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dipy data

Read test or example data

dipy.data.get_data(name='small_64D')

provides filenames of some test datasets

Parameters :

name: str :

the filename/s of which dataset to return, one of: ‘small_64D’ small region of interest nifti,bvecs,bvals 64 directions ‘small_101D’ small region of interest nifti,bvecs,bvals 101 directions ‘aniso_vox’ volume with anisotropic voxel size as Nifti ‘fornix’ 300 tracks in Trackvis format (from Pittsburgh Brain Competition)

Returns :

fnames : tuple

filenames for dataset

Examples

>>> import numpy as np
>>> from dipy.data import get_data
>>> fimg,fbvals,fbvecs=get_data('small_101D')
>>> bvals=np.loadtxt(fbvals)
>>> bvecs=np.loadtxt(fbvecs).T
>>> import nibabel as nib
>>> img=nib.load(fimg)
>>> data=img.get_data()
>>> data.shape
(6, 10, 10, 102)
>>> bvals.shape
(102,)
>>> bvecs.shape
(102, 3)
dipy.data.get_sim_voxels(name='fib1')

provide some simulated voxel data

Parameters :

name : str, which file?

‘fib0’, ‘fib1’ or ‘fib2’

Returns :

dix : dictionary, where dix[‘data’] returns a 2d array

where every row is a simulated voxel with different orientation

Notes

These sim voxels were provided by M.M. Correia using Rician noise.

Examples

>>> from dipy.data import get_sim_voxels
>>> sv=get_sim_voxels('fib1')
>>> sv['data'].shape
(100, 102)
>>> sv['fibres']
'1'
>>> sv['gradients'].shape
(102, 3)
>>> sv['bvals'].shape
(102,)
>>> sv['snr']
'60'
>>> sv2=get_sim_voxels('fib2')
>>> sv2['fibres']
'2'
>>> sv2['snr']
'80'
dipy.data.get_skeleton(name='C1')

provide skeletons generated from Local Skeleton Clustering (LSC)

Parameters :name : str, ‘C1’ or ‘C3’
Returns :dix : dictionary

Examples

>>> from dipy.data import get_skeleton
>>> C=get_skeleton('C1')
>>> len(C.keys())
117
>>> for c in C: break
>>> C[c].keys()
['indices', 'most', 'hidden', 'N']
dipy.data.get_sphere(name='symmetric363')

provide triangulated spheres

Parameters :

name : str

which sphere - one of: * ‘symmetric362’ * ‘symmetric642’

Returns :

vertices : ndarray

vertices for sphere

faces : ndarray

faces

Examples

>>> import numpy as np
>>> from dipy.data import get_sphere
>>> verts, faces = get_sphere('symmetric362')
>>> verts.shape
(362, 3)
>>> faces.shape
(720, 3)
>>> verts, faces = get_sphere('not a sphere name')
Traceback (most recent call last):
    ...
DataError: No sphere called "not a sphere name"