/
usefullVTKFunctions.py
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/
usefullVTKFunctions.py
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# -*- coding: utf-8 -*-
"""
Created on Mon Jan 16 17:26:54 2017
@author: broche
"""
import numpy as np
import vtk
from PyMca5.PyMca import PyMcaQt as qt
from time import gmtime, strftime
class VTK_Render_QT(qt.QFrame):
def __init__(self, parent = None):
qt.QFrame.__init__(self, parent)
self.v1 = qt.QVBoxLayout()
self.renWin = vtk.vtkRenderWindow()
@staticmethod
def exitCheck(obj, event):
if obj.GetEventPending() != 0:
obj.SetAbortRender(1)
@staticmethod
def image_float_to_int8(vol,minValue,maxValue):
"""
Format the volume to a 0-255 image uint16
"""
vol = (255 * (vol - minValue)) / (maxValue - minValue)
vol = vol.astype(np.uint8)
vol[vol < 0 ] = 0
vol[vol > 255 ] = 255
return vol
def MarchingCube(self,thresholdValue):
thresholdValue = float((255.0 * (thresholdValue - self.minValue)) / (self.maxValue - self.minValue))
threshold = vtk.vtkImageThreshold()
threshold.SetInputConnection(self.data_importer.GetOutputPort())
threshold.ThresholdByLower(thresholdValue) # remove all soft tissue
threshold.ReplaceInOn()
threshold.SetInValue(0) # set all values below 400 to 0
threshold.ReplaceOutOn()
threshold.SetOutValue(1) # set all values above 400 to 1
threshold.Update()
self.dmc = vtk.vtkDiscreteMarchingCubes()
self.dmc.SetInputConnection(threshold.GetOutputPort())
self.dmc.GenerateValues(1, 1, 1)
self.dmc.Update()
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName('./Data/' + strftime("%Y-%m-%d %H:%M:%S", gmtime())+'.stl')
stlWriter.SetInputConnection(self.dmc.GetOutputPort())
stlWriter.SetFileTypeToBinary()
stlWriter.Write()
def SmoothMesh(self,nbIter,RelaxFactor):
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInputConnection(self.dmc.GetOutputPort())
smoother.SetNumberOfIterations(nbIter)
smoother.SetRelaxationFactor(RelaxFactor)#this has little effect on the error!
self.dmc = vtk.vtkPolyDataNormals()
self.dmc.SetInputConnection(smoother.GetOutputPort())
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName('./Data/' + strftime("%Y-%m-%d %H:%M:%S", gmtime())+'.stl')
stlWriter.SetFileTypeToBinary()
stlWriter.SetInputConnection(self.dmc.GetOutputPort())
stlWriter.Write()
def init_all_VolumeRendering_component(self, flagMesh):
self.flagMesh = flagMesh
self.ren= vtk.vtkRenderer()
self.renWin.AddRenderer(self.ren)
self.iren = vtk.vtkXRenderWindowInteractor()
self.iren.SetRenderWindow(self.renWin)
self.ren.GetVolumes()
self.alpha_channel_function = vtk.vtkPiecewiseFunction()
self.alpha_channel_function.AddPoint(0, 0.0, 0.5, 0.0)
self.alpha_channel_function.AddPoint(255, 1, 0.5, 0.0)
self.color_function = vtk.vtkColorTransferFunction()
self.color_function.AddRGBPoint(0, 0, 0.0, 0.0, 0.5, 0.0)
self.color_function.AddRGBPoint(255, 1, 1, 1, 0.5, 0.0)
self.volume_property = vtk.vtkVolumeProperty()
self.volume_property.SetColor(self.color_function)
self.volume_property.SetScalarOpacity(self.alpha_channel_function)
self.data_importer = vtk.vtkImageImport()
if self.flagMesh :
self.volume_mapper = vtk.vtkPolyDataMapper()
else:
self.volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
self.volume = vtk.vtkVolume()
def import_numpy_array(self, np_array,minValue,maxValue):
self.minValue = minValue
self.maxValue = maxValue
np_array = self.image_float_to_int8(np_array, minValue,maxValue)
self.shape_data = np_array.shape
self.data_importer.CopyImportVoidPointer(np_array, np_array.nbytes)
self.data_importer.SetDataScalarTypeToUnsignedChar()
self.data_importer.SetNumberOfScalarComponents(1)
self.data_importer.SetDataExtent(0, self.shape_data[2] - 1, 0, self.shape_data[1] - 1, 0, self.shape_data[0] - 1)
self.data_importer.SetWholeExtent(0, self.shape_data[2] - 1, 0, self.shape_data[1] - 1, 0, self.shape_data[0] - 1)
def reset_alpha_channel(self):
self.alpha_channel_function.RemoveAllPoints()
def reset_color_channel(self):
self.color_function.RemoveAllPoints()
def set_color_channel(self, value, R, G, B, mid = 0.5, sharp = 0.0):
self.color_function.AddRGBPoint(value*255, R, G, B,mid, sharp)
def set_alpha_channel(self,value,alpha, mid = 0.5, sharp = 0.0):
self.alpha_channel_function.AddPoint(value*255, alpha,mid, sharp)
def set_volume_property(self, shade=True, ambient=0.1, diffuse=0.9, specular=0.2, specular_pw=10.0,
opacity_unit_dist=0.8919):
self.volume_property.SetColor(self.color_function)
self.volume_property.SetScalarOpacity(self.alpha_channel_function)
if shade:
self.volume_property.ShadeOn()
else:
self.volume_property.ShadeOff()
self.volume_property.SetAmbient(ambient)
self.volume_property.SetDiffuse(diffuse)
self.volume_property.SetSpecular(specular)
self.volume_property.SetSpecularPower(specular_pw)
self.volume_property.SetScalarOpacityUnitDistance(opacity_unit_dist)
def update_mapper(self, blend_mode='Composite'):
if not self.flagMesh:
if blend_mode == 'Composite':
self.volume_mapper.SetBlendModeToComposite()
elif blend_mode == 'MaxIntensity':
self.volume_mapper.SetBlendModeToMaximumIntensity()
self.volume_mapper.RemoveAllInputs()
if self.flagMesh:
self.volume_mapper.SetInputConnection(self.dmc.GetOutputPort())
else:
self.volume_mapper.SetInputConnection(self.data_importer.GetOutputPort())
self.volume_mapper.AutoAdjustSampleDistancesOn()
self.volume_mapper.IntermixIntersectingGeometryOn()
self.volume.SetMapper(self.volume_mapper)
self.volume.SetProperty(self.volume_property)
def add_PolyActor(self):
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.volume_mapper)
self.ren.AddActor(self.actor)
def add_volume_to_renderer(self):
self.ren.AddVolume(self.volume)
def update_renderer(self, background=[255.0, 255.0, 255.0], sizeW = [1600,1200]):
self.ren.SetBackground(1,1,1)
self.renWin.SetSize(sizeW[0],sizeW[1])
self.renWin.AddObserver("AbortCheckEvent", self.exitCheck)
def launch_render(self):
self.setLayout(self.v1)
self.iren.SetDesiredUpdateRate(25)
self.iren.Initialize()
self.renWin.Render()
self.iren.Start()
self.close_window()
del self.renWin, self.iren
def close_window(self):
self.renWin.Finalize()
self.iren.TerminateApp()
def take_screen_shot(self, file_name):
WindowToImageFilter = vtk.vtkWindowToImageFilter()
WindowToImageFilter.SetInput( self.renWin)
TIFFWriter = vtk.vtkTIFFWriter()
TIFFWriter.SetInputConnection(WindowToImageFilter.GetOutputPort())
self.renWin.SetSize(1600, 1200)
self.ren.Modified()
self.renWin.Modified()
self.renWin.Render()
TIFFWriter.SetFileName(file_name)
WindowToImageFilter.Modified()
WindowToImageFilter.Update()
TIFFWriter.Write()
def take_multi_rotation_screen_shot(self, path, angleRot):
WindowToImageFilter = vtk.vtkWindowToImageFilter()
WindowToImageFilter.SetInput(self.renWin)
TIFFWriter = vtk.vtkTIFFWriter()
TIFFWriter.SetInputConnection(WindowToImageFilter.GetOutputPort())
self.ren.GetActiveCamera().SetFocalPoint(self.shape_data[2]/2.0,self.shape_data[1]/2.0,1.3*self.shape_data[0])
self.ren.GetActiveCamera().Elevation(80)
self.ren.GetActiveCamera().Roll(180)
self.ren.GetActiveCamera().Zoom(0.7)
self.renderer.AddActor(self.actor)
for i in range(0,angleRot):
WindowToImageFilter.Modified()
WindowToImageFilter.Update()
TIFFWriter.SetFileName(path +'%4.4d'%i+'.tiff')
TIFFWriter.Write()
self.ren.GetActiveCamera().Azimuth(1)
self.ren.RemoveVolume(self.volume)
self.ren.RemoveActor(self.actor)
def add_arrow_field(self, arrow=[], shaft_reso=24, tip_reso=36):
if arrow != []:
for p in range(0,int(len(arrow[:, 0])),4):
arrow_source = vtk.vtkArrowSource()
arrow_source.SetShaftResolution(shaft_reso)
arrow_source.SetTipResolution(tip_reso)
start_point = [0 for i in range(3)]
start_point[0] = arrow[p, 2]
start_point[1] = arrow[p, 1]
start_point[2] = arrow[p, 0]
end_point = [0 for i in range(3)]
end_point[0] = arrow[p, 5]
end_point[1] = arrow[p, 4]
end_point[2] = arrow[p, 3]
normalized_x = [0 for i in range(3)]
normalized_y = [0 for i in range(3)]
normalized_z = [0 for i in range(3)]
normalized_x[0] = end_point[0] - start_point[0]
normalized_x[1] = end_point[1] - start_point[1]
normalized_x[2] = end_point[2] - start_point[2]
# The X axis is a vector from start to end
math = vtk.vtkMath()
length = math.Norm(normalized_x)
if length != 0:
math.Normalize(normalized_x)
# The Z axis is an arbitrary vector cross X
arbitrary = [0 for i in range(3)]
arbitrary[0] = 2048
arbitrary[1] = 2048
arbitrary[2] = 2048
math.Cross(normalized_x, arbitrary, normalized_z)
math.Normalize(normalized_z)
# The Y axis is Z cross X
math.Cross(normalized_z, normalized_x, normalized_y)
matrix = vtk.vtkMatrix4x4()
# Create the direction cosi1, 1, 1ne matrix
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalized_x[i])
matrix.SetElement(i, 1, normalized_y[i])
matrix.SetElement(i, 2, normalized_z[i])
# Apply the transforms
transform = vtk.vtkTransform()
transform.Translate(start_point)
transform.Concatenate(matrix)
transform.Scale(length, length, length)
# Transform the polydata
transformPD = vtk.vtkTransformPolyDataFilter()
transformPD.SetTransform(transform)
transformPD.SetInputConnection(arrow_source.GetOutputPort())
#Create a mapper and actor for the arrow
self.mapper = vtk.vtkPolyDataMapper()
self.actor = vtk.vtkActor()
arrow_source.SetTipLength(3.0/length)
arrow_source.SetTipRadius(1.0/length)
arrow_source.SetShaftRadius(0.5/length)
self.mapper.SetInputConnection(arrow_source.GetOutputPort())
self.actor.SetUserMatrix(transform.GetMatrix())
self.actor.GetProperty().SetColor(1,0,0)
self.actor.SetMapper(self.mapper)
self.ren.AddActor(self.actor)