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@wrap_input(0, 1)
def connect(ftr0, ftr1, port0=0, port1=0, add_conn=False):
"""Connection of two filters.
Connects the output port `port0` of filter `ftr0` with the input port
`port1` of filter `ftr1`.
Parameters
----------
ftr0 : vtkAlgorithm, vtkDataSet, BSAlgorithm or BSDataSet
The input filter. May be a filter or dataset.
ftr1 : vtkAlgorithm or BSAlgorithm
The output filter.
port0 : int, optional
Output port of `ftr0`. Not used if `ftr0` is a dataset. Default is 0.
port1 : int, optional
Input port of `ftr1`. Default is 0.
@wrap_input(0)
def _surface_selection(surf, array_name, low=-np.inf, upp=np.inf,
use_cell=False, keep=True):
"""Selection of points or cells meeting some thresholding criteria.
Parameters
----------
surf : vtkPolyData or BSPolyData
Input surface.
array_name : str or ndarray
Array used to perform selection.
low : float or -np.inf
Lower threshold. Default is -np.inf.
upp : float or np.inf
Upper threshold. Default is +np.inf.
use_cell : bool, optional
If True, apply selection to cells. Otherwise, use points.
@wrap_input(0)
def get_cells(surf):
"""Get surface cells.
Parameters
----------
surf : vtkDataSet or BSDataSet
Input surface.
Returns
-------
cells : ndarray, shape (n_cells, nd)
Array of cells. The value of nd depends on the topology. If vertex
(nd=1), line (nd=2) or poly (nd=3). Each element is a point id.
Raises
------
@wrap_input(0)
def downsample_with_parcellation(surf, labeling, name='parcel',
check_connected=True):
""" Downsample surface according to the labeling.
Such that, each parcel centroid is used as a point in the new donwsampled
surface. Connectivity is based on neighboring parcels.
Parameters
----------
surf : vtkPolyData or BSPolyData
Input surface.
labeling : str or 1D ndarray
Array of labels used to perform the downsampling. If str, it must be an
array in the PointData attributes of `surf`.
name : str, optional
Name of the downsampled parcellation appended to the PointData of the
@wrap_input(0)
def get_point2cell_connectivity(surf, mask=None, dtype=np.uint8):
"""Get point to cell connectivity.
Parameters
----------
surf : vtkDataSet or BSDataSet
Input surface.
mask : 1D ndarray, optional
Binary mask. If specified, only get points within the mask.
Default is None.
dtype : dtype, optional
Data type. Default is uint8.
Returns
-------
output : sparse matrix, shape (n_points, n_cells)
@wrap_input(0)
def _write_gifti(pd, opth):
# TODO: what about pointdata?
from nibabel.gifti.gifti import GiftiDataArray
if not pd.has_only_triangle:
raise ValueError('GIFTI writer only accepts triangles.')
points = GiftiDataArray(data=pd.Points, intent=INTENT_POINTS)
cells = GiftiDataArray(data=pd.GetCells2D(), intent=INTENT_CELLS)
# if data is not None:
# data_array = GiftiDataArray(data=data, intent=INTENT_POINTDATA)
# gii = nb.gifti.GiftiImage(darrays=[points, cells, data_array])
# else:
g = nb.gifti.GiftiImage(darrays=[points, cells])
nb.save(g, opth)
@wrap_input(0)
def to_data(ftr, port=0):
"""Extract data from filter.
Parameters
----------
ftr : vtkAlgorithm or :class:`.BSAlgorithm`
Input filter.
port : int, optional
Port to get data from. When port is -1, refers to all ports.
Default is 0.
Returns
-------
data : BSDataObject or list of BSDataObject
Returns the output of the filter. If port is -1 and number of output
ports > 1, then return list of outputs.
@wrap_input(0)
def get_point2edge_connectivity(surf, mask=None, dtype=np.uint8):
"""Get point to edge connectivity.
Parameters
----------
surf : vtkDataSet or BSDataSet
Input surface.
mask : 1D ndarray, optional
Binary mask. If specified, only use points within the mask.
Default is None.
dtype : dtype, optional
Data type. Default is uint8.
Returns
-------
output : sparse matrix, shape (n_points, n_edges)
@wrap_input(0)
def to_lines(surf):
"""Convert all cells in PolyData to lines.
Parameters
----------
surf : vtkPolyData or BSPolyData
Input surface.
Returns
-------
output : BSPolyData
PolyData with lines.
See Also
--------
:func:`to_vertex`
@wrap_input(0)
def get_cell2edge_connectivity(surf, mask=None, dtype=np.uint8):
"""Get cell to edge connectivity.
Parameters
----------
surf : vtkDataSet or BSDataSet
Input surface.
mask : 1D ndarray, optional
Binary mask. If specified, only use points within the mask.
Default is None.
dtype : dtype, optional
Data type. Default is uint8.
Returns
-------
output : sparse matrix, shape (n_cells, n_edges)