTkRenderWidget()
# Lets add an extra binding of the middle button in the image viewer
# to set the cursor location.
self.tkvw.bind('<Button-2>', SetCursorFromViewer)
self.tkvw.bind('<Shift-Button-1>', SetCursorFromViewer)
# Associate the functions with the buttons and label.
#
downButton.config(command=partial(ViewerDown, self.tkvw))
upButton.config(command=partial(ViewerUp, self.tkvw))
def visualize(txt_Wurl):
winSize = 800
#############################################
def LoadData(datapath):
'''
Function to load input image in NIFTI or DICOM
Argument: path to the input file
Returns: a vtkImageData '''
reader = vtk.vtkImageReader()
if (os.path.isdir(datapath)):
reader = vtk.vtkDICOMImageReader()
reader.SetDirectoryName(datapath)
else:
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(datapath)
reader.SetDataScalarType(vtk.VTK_UNSIGNED_SHORT)
reader.SetDataByteOrderToLittleEndian()
reader.SetNumberOfScalarComponents(1)
reader.Update()
return reader.GetOutput()
def Global_theresholding2(Image):
T1=random.randint(Image.GetScalarRange()[0],Image.GetScalarRange()[1])
T1=low
T2=high
T0=0
Height = Image.GetDimensions()[0]
Width = Image.GetDimensions()[1]
Depth = Image.GetDimensions()[2]
# Image newImage(3, Matrix(newImageHeight, Array(newImageWidth)))
newImage = np.zeros((Height, Width, Depth), float)
F1=[]
F2=[]
# for d in range(0,3):
for i in range(3, Height - 3):
for j in range(3, Width - 3):
for z in range(3, Depth - 3):
voxelValue = Image.GetScalarComponentAsFloat(i, j, z, 0)
if voxelValue>T1 and voxelValue<T2:
F1.append((voxelValue))
Image.SetScalarComponentFromFloat(i, j, z, 0, 255)
else:
F2.append((voxelValue))
Image.SetScalarComponentFromFloat(i, j, z, 0, 0)
return Image
# Display using image view\
# er convenience class
###################################################
def volume_renderer(img):
#Create the renderers, render window, and interactor
renWin=vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
ren=vtk.vtkRenderer()
ren.SetBackground(0.0, 0.0, 0.0)
renWin.AddRenderer(ren)
#Create a transfer function mapping scalar value to opacity
oTFun=vtk.vtkPiecewiseFunction()
# oTFun.AddSegment(0,1.0,256,0.1)
oTFun.AddPoint(0, 0.0)
oTFun.AddPoint(low, 0.1)
oTFun.AddPoint(high, 0.8)
oTFun.AddPoint(100, 0.05)
cTFun=vtk.vtkColorTransferFunction()
cTFun.AddRGBPoint(0, 0.0, 0.0, 0.0) # background
cTFun.AddRGBPoint(low, 0.7, 0.0, 0.3)
cTFun.AddRGBPoint(high, 0.0, 0.0, 0.5)
cTFun.AddRGBPoint(200, 1.0, 0.8, 0.5)
gradient = vtk.vtkPiecewiseFunction()
gradient.AddPoint(0, 0.0)
gradient.AddPoint(high, 0.5)
gradient.AddPoint(150, 1.0)
property =vtk.vtkVolumeProperty()
property.SetScalarOpacity(oTFun)
property.SetColor(cTFun)
property.SetInterpolationTypeToLinear()
mapper =vtk.vtkFixedPointVolumeRayCastMapper()
#mapper.SetBlendModeToMinimumIntensity()
mapper.SetInputData(img )
volume =vtk.vtkVolume()
volume.SetMapper(mapper)
volume.SetProperty(property)
volume.Update()
ren.AddViewProp(volume)
iren.Initialize()
iren.Start()
###################################################
def surface_renderer(img):
# get iso surface as polydata
marcher = vtk.vtkMarchingCubes()
marcher.SetInputData(img)
marcher.SetValue(0, 255)
marcher.ComputeNormalsOn()
marcher.Update()
# mapper-actor-render-renderwindow sequence
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(marcher.GetOutput())
mapper.ScalarVisibilityOff()
actor = vtk.vtkLODActor()
actor.SetMapper(mapper)
actor.SetNumberOfCloudPoints(1000000)
actor.GetProperty().SetColor(1.6, 0.0, 2)
actor.GetProperty().SetOpacity(0.5)
render = vtk.vtkRenderer()
render.AddActor(actor)
render.SetBackground(0.0, 0.0, 0.0)
window = vtk.vtkRenderWindow()
window.AddRenderer(render)
window.PolygonSmoothingOn()
window.SetSize(500, 500)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(window)
iren.Initialize()
window.Render()
iren.Start()
vtkImg = LoadData(txt_Wurl)
# filename='/Users/Fatemeh/Documents/Advance_Medical_Image_Datasets/head.nii'
#options of visualization
# option='volume'
option='surface'
low=70
high=3000
viewer = vtk.vtkImageViewer()
# Smooth the image data
gauss = vtk.vtkImageGaussianSmooth()
gauss.SetInputData(vtkImg)
gauss.SetDimensionality(3)
gauss.SetStandardDeviations([2.0,2.0,2.0])
gauss.SetRadiusFactors(1.0,1.0,1.0)
gauss.Update()
#theresholding image
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(gauss.GetOutput())
thresh.ThresholdBetween(low, high)
thresh.ReplaceInOn()
thresh.SetInValue(255)
thresh.ReplaceOutOn()
thresh.SetOutValue(0)
thresh.SetOutputScalarTypeToFloat()
thresh.Update()
if option == 'surface':
surface_renderer(thresh.GetOutput())
#surface_renderer(numpy_array)
if option == 'volume':
volume_renderer(vtkImg)
def SetUp(self):
"""
Set up cursor3D
"""
def OnClosing():
self.root.quit()
def ViewerDown(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() - 1)
def ViewerUp(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() + 1)
def ViewerSetZSlice(tkvw, z):
viewer = tkvw.GetImageViewer()
viewer.SetZSlice(z)
txt = "slice: " + str(z)
sliceLabel.configure(text=txt)
tkvw.Render()
def SetCursorFromViewer(event):
x = int(event.x)
y = int(event.y)
# We have to flip y axis because tk uses upper right origin.
self.root.update_idletasks()
height = int(self.tkvw.configure()["height"][4])
y = height - y
z = self.tkvw.GetImageViewer().GetZSlice()
SetCursor(x / IMAGE_MAG_X, y / IMAGE_MAG_Y, z / IMAGE_MAG_Z)
def SetCursor(x, y, z):
CURSOR_X = x
CURSOR_Y = y
CURSOR_Z = z
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X, CURSOR_Y * IMAGE_MAG_Y, CURSOR_Z * IMAGE_MAG_Z)
self.viewer.Render()
self.tkrw.Render()
# Pipeline stuff.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/neghip.slc")
# Cursor stuff
magnify = vtk.vtkImageMagnify()
magnify.SetInputConnection(reader.GetOutputPort())
magnify.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
imageCursor = vtk.vtkImageCursor3D()
imageCursor.SetInputConnection(magnify.GetOutputPort())
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X, CURSOR_Y * IMAGE_MAG_Y, CURSOR_Z * IMAGE_MAG_Z)
imageCursor.SetCursorValue(255)
imageCursor.SetCursorRadius(50 * IMAGE_MAG_X)
axes = vtk.vtkAxes()
axes.SymmetricOn()
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
axes.SetScaleFactor(50.0)
axes_mapper = vtk.vtkPolyDataMapper()
axes_mapper.SetInputConnection(axes.GetOutputPort())
axesActor = vtk.vtkActor()
axesActor.SetMapper(axes_mapper)
axesActor.GetProperty().SetAmbient(0.5)
# Image viewer stuff.
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageCursor.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(256)
viewer.SetColorLevel(128)
# Create transfer functions for opacity and color.
opacity_transfer_function = vtk.vtkPiecewiseFunction()
opacity_transfer_function.AddPoint(20, 0.0)
opacity_transfer_function.AddPoint(255, 0.2)
color_transfer_function = vtk.vtkColorTransferFunction()
color_transfer_function.AddRGBPoint(0, 0, 0, 0)
color_transfer_function.AddRGBPoint(64, 1, 0, 0)
color_transfer_function.AddRGBPoint(128, 0, 0, 1)
color_transfer_function.AddRGBPoint(192, 0, 1, 0)
color_transfer_function.AddRGBPoint(255, 0, 0.2, 0)
# Create properties, mappers, volume actors, and ray cast function.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_transfer_function)
# volume_property.SetColor(color_transfer_function[0],
# color_transfer_function[1],
# color_transfer_function[2])
volume_property.SetScalarOpacity(opacity_transfer_function)
volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volume_property)
# Create outline.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outline_mapper)
outlineActor.GetProperty().SetColor(1, 1, 1)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.AddActor(axesActor)
ren.AddVolume(volume)
ren.SetBackground(0.1, 0.2, 0.4)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(256, 256)
# Create the GUI: two renderer widgets and a quit button.
self.root = tkinter.Tk()
self.root.title("cursor3D")
# Define what to do when the user explicitly closes a window.
self.root.protocol("WM_DELETE_WINDOW", OnClosing)
# Help label, frame and quit button
helpLabel = tkinter.Label(self.root, text="MiddleMouse (or shift-LeftMouse) in image viewer to place cursor")
displayFrame = tkinter.Frame(self.root)
quitButton = tkinter.Button(self.root, text="Quit", command=OnClosing)
# Pack the GUI.
helpLabel.pack()
displayFrame.pack(fill=BOTH, expand=TRUE)
quitButton.pack(fill=X)
# Create the viewer widget.
viewerFrame = tkinter.Frame(displayFrame)
viewerFrame.pack(padx=3, pady=3, side=LEFT, anchor=N, fill=BOTH, expand=FALSE)
self.tkvw = vtkTkImageViewerWidget(viewerFrame, iv=viewer, width=264, height=264)
viewerControls = tkinter.Frame(viewerFrame)
viewerControls.pack(side=BOTTOM, anchor=S, fill=BOTH, expand=TRUE)
self.tkvw.pack(side=TOP, anchor=N, fill=BOTH, expand=FALSE)
downButton = tkinter.Button(viewerControls, text="Down", command=[ViewerDown, self.tkvw])
upButton = tkinter.Button(viewerControls, text="Up", command=[ViewerUp, self.tkvw])
sliceLabel = tkinter.Label(viewerControls, text="slice: " + str(CURSOR_Z * IMAGE_MAG_Z))
downButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
upButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
sliceLabel.pack(side=LEFT, expand=TRUE, fill=BOTH)
# Create the render widget
renderFrame = tkinter.Frame(displayFrame)
renderFrame.pack(padx=3, pady=3, side=LEFT, anchor=N, fill=BOTH, expand=TRUE)
self.tkrw = vtkTkRenderWidget(renderFrame, rw=renWin, width=264, height=264)
self.tkrw.pack(side=TOP, anchor=N, fill=BOTH, expand=TRUE)
# Bindings
self.tkvw.BindTkImageViewer()
self.tkrw.BindTkRenderWidget()
# Lets add an extra binding of the middle button in the image viewer
# to set the cursor location.
self.tkvw.bind("<Button-2>", SetCursorFromViewer)
self.tkvw.bind("<Shift-Button-1>", SetCursorFromViewer)
# Associate the functions with the buttons and label.
#
downButton.config(command=partial(ViewerDown, self.tkvw))
upButton.config(command=partial(ViewerUp, self.tkvw))
magnify2.SetInputConnection(reader.GetOutputPort())
magnify2.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
magnify2.ReleaseDataFlagOn()
# a filter that does in place processing (magnify ReleaseDataFlagOn)
cursor = vtk.vtkImageCursor3D()
cursor.SetInputConnection(magnify1.GetOutputPort())
cursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
cursor.SetCursorValue(255)
cursor.SetCursorRadius(50 * IMAGE_MAG_X)
# stream to increase coverage of in place filter.
# put the two together in one image
imageAppend = vtk.vtkImageAppend()
imageAppend.SetAppendAxis(0)
imageAppend.AddInputConnection(magnify2.GetOutputPort())
imageAppend.AddInputConnection(cursor.GetOutputPort())
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageAppend.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(200)
viewer.SetColorLevel(80)
# viewer DebugOn
viewer.Render()
viewer.SetPosition(50, 50)
# make interface
viewer.Render()
def main():
fileName = get_program_parameters()
colors = vtk.vtkNamedColors()
# Read the CT data of the human head.
reader = vtk.vtkMetaImageReader()
reader.SetFileName(fileName)
reader.Update()
cast = vtk.vtkImageCast()
cast.SetInputConnection(reader.GetOutputPort())
cast.SetOutputScalarTypeToFloat()
# Magnify the image.
magnify = vtk.vtkImageMagnify()
magnify.SetInputConnection(cast.GetOutputPort())
magnify.SetMagnificationFactors(2, 2, 1)
magnify.InterpolateOn()
# Smooth the data.
# Remove high frequency artifacts due to linear interpolation.
smooth = vtk.vtkImageGaussianSmooth()
smooth.SetInputConnection(magnify.GetOutputPort())
smooth.SetDimensionality(2)
smooth.SetStandardDeviations(1.5, 1.5, 0.0)
smooth.SetRadiusFactors(2.01, 2.01, 0.0)
# Compute the 2D gradient.
gradient = vtk.vtkImageGradient()
gradient.SetInputConnection(smooth.GetOutputPort())
gradient.SetDimensionality(2)
# Convert the data to polar coordinates.
# The image magnitude is mapped into saturation value,
# whilst the gradient direction is mapped into hue value.
polar = vtk.vtkImageEuclideanToPolar()
polar.SetInputConnection(gradient.GetOutputPort())
polar.SetThetaMaximum(255.0)
# Add a third component to the data.
# This is needed since the gradient filter only generates two components,
# and we need three components to represent color.
pad = vtk.vtkImageConstantPad()
pad.SetInputConnection(polar.GetOutputPort())
pad.SetOutputNumberOfScalarComponents(3)
pad.SetConstant(200.0)
# At this point we have Hue, Value, Saturation.
# Permute components so saturation will be constant.
# Re-arrange components into HSV order.
permute = vtk.vtkImageExtractComponents()
permute.SetInputConnection(pad.GetOutputPort())
permute.SetComponents(0, 2, 1)
# Convert back into RGB values.
rgb = vtk.vtkImageHSVToRGB()
rgb.SetInputConnection(permute.GetOutputPort())
rgb.SetMaximum(255.0)
# Set up a viewer for the image.
# Note that vtkImageViewer and vtkImageViewer2 are convenience wrappers around
# vtkActor2D, vtkImageMapper, vtkRenderer, and vtkRenderWindow.
# So all that needs to be supplied is the interactor.
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(rgb.GetOutputPort())
viewer.SetZSlice(22)
viewer.SetColorWindow(255.0)
viewer.SetColorLevel(127.0)
viewer.GetRenderWindow().SetSize(512, 512)
viewer.GetRenderer().SetBackground(colors.GetColor3d("Silver"))
# Create the RenderWindowInteractor.
iren = vtk.vtkRenderWindowInteractor()
viewer.SetupInteractor(iren)
viewer.Render()
iren.Initialize()
iren.Start()
p2.SetPoint(7, 96, 96, 0) thinPlate = vtk.vtkThinPlateSplineTransform() thinPlate.SetSourceLandmarks(p2) thinPlate.SetTargetLandmarks(p1) thinPlate.SetBasisToR2LogR() # convert the thin plate spline into a grid transformToGrid = vtk.vtkTransformToGrid() transformToGrid.SetInput(thinPlate) transformToGrid.SetGridSpacing(16, 16, 1) transformToGrid.SetGridOrigin(-0.5, -0.5, 0) transformToGrid.SetGridExtent(0, 16, 0, 16, 0, 0) transformToGrid.Update() transform = vtk.vtkGridTransform() transform.SetDisplacementGridConnection(transformToGrid.GetOutputPort()) transform.SetInterpolationModeToCubic() # you must invert the transform before passing it to vtkImageReslice transform.Inverse() # apply the grid warp to the image reslice = vtk.vtkImageReslice() reslice.SetInputConnection(blend.GetOutputPort()) reslice.SetResliceTransform(transform) reslice.SetInterpolationModeToLinear() # set the window/level to 255.0/127.5 to view full range viewer = vtk.vtkImageViewer() viewer.SetInputConnection(reslice.GetOutputPort()) viewer.SetColorWindow(255.0) viewer.SetColorLevel(127.5) viewer.SetZSlice(0) viewer.Render() # --- end of script --
def main():
fn = get_program_parameters()
# A script to test the stencil filter with a polydata stencil.
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetDataSpacing(0.8, 0.8, 1.5)
reader.SetDataOrigin(0.0, 0.0, 0.0)
reader.SetFileName(fn)
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(12)
sphere.SetThetaResolution(12)
sphere.SetCenter(102, 102, 0)
sphere.SetRadius(60)
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(sphere.GetOutputPort())
stripper = vtk.vtkStripper()
stripper.SetInputConnection(triangle.GetOutputPort())
dataToStencil = vtk.vtkPolyDataToImageStencil()
dataToStencil.SetInputConnection(stripper.GetOutputPort())
dataToStencil.SetOutputSpacing(0.8, 0.8, 1.5)
dataToStencil.SetOutputOrigin(0.0, 0.0, 0.0)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(reader.GetOutputPort())
stencil.SetStencilConnection(dataToStencil.GetOutputPort())
stencil.ReverseStencilOn()
stencil.SetBackgroundValue(500)
# test again with a contour
reader2 = vtk.vtkPNGReader()
reader2.SetDataSpacing(0.8, 0.8, 1.5)
reader2.SetDataOrigin(0.0, 0.0, 0.0)
reader2.SetFileName(fn)
plane = vtk.vtkPlane()
plane.SetOrigin(0, 0, 0)
plane.SetNormal(0, 0, 1)
cutter = vtk.vtkCutter()
cutter.SetInputConnection(sphere.GetOutputPort())
cutter.SetCutFunction(plane)
stripper2 = vtk.vtkStripper()
stripper2.SetInputConnection(cutter.GetOutputPort())
dataToStencil2 = vtk.vtkPolyDataToImageStencil()
dataToStencil2.SetInputConnection(stripper2.GetOutputPort())
dataToStencil2.SetOutputSpacing(0.8, 0.8, 1.5)
dataToStencil2.SetOutputOrigin(0.0, 0.0, 0.0)
stencil2 = vtk.vtkImageStencil()
stencil2.SetInputConnection(reader2.GetOutputPort())
stencil2.SetStencilConnection(dataToStencil2.GetOutputPort())
stencil2.SetBackgroundValue(500)
imageAppend = vtk.vtkImageAppend()
imageAppend.SetInputConnection(stencil.GetOutputPort())
imageAppend.AddInputConnection(stencil2.GetOutputPort())
viewer = vtk.vtkImageViewer()
interator = vtk.vtkRenderWindowInteractor()
viewer.SetInputConnection(imageAppend.GetOutputPort())
viewer.SetupInteractor(interator)
viewer.SetZSlice(0)
viewer.SetColorWindow(2000)
viewer.SetColorLevel(1000)
viewer.GetRenderWindow().SetWindowName('PolyDataToImageDataStencil')
viewer.Render()
interator.Start()
