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Values from streamlines object #1524

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merged 4 commits into from May 16, 2018
Merged

Values from streamlines object #1524

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b5001ba
TST: We should be able to read values with Streamline objects.
arokem May 16, 2018
a710850
BF: Enables extracting values with Streamline objects.
arokem May 16, 2018
202028d
PEP8
arokem May 16, 2018
23cb625
PEP8 the entire thing.
arokem May 16, 2018
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67 changes: 35 additions & 32 deletions dipy/tracking/streamline.py
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Expand Up @@ -29,16 +29,19 @@

MEGABYTE = 1024 * 1024


class _BuildCache(object):
def __init__(self, arr_seq, common_shape, dtype):
self.offsets = list(arr_seq._offsets)
self.lengths = list(arr_seq._lengths)
self.next_offset = arr_seq._get_next_offset()
self.bytes_per_buf = arr_seq._buffer_size * MEGABYTE
# Use the passed dtype only if null data array
self.dtype = dtype if arr_seq._data.size == 0 else arr_seq._data.dtype
if arr_seq.common_shape != () and common_shape != arr_seq.common_shape:
if arr_seq._data.size == 0:
self.dtype = dtype
else:
arr_seq._data.dtype
if (arr_seq.common_shape != () and
common_shape != arr_seq.common_shape):
raise ValueError(
"All dimensions, except the first one, must match exactly")
self.common_shape = common_shape
Expand All @@ -50,34 +53,32 @@ def update_seq(self, arr_seq):
arr_seq._offsets = np.array(self.offsets)
arr_seq._lengths = np.array(self.lengths)


class Streamlines(ArraySequence):

def __init__(self, *args, **kwargs):
super(Streamlines, self).__init__(*args, **kwargs)

def append(self, element, cache_build=False):
""" Appends `element` to this array sequence.
"""
Appends `element` to this array sequence.

Append can be a lot faster if it knows that it is appending several
elements instead of a single element. In that case it can cache the
parameters it uses between append operations, in a "build cache". To
tell append to do this, use ``cache_build=True``. If you use
``cache_build=True``, you need to finalize the append operations with
:meth:`finalize_append`.
elements instead of a single element. In that case it can cache
the parameters it uses between append operations, in a "build
cache". To tell append to do this, use ``cache_build=True``. If
you use ``cache_build=True``, you need to finalize the append
operations with :meth:`finalize_append`.

Parameters
----------
element : ndarray
Element to append. The shape must match already inserted elements
shape except for the first dimension.
cache_build : {False, True}
Whether to save the build cache from this append routine. If True,
append can assume it is the only player updating `self`, and the
caller must finalize `self` after all append operations, with
``self.finalize_append()``.
Returns
element : ndarray Element to append. The shape must match already
inserted elements shape except for the first dimension.
cache_build : {False, True} Whether to save the build cache
from this append routine. If True, append can assume it is the
only player updating `self`, and the caller must finalize
`self` after all append operations, with
``self.finalize_append()``. Returns
-------
None
Notes
None Notes
-----
If you need to add multiple elements you should consider
`ArraySequence.extend`.
Expand Down Expand Up @@ -124,19 +125,20 @@ def extend(self, elements):
""" Appends all `elements` to this array sequence.
Parameters
----------
elements : iterable of ndarrays or :class:`ArraySequence` object
If iterable of ndarrays, each ndarray will be concatenated along
the first dimension then appended to the data of this
elements : iterable of ndarrays or :class:`ArraySequence` instance

If iterable of ndarrays, each ndarray will be concatenated
along the first dimension then appended to the data of this
ArraySequence.
If :class:`ArraySequence` object, its data are simply appended to
the data of this ArraySequence.
If :class:`ArraySequence` object, its data are simply appended
to the data of this ArraySequence.

Returns
-------
None
Notes
None Notes
-----
The shape of the elements to be added must match the one of the data of
this :class:`ArraySequence` except for the first dimension.
The shape of the elements to be added must match the one of the
data of this :class:`ArraySequence` except for the first dimension.
"""
# If possible try pre-allocating memory.
try:
Expand Down Expand Up @@ -597,7 +599,8 @@ def _extract_vals(data, streamlines, affine=None, threedvec=False):
"""
data = data.astype(np.float)
if (isinstance(streamlines, list) or
isinstance(streamlines, types.GeneratorType)):
isinstance(streamlines, types.GeneratorType) or
isinstance(streamlines, Streamlines)):
if affine is not None:
streamlines = ut.move_streamlines(streamlines,
np.linalg.inv(affine))
Expand Down
3 changes: 3 additions & 0 deletions dipy/tracking/tests/test_streamline.py
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Expand Up @@ -1027,6 +1027,9 @@ def test_values_from_volume():
vv = values_from_volume(data, np.array(sl1))
npt.assert_almost_equal(vv, ans1, decimal=decimal)

vv = values_from_volume(data, Streamlines(sl1))
npt.assert_almost_equal(vv, ans1, decimal=decimal)

affine = np.eye(4)
affine[:, 3] = [-100, 10, 1, 1]
x_sl1 = ut.move_streamlines(sl1, affine)
Expand Down