def __init__(self):
self.interactor = None
self.image_original = None
self.image_threshold = None
self.render = None
self.lut = vtkLookupTable()
self.lut_original = vtkLookupTable()
self.image_color = vtkImageMapToColors()
self.blend = blend = vtkImageBlend()
self.map = map = vtkImageMapper()
self.actor = actor = vtkImageActor()
self.actor2 = actor2 = vtkImageActor()
self.actor3 = actor3 = vtkImageActor()
self.image_color_o = vtkImageMapToColors()
self.operation_type = 0
self.w = None
self.slice = 0
self.clicked = 0
self.orientation = AXIAL
self.w = (200, 1200)
def _set_colour(self, imagedata, colour):
scalar_range = int(imagedata.GetScalarRange()[1])
r, g, b = colour[:3]
# map scalar values into colors
lut_mask = vtkLookupTable()
lut_mask.SetNumberOfColors(256)
lut_mask.SetHueRange(const.THRESHOLD_HUE_RANGE)
lut_mask.SetSaturationRange(1, 1)
lut_mask.SetValueRange(0, 255)
lut_mask.SetRange(0, 255)
lut_mask.SetNumberOfTableValues(256)
lut_mask.SetTableValue(0, 0, 0, 0, 0.0)
lut_mask.SetTableValue(1, 1-r, 1-g, 1-b, 0.50)
lut_mask.SetRampToLinear()
lut_mask.Build()
# map the input image through a lookup table
img_colours_mask = vtkImageMapToColors()
img_colours_mask.SetLookupTable(lut_mask)
img_colours_mask.SetOutputFormatToRGBA()
img_colours_mask.SetInputData(imagedata)
img_colours_mask.Update()
return img_colours_mask.GetOutput()
def __init__(self, model_file, genie):
super(View3D, self).__init__()
self.lut = vtkLookupTable()
self.lut.SetScaleToLog10()
ColorMapPreset.use_colormap(current_inv_colormap_filename(genie),
self.lut)
self.init_docks()
self.cut_plane_panel = CutPlanePanel()
self.cut_plane_dock.setWidget(self.cut_plane_panel)
self.vtk_view = VTKWidget(model_file, self.lut, genie,
self.cut_plane_panel)
self.vtk_view.update_scalar_range(*self.vtk_view.model.scalar_range)
self.setCentralWidget(self.vtk_view)
self.visibility_panel = VisibilityPanel(
self.vtk_view.model.data_fields_names)
self.visibility_dock.setWidget(self.visibility_panel)
self.color_map_panel = ColorMapPanel(*self.vtk_view.model.scalar_range,
genie, self.lut)
self.color_map_dock.setWidget(self.color_map_panel)
self.resizeDocks([self.cut_plane_dock],
[self.cut_plane_panel.minimumSizeHint().width() + 1],
Qt.Horizontal)
self.init_connections()
def map_img(self, ): # greyscale lookup table
self.img_table = vtkLookupTable()
self.img_color = vtkImageMapToColors()
self.img_table.SetRange(0, 2000) # image intensity range
self.img_table.SetValueRange(0.0, 1.0) # from black to white
self.img_table.SetSaturationRange(0.0, 0.0) # no color saturation
self.img_table.SetRampToSQRT()
self.img_table.Build()
self.connect_window_level()
img_actor = vtkImageActor()
img_actor.GetMapper().SetInputConnection(
self.img_color.GetOutputPort())
return img_actor
def make_new_lut(self, lut, pixmap=None):
new_lut = vtkLookupTable()
self.copy_lut_settings(lut, new_lut)
new_lut.SetNumberOfTableValues(200)
if pixmap == None:
map = QImage(self.bar.pixmap())
else:
map = QImage(pixmap)
for index in range(200):
pixel = map.pixel(index, 0)
new_lut.SetTableValue(index,
qRed(pixel) / 255,
qGreen(pixel) / 255,
qBlue(pixel) / 255, 1)
new_lut.Build()
return new_lut
def map_roi(self): # colored lookup table
self.roi_table = vtkLookupTable()
self.roi_table.SetNumberOfTableValues(2)
self.roi_table.SetRange(0.0, 1.0)
self.roi_table.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
self.roi_table.SetTableValue(1, 0.0, 1.0, 0.0,
1.0) # value, r, g, b, a
self.roi_table.Build()
self.roi_color = vtkImageMapToColors()
self.roi_color.SetLookupTable(self.roi_table)
self.roi_color.SetInputConnection(self.roi_reslice.GetOutputPort())
roi_actor = vtkImageActor()
roi_actor.GetMapper().SetInputConnection(
self.roi_color.GetOutputPort())
return roi_actor
def _set_volume_range(self, volume, ctable, alpha, scalar_bar, rng):
color_tf = vtkColorTransferFunction()
opacity_tf = vtkPiecewiseFunction()
for loc, color in zip(np.linspace(*rng, num=len(ctable)), ctable):
color_tf.AddRGBPoint(loc, *(color[:-1] / 255.))
opacity_tf.AddPoint(loc, color[-1] * alpha / 255.)
color_tf.ClampingOn()
opacity_tf.ClampingOn()
prop = volume.GetProperty()
prop.SetColor(color_tf)
prop.SetScalarOpacity(opacity_tf)
prop.ShadeOn()
prop.SetInterpolationTypeToLinear()
if scalar_bar is not None:
lut = vtkLookupTable()
lut.SetRange(*rng)
lut.SetTable(numpy_to_vtk(ctable))
scalar_bar.SetLookupTable(lut)
def main():
VTK_DATA_ROOT = vtkGetDataRoot()
folder = "/Users/nandana/Downloads/image_ex"
#read dicom files from specified directory
reader = vtkDICOMImageReader()
reader.SetDirectoryName(folder)
reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetDataOrigin(-150.0, 150.0, 3.0)
reader.SetDataScalarTypeToUnsignedShort()
reader.UpdateWholeExtent()
# Calculate the center of the volume
reader.Update()
(xMin, xMax, yMin, yMax, zMin,
zMax) = reader.GetExecutive().GetWholeExtent(
reader.GetOutputInformation(0))
(xSpacing, ySpacing, zSpacing) = reader.GetOutput().GetSpacing()
(x0, y0, z0) = reader.GetOutput().GetOrigin()
center = [
x0 + xSpacing * 0.5 * (xMin + xMax),
y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)
]
yd = ((yMax - yMin) + 1) * ySpacing
"""
# Matrices for axial, coronal, sagittal, oblique view orientations
axial = vtkMatrix4x4()
axial.DeepCopy((1, 0, 0, center[0],
0, 1, 0, center[1],
0, 0, 1, center[2],
0, 0, 0, 1))
coronal = vtkMatrix4x4()
coronal.DeepCopy((1, 0, 0, center[0],
0, 0, 1, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
sagittal = vtkMatrix4x4
sagittal.DeepCopy((0, 0,-1, center[0],
1, 0, 0, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
oblique = vtkMatrix4x4()
oblique.DeepCopy((1, 0, 0, center[0],
0, 0.866025, -0.5, center[1],
0, 0.5, 0.866025, center[2],
0, 0, 0, 1))
reslice = vtkImageReslice()
outputPort = reader.GetOutputPort()
#reslice.SetInputConnection(reader.GetOutputPort())
reslice.SetInputConnection(0, reader.GetOutputPort())
print(reader.GetOutput().GetExtent())
reslice.SetOutputExtent(reader.GetOutput().GetExtent())
reslice.SetOutputDimensionality(2)
reslice.SetResliceAxes(coronal)
reslice.SetInterpolationModeToLinear()
"""
# Visualize
imageViewer = vtkResliceImageViewer()
imageViewer.SetSliceOrientationToXY()
#imageViewer.SetSlice(9)
imageViewer.SetResliceModeToAxisAligned()
imageViewer.SliceScrollOnMouseWheelOff()
imageViewer.SetInputData(reader.GetOutput())
#imageViewer.Render()
camera = imageViewer.GetRenderer().GetActiveCamera()
print(camera.GetOrientationWXYZ())
# slice status message
sliceTextProp = vtkTextProperty()
sliceTextProp.SetFontFamilyToCourier()
sliceTextProp.SetFontSize(20)
sliceTextProp.SetVerticalJustificationToBottom()
sliceTextProp.SetJustificationToLeft()
sliceTextMapper = vtkTextMapper()
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
sliceTextMapper.SetTextProperty(sliceTextProp)
sliceTextActor = vtkActor2D()
sliceTextActor.SetMapper(sliceTextMapper)
sliceTextActor.SetPosition(100, 10)
# coordinate display
coordTextProp = vtkTextProperty()
coordTextProp.SetFontFamilyToCourier()
coordTextProp.SetFontSize(20)
coordTextProp.SetVerticalJustificationToBottom()
coordTextProp.SetJustificationToLeft()
coordTextMapper = vtkTextMapper()
coordTextMapper.SetInput("Pixel Coordinates: (--, --)")
coordTextMapper.SetTextProperty(coordTextProp)
coordTextActor = vtkActor2D()
coordTextActor.SetMapper(coordTextMapper)
coordTextActor.SetPosition(500, 10)
worldCoordTextProp = vtkTextProperty()
worldCoordTextProp.SetFontFamilyToCourier()
worldCoordTextProp.SetFontSize(20)
worldCoordTextProp.SetVerticalJustificationToBottom()
worldCoordTextProp.SetJustificationToLeft()
worldCoordTextMapper = vtkTextMapper()
worldCoordTextMapper.SetInput("World Coordinates: (--, --)")
worldCoordTextMapper.SetTextProperty(worldCoordTextProp)
worldCoordTextActor = vtkActor2D()
worldCoordTextActor.SetMapper(worldCoordTextMapper)
worldCoordTextActor.SetPosition(500, 30)
# usage hint message
usageTextProp = vtkTextProperty()
usageTextProp.SetFontFamilyToCourier()
usageTextProp.SetFontSize(14)
usageTextProp.SetVerticalJustificationToTop()
usageTextProp.SetJustificationToLeft()
usageTextMapper = vtkTextMapper()
usageTextMapper.SetInput(
"- Slice with mouse wheel\n- Zoom with pressed right\n mouse button while dragging\n- Press i to toggle cursor line on/off"
)
usageTextMapper.SetTextProperty(usageTextProp)
usageTextActor = vtkActor2D()
usageTextActor.SetMapper(usageTextMapper)
usageTextActor.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedDisplay()
usageTextActor.GetPositionCoordinate().SetValue(0.05, 0.95)
actor = imageViewer.GetImageActor()
#image = vtkImageActor()
#actor.GetMapper().SetInputData(reader.GetOutput())
image = imageViewer.GetInput()
roiData = vtkImageData()
roiImage = vtkImageActor()
roiData.DeepCopy(image)
extent = roiData.GetExtent()
for i in range(extent[0], extent[1]):
for j in range(extent[2], extent[3]):
for k in range(extent[4], extent[5]):
if image.GetScalarComponentAsDouble(i, j, k, 0) > -100:
roiData.SetScalarComponentFromDouble(i, j, k, 0, 1)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 1)
else: #just in case
roiData.SetScalarComponentFromDouble(i, j, k, 0, 0.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 0.0)
"""
for i in range(extent[0], extent[1]):
for j in range(extent[2], extent[3]):
#for k in range(extent[4], extent[5]):
#k = 0
roiData.SetScalarComponentFromDouble(i, j, k, 0, 0.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 0.0)
"""
print(extent)
table = vtkLookupTable()
table.SetNumberOfTableValues(2)
table.SetRange(0.0, 1.0)
table.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
table.SetTableValue(1, 0.0, 1.0, 0.0, 1.0)
table.Build()
mapToColor = vtkImageMapToColors()
mapToColor.SetLookupTable(table)
mapToColor.PassAlphaToOutputOn()
mapToColor.SetInputData(roiData)
#actor.GetMapper().SetInputConnection(mapToColor.GetOutputPort())
roiImage.GetMapper().SetInputConnection(mapToColor.GetOutputPort())
imageViewer.SetInputData(image)
interactorStyle = vtkInteractorStyleImage()
interactor = vtkRenderWindowInteractor()
imageViewer.SetupInteractor(interactor)
interactor.SetInteractorStyle(interactorStyle)
# add slice status message and usage hint message to the renderer
imageViewer.GetRenderer().AddActor2D(coordTextActor)
imageViewer.GetRenderer().AddActor2D(sliceTextActor)
imageViewer.GetRenderer().AddActor2D(usageTextActor)
imageViewer.GetRenderer().AddActor2D(worldCoordTextActor)
imageViewer.GetRenderer().AddActor(roiImage)
#imageViewer.GetRenderer().AddViewProp(stack)
# initialize rendering and interaction
#imageViewer.SetSlice(35)
imageViewer.GetRenderWindow().SetSize(1000, 1000)
imageViewer.GetRenderer().SetBackground(0.2, 0.3, 0.4)
imageViewer.GetWindowLevel().SetWindow(1000)
imageViewer.GetWindowLevel().SetLevel(-1000)
imageViewer.Render()
yd = (yMax - yMin + 1) * ySpacing
xd = (xMax - xMin + 1) * xSpacing
d = camera.GetDistance()
camera.SetParallelScale(0.5 * xd)
camera.SetFocalPoint(center[0], center[1], 0)
camera.SetPosition(center[0], center[1], +d)
actions = {}
actions["Dolly"] = -1
actions["Cursor"] = 0
def middlePressCallback(obj, event):
# if middle + ctrl pressed, zoom in/out
# otherwise slice through image (handled by mouseMoveCallback)
if (interactor.GetControlKey()):
actions["Dolly"] = 0
interactorStyle.OnRightButtonDown()
else:
actions["Dolly"] = 1
def middleReleaseCallback(obj, event):
if (actions["Dolly"] == 0):
interactorStyle.OnRightButtonUp()
elif (actions["Dolly"] == 1):
actions["Dolly"] = 0
def mouseMoveCallback(obj, event):
# if the middle button is pressed + mouse is moved, slice through image
# otherwise, update world/pixel coords as mouse is moved
if (actions["Dolly"] == 1):
(lastX, lastY) = interactor.GetLastEventPosition()
(curX, curY) = interactor.GetEventPosition()
deltaY = curY - lastY
if (deltaY > 0):
imageViewer.IncrementSlice(1)
elif (deltaY < 0):
imageViewer.IncrementSlice(-1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
else:
(mouseX, mouseY) = interactor.GetEventPosition()
bounds = actor.GetMapper().GetInput().GetBounds()
testCoord = vtkCoordinate()
testCoord.SetCoordinateSystemToDisplay()
testCoord.SetValue(mouseX, mouseY, 0)
(posX, posY,
posZ) = testCoord.GetComputedWorldValue(imageViewer.GetRenderer())
inBounds = True
if posX < bounds[0] or posX > bounds[1] or posY < bounds[
2] or posY > bounds[3]:
inBounds = False
if inBounds:
wMousePos = "World Coordinates: (" + "{:.2f}".format(
posX) + ", " + "{:.2f}".format(
posY) + ", " + "{:.2f}".format(posZ) + ")"
pMousePos = "Pixel Coordinates: (" + "{:.2f}".format(
mouseX) + ", " + "{:.2f}".format(mouseY) + ")"
worldCoordTextMapper.SetInput(wMousePos)
coordTextMapper.SetInput(pMousePos)
imageViewer.Render()
interactorStyle.OnMouseMove()
def scrollForwardCallback(obj, event):
# slice through image on scroll, update slice text
imageViewer.IncrementSlice(1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
def scrollBackwardCallback(obj, event):
imageViewer.IncrementSlice(-1)
msg = "Slice {} out of {}".format(imageViewer.GetSlice() + 1, \
imageViewer.GetSliceMax() + 1)
sliceTextMapper.SetInput(msg)
imageViewer.Render()
def windowModifiedCallback(obj, event):
# track render window width so coordinate text aligns itself
# to the right side of the screen
width = imageViewer.GetRenderWindow().GetSize()[0]
coordTextActor.SetPosition(width - 550, 10)
worldCoordTextActor.SetPosition(width - 550, 30)
imageViewer.Render()
def keyPressCallback(obj, event):
# toggle cursor on/off when t key is pressed
key = interactor.GetKeySym()
if (key == "t"):
if (actions["Cursor"] == 0):
imageViewer.GetRenderWindow().HideCursor()
actions["Cursor"] = 1
elif (actions["Cursor"] == 1):
imageViewer.GetRenderWindow().ShowCursor()
actions["Cursor"] = 0
interactorStyle.AddObserver("MiddleButtonPressEvent", middlePressCallback)
interactorStyle.AddObserver("MiddleButtonReleaseEvent",
middleReleaseCallback)
interactorStyle.AddObserver("MouseMoveEvent", mouseMoveCallback)
interactorStyle.AddObserver("MouseWheelForwardEvent",
scrollForwardCallback)
interactorStyle.AddObserver("MouseWheelBackwardEvent",
scrollBackwardCallback)
interactorStyle.AddObserver("KeyPressEvent", keyPressCallback)
imageViewer.GetRenderWindow().AddObserver("ModifiedEvent",
windowModifiedCallback)
interactor.Start()
for i in range(extent[0], extent[1]):
for j in range(extent[2], extent[3]):
for k in range(extent[4], extent[5]):
if image.GetScalarComponentAsDouble(i, j, k, 0) > -100:
roiData.SetScalarComponentFromDouble(i, j, k, 0, 1.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 1)
else: #just in case
roiData.SetScalarComponentFromDouble(i, j, k, 0, 0.0)
#roiData.SetScalarComponentFromDouble(0, i, j, k, 0.0)
print(extent)
"""
print("creating LookupTable...")
table = vtkLookupTable()
table.SetNumberOfTableValues(2)
table.SetRange(0.0, 1.0)
table.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
table.SetTableValue(1, 0.0, 1.0, 0.0, 1.0) # value, r, g, b, a
table.Build()
# Create a greyscale lookup table
table2 = vtkLookupTable()
table2.SetRange(0, 2000) # image intensity range
table2.SetValueRange(0.0, 1.0) # from black to white
table2.SetSaturationRange(0.0, 0.0) # no color saturation
table2.SetRampToSQRT()
table2.Build()
def __init__(self):
VTK_DATA_ROOT = vtkGetDataRoot()
self.reader = vtkDICOMImageReader()
self.folder = "/Users/nandana/Downloads/image_ex"
self.reader.SetDirectoryName(self.folder)
self.reader.SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
self.reader.SetDataExtent(0, 63, 0, 63, 1, 93)
self.reader.SetDataSpacing(3.2, 3.2, 1.5)
self.reader.SetDataOrigin(0.0, 0.0, 0.0)
self.reader.SetDataScalarTypeToUnsignedShort()
self.reader.UpdateWholeExtent()
self.reader.Update()
self.center = self.calculate_center()
self.axial = vtkMatrix4x4()
self.axial.DeepCopy((1, 0, 0, self.center[0], 0, 1, 0, self.center[1],
0, 0, 1, self.center[2], 0, 0, 0, 1))
self.coronal = vtkMatrix4x4()
self.coronal.DeepCopy(
(1, 0, 0, self.center[0], 0, 0, 1, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
self.sagittal = vtkMatrix4x4()
self.sagittal.DeepCopy(
(0, 0, -1, self.center[0], 1, 0, 0, self.center[1], 0, -1, 0,
self.center[2], 0, 0, 0, 1))
self.oblique = vtkMatrix4x4()
self.oblique.DeepCopy(
(1, 0, 0, self.center[0], 0, 0.866025, -0.5, self.center[1], 0,
0.5, 0.866025, self.center[2], 0, 0, 0, 1))
self.img_reslice = vtkImageReslice()
self.roi_reslice = vtkImageReslice()
self.img_reslice.SetInputConnection(0, self.reader.GetOutputPort())
self.img_reslice.SetOutputDimensionality(2)
self.img_reslice.SetInterpolationModeToLinear()
self.roi_reslice.SetInputConnection(0, self.reader.GetOutputPort())
self.roi_reslice.SetOutputDimensionality(2)
self.roi_reslice.SetInterpolationModeToLinear()
self.set_orientation(self.axial)
self.img_table = vtkLookupTable()
self.roi_table = vtkLookupTable()
self.window_level = vtkImageMapToWindowLevelColors()
self.img_color = vtkImageMapToColors()
self.roi_color = vtkImageMapToColors()
self.img = self.map_img()
self.roi = self.map_roi()
self.px_coord_text_prop = vtkTextProperty()
self.px_coord_text_mapper = vtkTextMapper()
self.px_coord_text_actor = vtkActor2D()
self.world_coord_text_prop = vtkTextProperty()
self.world_coord_text_mapper = vtkTextMapper()
self.world_coord_text_actor = vtkActor2D()
self.usage_text_prop = vtkTextProperty()
self.usage_text_mapper = vtkTextMapper()
self.usage_text_actor = vtkActor2D()
self.renderer = vtkRenderer()
self.add_text()
self.renderer.AddActor(self.img)
self.renderer.AddActor(self.roi)
self.renderer.SetBackground(0.2, 0.3, 0.4)
self.window = vtkRenderWindow()
self.window.AddRenderer(self.renderer)
self.window.SetSize(1000, 1000)
self.interactor_style = vtkInteractorStyleImage()
self.interactor_style.SetInteractionModeToImageSlicing()
self.interactor = vtkRenderWindowInteractor()
self.interactor.SetInteractorStyle(self.interactor_style)
self.window.SetInteractor(self.interactor)
self.window_level.SetWindow(1000)
self.window_level.SetLevel(200)
self.window_level.Update()
self.window.Render()
self.interactor_style.AddObserver("MouseWheelForwardEvent",
self.scroll_forward_callback)
self.interactor_style.AddObserver("MouseWheelBackwardEvent",
self.scroll_backward_callback)
self.interactor_style.AddObserver("MouseMoveEvent",
self.mouse_move_callback)
self.interactor_style.AddObserver("KeyPressEvent",
self.key_press_callback)
self.interactor_style.AddObserver("LeftButtonPressEvent",
self.left_press_callback)
self.window.AddObserver("ModifiedEvent", self.window_mod_callback)
self.actions = {
"Slicing": 0,
"Cursor": 0,
"CurrentPos": -1,
"LastPos": -1,
"DoubleClick": 0
}