DemonsRegistration2/DemonsRegistration2.py

#!/usr/bin/env python
#=========================================================================
#
#  Copyright Insight Software Consortium
#
#  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.
#
#=========================================================================

from __future__ import print_function

import SimpleITK as sitk
import sys
import os


def command_iteration(filter) :
    print("{0:3} = {1:10.5f}".format(filter.GetElapsedIterations(),
                                    filter.GetMetric()))

if len ( sys.argv ) < 4:
    print( "Usage: {0} <fixedImageFilter> <movingImageFile> [initialTransformFile] <outputTransformFile>".format(sys.argv[0]))
    sys.exit ( 1 )


fixed = sitk.ReadImage(sys.argv[1])

moving = sitk.ReadImage(sys.argv[2])

matcher = sitk.HistogramMatchingImageFilter()
if ( fixed.GetPixelID() in ( sitk.sitkUInt8, sitk.sitkInt8 ) ):
    matcher.SetNumberOfHistogramLevels(128)
else:
    matcher.SetNumberOfHistogramLevels(1024)
matcher.SetNumberOfMatchPoints(7)
matcher.ThresholdAtMeanIntensityOn()
moving = matcher.Execute(moving,fixed)

# The fast symmetric forces Demons Registration Filter
# Note there is a whole family of Demons Registration algorithms included in SimpleITK
demons = sitk.FastSymmetricForcesDemonsRegistrationFilter()
demons.SetNumberOfIterations(200)
# Standard deviation for Gaussian smoothing of displacement field
demons.SetStandardDeviations(1.0)

demons.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration(demons) )

if len( sys.argv ) > 4:
    initialTransform = sitk.ReadTransform(sys.argv[3])
    sys.argv[-1] = sys.argv.pop()

    toDisplacementFilter = sitk.TransformToDisplacementFieldFilter()
    toDisplacementFilter.SetReferenceImage(fixed)

    displacementField = toDisplacementFilter.Execute(initialTransform)

    displacementField = demons.Execute(fixed, moving, displacementField)

else:

    displacementField = demons.Execute(fixed, moving)


print("-------")
print("Number Of Iterations: {0}".format(demons.GetElapsedIterations()))
print(" RMS: {0}".format(demons.GetRMSChange()))

outTx = sitk.DisplacementFieldTransform(displacementField)

sitk.WriteTransform(outTx, sys.argv[3])

if (not "SITK_NOSHOW" in os.environ):

    resampler = sitk.ResampleImageFilter()
    resampler.SetReferenceImage(fixed);
    resampler.SetInterpolator(sitk.sitkLinear)
    resampler.SetDefaultPixelValue(100)
    resampler.SetTransform(outTx)

    out = resampler.Execute(moving)
    simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
    simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
    cimg = sitk.Compose(simg1, simg2, simg1//2.+simg2//2.)
    sitk.Show( cimg, "DeformableRegistration1 Composition" )