# Check opacity
if args.opacity > 1 or args.opacity < 0:
os.sys.exit('Opaicty must be between zeor and one. Given {o}. Exiting...'.format(o=args.opacity))
# Read both images
inputReader = vtk.vtkImageReader2Factory.CreateImageReader2(args.inputImage)
if inputReader is None:
if args.inputImage.lower().endswith('.nii'):
inputReader = vtk.vtkNIFTIImageReader()
elif args.inputImage.lower().endswith('.dcm'):
inputReader = vtk.vtkDICOMImageReader()
elif vtkboneImported and args.inputImage.lower().endswith('.aim'):
inputReader = vtkbone.vtkboneAIMReader()
inputReader.DataOnCellsOff()
elif vtkbonelabImported and args.inputImage.lower().endswith('.aim'):
inputReader = vtkbonelab.vtkbonelabAIMReader()
inputReader.DataOnCellsOff()
else:
os.sys.exit('Unable to find a reader for \"{fileName}\". Exiting...'.format(fileName=args.inputImage))
inputReader.SetFileName(args.inputImage)
print('Loading {}...'.format(args.inputImage))
inputReader.Update()
segReader = vtk.vtkImageReader2Factory.CreateImageReader2(args.inputSegmentation)
if segReader is None:
if args.inputSegmentation.lower().endswith('.nii'):
segReader = vtk.vtkNIFTIImageReader()
elif args.inputSegmentation.lower().endswith('.dcm'):
segReader = vtk.vtkDICOMImageReader()
elif vtkboneImported and args.inputSegmentation.lower().endswith('.aim'):
segReader = vtkbone.vtkboneAIMReader()
os.sys.exit(
'Number of threads must be one or greater. Given {n}. Exiting...'.
format(n=args.nThreads))
# Read in inputs
reader1 = vtk.vtkImageReader2Factory.CreateImageReader2(args.inputImage1)
if reader1 is None:
if args.inputImage1.lower().endswith('.nii'):
reader1 = vtk.vtkNIFTIImageReader()
elif args.inputImage1.lower().endswith('.dcm'):
reader1 = vtk.vtkDICOMImageReader()
elif vtkboneImported and args.inputImage1.lower().endswith('.aim'):
reader1 = vtkbone.vtkboneAIMReader()
reader1.DataOnCellsOff()
elif vtkbonelabImported and args.inputImage1.lower().endswith('.aim'):
reader1 = vtkbonelab.vtkbonelabAIMReader()
reader1.DataOnCellsOff()
else:
os.sys.exit(
'Unable to find a reader for \"{fileName}\". Exiting...'.format(
fileName=args.inputImage1))
reader1.SetFileName(args.inputImage1)
print('Loading {}...'.format(args.inputImage1))
reader1.Update()
reader2 = vtk.vtkImageReader2Factory.CreateImageReader2(args.inputImage1)
if reader2 is None:
if args.inputImage2.lower().endswith('.nii'):
reader2 = vtk.vtkNIFTIImageReader()
elif args.inputImage2.lower().endswith('.dcm'):
reader2 = vtk.vtkDICOMImageReader()
# Imports
import argparse
import vtk
import re
import os
try:
import vtkbone
reader = vtkbone.vtkboneAIMReader()
except ImportError:
try:
import vtkn88
reader = vtkn88.vtkn88AIMReader()
except ImportError:
try:
import vtkbonelab
reader = vtkbonelab.vtkbonelabAIMReader()
except ImportError:
os.sys.exit(
'Unable to import vtkbone, vtkn88, or vtkbonelab. Exiting...')
# Argument parser
parser = argparse.ArgumentParser(
description='Subget medical data',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('inputImage', help='The input AIM (*.aim) image)')
parser.add_argument('outputImage', help='The output NIfTI (*.nii) image)')
parser.add_argument('-f',
'--force',
action='store_true',
help='Set to overwrite output without asking')
args = parser.parse_args()