def _extract_vals(data, streamlines, affine=None, threedvec=False):
"""
Helper function for use with `values_from_volume`.
Parameters
----------
data : 3D or 4D array
Scalar (for 3D) and vector (for 4D) values to be extracted. For 4D
data, interpolation will be done on the 3 spatial dimensions in each
volume.
streamlines : ndarray or list
If array, of shape (n_streamlines, n_nodes, 3)
If list, len(n_streamlines) with (n_nodes, 3) array in
each element of the list.
affine : ndarray, shape (4, 4)
Affine transformation from voxels (image coordinates) to streamlines.
Default: identity.
threedvec : bool
Whether the last dimension has length 3. This is a special case in
which we can use :func:`vfu.interpolate_vector_3d` for the
interploation of 4D volumes without looping over the elements of the
last dimension.
Return
------
array or list (depending on the input) : values interpolate to each
coordinate along the length of each streamline
"""
data = data.astype(np.float)
if (isinstance(streamlines, list)
or isinstance(streamlines, types.GeneratorType)):
if affine is not None:
streamlines = ut.move_streamlines(streamlines,
np.linalg.inv(affine))
vals = []
for sl in streamlines:
if threedvec:
vals.append(
list(
vfu.interpolate_vector_3d(data,
sl.astype(np.float))[0]))
else:
vals.append(
list(
vfu.interpolate_scalar_3d(data,
sl.astype(np.float))[0]))
elif isinstance(streamlines, np.ndarray):
sl_shape = streamlines.shape
sl_cat = streamlines.reshape(sl_shape[0] * sl_shape[1],
3).astype(np.float)
if affine is not None:
inv_affine = np.linalg.inv(affine)
sl_cat = (np.dot(sl_cat, inv_affine[:3, :3]) + inv_affine[:3, 3])
# So that we can index in one operation:
if threedvec:
vals = np.array(vfu.interpolate_vector_3d(data, sl_cat)[0])
else:
vals = np.array(vfu.interpolate_scalar_3d(data, sl_cat)[0])
vals = np.reshape(vals, (sl_shape[0], sl_shape[1], -1))
if vals.shape[-1] == 1:
vals = np.reshape(vals, vals.shape[:-1])
else:
raise RuntimeError("Extracting values from a volume ",
"requires streamlines input as an array, ",
"a list of arrays, or a streamline generator.")
return vals
def _extract_vals(data, streamlines, affine=None, threedvec=False):
"""
Helper function for use with `values_from_volume`.
Parameters
----------
data : 3D or 4D array
Scalar (for 3D) and vector (for 4D) values to be extracted. For 4D
data, interpolation will be done on the 3 spatial dimensions in each
volume.
streamlines : ndarray or list
If array, of shape (n_streamlines, n_nodes, 3)
If list, len(n_streamlines) with (n_nodes, 3) array in
each element of the list.
affine : ndarray, shape (4, 4)
Affine transformation from voxels (image coordinates) to streamlines.
Default: identity.
threedvec : bool
Whether the last dimension has length 3. This is a special case in
which we can use :func:`vfu.interpolate_vector_3d` for the
interploation of 4D volumes without looping over the elements of the
last dimension.
Return
------
array or list (depending on the input) : values interpolate to each
coordinate along the length of each streamline
"""
data = data.astype(np.float)
if (isinstance(streamlines, list) or
isinstance(streamlines, types.GeneratorType)):
if affine is not None:
streamlines = ut.move_streamlines(streamlines,
np.linalg.inv(affine))
vals = []
for sl in streamlines:
if threedvec:
vals.append(list(vfu.interpolate_vector_3d(data,
sl.astype(np.float))[0]))
else:
vals.append(list(vfu.interpolate_scalar_3d(data,
sl.astype(np.float))[0]))
elif isinstance(streamlines, np.ndarray):
sl_shape = streamlines.shape
sl_cat = streamlines.reshape(sl_shape[0] *
sl_shape[1], 3).astype(np.float)
if affine is not None:
inv_affine = np.linalg.inv(affine)
sl_cat = (np.dot(sl_cat, inv_affine[:3, :3]) +
inv_affine[:3, 3])
# So that we can index in one operation:
if threedvec:
vals = np.array(vfu.interpolate_vector_3d(data, sl_cat)[0])
else:
vals = np.array(vfu.interpolate_scalar_3d(data, sl_cat)[0])
vals = np.reshape(vals, (sl_shape[0], sl_shape[1], -1))
if vals.shape[-1] == 1:
vals = np.reshape(vals, vals.shape[:-1])
else:
raise RuntimeError("Extracting values from a volume ",
"requires streamlines input as an array, ",
"a list of arrays, or a streamline generator.")
return vals
