def testEstimateECQMMFMultimodalDeformationField2DMultiScale_synthetic():
##################parameters############
maxGTDisplacement=2
maxPyramidLevel=0
lambdaMeasureField=0.02
lambdaDisplacement=200
mu=0.001
maxOuterIter=20
maxInnerIter=50
tolerance=1e-5
displacementList=[]
#######################################3
#fname0='IBSR_01_to_02.nii.gz'
#fname1='data/t1/IBSR18/IBSR_02/IBSR_02_ana_strip.nii.gz'
fnameMoving='data/t2/t2_icbm_normal_1mm_pn0_rf0_peeled.nii.gz'
fnameFixed='data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz'
nib_moving = nib.load(fnameMoving)
nib_fixed = nib.load(fnameFixed)
moving=nib_moving.get_data().squeeze().astype(np.float64)
fixed=nib_fixed.get_data().squeeze().astype(np.float64)
sm=moving.shape
sf=fixed.shape
#---coronal---
moving=moving[:,sm[1]//2,:].copy()
fixed=fixed[:,sf[1]//2,:].copy()
moving=(moving-moving.min())/(moving.max()-moving.min())
fixed=(fixed-fixed.min())/(fixed.max()-fixed.min())
#----apply synthetic deformation field to fixed image
GT=rcommon.createDeformationField_type2(fixed.shape[0], fixed.shape[1], maxGTDisplacement)
fixed=rcommon.warpImage(fixed,GT)
maskMoving=moving>0
maskFixed=fixed>0
movingPyramid=[img for img in rcommon.pyramid_gaussian_2D(moving, maxPyramidLevel, maskMoving)]
fixedPyramid=[img for img in rcommon.pyramid_gaussian_2D(fixed, maxPyramidLevel, maskFixed)]
plt.figure()
plt.subplot(1,2,1)
plt.imshow(moving, cmap=plt.cm.gray)
plt.title('Moving')
plt.subplot(1,2,2)
plt.imshow(fixed, cmap=plt.cm.gray)
plt.title('Fixed')
rcommon.plotOverlaidPyramids(movingPyramid, fixedPyramid)
displacement=estimateECQMMFMultimodalDeformationField2DMultiScale(fixedPyramid, movingPyramid, lambdaMeasureField, lambdaDisplacement, mu, maxOuterIter, maxInnerIter, tolerance, 0,displacementList)
warpedPyramid=[rcommon.warpImage(movingPyramid[i], displacementList[i]) for i in range(maxPyramidLevel+1)]
rcommon.plotOverlaidPyramids(warpedPyramid, fixedPyramid)
rcommon.overlayImages(warpedPyramid[0], fixedPyramid[0])
rcommon.plotDeformationField(displacement)
displacement[...,0]*=(maskMoving + maskFixed)
displacement[...,1]*=(maskMoving + maskFixed)
nrm=np.sqrt(displacement[...,0]**2 + displacement[...,1]**2)
maxNorm=np.max(nrm)
rcommon.plotDeformationField(displacement)
residual=((displacement-GT))**2
meanDisplacementError=np.sqrt(residual.sum(2)*(maskMoving + maskFixed)).mean()
stdevDisplacementError=np.sqrt(residual.sum(2)*(maskMoving + maskFixed)).std()
print 'Max global displacement: ', maxNorm
print 'Mean displacement error: ', meanDisplacementError,'(',stdevDisplacementError,')'
def testEstimateMonomodalSyNField2DMultiScale(lambdaParam):
fname0 = 'IBSR_01_to_02.nii.gz'
fname1 = 'data/t1/IBSR18/IBSR_02/IBSR_02_ana_strip.nii.gz'
nib_moving = nib.load(fname0)
nib_fixed = nib.load(fname1)
moving = nib_moving.get_data().squeeze()
fixed = nib_fixed.get_data().squeeze()
moving = np.copy(moving, order='C')
fixed = np.copy(fixed, order='C')
sl = moving.shape
sr = fixed.shape
level = 5
#---sagital---
moving = moving[sl[0] // 2, :, :].copy()
fixed = fixed[sr[0] // 2, :, :].copy()
#---coronal---
#moving=moving[:,sl[1]//2,:].copy()
#fixed=fixed[:,sr[1]//2,:].copy()
#---axial---
#moving=moving[:,:,sl[2]//2].copy()
#fixed=fixed[:,:,sr[2]//2].copy()
maskMoving = moving > 0
maskFixed = fixed > 0
movingPyramid = [
img for img in rcommon.pyramid_gaussian_2D(moving, level, maskMoving)
]
fixedPyramid = [
img for img in rcommon.pyramid_gaussian_2D(fixed, level, maskFixed)
]
rcommon.plotOverlaidPyramids(movingPyramid, fixedPyramid)
displacementList = []
maxIter = 200
displacement = estimateMonomodalSyNField2DMultiScale(
movingPyramid, fixedPyramid, lambdaParam, maxIter, 0, displacementList)
warpPyramid = [
rcommon.warpImage(movingPyramid[i], displacementList[i])
for i in range(level + 1)
]
rcommon.plotOverlaidPyramids(warpPyramid, fixedPyramid)
rcommon.overlayImages(warpPyramid[0], fixedPyramid[0])
rcommon.plotDeformationField(displacement)
nrm = np.sqrt(displacement[..., 0]**2 + displacement[..., 1]**2)
maxNorm = np.max(nrm)
displacement[..., 0] *= (maskMoving + maskFixed)
displacement[..., 1] *= (maskMoving + maskFixed)
rcommon.plotDeformationField(displacement)
#nrm=np.sqrt(displacement[...,0]**2 + displacement[...,1]**2)
#plt.figure()
#plt.imshow(nrm)
print 'Max global displacement: ', maxNorm
def testEstimateMonomodalSyNField2DMultiScale(lambdaParam):
fname0='IBSR_01_to_02.nii.gz'
fname1='data/t1/IBSR18/IBSR_02/IBSR_02_ana_strip.nii.gz'
nib_moving = nib.load(fname0)
nib_fixed= nib.load(fname1)
moving=nib_moving.get_data().squeeze()
fixed=nib_fixed.get_data().squeeze()
moving=np.copy(moving, order='C')
fixed=np.copy(fixed, order='C')
sl=moving.shape
sr=fixed.shape
level=5
#---sagital---
moving=moving[sl[0]//2,:,:].copy()
fixed=fixed[sr[0]//2,:,:].copy()
#---coronal---
#moving=moving[:,sl[1]//2,:].copy()
#fixed=fixed[:,sr[1]//2,:].copy()
#---axial---
#moving=moving[:,:,sl[2]//2].copy()
#fixed=fixed[:,:,sr[2]//2].copy()
maskMoving=moving>0
maskFixed=fixed>0
movingPyramid=[img for img in rcommon.pyramid_gaussian_2D(moving, level, maskMoving)]
fixedPyramid=[img for img in rcommon.pyramid_gaussian_2D(fixed, level, maskFixed)]
rcommon.plotOverlaidPyramids(movingPyramid, fixedPyramid)
displacementList=[]
maxIter=200
displacement=estimateMonomodalSyNField2DMultiScale(movingPyramid, fixedPyramid, lambdaParam, maxIter, 0,displacementList)
warpPyramid=[rcommon.warpImage(movingPyramid[i], displacementList[i]) for i in range(level+1)]
rcommon.plotOverlaidPyramids(warpPyramid, fixedPyramid)
rcommon.overlayImages(warpPyramid[0], fixedPyramid[0])
rcommon.plotDeformationField(displacement)
nrm=np.sqrt(displacement[...,0]**2 + displacement[...,1]**2)
maxNorm=np.max(nrm)
displacement[...,0]*=(maskMoving + maskFixed)
displacement[...,1]*=(maskMoving + maskFixed)
rcommon.plotDeformationField(displacement)
#nrm=np.sqrt(displacement[...,0]**2 + displacement[...,1]**2)
#plt.figure()
#plt.imshow(nrm)
print 'Max global displacement: ', maxNorm
def testEstimateECQMMFMultimodalDeformationField2DMultiScale_synthetic():
##################parameters############
maxGTDisplacement = 2
maxPyramidLevel = 0
lambdaMeasureField = 0.02
lambdaDisplacement = 200
mu = 0.001
maxOuterIter = 20
maxInnerIter = 50
tolerance = 1e-5
displacementList = []
#######################################3
#fname0='IBSR_01_to_02.nii.gz'
#fname1='data/t1/IBSR18/IBSR_02/IBSR_02_ana_strip.nii.gz'
fnameMoving = 'data/t2/t2_icbm_normal_1mm_pn0_rf0_peeled.nii.gz'
fnameFixed = 'data/t1/t1_icbm_normal_1mm_pn0_rf0_peeled.nii.gz'
nib_moving = nib.load(fnameMoving)
nib_fixed = nib.load(fnameFixed)
moving = nib_moving.get_data().squeeze().astype(np.float64)
fixed = nib_fixed.get_data().squeeze().astype(np.float64)
sm = moving.shape
sf = fixed.shape
#---coronal---
moving = moving[:, sm[1] // 2, :].copy()
fixed = fixed[:, sf[1] // 2, :].copy()
moving = (moving - moving.min()) / (moving.max() - moving.min())
fixed = (fixed - fixed.min()) / (fixed.max() - fixed.min())
#----apply synthetic deformation field to fixed image
GT = rcommon.createDeformationField_type2(fixed.shape[0], fixed.shape[1],
maxGTDisplacement)
fixed = rcommon.warpImage(fixed, GT)
maskMoving = moving > 0
maskFixed = fixed > 0
movingPyramid = [
img for img in rcommon.pyramid_gaussian_2D(moving, maxPyramidLevel,
maskMoving)
]
fixedPyramid = [
img for img in rcommon.pyramid_gaussian_2D(fixed, maxPyramidLevel,
maskFixed)
]
plt.figure()
plt.subplot(1, 2, 1)
plt.imshow(moving, cmap=plt.cm.gray)
plt.title('Moving')
plt.subplot(1, 2, 2)
plt.imshow(fixed, cmap=plt.cm.gray)
plt.title('Fixed')
rcommon.plotOverlaidPyramids(movingPyramid, fixedPyramid)
displacement = estimateECQMMFMultimodalDeformationField2DMultiScale(
fixedPyramid, movingPyramid, lambdaMeasureField, lambdaDisplacement,
mu, maxOuterIter, maxInnerIter, tolerance, 0, displacementList)
warpedPyramid = [
rcommon.warpImage(movingPyramid[i], displacementList[i])
for i in range(maxPyramidLevel + 1)
]
rcommon.plotOverlaidPyramids(warpedPyramid, fixedPyramid)
rcommon.overlayImages(warpedPyramid[0], fixedPyramid[0])
rcommon.plotDeformationField(displacement)
displacement[..., 0] *= (maskMoving + maskFixed)
displacement[..., 1] *= (maskMoving + maskFixed)
nrm = np.sqrt(displacement[..., 0]**2 + displacement[..., 1]**2)
maxNorm = np.max(nrm)
rcommon.plotDeformationField(displacement)
residual = ((displacement - GT))**2
meanDisplacementError = np.sqrt(
residual.sum(2) * (maskMoving + maskFixed)).mean()
stdevDisplacementError = np.sqrt(
residual.sum(2) * (maskMoving + maskFixed)).std()
print 'Max global displacement: ', maxNorm
print 'Mean displacement error: ', meanDisplacementError, '(', stdevDisplacementError, ')'
