Ejemplo n.º 1
0
    def discrete_to_roi_features(self, fid, method='average'):
        """
        Compute an ROI-level feature given the discrete features
        
        Parameters
        ----------
        fid(string) the discrete feature under consideration
        method='average' the assessment method
        
        Results
        ------
        the computed roi-feature is returned
        """
        if method not in['min','max','average','cumulated_average']:
            raise  ValueError, 'unknown method'
        if method=='cumulated_average':
            df = self.discrete_features[fid]
            data = self.discrete_features[fid]
            d0 = data[0]
            if np.size(d0) == np.shape(d0)[0]:
                np.reshape(d0,(np.size(d0),1))
            fdim = d0.shape[1]
            ldata = np.zeros((self.k,fdim))
            for k in range(self.k):
                dk = self.get_descendents(k)
                card = np.sum(self.get_size()[dk])
                for ch in dk:
                    ldata[k] += np.sum(data[ch],0)  
                ldata[k]/=card
            self.set_roi_feature(fid,ldata)
        else:
            ldata = MultipleROI.discrete_to_roi_features(self, fid, method)

        return ldata
Ejemplo n.º 2
0
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], position[1], position[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', InputImage)
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',InputImage)
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" %\