import PyCA.Common as common
import PyCA.Display as display
# vector momentum modules
from Libraries import CAvmCommon
# others
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
import mpi4py
StudySpec = {
'numSubjects':
Config.Param(default=4, required=True,
comment="Total number of subjects."),
'subjectIds':
Config.Param(
default=['sid1', 'sid2', 'sid3', 'sid4'],
required=True,
comment=
"List of subject ids. This should be unique names for each individuals"
),
'subjectImages':
Config.Param(default=[
'subject1_I.mhd', 'subject2_I.mhd', 'subject3_I.mhd', 'subject4_I.mhd'
],
required=True,
comment="List of subject image files"),
'subjectWeights':
Config.Param(default=[1.0, 1.0, 1.0, 1.0],
from Libraries import CAvmCommon
# others
import numpy as np
import matplotlib.pyplot as plt
import os, errno
import logging
import copy
import math
import time
StudySpec = {
'I0':
Config.Param(default='subject1.mhd',
required=True,
comment="Initial (moving) image file"),
'I1':
Config.Param(default='subject2.mhd',
required=True,
comment="Target (fixed) image file")
}
MatchingConfigSpec = {
'compute': Compute.ComputeConfigSpec,
'vectormomentum': VMConfig.VMConfigSpec,
'study': StudySpec,
'optim': Optim.OptimConfigSpec,
'io': {
'plotEvery':
Config.Param(default=10, comment="Update plots every N iterations"),
from Libraries import CAvmHGMCommon
# HGM application module
from Applications import CAvmHGM
# others
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
#import mpi4py
StudySpec = {
'I':
Config.Param(default='I.mhd',
required=True,
comment="Initial (moving) image file, I to be matched to J"),
'm':
Config.Param(default='m.mhd',
required=True,
comment="Initial momenta, m at I to be matched to n"),
'J':
Config.Param(default='J.mhd',
required=True,
comment="Target (fixed) image file, J"),
'n':
Config.Param(default='n.mhd',
required=True,
comment="Initial momenta, n at the target J")
}
# HGM application module
from Applications import CAvmHGM
# others
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
import csv
#import mpi4py
StudySpec = {
'I':
Config.Param(default='I.mhd',
required=True,
comment="Initial (moving) image file, I to be matched to J"),
'm':
Config.Param(default='m.mhd',
required=True,
comment="Initial momenta, m at I to be matched to n"),
'J':
Config.Param(default='J.mhd',
required=True,
comment="Target (fixed) image file, J"),
'n':
Config.Param(default='n.mhd',
required=True,
comment="Initial momenta, n at the target J")
}
# others
import numpy as np
import matplotlib.pyplot as plt
import os, errno
import logging
import sys
import copy
import math
import time
StudySpec = {
'I0':
Config.Param(default='I0.mhd',
required=True,
comment="Initial (moving) image file"),
'm0':
Config.Param(default='m0.mhd',
required=True,
comment="Initial momenta direction to shoot towards"),
'scaleMomenta':
Config.Param(default=1.0,
required=True,
comment="Scale initial momenta before shooting.")
}
GeodesicShootingConfigSpec = {
'study':
StudySpec,
'diffOpParams':
# HGM modules
from Libraries import CAvmHGMCommon
# others
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
import mpi4py
import csv
import socket
import datetime
StudySpec = {
'numSubjects':
Config.Param(default=4, required=True,
comment="Total number of subjects."),
'subjectIds':
Config.Param(
default=['sid1', 'sid2', 'sid3', 'sid4'],
required=True,
comment=
"List of subject ids. This should be unique names for each individuals"
),
'subjectIntercepts':
Config.Param(
default=[
'subject1_I.mhd', 'subject2_I.mhd', 'subject3_I.mhd',
'subject4_I.mhd'
],
required=True,
comment=
from Libraries import CAvmCommon
# HGM modules
# from Libraries import CAvmHGMCommon
# others
import matplotlib.pyplot as plt
import os
import sys
import numpy as np
import mpi4py
import itertools
import csv
StudySpec = {
'numSubjects':
Config.Param(default=4, required=True,
comment="Total number of subjects."),
'subjectFile':
Config.Param(
default="FilePath.csv",
comment=
"Path to the file that lists details of all subjects every timepoint, as pair of rows of images and times. Each row should be comma separated."
),
'initializationsFile':
Config.Param(
default=None,
comment=
"Path to the file that lists details of all initializations of initial image and momenta."
),
'setUnitSpacing':
Config.Param(default=True,
comment="Ignore the spacing in images and set it to (1,1,1)"),