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Streamline_tools example stops working when I change density from 1 to 2 #307

Garyfallidis opened this Issue Jan 4, 2014 · 1 comment


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Garyfallidis commented Jan 4, 2014

I just changed this line in the streamline_tools example

seeds = utils.seeds_from_mask(white_matter, density=2)

and I am getting this error. Please also after solving this problem write a better docstring for seeds_from_mask

All files already in /home/user/.dipy/stanford_hardi.

AttributeError Traceback (most recent call last)
/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)
176 else:
177 filename = fname
--> 178 builtin.execfile(filename, *where)

/home/user/Documents/dipy_paper/code/ in ()
53 """
---> 55 seeds = utils.seeds_from_mask(white_matter, density=2)
56 streamline_generator = EuDX(csapeaks.peak_values, csapeaks.peak_indices,
57 odf_vertices=peaks.default_sphere.vertices,

/home/user/Devel/dipy/dipy/tracking/_utils.pyc in seeds_from_mask(mask, density, voxel_size, affine)
406 where = np.argwhere(mask)
407 seeds = where[:, np.newaxis, :] + grid[np.newaxis, :, :]
--> 408 seeds.shape = (-1, 3)
410 # Apply the spacial transform

AttributeError: incompatible shape for a non-contiguous array


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MrBago commented Jan 8, 2014

Based on the trace it looks like line 408 should be replaced with seeds = seeds.reshape((-1, 3)). I'll have time to work on this maybe Friday or Monday.

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