def test_roi1(verbose=0):
nim = load(RefImage)
affine = nim.get_affine()
shape = nim.get_shape()
lroi = DiscreteROI("myroi", affine, shape)
lroi.from_position(np.array([0,0,0]),5.0)
roiPath = os.path.join(WriteDir,"myroi.nii")
lroi.make_image(roiPath)
assert(os.path.isfile(roiPath))
average_activation = nroi.representative_feature('activation')
bmap = -np.zeros(domain.size)
for k in range(nroi.k):
bmap[nroi.label==k] = average_activation[k]
# saving the blob image,i. e. a label image
wlabel = -2*np.ones(shape)
wlabel[data!=0] = nroi.label
blobPath = os.path.join(swd, "blob.nii")
wim = Nifti1Image(wlabel, affine)
wim.get_header()['descrip'] = 'blob image extracted from %s'%input_image
save(wim, blobPath)
# --- 2.b take blob labelled "1" as an ROI
roi = DiscreteROI( affine=affine, shape=shape)
roi.from_labelled_image(blobPath, 1)
roiPath2 = os.path.join(swd, "roi_blob_1.nii")
roi.make_image(roiPath2)
# --- 2.c take the blob closest to 'position as an ROI'
roiPath3 = os.path.join(swd, "blob_closest_to_%d_%d_%d.nii")%\
(position[0][0], position[0][1], position[0][2])
roi.from_position_and_image(blobPath, np.array(position))
roi.make_image(roiPath3)
# --- 2.d make a set of ROIs from all the blobs
mroi = MultipleROI( affine=affine, shape=shape)
mroi.from_labelled_image(blobPath)
roiPath4 = os.path.join(swd, "roi_all_blobs.nii")
mroi.make_image(roiPath4)
# paths
swd = tempfile.mkdtemp()
data_dir = os.path.expanduser(os.path.join('~', '.nipy', 'tests', 'data'))
InputImage = os.path.join(data_dir,'spmT_0029.nii.gz')
MaskImage = os.path.join(data_dir,'mask.nii.gz')
# -----------------------------------------------------
# example 1: create the ROI froma a given position
# -----------------------------------------------------
position = [0,0,0]
nim = load(MaskImage)
affine = nim.get_affine()
shape = nim.get_shape()
roi = DiscreteROI("myroi", affine,shape)
roi.from_position(np.array(position), 5.0)
roi.make_image(os.path.join(swd,"myroi.nii"))
roi.set_feature_from_image('activ',InputImage)
roi.plot_feature('activ')
print 'Wrote an ROI mask image in %s' %os.path.join(swd,"myroi.nii")
# ----------------------------------------------------
# ---- example 2: create ROIs from a blob image ------
# ----------------------------------------------------
# --- 2.a create the blob image
import nipy.neurospin.graph.field as ff
import nipy.neurospin.spatial_models.hroi as hroi
