def clean(self, valid):
"""
remove the rois for which valid==0
and update the hierarchy accordingly
In case sum(valid)==0, 0 is returned
"""
if np.sum(valid)==0:
return None
# fixme: is None a correct way of dealing with k=0 ?
# first clean as a forest
sf = self.subforest(valid)
Forest.__init__(self, sf.V, sf.parents)
# then clean as a multiple ROI
MultipleROI.clean(self, valid)
return self.V
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)
mroi.set_discrete_feature_from_image('activ', input_image)
mroi.discrete_to_roi_features('activ')
mroi.plot_roi_feature('activ')
# ---- 2.e the same, a bit more complex
mroi = MultipleROI( affine=affine, shape=shape)
mroi.as_multiple_balls(np.array([[-10.,0.,10.]]),np.array([7.0]))
mroi.from_labelled_image(blobPath,np.arange(1,20))
mroi.from_labelled_image(blobPath,np.arange(31,50))
roiPath5 = os.path.join(swd,"roi_some_blobs.nii")
mroi.set_discrete_feature_from_image('activ',input_image)
mroi.discrete_to_roi_features('activ')
valid = mroi.get_roi_feature('activ')>4.0
mroi.clean(valid)
mroi.make_image(roiPath5)
print "Wrote ROI mask images in %s, \n %s \n %s \n and %s" %\
(roiPath2, roiPath3, roiPath4, roiPath5)
mp.show()
