使用 python 将 PNG 序列加载到 vtkImageData 以进行 3D 体积渲染

Question

I have a sequence of about 100 PNG files containing 512x512 pre-segmented CAT scan data. I want to use vtk on Python to create a 3D model using marching cubes algorithm. The part that I don't know how to do is to load the sequence of PNG files and convert them to a single vtk pixel data object suitable for sending to the vtkDiscreteMarchingCubes algorithm.

I also think that I need to convert the pixel values of the PNG data because right now the data is in the alpha channel, so this needs to be converted into scalar data with values of zero and 1.

Answer 1

use vtkPNGreader and load in individual slices and then populate a vtkImageData which you can define the dimensions as and for each z-slice or image fill the image data form the output of the reader into your vtkImageData.

Rough pseudocode - not checked for bugs :)

import vtk
from vtk.util import numpy_support

pngfiles = glob.glob('*.png')

png_reader = vtk.vtkPNGReader()
png_reader.SetFileName(pngfiles[0])
x,y = png_reader.GetOutput().GetDimensions()

data_3d = np.zeros([x,y,len(pngfiles)])

for i,p in enumerate(png):
    png_reader.SetFileName(pngfiles[0])
    png_reader.Update()
    img_data = png_reader.GetOutput()
    data_3D[:,:,i] = numpy_support.vtk_to_numpy(img_data)

#save your 3D numpy array out.
data_3Dvtk = numpy_support.numpy_to_vtk(data_3D)

Answer 2

Just in case anyone stumbles on here looking for another way to do this only using vtk, you can use vtkImageAppend class.

def ReadImages(files):
    reader = vtk.vtkPNGReader()
    image3D = vtk.vtkImageAppend()
    image3D.SetAppendAxis(2)
    
    for f in files:
        reader.SetFileName(f)
        reader.Update()
        t_img = vtk.vtkImageData()
        t_img.DeepCopy(reader.GetOutput())
        image3D.AddInputData(t_img)

    image3D.Update()

    return image3D.GetOutput()

for converting the data you can take a look at what the output of t_img.GetPointData().GetArray('PNGImage') gives and see if it is the expected value.