def fx(sl, dataset, roi_ids, results):
"""this requires the searchlight conditional attribute 'roi_feature_ids'
to be enabled"""
import numpy as np
from mvpa2.datasets import Dataset
resmap = None
probmap = None
for resblock in results:
for res in resblock:
if resmap is None:
# prepare the result container
resmap = np.zeros((len(res), dataset.nfeatures), dtype=res.samples.dtype)
observ_counter = np.zeros(dataset.nfeatures, dtype=int)
#project the result onto all features -- love broadcasting!
resmap[:, res.a.roi_feature_ids] += res.samples
# increment observation counter for all relevant features
observ_counter[res.a.roi_feature_ids] += 1
# when all results have been added up average them according to the number
# of observations
observ_mask = observ_counter > 0
resmap[:, observ_mask] /= observ_counter[observ_mask]
# transpose to make broadcasting work -- creates a view, so in-place
# modification still does the job
result_ds = Dataset(resmap,
fa={'observations': observ_counter})
if 'mapper' in dataset.a:
import copy
result_ds.a['mapper'] = copy.copy(dataset.a.mapper)
return result_ds
def run_bootstrap(ds, sts, niter=1000):
"""
dataset: Input fmri dataset with targets and chunks, should be preprocessed
Q: The loading matrix from statis
niter: number of iteration for bootstrap
This function iteratively samples random chunks from dataset with
replacement and computes each statis solution.
The factor scores from each statis are then projected into original compromise
matrix space using Q
OUTPUT: FBoot collects all projected factor scores
"""
ntables = sts.ntables
rows, nfactors = ds.shape
nrows = rows/ntables
boot = np.zeros((nrows,nfactors,niter))
X = ds.a['X'].value
X = X.samples
ignore = 0 # Hack: for some reasone inter_table_Rv_analysis chokes...
ident = np.unique(sts.subtable_idx)
for i in range(niter):
idx = ident[np.random.random_integers(0,ntables-1,size=(ntables,))]
Y = None
Y_idx = None
fselect = np.zeros((nrows,nfactors,ntables))
for k,j in enumerate(idx):
Y_t = X[:,sts.subtable_idx==j]
if Y_idx is None:
Y_idx = np.ones((Y_t.shape[1]))*k
else:
Y_idx = np.hstack((Y_idx,np.ones((Y_t.shape[1]))*k))
if Y == None:
Y = Y_t
else:
Y = np.hstack((Y,Y_t))
fselect[:,:,k] = ds.samples[ds.chunks==np.unique(ds.chunks)[j],:]
(A,alpha,C,G) = inter_table_Rv_analysis(Y,Y_idx)
if G is None:
ignore += 1
continue
#print "shape alpha:", alpha.shape
#print "shape fselect", fselect.shape
#print alpha
#print fselect
boot[:,:,i] = np.sum(fselect*alpha.flatten(),2)
if i%100==0:
sys.stdout.write("iter:%s/%s\r"% (i,niter))
sys.stdout.flush()
print "completed %s/%s bootstraps." % (niter-ignore,niter)
boot = Dataset(boot)
boot.sa['targets'] = ds.targets[:nrows]
return boot
def packing(dataset, radius=4, nifti=False, randoffset=False):
"""return a hexagonal close sphere packing grid for a PyMVPA fMRI dataset
Keyword arguments:
radius-- radius in voxels of the spheres to pack (default 4)
nifti-- write out a seed voxel mask as a nifti
randomoffset-- random jitter of the seed voxel grid
"""
from pylab import find, random
from numpy import ones, zeros, arange, sqrt, remainder
from mvpa2.suite import fmri_dataset, Dataset
import os
if randoffset:
ro = random(3)
else:
ro = zeros(3)
minco = dataset.fa.voxel_indices.min(0)
maxco = dataset.fa.voxel_indices.max(0)
rect = ones(dataset.a.voxel_dim)
fac = sqrt(6)*2*radius/3
for iz,z in enumerate(arange(minco[2], maxco[2], fac)):
for iy,y in enumerate(arange(minco[1], maxco[1], fac)):
for x in arange(minco[0], maxco[0], 2*radius):
hx = x + remainder(iy, 2)*radius + ro[0]*radius
hy = y + remainder(iz, 2)*fac + ro[1]*radius
hz = z + ro[2]*radius
if hz <= maxco[2]:
rect [hx, hy, hz] += 1
maskedrect = dataset.mapper.forward1(rect)
roiIndex = find((maskedrect == 2))
print 'number of seed voxel: '+str(len(roiIndex))
maskedrectds = Dataset([maskedrect])
maskedrectds.a = dataset.a.copy()
maskedrectds.fa = dataset.fa.copy()
if nifti:
from nibabel import Nifti1Image
Nifti1Image(maskedrectds.O.squeeze(),
dataset.a.imghdr.get_best_affine()
).to_filename(os.path.join('sparse'+str(int(radius))+'.nii.gz'))
return roiIndex, maskedrectds
def _forward_dataset(self, ds):
targ = np.copy(ds.targets)
mapped = None
X = None
i,j = ds.shape
if self._stack=='v':
chunks = np.unique(ds.sa[self._chunks_attr].value)
else:
chunks = np.unique(ds.fa[self._chunks_attr].value)
for ch,chunk in enumerate(chunks):
if self._stack == 'v':
table = ds[ds.sa[self._chunks_attr].value==chunk,:]
if self._stack == 'h':
table = ds[:,ds.fa[self._chunks_attr].value==chunk]
table = self.center_and_norm_table(table,
col_mean=self._subtable_stats[ch]['col_mean'],
col_norm=self._subtable_stats[ch]['col_norm'],
table_norm = self._subtable_stats[ch]['table_norm'])[0]
if self._stack =='v':
# Assume features align, use average Q
Q_ = None
for subtab in np.unique(self.subtable_idx):
if Q_ is None:
Q_ = self.Q[self.subtable_idx==subtab,:]
else:
Q_ = Q_ + self.Q[self.subtable_idx==subtab,:]
Q_ = Q_ / len(np.unique(self.subtable_idx))
part = Dataset(np.dot(table.samples,Q_))
part.sa = table.sa
if self._stack =='h':
# Assume same number of features as in X
part = Dataset(np.dot(table,self.Q[self.subtable_idx==chunk,:]))
part.sa = table.sa
part.sa['chunks'] = [chunk]*part.shape[0]
if mapped is None:
mapped = part.copy()
X = table
else:
mapped.append(part.copy())
X.append(table,'h')
mapped.a['X'] = X
if self.keep_dims == 'all':
self.keep_dims = range(mapped.shape[1])
return mapped[:,self.keep_dims]
def _call(self, ds):
data_dsm = 1 - pdist(ds.samples, metric='correlation')
data_dsm = np.arctanh(data_dsm) # Fisher z transformation
data_dsm = data_dsm[self.labels != 0]
labels = self.labels[self.labels != 0]
data_dsm = zscore(data_dsm)
# difference between distances of same types of trials across run (labeled 1)
# and different types of trals across run (labeled 2)
sim = np.mean(data_dsm[labels == 1]) - np.mean(data_dsm[labels == 2])
return Dataset([sim])
def load_eeg_dataset(path, filename, attrib, TR, eliminated_vols=None, **kwargs):
"""
**kwargs:
- type:
* 'psd': Power Spectrum Density using matplotlib.specgram
additional parameters to be included NFFT and noverlap
* 'fft': Power Spectrum and Phase using scipy.fft
* 'time': EEG timecourse in every TR.
"""
type = "time"
for arg in kwargs:
if arg == "type":
type = kwargs[arg]
print "type = " + type
# load eeg data
[data, eeg_info] = load_eeg_data(path, filename, TR, eliminatedVols=eliminated_vols)
channel_ids = eeg_info["channel_ids"]
dt = eeg_info["dt"]
kwargs["dt"] = dt
if (type == "psd") or (type == "fft"):
[samples, freq] = spectrum_eeg(data, **kwargs)
data = samples.reshape(samples.shape[0], samples.shape[1], -1)
# mvpa analysis: attributes and dataset
attr = SampleAttributes(attrib)
print "Building dataset..."
ds = Dataset.from_channeltimeseries(data, channelids=channel_ids, targets=attr.targets, chunks=attr.chunks)
if (type == "psd") or (type == "fft"):
ds.a["frequiencies"] = freq
ds.a["shape"] = samples.shape
ds.a["timepoints"] = np.arange(0, TR, dt)
del data
if "samples" in locals():
del samples
return ds
for j in channelSelected:
start = markers[i][1] + (onSet / dt)
stop = start + (nSamples / dt)
nVec = np.array(data.T[j][start:stop])
if nVec.shape[0] != (nSamples / dt):
nVec.resize(nSamples / dt)
print "yes"
dataRes[j][i] = nVec
# Select data based on channels Selected
dataResSel = np.take(dataRes, channelSelected, axis=0)
ch_infoSel = np.take(ch_info, channelSelected)
# reshape data to feed Dataset
dataResSel = np.reshape(dataResSel, (nTrials, -1, nSamples / dt))
# Eliminate first n. runs
volToEliminate = 5
dataResSel = dataResSel[: nTrials - volToEliminate]
# mvpa analysis: attributes and dataset
attr = SampleAttributes("/home/robbis/fmri_datasets/monks/monks_attrib_pymvpa.txt")
ds = Dataset.from_channeltimeseries(
dataResSel, t0=0, dt=dt, channelids=ch_infoSel, targets=attr.targets, chunks=attr.chunks
)
del dataRes, dataResSel
def _call(self, ds):
data_dsm = pdist(ds.samples, metric='correlation') # 'euclidean'
corr = spearmanr(data_dsm, self.labels, axis=None).correlation
return Dataset([corr])
