Usage

Example

• Run the helloRadiomics example, using sample data provided in pyradiomics/data:
  • python bin/helloRadiomics.py

Interactive Use

• Add pyradiomics to the environment variable PYTHONPATH:

  • setenv PYTHONPATH /path/to/pyradiomics/radiomics

• Start the python interactive session:

  • python

• Import the necessary classes:

  from radiomics import firstorder, glcm, imageoperations, shape, glrlm, glszm
  import SimpleITK as sitk
  import sys, os
  

• Set up a data directory variable:

  dataDir = '/path/to/pyradiomics/data'
  

• You will find sample data files brain1_image.nrrd and brain1_label.nrrd in that directory.

• Use SimpleITK to read a the brain image and mask:

  imageName = str(dataDir + os.path.sep + 'brain1_image.nrrd')
  maskName = str(dataDir + os.path.sep + 'brain1_label.nrrd')
  image = sitk.ReadImage(imageName)
  mask = sitk.ReadImage(maskName)
  

• Calculate the first order features:

  firstOrderFeatures = firstorder.RadiomicsFirstOrder(image,mask)
  firstOrderFeatures.calculateFeatures()
  for (key,val) in firstOrderFeatures.featureValues.iteritems():
    print '  ',key,':',val
  

• See the radomics package for more features that you can calculate.