cycletools

calc_topological_charge(phase_diffs, orientation)

Calculate the topological charge from phase differences.

Parameters:

Name	Type	Description	Default
phase_diffs	ndarray	Array of phase differences.	required
orientation	int	Orientation factor, either 1 or -1.	required

Returns:

Type	Description
ndarray	np.array: The calculated topological charge and wave number.

extract_boundary_cycles(phasefield)

Extract boundary cycles from mesh boundaries.

Parameters:

Name	Type	Description	Default
phasefield	PhaseField	Phasefield mesh containing vertices, faces, edges, and face_masks.	required

Returns:

Type	Description
DataFrame	pd.DataFrame: DataFrame representing cycles with columns: 'time_axis', 'nodes', 'top_charge', 'wave_number', 'n_nodes'.

extract_face_cycles(phasefield)

Extract mesh face cycles.

Parameters:

Name	Type	Description	Default
phasefield	PhaseField	Phasefield mesh containing faces, phase differences for each face, and face_masks.	required

Returns:

Type	Description
DataFrame	pd.DataFrame: DataFrame representing cycles with columns: 'time_axis', 'nodes', 'top_charge', 'wave_number', 'n_nodes'.

get_boundaries(polydata)

Extract boundary loops from a polydata object.

Parameters:

Name	Type	Description	Default
polydata	PolyData	The input mesh.	required

Returns:

Type	Description
list[list[int]]	list[list[int]]: A list of boundary loops, where each loop is a list of point indices.

get_cutout_polydata(points, faces, face_mask)

Create a PyVista PolyData object from filtered faces.

Parameters:

Name	Type	Description	Default
points	ndarray	Array of mesh points.	required
faces	ndarray	Array of mesh faces.	required
face_mask	ndarray	Boolean mask to filter faces.	required

Returns:

Type	Description
PolyData	pv.PolyData: The resulting PolyData object.

orient_boundary(boundary, boundary_first_edge_id, filtered_edges_id)

Orient a boundary based on the presence of its first edge in filtered edges.

Parameters:

Name	Type	Description	Default
boundary	list[int]	The boundary to orient.	required
boundary_first_edge_id	int	ID of the first edge in the boundary.	required
filtered_edges_id	ndarray	Array of filtered edge IDs.	required

Returns:

Type	Description
tuple[list[int], int]	tuple[list[int], int]: The oriented boundary and its orientation factor (1 or -1).

split_boundaries(boundaries)

Split boundaries into simple loops.

A simple loop is defined as a boundary that does not intersect itself.

Parameters:

Name	Type	Description	Default
boundaries	list[list[int]]	List of boundary loops.	required

Returns:

Type	Description
list[list[int]]	list[list[int]]: List of simple boundary loops.

split_boundary(boundary)

Split a boundary into simple loops using networkx.

Parameters:

Name	Type	Description	Default
boundary	list[int]	List of point indices forming a boundary.	required

Returns:

Type	Description
list[list[int]]	list[list[int]]: List of simple boundary loops.