core.utils.generators

Module: core.utils.generators

This module defines a few common generators for slicing over arrays.

They are defined on ndarray, so they do not depend on Image.

  • data_generator: return (item, data[item]) tuples from an iterable object
  • slice_generator: return slices through an ndarray, possibly over many indices
  • f_generator: return a generator that applies a function to the output of another generator

The above three generators return 2-tuples.

  • write_data: write the output of a generator to an ndarray
  • parcels: return binary array of the unique components of data

Functions

nipy.core.utils.generators.data_generator(data, iterable=None)

Return generator for [(i, data[i]) for i in iterable]

If iterable is None, it defaults to range(data.shape[0])

Examples

>>> a = np.asarray([[True,False],[False,True]])
>>> b = np.asarray([[False,False],[True,False]])
>>> for i, d in data_generator(np.asarray([[1,2],[3,4]]), [a,b]):
...     print(d)
...
[1 4]
[3]
nipy.core.utils.generators.f_generator(f, iterable)

Return a generator for [(i, f(x)) for i, x in iterable]

Examples

>>> for i, d in f_generator(lambda x: x**2, data_generator([[1,2],[3,4]])):
...     print(i, d)
...
0 [1 4]
1 [ 9 16]
nipy.core.utils.generators.matrix_generator(img)

From a generator of items (i, r), return (i, rp) where rp is a 2d array with rp.shape = (r.shape[0], prod(r.shape[1:]))

nipy.core.utils.generators.parcels(data, labels=None, exclude=())

Return a generator for [data == label for label in labels]

If labels is None, labels = numpy.unique(data). Each label in labels can be a sequence, in which case the value returned for that label union:

[numpy.equal(data, l) for l in label]
Parameters:

data : image or array-like

Either an image (with get_data method returning ndarray) or an array-like

labels : iterable, optional

A sequence of labels for which to return indices within data. The elements in labels can themselves be lists, tuples, in which case the indices returned are for all values in data matching any of the items in the list, tuple.

exclude : iterable, optional

Values in labels for which you do not want to return a parcel.

Returns:

gen : generator

generator yielding a array of boolean indices into data for which data == label, for each element in label.

Examples

>>> for p in parcels([[1,1],[2,1]]):
...     print(p)
...
[[ True  True]
 [False  True]]
[[False False]
 [ True False]]
>>> for p in parcels([[1,1],[2,3]], labels=[2,3]):
...     print(p)
...
[[False False]
 [ True False]]
[[False False]
 [False  True]]
>>> for p in parcels([[1,1],[2,3]], labels=[(2,3),2]):
...     print(p)
...
[[False False]
 [ True  True]]
[[False False]
 [ True False]]
nipy.core.utils.generators.shape_generator(img, shape)

From a generator of items (i, r), return (i, r.reshape(shape))

nipy.core.utils.generators.slice_generator(data, axis=0)

Return generator for yielding slices along axis

Parameters:

data : array-like

axis : int or list or tuple

If int, gives the axis. If list or tuple, gives the combination of axes over which to iterate. First axis is fastest changing in output.

Examples

>>> for i,d in slice_generator([[1,2],[3,4]]):
...     print(i, d)
...
(0,) [1 2]
(1,) [3 4]
>>> for i,d in slice_generator([[1,2],[3,4]], axis=1):
...     print(i, d)
...
(slice(None, None, None), 0) [1 3]
(slice(None, None, None), 1) [2 4]
nipy.core.utils.generators.slice_parcels(data, labels=None, axis=0)

A generator for slicing through parcels and slices of data…

hmmm… a better description is needed

>>> x=np.array([[0,0,0,1],[0,1,0,1],[2,2,0,1]])
>>> for a in slice_parcels(x):
...     print(a, x[a])
...
((0,), array([ True,  True,  True, False], dtype=bool)) [0 0 0]
((0,), array([False, False, False,  True], dtype=bool)) [1]
((1,), array([ True, False,  True, False], dtype=bool)) [0 0]
((1,), array([False,  True, False,  True], dtype=bool)) [1 1]
((2,), array([False, False,  True, False], dtype=bool)) [0]
((2,), array([False, False, False,  True], dtype=bool)) [1]
((2,), array([ True,  True, False, False], dtype=bool)) [2 2]
>>> for a in slice_parcels(x, axis=1):
...     b, c = a
...     print(a, x[b][c])
...
((slice(None, None, None), 0), array([ True,  True, False], dtype=bool)) [0 0]
((slice(None, None, None), 0), array([False, False,  True], dtype=bool)) [2]
((slice(None, None, None), 1), array([ True, False, False], dtype=bool)) [0]
((slice(None, None, None), 1), array([False,  True, False], dtype=bool)) [1]
((slice(None, None, None), 1), array([False, False,  True], dtype=bool)) [2]
((slice(None, None, None), 2), array([ True,  True,  True], dtype=bool)) [0 0 0]
((slice(None, None, None), 3), array([ True,  True,  True], dtype=bool)) [1 1 1]
nipy.core.utils.generators.write_data(output, iterable)

Write (index, data) iterable to output

Write some data to output. Iterable should return 2-tuples of the form index, data such that:

output[index] = data

makes sense.

Examples

>>> a=np.zeros((2,2))
>>> write_data(a, data_generator(np.asarray([[1,2],[3,4]])))
>>> a
array([[ 1.,  2.],
       [ 3.,  4.]])