Installation and Usage

This is a work in progress addressing https://github.com/Radiomics/pyradiomics/issues/102

• To get the code:

  Clone the repository: git clone git://github.com/Radiomics/pyradiomics

• Install on your system:

  For mac/linux: cd pyradiomics; sudo python setup.py install

• If you don't have sudo/admin rights on your maching, you need to locally install numpy, SimpleITK, tqdm, PyWavelets

• Run the example, helloRadiomics: python bin/helloRadiomics.py

• Interactively:

  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, rlgl, glszm
import SimpleITK as sitk
import sys, os

Set up a data directory variable: `dataDir = '/path/to/data'

Use SimpleITK to read an image and mask:

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

Calculate some first order features:

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