import os
import glob
import SimpleITK as sitk
import numpy as np
import vtk
from vtkmodules.util import numpy_support
import cv2
slice_image_folder = R'path_to_imgs'
mask_image_folder = R'path_to_masks'
slice_image_files = sorted(glob.glob(os.path.join(slice_image_folder, '*.jpg')))
mask_image_files = sorted(glob.glob(os.path.join(mask_image_folder, '*.png')))
def read_images(slice_files, mask_files):
slices = [cv2.imread(file, cv2.IMREAD_GRAYSCALE) for file in slice_files]
masks = [cv2.imread(file, cv2.IMREAD_GRAYSCALE) for file in mask_files]
if len(slices) != len(masks):
raise ValueError("Number of slice images and mask images must be the same.")
slices_array = np.stack(slices, axis=2)
pre_mask = []
for m in masks:
m[m == 50] = 0
_, binary_mask = cv2.threshold(m, 1, 255, cv2.THRESH_BINARY)
pre_mask.append(binary_mask)
masks_array = np.stack(pre_mask, axis=2)
return slices_array, masks_array
def numpy_to_sitk(image_array):
sitk_image = sitk.GetImageFromArray(image_array)
return sitk_image
def plot_3d(image_array, mask_array):
try:
vtk_image = vtk.vtkImageData()
vtk_image.SetDimensions(image_array.shape)
vtk_image.SetSpacing((1.0, 1.0, 1.0))
flat_image_array = image_array.ravel(order='F')
vtk_image_array = numpy_support.numpy_to_vtk(num_array=flat_image_array, deep=True, array_type=vtk.VTK_FLOAT)
vtk_image.GetPointData().SetScalars(vtk_image_array)
flat_mask_array = mask_array.ravel(order='F')
vtk_mask_array = numpy_support.numpy_to_vtk(num_array=flat_mask_array, deep=True, array_type=vtk.VTK_FLOAT)
vtk_mask_image = vtk.vtkImageData()
vtk_mask_image.SetDimensions(mask_array.shape)
vtk_mask_image.SetSpacing((1.0, 1.0, 1.0))
vtk_mask_image.GetPointData().SetScalars(vtk_mask_array)
colorFunc = vtk.vtkColorTransferFunction()
colorFunc.AddRGBPoint(0, 0.0, 0.0, 0.0)
colorFunc.AddRGBPoint(255, 1.0, 1.0, 1.0)
opacityFunc = vtk.vtkPiecewiseFunction()
opacityFunc.AddPoint(0, 0.0)
opacityFunc.AddPoint(255, 1.0)
renderer = vtk.vtkRenderer()
volumeMapper = vtk.vtkSmartVolumeMapper()
volumeMapper.SetInputData(vtk_image)
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorFunc)
volumeProperty.SetScalarOpacity(opacityFunc)
volumeProperty.ShadeOn()
volumeProperty.SetInterpolationTypeToLinear()
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
renderer.AddVolume(volume)
maskMapper = vtk.vtkSmartVolumeMapper()
maskMapper.SetInputData(vtk_mask_image)
maskOpacityFunc = vtk.vtkPiecewiseFunction()
maskOpacityFunc.AddPoint(0, 0.0)
maskOpacityFunc.AddPoint(1, 1.0)
maskColorFunc = vtk.vtkColorTransferFunction()
maskColorFunc.AddRGBPoint(0, 0.0, 0.0, 0.0)
maskColorFunc.AddRGBPoint(1, 1.0, 0.0, 0.0)
maskProperty = vtk.vtkVolumeProperty()
maskProperty.SetColor(maskColorFunc)
maskProperty.SetScalarOpacity(maskOpacityFunc)
maskProperty.ShadeOn()
maskProperty.SetInterpolationTypeToLinear()
maskVolume = vtk.vtkVolume()
maskVolume.SetMapper(maskMapper)
maskVolume.SetProperty(maskProperty)
renderer.AddVolume(maskVolume)
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindow.Render()
renderWindowInteractor.Start()
except Exception as e:
print(f"An error occurred: {e}")
def main():
try:
slices_array, masks_array = read_images(slice_image_files, mask_image_files)
plot_3d(slices_array, masks_array)
except Exception as e:
print(f"An error occurred in main function: {e}")
if __name__ == '__main__':
main()
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