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 }