[PYTHON] Convert MetaImageIO (* .mha, * .mhd) to tiff stack

Use SimpleITK with python

The core part is as follows. If you specify tiff in the output, it will automatically become a stack file.

import SimpleITK as sitk

reader = sitk.ImageFileReader()
reader.SetImageIO("MetaImageIO")
reader.SetFileName(inputImageFileName)
image = reader.Execute();

writer = sitk.ImageFileWriter()
writer.SetImageIO("TIFFImageIO")
writer.SetFileName(outputImageFileName)
writer.Execute(image)

You can read and write other files by changing SetImageIO.

To make it easier to use in the terminal, I do the following:

mhd2tif

#!/usr/bin/env python3
import os,sys
import SimpleITK as sitk

if len(sys.argv)!=3 :
    print("usage: mhd2tif infile.mhd out.tif")
    exit()

inputImageFileName = sys.argv[1]
outputImageFileName = sys.argv[2]

if os.path.isfile(inputImageFileName)==False :
    print(inputImageFileName + ": not found.")
    exit()

reader = sitk.ImageFileReader()
reader.SetImageIO("MetaImageIO")
reader.SetFileName(inputImageFileName)
image = reader.Execute();

writer = sitk.ImageFileWriter()
writer.SetImageIO("TIFFImageIO")
writer.SetFileName(outputImageFileName)
writer.Execute(image)

reference

https://simpleitk.readthedocs.io/en/master/IO.html