Python/ExtractSlice.py

#!/usr/bin/env python
# =========================================================================
#
#  Copyright NumFOCUS
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0.txt
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
# =========================================================================
 
""" An example script using SimpleITK's ExtractImageFilter to extact a slice from a 3D image. """
 
import sys
import os
import SimpleITK as sitk
 
if len(sys.argv) != 4:
    print(f"Usage: {sys.argv[0]} inputImage sliceNumber outputImage")
    sys.exit(1)
 
zslice = int(sys.argv[2])
 
inputImage = sitk.ReadImage(str(sys.argv[1]))
 
size = list(inputImage.GetSize())
size[2] = 0
 
index = [0, 0, zslice]
 
Extractor = sitk.ExtractImageFilter()
Extractor.SetSize(size)
Extractor.SetIndex(index)
 
sitk.WriteImage(Extractor.Execute(inputImage), str(sys.argv[3]))
 
if "SITK_NOSHOW" not in os.environ:
    sitk.Show(Extractor.Execute(inputImage))