def compute():
outputDir='/Users/younes/Development/Results/atlasSections'
if __name__ == "__main__":
loggingUtils.setup_default_logging(outputDir, fileName='info')
else:
loggingUtils.setup_default_logging()
## Build Two colliding ellipses
fv01 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas02_curve01.txt')
fv02 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas02_curve02.txt')
fv03 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas02_curve03.txt')
fv11 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas08_curve01.txt')
fv12 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas08_curve02.txt')
fv13 = Curve(filename='/cis/home/younes/MorphingData/MostofskyCurves/atlas08_curve03.txt')
## Object kernel
K1 = Kernel(name='laplacian', sigma = 10.0)
## Background kernel
K2 = Kernel(name='laplacian', sigma = 1.0)
sm = CurveMatchingParam(timeStep=0.1, KparDiff=K1, KparDiffOut=K2, sigmaDist=2., sigmaError=.1, errorType='measure')
f = (CurveMatching(Template=(fv01,fv02,fv03), Target=(fv11,fv12,fv13), outputDir=outputDir,
param=sm, mu=1.,regWeightOut=1., testGradient=False,
typeConstraint='stitched', maxIter_cg=10000, maxIter_al=100, affine='none', rotWeight=10))
f.optimizeMatching()
return f
def compute():
outputDir = '/Users/younes/Development/Results/threeBallsSplineAndMomentum'
#outputDir = '/cis/home/younes/MorphingData/twoBallsStitched'
#outputDir = '/Users/younes/Development/Results/tight_stitched_rigid2_10'
if __name__ == "__main__":
loggingUtils.setup_default_logging(outputDir, fileName='info')
else:
loggingUtils.setup_default_logging()
Tg = 2000
npt = 100.0
## Build Two colliding ellipses
[x,y,z] = np.mgrid[0:2*npt, 0:2*npt, 0:2*npt]/npt
y = y-1
z = z-1
x = x-1
s2 = np.sqrt(2)
I1 = .06 - ((x)**2 + 0.5*((y)**2) + (z)**2)
fv1 = Surface() ;
fv1.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
I1 = .08 - ((x+.05)**2 + 0.3*(y-0.05)**2 + (z)**2)
fv2 = Surface() ;
fv2.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
I1 = .06 - (1.25*(x)**2 + 0.5*(y-0.25)**2 + 0.75*(z)**2)
fv3 = Surface() ;
fv3.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
## Object kernel
K1 = Kernel(name='laplacian', sigma = 50.0, order=4)
sm = surfaceMatching.SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, sigmaDist=50., sigmaError=10., errorType='measure')
f = (match.SurfaceMatching(Template=fv1, Targets=(fv2,fv3), outputDir=outputDir, param=sm, typeRegression='both',
testGradient=False, maxIter=1000))
#, affine='none', rotWeight=0.1))
f.optimizeMatching()
return f
def compute():
#outputDir = '/Users/younes/Development/Results/biocardTS/spline'
outputDir = '/Users/younes/Development/Results/biocardTS/geodesic'
#outputDir = '/cis/home/younes/MorphingData/twoBallsStitched'
#outputDir = '/Users/younes/Development/Results/tight_stitched_rigid2_10'
if __name__ == "__main__":
loggingUtils.setup_default_logging(outputDir, fileName='info')
else:
loggingUtils.setup_default_logging()
rdir = '/cis/project/biocard/data/2mm_complete_set_surface_mapping_10212012/hippocampus/6_mappings_baseline_template_all/0_template_to_all/' ;
sub = '2840698'
#sub = '2729611'
if sub == '2840698':
fv1 = surfaces.Surface(filename=rdir+'2840698_2_4_hippo_L_reg.byu_10_6.5_2.5.byu')
fv2 = surfaces.Surface(filename=rdir+'2840698_3_4_hippo_L_reg.byu_10_6.5_2.5.byu')
fv3 = surfaces.Surface(filename=rdir+'2840698_4_8_hippo_L_reg.byu_10_6.5_2.5.byu')
fv4 = surfaces.Surface(filename=rdir+'2840698_5_6_hippo_L_reg.byu_10_6.5_2.5.byu')
if sub == '2729611':
fv1 = surfaces.Surface(filename=rdir+sub+'_1_4_hippo_L_reg.byu_10_6.5_2.5.byu')
fv2 = surfaces.Surface(filename=rdir+sub+'_2_4_hippo_L_reg.byu_10_6.5_2.5.byu')
fv3 = surfaces.Surface(filename=rdir+sub+'_3_7_hippo_L_reg.byu_10_6.5_2.5.byu')
fv4 = surfaces.Surface(filename=rdir+sub+'_4_6_hippo_L_reg.byu_10_6.5_2.5.byu')
## Object kernel
K1 = Kernel(name='laplacian', sigma = 6.5, order=4)
sm = surfaceMatching.SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, sigmaDist=2.5, sigmaError=1., errorType='varifold')
f = (match.SurfaceMatching(Template=fv1, Targets=(fv2,fv3,fv4), outputDir=outputDir, param=sm,
typeRegression='geodesic',
affine='euclidean', testGradient=False, affineWeight=.1, maxIter=1000, controlWeight=1.))
#, affine='none', rotWeight=0.1))
f.optimizeMatching()
return f
def main():
loggingUtils.setup_default_logging()
parser = argparse.ArgumentParser(description='runs surface matching registration over directories (relative to the template)')
parser.add_argument('template', metavar='template', type = str, help='template')
parser.add_argument('target', metavar='target', type = str, help='target')
parser.add_argument('--typeKernel', metavar='typeKernel', type=str, dest='typeKernel', default = 'gauss', help='kernel type')
parser.add_argument('--sigmaKernel', metavar='sigmaKernel', type=float, dest='sigmaKernel', default = 6.5, help='kernel width')
parser.add_argument('--sigmaDist', metavar='sigmaDist', type=float, dest='sigmaDist', default = 2.5, help='kernel width (error term); (default = 2.5)')
parser.add_argument('--sigmaError', metavar='sigmaError', type=float, dest='sigmaError', default = 1.0, help='std error; (default = 1.0)')
parser.add_argument('--typeError', metavar='typeError', type=str, dest='typeError', default = 'varifold', help='type error term (default: varifold)')
parser.add_argument('--dirOut', metavar = 'dirOut', type = str, dest = 'dirOut', default = '', help='Output directory')
parser.add_argument('--tmpOut', metavar = 'tmpOut', type = str, dest = 'tmpOut', default = '', help='info files directory')
parser.add_argument('--rigid', action = 'store_true', dest = 'rigid', default = False, help='Perform Rigid Registration First')
parser.add_argument('--logFile', metavar = 'logFile', type = str, dest = 'logFile', default = 'info.txt', help='Output log file')
parser.add_argument('--stdout', action = 'store_true', dest = 'stdOutput', default = False, help='To also print on standard output')
parser.add_argument('--scaleFactor', metavar='scaleFactor', type=float, dest='scaleFactor',
default = 1, help='scale factor for all surfaces')
parser.add_argument('--atrophy', action = 'store_true', dest = 'atrophy', default = False, help='force atrophy')
parser.add_argument('--symmetric', action = 'store_true', dest = 'symmetric', default = False, help='Use error term on both template and target')
args = parser.parse_args()
if args.dirOut == '':
args.dirOut = '.'
if args.tmpOut == '':
args.tmpOut = args.dirOut + '/tmp'
if not os.path.exists(args.dirOut):
os.makedirs(args.dirOut)
if not os.path.exists(args.tmpOut):
os.makedirs(args.tmpOut)
loggingUtils.setup_default_logging(fileName=args.tmpOut+'/'+args.logFile, stdOutput = args.stdOutput)
if args.atrophy:
import surfaceMatchingAtrophy as smt
else:
import surfaceMatching as smt
tmpl = surfaces.Surface(filename=args.template)
tmpl.vertices *= args.scaleFactor
K1 = Kernel(name=args.typeKernel, sigma = args.sigmaKernel)
sm = smt.SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, sigmaDist=args.sigmaDist, sigmaError=args.sigmaError, errorType=args.typeError)
fv = surfaces.Surface(filename=args.target)
fv.vertices *= args.scaleFactor
#print fv.vertices
if args.rigid:
R0, T0 = rigidRegistration(surfaces = (fv.vertices, tmpl.vertices), verb=False, temperature=10., annealing=True)
fv.updateVertices(np.dot(fv.vertices, R0.T) + T0)
#print fv.vertices
if args.atrophy:
f = smt.SurfaceMatching(Template=tmpl, Target=fv, outputDir=args.tmpOut,param=sm, testGradient=False, mu = 0.001, symmetric=args.symmetric,
maxIter_cg=1000, affine= 'euclidean', rotWeight=.01, transWeight = .01, scaleWeight=10., affineWeight=100.)
else:
f = smt.SurfaceMatching(Template=tmpl, Target=fv, outputDir=args.tmpOut,param=sm, testGradient=False, symmetric=args.symmetric,
maxIter=1000, affine= 'euclidean', rotWeight=.01, transWeight = .01, scaleWeight=10., affineWeight=100.)
f.optimizeMatching()
u = path.split(args.target)
[nm,ext] = path.splitext(u[1])
f.fvDef.savebyu(args.dirOut+'/'+nm+'Def.byu')
def computeMatching(self):
(rg,N,T) = self.getSimData()
for it in range(500):
self.optimizeN()
conjugateGradient.cg(self, True, \
maxIter = self.nonlinear_cg_max_iter, \
TestGradient=True, epsInit=self.cg_init_eps)
if (it % self.write_iter == 0):
self.writeData("iter%d" % (it))
return self
if __name__ == "__main__":
# set permanent options
output_directory_base = metamorphosisConfig.compute_output_dir
#output_directory_base = "./"
# set options from command line
parser = optparse.OptionParser()
parser.add_option("-o", "--output_dir", dest="output_dir")
parser.add_option("-c", "--config_name", dest="config_name")
(options, args) = parser.parse_args()
output_dir = output_directory_base + options.output_dir
# remove any old results in the output directory
if os.access(output_dir, os.F_OK):
shutil.rmtree(output_dir)
os.mkdir(output_dir)
loggingUtils.setup_default_logging(output_dir, metamorphosisConfig)
logging.info(options)
sim = Metamorphosis(output_dir, options.config_name)
sim.computeMatching()
sim.writeData("final")
import imageTimeSeries
import imageTimeSeriesConfig
import optparse
import os
import shutil
import logging
import loggingUtils
output_directory_base = imageTimeSeriesConfig.compute_output_dir
# set options from command line
parser = optparse.OptionParser()
parser.add_option("-o", "--output_dir", dest="output_dir")
parser.add_option("-c", "--config_name", dest="config_name")
parser.add_option("-f", "--file_base", dest="fbase")
(options, args) = parser.parse_args()
output_dir = output_directory_base + options.output_dir
# remove any old results in the output directory
if os.access(output_dir, os.F_OK):
shutil.rmtree(output_dir)
os.mkdir(output_dir)
loggingUtils.setup_default_logging(output_dir, imageTimeSeriesConfig)
logging.info(options)
its = imageTimeSeries.ImageTimeSeries(output_dir, options.config_name)
its.loadData(options.fbase)
logging.info("Begin computing maps.")
its.computeMaps()
logging.info("Done.")
def compute():
outputDir = '/Users/younes/Development/Results/twoBallsStitched2'
#outputDir = '/cis/home/younes/MorphingData/twoBallsStitched'
#outputDir = '/Users/younes/Development/Results/tight_stitched_rigid2_10'
if __name__ == "__main__":
loggingUtils.setup_default_logging(outputDir, fileName='info')
else:
loggingUtils.setup_default_logging()
if False:
Tg = 2000
npt = 100.0
## Build Two colliding ellipses
[x,y,z] = np.mgrid[0:2*npt, 0:2*npt, 0:2*npt]/npt
y = y-1
z = z-1
x = x-1
s2 = np.sqrt(2)
I1 = .06 - ((x+.2)**2 + 0.5*(y-0.25)**2 + (z)**2)
fv1 = Surface() ;
fv1.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
I1 = .06 - ((x-.2)**2 + 0.5*(y+0.25)**2 + (z)**2)
fv2 = Surface() ;
fv2.Isosurface(I1, value=0, target=Tg, scales=[1, 1, 1])
u = (z + y)/s2
v = (z - y)/s2
I1 = .095 - ((x+.25)**2 + (v)**2 + 0.5*(u+.25)**2)
fv3 = Surface() ;
fv3.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
u = (z + y)/s2
v = (z - y)/s2
I1 = .095 - ((x-.25)**2 + (v)**2 + 0.5*(u-.25)**2)
fv4 = Surface() ;
fv4.Isosurface(I1, value=0, target=Tg, scales=[1, 1, 1])
else:
fv1 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere1.obj')
fv2 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere2.obj')
fv3 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere1b.obj')
fv4 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere2b.obj')
fv1.vertices *= 100 ;
fv2.vertices *= 100 ;
fv3.vertices *= 100 ;
fv4.vertices *= 100 ;
## Object kernel
K1 = Kernel(name='laplacian', sigma = 50.0, order=4)
## Background kernel
K2 = Kernel(name='laplacian', sigma = 10.0, order=2)
sm = SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, KparDiffOut=K2, sigmaDist=50., sigmaError=10., errorType='varifold')
f = (SurfaceMatching(Template=(fv1,fv2), Target=(fv3,fv4), outputDir=outputDir, param=sm, mu=.1,regWeightOut=1.,
testGradient=False, typeConstraint='stitched', maxIter_cg=1000, maxIter_al=100, affine='none', rotWeight=0.1))
f.optimizeMatching()
return f
letter_match = None
if options.config_name == "letter":
digitId = 11
templateId = 18
output_dir_old = output_dir
for targetId in range(39):
letter_match = (digitId,templateId,targetId)
output_dir = "%s_%d_%d_%d" % (output_dir_old, letter_match[0],\
letter_match[1], letter_match[2])
# remove any old results in the output directory
if os.access(output_dir, os.F_OK):
shutil.rmtree(output_dir)
os.mkdir(output_dir)
if targetId == 0:
loggingUtils.setup_default_logging(output_dir, smoothImageConfig)
logging.info(options)
sim = SmoothImageMeta(output_dir, options.config_name, letter_match)
sim.computeMatching()
sim.writeData("final")
else:
# remove any old results in the output directory
if os.access(output_dir, os.F_OK):
shutil.rmtree(output_dir)
os.mkdir(output_dir)
loggingUtils.setup_default_logging(output_dir, smoothImageConfig)
logging.info(options)
sim = SmoothImageMeta(output_dir, options.config_name, None)
sim.computeMatching()
sim.writeData("final")
def compute(args=None, noArgs=True):
if noArgs:
outputDir = '/Users/younes/Development/Results/multiShapes'
#outputDir = '/cis/home/younes/MorphingData/twoBallsStitched'
#outputDir = '/Users/younes/Development/Results/tight_stitched_rigid2_10'
loggingUtils.setup_default_logging()
if False:
Tg = 2000
npt = 100.0
## Build Two colliding ellipses
[x,y,z] = np.mgrid[0:2*npt, 0:2*npt, 0:2*npt]/npt
y = y-1
z = z-1
x = x-1
s2 = np.sqrt(2)
I1 = .06 - ((x+.2)**2 + 0.5*(y-0.25)**2 + (z)**2)
fv1 = Surface() ;
fv1.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
I1 = .06 - ((x-.2)**2 + 0.5*(y+0.25)**2 + (z)**2)
fv2 = Surface() ;
fv2.Isosurface(I1, value=0, target=Tg, scales=[1, 1, 1])
u = (z + y)/s2
v = (z - y)/s2
I1 = .095 - ((x+.25)**2 + (v)**2 + 0.5*(u+.25)**2)
fv3 = Surface() ;
fv3.Isosurface(I1, value = 0, target=Tg, scales=[1, 1, 1])
u = (z + y)/s2
v = (z - y)/s2
I1 = .095 - ((x-.25)**2 + (v)**2 + 0.5*(u-.25)**2)
fv4 = Surface() ;
fv4.Isosurface(I1, value=0, target=Tg, scales=[1, 1, 1])
else:
fv1 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere1.obj')
fv2 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere2.obj')
fv3 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere1b.obj')
fv4 = Surface(filename='/Users/younes/Development/Data/Surfaces/fshpere2b.obj')
fv1.vertices *= 100
fv2.vertices *= 100
fv3.vertices *= 100
fv4.vertices *= 100
fTmpl = (fv1, fv2)
fTarg = (fv3, fv4)
## Object kernel
K1 = Kernel(name='laplacian', sigma = 50.0, order=4)
## Background kernel
K2 = Kernel(name='laplacian', sigma = 10.0, order=2)
typeConstraint = 'stitched'
sm = SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, KparDiffOut=K2,
sigmaDist=50., sigmaError=10., errorType='varifold')
mu = 0.1 ;
else:
fTmpl = []
for name in args.template:
fTmpl.append(Surface(filename=name))
for f in fTmpl:
f.vertices *= args.scaleFactor
fTarg = []
for name in args.target:
fTarg.append(Surface(filename=name))
for f in fTarg:
f.vertices *= args.scaleFactor
## Object kernel
K1 = Kernel(name='laplacian', sigma = args.sigmaKernelIn, order=4)
## Background kernel
K2 = Kernel(name='laplacian', sigma = args.sigmaKernelOut, order=2)
sm = SurfaceMatchingParam(timeStep=0.1, KparDiff=K1, KparDiffOut=K2,
sigmaDist=args.sigmaDist, sigmaError=args.sigmaError, errorType=args.typeError)
outputDir = args.dirOut
loggingUtils.setup_default_logging(fileName=outputDir+args.logFile, stdOutput = args.stdOutput)
if args.sliding:
typeConstraint = 'slidingV2'
else:
typeConstraint = 'stitched'
mu = args.mu
f = (SurfaceMatching(Template=fTmpl, Target=fTarg, outputDir=outputDir, param=sm, mu=mu,regWeightOut=1.,
testGradient=False, typeConstraint=typeConstraint, maxIter_cg=1000, maxIter_al=100, affine='none', rotWeight=0.1))
f.optimizeMatching()
return f