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DOC: Update docstrings with a few more links and array_like
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‎nibabel/cifti2/cifti2_axes.py

Lines changed: 35 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -252,20 +252,20 @@ def __init__(self, name, voxel=None, vertex=None, affine=None,
252252
253253
Parameters
254254
----------
255-
name : str or np.ndarray
255+
name : array_like
256256
brain structure name or (N, ) string array with the brain structure names
257-
voxel : np.ndarray
257+
voxel : array_like, optional
258258
(N, 3) array with the voxel indices (can be omitted for CIFTI-2 files only
259259
covering the surface)
260-
vertex : np.ndarray
260+
vertex : array_like, optional
261261
(N, ) array with the vertex indices (can be omitted for volumetric CIFTI-2 files)
262-
affine : np.ndarray
262+
affine : array_like, optional
263263
(4, 4) array mapping voxel indices to mm space (not needed for CIFTI-2 files only
264264
covering the surface)
265-
volume_shape : tuple of three integers
265+
volume_shape : tuple of three integers, optional
266266
shape of the volume in which the voxels were defined (not needed for CIFTI-2 files only
267267
covering the surface)
268-
nvertices : dict from string to integer
268+
nvertices : dict from string to integer, optional
269269
maps names of surface elements to integers (not needed for volumetric CIFTI-2 files)
270270
"""
271271
if voxel is None:
@@ -304,7 +304,7 @@ def __init__(self, name, voxel=None, vertex=None, affine=None,
304304
if affine is None or volume_shape is None:
305305
raise ValueError("Affine and volume shape should be defined "
306306
"for BrainModelAxis containing voxels")
307-
self.affine = affine
307+
self.affine = np.asanyarray(affine)
308308
self.volume_shape = volume_shape
309309

310310
if np.any(self.vertex[surface_mask] < 0):
@@ -325,12 +325,12 @@ def from_mask(cls, mask, name='other', affine=None):
325325
326326
Parameters
327327
----------
328-
mask : np.ndarray
328+
mask : array_like
329329
all non-zero voxels will be included in the BrainModelAxis axis
330330
should be (Nx, Ny, Nz) array for volume mask or (Nvertex, ) array for surface mask
331-
name : str
331+
name : str, optional
332332
Name of the brain structure (e.g. 'CortexRight', 'thalamus_left' or 'brain_stem')
333-
affine : np.ndarray
333+
affine : array_like, optional
334334
(4, 4) array with the voxel to mm transformation (defaults to identity matrix)
335335
Argument will be ignored for surface masks
336336
@@ -362,7 +362,7 @@ def from_surface(cls, vertices, nvertex, name='Other'):
362362
363363
Parameters
364364
----------
365-
vertices : np.ndarray
365+
vertices : array_like
366366
indices of the vertices on the surface
367367
nvertex : int
368368
total number of vertices on the surface
@@ -384,7 +384,7 @@ def from_index_mapping(cls, mim):
384384
385385
Parameters
386386
----------
387-
mim : cifti2.Cifti2MatrixIndicesMap
387+
mim : :class:`.cifti2.Cifti2MatrixIndicesMap`
388388
389389
Returns
390390
-------
@@ -422,7 +422,7 @@ def to_mapping(self, dim):
422422
423423
Returns
424424
-------
425-
cifti2.Cifti2MatrixIndicesMap
425+
:class:`.cifti2.Cifti2MatrixIndicesMap`
426426
"""
427427
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_BRAIN_MODELS')
428428
for name, to_slice, bm in self.iter_structures():
@@ -720,22 +720,22 @@ def __init__(self, name, voxels, vertices, affine=None, volume_shape=None, nvert
720720
721721
Parameters
722722
----------
723-
name : np.ndarray
723+
name : array_like
724724
(N, ) string array with the parcel names
725-
voxels : np.ndarray
725+
voxels : array_like
726726
(N, ) object array each containing a sequence of voxels.
727727
For each parcel the voxels are represented by a (M, 3) index array
728-
vertices : np.ndarray
728+
vertices : array_like
729729
(N, ) object array each containing a sequence of vertices.
730730
For each parcel the vertices are represented by a mapping from brain structure name to
731731
(M, ) index array
732-
affine : np.ndarray
732+
affine : array_like, optional
733733
(4, 4) array mapping voxel indices to mm space (not needed for CIFTI-2 files only
734734
covering the surface)
735-
volume_shape : tuple of three integers
735+
volume_shape : tuple of three integers, optional
736736
shape of the volume in which the voxels were defined (not needed for CIFTI-2 files only
737737
covering the surface)
738-
nvertices : dict[String -> int]
738+
nvertices : dict from string to integer, optional
739739
maps names of surface elements to integers (not needed for volumetric CIFTI-2 files)
740740
"""
741741
self.name = np.asanyarray(name, dtype='U')
@@ -748,7 +748,7 @@ def __init__(self, name, voxels, vertices, affine=None, volume_shape=None, nvert
748748
voxels[idx] = as_array[idx]
749749
self.voxels = np.asanyarray(voxels, dtype='object')
750750
self.vertices = np.asanyarray(vertices, dtype='object')
751-
self.affine = affine
751+
self.affine = np.asanyarray(affine) if affine is not None else None
752752
self.volume_shape = volume_shape
753753
if nvertices is None:
754754
self.nvertices = {}
@@ -813,7 +813,7 @@ def from_index_mapping(cls, mim):
813813
814814
Parameters
815815
----------
816-
mim : cifti2.Cifti2MatrixIndicesMap
816+
mim : :class:`cifti2.Cifti2MatrixIndicesMap`
817817
818818
Returns
819819
-------
@@ -859,7 +859,7 @@ def to_mapping(self, dim):
859859
860860
Returns
861861
-------
862-
cifti2.Cifti2MatrixIndicesMap
862+
:class:`cifti2.Cifti2MatrixIndicesMap`
863863
"""
864864
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_PARCELS')
865865
if self.affine is not None:
@@ -1008,7 +1008,8 @@ def get_element(self, index):
10081008
tuple with 3 elements
10091009
- unicode name of the parcel
10101010
- (M, 3) int array with voxel indices
1011-
- Dict[String -> (K, ) int array] with vertex indices for a specific surface brain structure
1011+
- dict from string to (K, ) int array with vertex indices
1012+
for a specific surface brain structure
10121013
"""
10131014
return self.name[index], self.voxels[index], self.vertices[index]
10141015

@@ -1023,9 +1024,9 @@ def __init__(self, name, meta=None):
10231024
"""
10241025
Parameters
10251026
----------
1026-
name : np.ndarray of string
1027+
name : array_like
10271028
(N, ) string array with the parcel names
1028-
meta : np.ndarray of dict
1029+
meta : array_like
10291030
(N, ) object array with a dictionary of metadata for each row/column.
10301031
Defaults to empty dictionary
10311032
"""
@@ -1046,7 +1047,7 @@ def from_index_mapping(cls, mim):
10461047
10471048
Parameters
10481049
----------
1049-
mim : cifti2.Cifti2MatrixIndicesMap
1050+
mim : :class:`.cifti2.Cifti2MatrixIndicesMap`
10501051
10511052
Returns
10521053
-------
@@ -1067,7 +1068,7 @@ def to_mapping(self, dim):
10671068
10681069
Returns
10691070
-------
1070-
cifti2.Cifti2MatrixIndicesMap
1071+
:class:`.cifti2.Cifti2MatrixIndicesMap`
10711072
"""
10721073
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_SCALARS')
10731074
for name, meta in zip(self.name, self.meta):
@@ -1151,13 +1152,13 @@ def __init__(self, name, label, meta=None):
11511152
"""
11521153
Parameters
11531154
----------
1154-
name : np.ndarray
1155+
name : array_like
11551156
(N, ) string array with the parcel names
1156-
label : np.ndarray
1157+
label : array_like
11571158
single dictionary or (N, ) object array with dictionaries mapping
11581159
from integers to (name, (R, G, B, A)), where name is a string and R, G, B, and A are
11591160
floats between 0 and 1 giving the colour and alpha (i.e., transparency)
1160-
meta : np.ndarray
1161+
meta : array_like, optional
11611162
(N, ) object array with a dictionary of metadata for each row/column
11621163
"""
11631164
self.name = np.asanyarray(name, dtype='U')
@@ -1180,7 +1181,7 @@ def from_index_mapping(cls, mim):
11801181
11811182
Parameters
11821183
----------
1183-
mim : cifti2.Cifti2MatrixIndicesMap
1184+
mim : :class:`.cifti2.Cifti2MatrixIndicesMap`
11841185
11851186
Returns
11861187
-------
@@ -1202,7 +1203,7 @@ def to_mapping(self, dim):
12021203
12031204
Returns
12041205
-------
1205-
cifti2.Cifti2MatrixIndicesMap
1206+
:class:`.cifti2.Cifti2MatrixIndicesMap`
12061207
"""
12071208
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_LABELS')
12081209
for name, label, meta in zip(self.name, self.label, self.meta):
@@ -1324,7 +1325,7 @@ def from_index_mapping(cls, mim):
13241325
13251326
Parameters
13261327
----------
1327-
mim : cifti2.Cifti2MatrixIndicesMap
1328+
mim : :class:`.cifti2.Cifti2MatrixIndicesMap`
13281329
13291330
Returns
13301331
-------
@@ -1345,7 +1346,7 @@ def to_mapping(self, dim):
13451346
13461347
Returns
13471348
-------
1348-
cifti2.Cifti2MatrixIndicesMap
1349+
:class:`cifti2.Cifti2MatrixIndicesMap`
13491350
"""
13501351
mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_SERIES')
13511352
mim.series_exponent = 0

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