def apply_repro_analysis_analysis(dataset, thresholds=[3.0], method = 'crfx'):
"""
perform the reproducibility analysis according to the
"""
from nipy.io.imageformats import Nifti1Image
nsubj, dimx, dimy = dataset.shape
func = np.reshape(dataset,(nsubj, dimx*dimy)).T
var = np.ones((dimx*dimy, nsubj))
#xyz = np.reshape(np.indices((dimx, dimy,1)).T,(dimx*dimy,3))
#coord = xyz.astype(np.float)
mask = Nifti1Image(np.ones((dimx, dimy, 1)),np.eye(4))
ngroups = 10
sigma = 2.0
csize = 10
niter = 10
verbose = 0
swap = False
kap = []
clt = []
for threshold in thresholds:
kappa = []
cls = []
kwargs={'threshold':threshold,'csize':csize}
for i in range(niter):
k = voxel_reproducibility(func, var, mask, ngroups,
method, swap, verbose, **kwargs)
kappa.append(k)
cld = cluster_reproducibility(func, var, mask, ngroups, sigma,
method, swap, verbose, **kwargs)
cls.append(cld)
kap.append(np.array(kappa))
clt.append(np.array(cls))
kap = np.array(kap)
clt = np.array(clt)
return kap,clt
# do not use permutations
swap = False
kap = []
clt = []
pk = []
sens = []
for threshold in thresholds:
kwargs={'threshold':threshold,'csize':csize}
kappa = []
cls = []
sent = []
peaks = []
for i in range(niter):
k = voxel_reproducibility(func, var, mask, ngroups,
method, swap, verbose, **kwargs)
kappa.append(k)
cld = cluster_reproducibility(func, var, mask, ngroups, sigma,
method, swap, verbose, **kwargs)
cls.append(cld)
peak = peak_reproducibility(func, var, mask, ngroups, sigma,
method, swap, verbose, **kwargs)
peaks.append(peak)
seni = map_reproducibility(func, var, mask, ngroups,
method, True, verbose, threshold=threshold,
csize=csize).mean()/ngroups
sent.append(seni)
sens.append(np.array(sent))
kap.append(np.array(kappa))
clt.append(np.array(cls))
pk.append(np.array(peaks))
method = "crfx"
verbose = 0
# apply random sign swaps to the data to test the reproducibility
# under the H0 hypothesis
swap = False
kap = []
clt = []
for threshold in thresholds:
kappa = []
cls = []
kwargs = {"threshold": threshold, "csize": csize}
for i in range(niter):
k = voxel_reproducibility(Functional, VarFunctional, xyz, ngroups, method, swap, verbose, **kwargs)
kappa.append(k)
cld = cluster_reproducibility(
Functional, VarFunctional, xyz, ngroups, coord, sigma, method, swap, verbose, **kwargs
)
cls.append(cld)
kap.append(np.array(kappa))
clt.append(np.array(cls))
import matplotlib.pylab as mp
mp.figure()
mp.subplot(1, 2, 1)
mp.boxplot(kap)
mp.title("voxel-level reproducibility")
