SimpleITK  
Python/BoarderSegmentation.py
1#!/usr/bin/env python
2# =========================================================================
3#
4# Copyright NumFOCUS
5#
6# Licensed under the Apache License, Version 2.0 (the "License");
7# you may not use this file except in compliance with the License.
8# You may obtain a copy of the License at
9#
10# http://www.apache.org/licenses/LICENSE-2.0.txt
11#
12# Unless required by applicable law or agreed to in writing, software
13# distributed under the License is distributed on an "AS IS" BASIS,
14# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15# See the License for the specific language governing permissions and
16# limitations under the License.
17#
18# =========================================================================
19
20""" An example script demonstrating boarder segmentation in SimpleITK. """
21
22import sys
23import os
24import SimpleITK as sitk
25
26# verify that we have the correct number of arguments
27if len(sys.argv) != 5:
28 sys.stderr.write("Usage: {sys.argv[0]} inputFile outputFile replaceValue upperThreshold\n")
29 sys.exit(1)
30
31# copy the arguments in to variables
32inputFileName = sys.argv[1]
33outputFileName = sys.argv[2]
34replaceValue = int(sys.argv[3])
35upperThreshold = float(sys.argv[4])
36
37# Read the file into an sitkImage
38image = sitk.ReadImage(inputFileName)
39
40# Threshold the value [0,2), results in values inside the range 1, 0 otherwise
41boundary = sitk.BinaryThreshold(image, 0, upperThreshold, 1, 0)
42
43boundary = sitk.BinaryMorphologicalClosing(boundary, [1] * image.GetDimension())
44
45# Remove any label pixel not connected to the boarder
46boundary = sitk.BinaryGrindPeak(boundary)
47
48boundary = sitk.Cast(boundary, image.GetPixelID())
49
50# Multiply, the input image by not the boarder.
51# This will multiply the image by 0 or 1, where 0 is the
52# boarder. Making the board 0
53image = image * ~boundary
54
55# add the replace value to the pixel on the board
56image = image + (boundary * replaceValue)
57
58if "SITK_NOSHOW" not in os.environ:
59 sitk.Show(image, "Boarder Segmentation")
Image BinaryMorphologicalClosing(const Image &image1, std::vector< unsigned int > kernelRadius=std::vector< uint32_t >(3, 1), KernelEnum kernelType=itk::simple::sitkBall, double foregroundValue=1.0, bool safeBorder=true)
binary morphological closing of an image.
SITKIO_EXPORT Image ReadImage(const PathType &filename, PixelIDValueEnum outputPixelType=sitkUnknown, const std::string &imageIO="")
ReadImage is a procedural interface to the ImageFileReader class which is convenient for most image r...
Image BinaryGrindPeak(const Image &image1, bool fullyConnected=false, double foregroundValue=1.0, double backgroundValue=0)
Remove the objects not connected to the boundary of the image.
void SITKIO_EXPORT Show(const Image &image, const std::string &title="", const bool debugOn=ProcessObject::GetGlobalDefaultDebug())
Image BinaryThreshold(Image &&image1, double lowerThreshold=0.0, double upperThreshold=255.0, uint8_t insideValue=1u, uint8_t outsideValue=0u)
Binarize an input image by thresholding.
Image Cast(const Image &image, PixelIDValueEnum pixelID)