API Reference

morphsync.MorphSync

Methods:

Name	Description
__repr__	Return a string representation of the MorphSync.
add_graph	Add a graph layer to the MorphSync.
add_layer	Add a layer of the specified type to the MorphSync.
add_link	Add a mapping link between two layers.
add_mesh	Add a mesh layer to the MorphSync.
add_points	Add a points layer to the MorphSync.
add_table	Add a table layer to the MorphSync.
apply_mask	Create a new MorphSync with a masked version of the specified layer.
apply_mask_by_node_index	Create a new MorphSync with a layer subset by node index.
assign_from_mapping	Assign values from the target layer to the source layer based on mapping.
drop_layer	Remove a layer from the MorphSync.
get_layer	Get a layer by name.
get_link	Get the mapping DataFrame between two layers.
get_link_as_layer	Create a Graph layer representing the mapping between two layers.
get_link_path	Find the shortest path of mappings between two layers.
get_mapped_nodes	Get features from the target layer for nodes mapped from the source layer.
get_mapping	Find mappings from source to target layers using the entire link graph.
get_mapping_paths	Find mappings from source to target layers using the entire link graph, and
get_masking	Get unique target indices that map to any of the specified source indices.
get_params	Get the parameters used to initialize this MorphSync container.
has_layer	Check if a layer with the given name exists.
query_nodes	Create a new MorphSync by querying nodes in a specific layer.

Attributes:

Name	Type	Description
layer_names	list[str]	List of all layer names in the container.
layer_types	dict	Dictionary mapping layer names to their class types.
link_graph	DiGraph	NetworkX graph representing the connectivity between layers.

layer_names property

List of all layer names in the container.

layer_types property

Dictionary mapping layer names to their class types.

link_graph property

NetworkX graph representing the connectivity between layers.

Returns:

Type	Description
DiGraph	Graph where nodes are layer names and edges represent mappings.

__repr__()

Return a string representation of the MorphSync.

add_graph(name, graph, copy=True, **kwargs)

Add a graph layer to the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name for the new graph layer.	required
graph		Graph data - either an object with 'vertices' and 'edges' attributes or a tuple of (vertices, edges).	required
copy	bool	Whether to copy the input data.	True
**kwargs		Additional arguments passed to the Graph constructor.	{}

add_layer(name, data, layer_type, copy=True, **kwargs)

Add a layer of the specified type to the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name for the new layer.	required
data	Any	Data for the layer, format depends on layer_type.	required
layer_type	str	Type of layer to create. Must be one of 'mesh', 'points', 'graph', or 'table'.	required
copy	bool	Whether to copy the input data.	True
**kwargs		Additional arguments passed to the layer constructor.	{}

Raises:

Type	Description
ValueError	If layer_type is not one of the supported types.

add_link(source, target, mapping='closest')

Add a mapping link between two layers.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required
mapping	Union[str, ndarray, DataFrame, Series, dict]	Mapping specification. Options: - "closest": Map to nearest neighbors based on spatial coordinates - "index": Map by matching indices - np.ndarray: 1D array of target indices for each source element - pd.DataFrame: DataFrame with source and target columns - pd.Series: Series mapping source to target indices - dict: Dictionary mapping source to target indices	'closest'

add_mesh(name, mesh, copy=True, **kwargs)

Add a mesh layer to the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name for the new mesh layer.	required
mesh		Mesh data - either an object with 'vertices' and 'faces' attributes or a tuple of (vertices, faces).	required
copy	bool	Whether to copy the input data.	True
**kwargs		Additional arguments passed to the Mesh constructor.	{}

add_points(name, points, copy=True, **kwargs)

Add a points layer to the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name for the new points layer.	required
points		Point coordinates as an array, DataFrame, or tuple containing points.	required
copy	bool	Whether to copy the input data.	True
**kwargs		Additional arguments passed to the Points constructor.	{}

add_table(name, table, copy=True, **kwargs)

Add a table layer to the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name for the new table layer.	required
table	DataFrame	DataFrame containing tabular data.	required
copy	bool	Whether to copy the input data.	True
**kwargs		Additional arguments passed to the Table constructor.	{}

apply_mask(layer_name, mask)

Create a new MorphSync with a masked version of the specified layer.

Parameters:

Name	Type	Description	Default
layer_name	str	Name of the layer to mask.	required
mask	Union[ndarray, list]	Boolean mask or indices to apply to the layer.	required

Returns:

Type	Description
MorphSync	New MorphSync with the masked layer and corresponding mappings to other layers.

apply_mask_by_node_index(layer_name, new_index)

Create a new MorphSync with a layer subset by node index.

Parameters:

Name	Type	Description	Default
layer_name	str	Name of the layer to subset.	required
new_index	Union[Index, ndarray, list]	Node indices to keep in the new layer.	required

Returns:

Type	Description
MorphSync	New MorphSync container with the subset layer and corresponding mappings to other layers.

assign_from_mapping(source, target, columns)

Assign values from the target layer to the source layer based on mapping.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer that will receive the values.	required
target	str	Name of the target layer that provides the values.	required
columns	Union[str, list, dict]	Column specification: - str: Single column name to copy - list: List of column names to copy - dict: Mapping from source column names to target column names	required

Notes

This modifies the source layer in place by adding/updating the specified columns.

drop_layer(name)

Remove a layer from the MorphSync.

Parameters:

Name	Type	Description	Default
name	str	Name of the layer to remove.	required

get_layer(name)

Get a layer by name.

Parameters:

Name	Type	Description	Default
name	str	Name of the layer to retrieve.	required

Returns:

Type	Description
Layer	The requested layer.

Raises:

Type	Description
KeyError	If the layer does not exist.

get_link(source, target)

Get the mapping DataFrame between two layers.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required

Returns:

Type	Description
DataFrame	DataFrame containing the mapping between source and target layers.

get_link_as_layer(source, target)

Create a Graph layer representing the mapping between two layers.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required

Returns:

Type	Description
Graph	Graph layer where edges connect mapped nodes between source and target layers. Source nodes come first in the node list, followed by target nodes.

get_link_path(source, target)

Find the shortest path of mappings between two layers.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required

Returns:

Type	Description
list[str]	List of layer names representing the shortest path from source to target.

get_mapped_nodes(source, target, source_index=None, replace_index=True, validate=None)

Get features from the target layer for nodes mapped from the source layer.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required
source_index	Optional[Union[ndarray, Index, Series]]	Source indices to get mappings for. If None, uses all source indices.	None
replace_index	bool	Whether to replace the target indices with source indices in the result.	True
validate	Optional[str]	Whether to validate the mapping at each step. If specified, checks if each mapping between layers is of the specified type. Options are: - "one_to_one" or "1:1": check if join keys are unique in both source and target layers. - "one_to_many" or "1:m": check if join keys are unique in the source dataset. - "many_to_one" or "m:1": check if join keys are unique in the target dataset. - "many_to_many" or "m:m": allowed, but does not result in checks.	None

Returns:

Type	Description
DataFrame	DataFrame containing target layer features for the mapped nodes.

get_mapping(source, target, source_index=None, validate=None, dropna=False)

Find mappings from source to target layers using the entire link graph.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required
source_index	Optional[Union[ndarray, Index, Series]]	Index of the source layer to map from. If None, uses all indices in the source layer.	None
validate	Optional[str]	Whether to validate the mapping at each step. If specified, checks if each mapping between layers is of the specified type. Options are: - "one_to_one" or "1:1": check if join keys are unique in both source and target layers. - "one_to_many" or "1:m": check if join keys are unique in the source dataset. - "many_to_one" or "m:1": check if join keys are unique in the target dataset. - "many_to_many" or "m:m": allowed, but does not result in checks.	None
dropna	bool	Whether to drop entries with null mappings. If False, returns NaN/pd.NA values for missing mappings.	False

Returns:

Type	Description
Series	Series with nodes in the source layer as the index and mapped nodes in the target layer as the values. Format depends on dropna parameter.

Notes

This function is a convenience wrapper around get_mapping_paths that returns just the final mapping as a Series. If you need to see the full mapping at each step, use get_mapping_paths.

get_mapping_paths(source, target, source_index=None, validate=None, dropna=False)

Find mappings from source to target layers using the entire link graph, and describe the mapping at each step.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required
source_index	Optional[Union[ndarray, Index]]	Index of the source layer to map from. If None, uses all indices in the source layer.	None
validate	Optional[str]	Whether to validate the mapping at each step. If specified, checks if each mapping between layers is of the specified type. Options are: - "one_to_one" or "1:1": check if join keys are unique in both source and target layers. - "one_to_many" or "1:m": check if join keys are unique in the source dataset. - "many_to_one" or "m:1": check if join keys are unique in the target dataset. - "many_to_many" or "m:m": allowed, but does not result in checks.	None
dropna	bool	Whether to drop entries with null mappings. If False, returns NaN/pd.NA values for missing mappings.	False

Returns:

Type	Description
DataFrame	Mapped indices in the target layer corresponding to the source_index in the source layer. Format depends on dropna parameter.

get_masking(source, target, source_index=None)

Get unique target indices that map to any of the specified source indices.

Parameters:

Name	Type	Description	Default
source	str	Name of the source layer.	required
target	str	Name of the target layer.	required
source_index	Optional[Union[ndarray, Index, Series]]	Source indices to find mappings for. If None, uses all source indices.	None

Returns:

Type	Description
ndarray	Array of unique target indices that map to the source indices.

get_params()

Get the parameters used to initialize this MorphSync container.

Returns:

Type	Description
dict	Dictionary containing initialization parameters.

has_layer(name)

Check if a layer with the given name exists.

Parameters:

Name	Type	Description	Default
name	str	Name of the layer to check.	required

Returns:

Type	Description
bool	True if the layer exists, False otherwise.

query_nodes(layer_name, query_str)

Create a new MorphSync by querying nodes in a specific layer.

Parameters:

Name	Type	Description	Default
layer_name	str	Name of the layer to query.	required
query_str	str	Query string to pass to pandas DataFrame.query() method.	required

Returns:

Type	Description
MorphSync	New MorphSync container with the queried layer and corresponding mappings to other layers.

Layers

morphsync.Layer

Methods:

Name	Description
get_params	Get the parameters used to initialize this layer.
mask_by_node_index	Create a new layer containing only the specified nodes and their facets.
mask_nodes	Mask the nodes DataFrame and return a new layer with the
query_nodes	Query the nodes DataFrame and return a new layer with the

Attributes:

Name	Type	Description
edge_index	Index	Index of the edges. Alias for facets_index.
facets_index	Index	Index of the facets DataFrame.
facets_positional	ndarray	Array of the facets in positional indexing, such that 0 corresponds to the
layer_type	str	String identifier of the layer type (e.g., 'mesh', 'points', 'graph').
n_facets	int	Number of facets (edges/faces) in the layer.
n_nodes	int	Number of nodes in the layer.
n_points	int	Number of points in the layer. Alias for n_nodes.
n_vertices	int	Number of vertices in the layer. Alias for n_nodes.
nodes_index	Index	Index of the nodes DataFrame.
points	ndarray	Alias for vertices
points_index	Index	Index of the points. Alias for nodes_index.
vertices	ndarray	Array of the spatial coordinates of the vertices
vertices_df	DataFrame	DataFrame of the spatial coordinates of the vertices
vertices_index	Index	Index of the vertices. Alias for nodes_index.

edge_index property

Index of the edges. Alias for facets_index.

facets_index property

Index of the facets DataFrame.

facets_positional property

Array of the facets in positional indexing, such that 0 corresponds to the first node in its current node index ordering

layer_type property

String identifier of the layer type (e.g., 'mesh', 'points', 'graph').

n_facets property

Number of facets (edges/faces) in the layer.

n_nodes property

Number of nodes in the layer.

n_points property

Number of points in the layer. Alias for n_nodes.

n_vertices property

Number of vertices in the layer. Alias for n_nodes.

nodes_index property

Index of the nodes DataFrame.

points property

Alias for vertices

points_index property

Index of the points. Alias for nodes_index.

vertices property

Array of the spatial coordinates of the vertices

vertices_df property

DataFrame of the spatial coordinates of the vertices

vertices_index property

Index of the vertices. Alias for nodes_index.

get_params()

Get the parameters used to initialize this layer.

Returns:

Type	Description
dict	Dictionary containing layer initialization parameters.

mask_by_node_index(new_index, new_nodes=None)

Create a new layer containing only the specified nodes and their facets.

Parameters:

Name	Type	Description	Default
new_index	Union[ndarray, Index, Series]	Index of nodes to keep in the new layer.	required
new_nodes	Optional[DataFrame]	Pre-filtered nodes DataFrame. If None, nodes will be filtered automatically based on new_index.	None

Returns:

Type	Description
	A new layer instance containing only the specified nodes and facets that reference those nodes.

Notes

Only facets that reference exclusively the nodes in new_index are kept.

mask_nodes(mask)

Mask the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
mask	ndarray	A boolean mask array to filter the nodes DataFrame. This masking is applied in positional indexing (i.e. order, not key matters).	required

Returns:

Type	Description
	A new layer with the masked nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

query_nodes(query_str)

Query the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
query_str	str	A query string to pass to pd.DataFrame.query on the nodes DataFrame.	required

Returns:

Type	Description
	A new layer with the queried nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

morphsync.Table

Bases: Layer

Methods:

Name	Description
__repr__	Return a string representation of the Table.
get_params	Get the parameters used to initialize this layer.
mask_by_node_index	Create a new layer containing only the specified nodes and their facets.
mask_nodes	Mask the nodes DataFrame and return a new layer with the
query_nodes	Query the nodes DataFrame and return a new layer with the

Attributes:

Name	Type	Description
edge_index	Index	Index of the edges. Alias for facets_index.
facets_index	Index	Index of the facets DataFrame.
facets_positional	ndarray	Array of the facets in positional indexing, such that 0 corresponds to the
layer_type	str	String identifier of the layer type (e.g., 'mesh', 'points', 'graph').
n_facets	int	Number of facets (edges/faces) in the layer.
n_nodes	int	Number of nodes in the layer.
n_points	int	Number of points in the layer. Alias for n_nodes.
n_vertices	int	Number of vertices in the layer. Alias for n_nodes.
nodes_index	Index	Index of the nodes DataFrame.
points	ndarray	Alias for vertices
points_index	Index	Index of the points. Alias for nodes_index.
table	DataFrame	Access the table data as a DataFrame. Alias for nodes.
vertices	ndarray	Array of the spatial coordinates of the vertices
vertices_df	DataFrame	DataFrame of the spatial coordinates of the vertices
vertices_index	Index	Index of the vertices. Alias for nodes_index.

edge_index property

Index of the edges. Alias for facets_index.

facets_index property

Index of the facets DataFrame.

facets_positional property

Array of the facets in positional indexing, such that 0 corresponds to the first node in its current node index ordering

layer_type property

String identifier of the layer type (e.g., 'mesh', 'points', 'graph').

n_facets property

Number of facets (edges/faces) in the layer.

n_nodes property

Number of nodes in the layer.

n_points property

Number of points in the layer. Alias for n_nodes.

n_vertices property

Number of vertices in the layer. Alias for n_nodes.

nodes_index property

Index of the nodes DataFrame.

points property

Alias for vertices

points_index property

Index of the points. Alias for nodes_index.

table property

Access the table data as a DataFrame. Alias for nodes.

vertices property

Array of the spatial coordinates of the vertices

vertices_df property

DataFrame of the spatial coordinates of the vertices

vertices_index property

Index of the vertices. Alias for nodes_index.

__repr__()

Return a string representation of the Table.

get_params()

Get the parameters used to initialize this layer.

Returns:

Type	Description
dict	Dictionary containing layer initialization parameters.

mask_by_node_index(new_index, new_nodes=None)

Create a new layer containing only the specified nodes and their facets.

Parameters:

Name	Type	Description	Default
new_index	Union[ndarray, Index, Series]	Index of nodes to keep in the new layer.	required
new_nodes	Optional[DataFrame]	Pre-filtered nodes DataFrame. If None, nodes will be filtered automatically based on new_index.	None

Returns:

Type	Description
	A new layer instance containing only the specified nodes and facets that reference those nodes.

Notes

Only facets that reference exclusively the nodes in new_index are kept.

mask_nodes(mask)

Mask the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
mask	ndarray	A boolean mask array to filter the nodes DataFrame. This masking is applied in positional indexing (i.e. order, not key matters).	required

Returns:

Type	Description
	A new layer with the masked nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

query_nodes(query_str)

Query the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
query_str	str	A query string to pass to pd.DataFrame.query on the nodes DataFrame.	required

Returns:

Type	Description
	A new layer with the queried nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

morphsync.Points

Bases: Layer

Methods:

Name	Description
__repr__	Return a string representation of the Points.
get_params	Get the parameters used to initialize this layer.
mask_by_node_index	Create a new layer containing only the specified nodes and their facets.
mask_nodes	Mask the nodes DataFrame and return a new layer with the
query_nodes	Query the nodes DataFrame and return a new layer with the

Attributes:

Name	Type	Description
edge_index	Index	Index of the edges. Alias for facets_index.
facets_index	Index	Index of the facets DataFrame.
facets_positional	ndarray	Array of the facets in positional indexing, such that 0 corresponds to the
index	Index	Index of the points. Alias for nodes.index.
is_spatially_valid	bool	Check if the points have valid spatial structure.
layer_type	str	String identifier of the layer type (e.g., 'mesh', 'points', 'graph').
n_facets	int	Number of facets (edges/faces) in the layer.
n_nodes	int	Number of nodes in the layer.
n_points	int	Number of points in the layer. Alias for n_nodes.
n_vertices	int	Number of vertices in the layer. Alias for n_nodes.
nodes_index	Index	Index of the nodes DataFrame.
points	ndarray	Alias for vertices
points_index	Index	Index of the points. Alias for nodes_index.
vertices	ndarray	Array of the spatial coordinates of the vertices
vertices_df	DataFrame	DataFrame of the spatial coordinates of the vertices
vertices_index	Index	Index of the vertices. Alias for nodes_index.

edge_index property

Index of the edges. Alias for facets_index.

facets_index property

Index of the facets DataFrame.

facets_positional property

Array of the facets in positional indexing, such that 0 corresponds to the first node in its current node index ordering

index property

Index of the points. Alias for nodes.index.

is_spatially_valid property

Check if the points have valid spatial structure.

Returns:

Type	Description
bool	True if points are 3D and non-empty.

layer_type property

String identifier of the layer type (e.g., 'mesh', 'points', 'graph').

n_facets property

Number of facets (edges/faces) in the layer.

n_nodes property

Number of nodes in the layer.

n_points property

Number of points in the layer. Alias for n_nodes.

n_vertices property

Number of vertices in the layer. Alias for n_nodes.

nodes_index property

Index of the nodes DataFrame.

points property

Alias for vertices

points_index property

Index of the points. Alias for nodes_index.

vertices property

Array of the spatial coordinates of the vertices

vertices_df property

DataFrame of the spatial coordinates of the vertices

vertices_index property

Index of the vertices. Alias for nodes_index.

__repr__()

Return a string representation of the Points.

get_params()

Get the parameters used to initialize this layer.

Returns:

Type	Description
dict	Dictionary containing layer initialization parameters.

mask_by_node_index(new_index, new_nodes=None)

Create a new layer containing only the specified nodes and their facets.

Parameters:

Name	Type	Description	Default
new_index	Union[ndarray, Index, Series]	Index of nodes to keep in the new layer.	required
new_nodes	Optional[DataFrame]	Pre-filtered nodes DataFrame. If None, nodes will be filtered automatically based on new_index.	None

Returns:

Type	Description
	A new layer instance containing only the specified nodes and facets that reference those nodes.

Notes

Only facets that reference exclusively the nodes in new_index are kept.

mask_nodes(mask)

Mask the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
mask	ndarray	A boolean mask array to filter the nodes DataFrame. This masking is applied in positional indexing (i.e. order, not key matters).	required

Returns:

Type	Description
	A new layer with the masked nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

query_nodes(query_str)

Query the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
query_str	str	A query string to pass to pd.DataFrame.query on the nodes DataFrame.	required

Returns:

Type	Description
	A new layer with the queried nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

morphsync.Graph

Bases: Layer

Methods:

Name	Description
__repr__	Return a string representation of the Graph.
get_params	Get the parameters used to initialize this layer.
mask_by_node_index	Create a new layer containing only the specified nodes and their facets.
mask_nodes	Mask the nodes DataFrame and return a new layer with the
query_nodes	Query the nodes DataFrame and return a new layer with the
to_adjacency	Convert the graph to an adjacency matrix.

Attributes:

Name	Type	Description
edge_index	Index	Index of the edges. Alias for facets_index.
edges	ndarray	Edges as a numpy array of shape (n_edges, 2).
edges_df	DataFrame	Edges as a DataFrame containing node indices.
edges_positional	ndarray	Edges in positional indexing.
facets_index	Index	Index of the facets DataFrame.
facets_positional	ndarray	Array of the facets in positional indexing, such that 0 corresponds to the
is_spatially_valid	bool	Check if the graph has valid spatial structure.
layer_type	str	String identifier of the layer type (e.g., 'mesh', 'points', 'graph').
n_edges	int	Number of edges in the graph.
n_facets	int	Number of facets (edges/faces) in the layer.
n_nodes	int	Number of nodes in the layer.
n_points	int	Number of points in the layer. Alias for n_nodes.
n_vertices	int	Number of vertices in the layer. Alias for n_nodes.
nodes_index	Index	Index of the nodes DataFrame.
points	ndarray	Alias for vertices
points_index	Index	Index of the points. Alias for nodes_index.
vertices	ndarray	Array of the spatial coordinates of the vertices
vertices_df	DataFrame	DataFrame of the spatial coordinates of the vertices
vertices_index	Index	Index of the vertices. Alias for nodes_index.

edge_index property

Index of the edges. Alias for facets_index.

edges property

Edges as a numpy array of shape (n_edges, 2).

edges_df property

Edges as a DataFrame containing node indices.

edges_positional property

Edges in positional indexing.

facets_index property

Index of the facets DataFrame.

facets_positional property

Array of the facets in positional indexing, such that 0 corresponds to the first node in its current node index ordering

is_spatially_valid property

Check if the graph has valid spatial structure.

Returns:

Type	Description
bool	True if vertices are 3D and both vertices and edges are non-empty.

layer_type property

String identifier of the layer type (e.g., 'mesh', 'points', 'graph').

n_edges property

Number of edges in the graph.

n_facets property

Number of facets (edges/faces) in the layer.

n_nodes property

Number of nodes in the layer.

n_points property

Number of points in the layer. Alias for n_nodes.

n_vertices property

Number of vertices in the layer. Alias for n_nodes.

nodes_index property

Index of the nodes DataFrame.

points property

Alias for vertices

points_index property

Index of the points. Alias for nodes_index.

vertices property

Array of the spatial coordinates of the vertices

vertices_df property

DataFrame of the spatial coordinates of the vertices

vertices_index property

Index of the vertices. Alias for nodes_index.

__repr__()

Return a string representation of the Graph.

get_params()

Get the parameters used to initialize this layer.

Returns:

Type	Description
dict	Dictionary containing layer initialization parameters.

mask_by_node_index(new_index, new_nodes=None)

Create a new layer containing only the specified nodes and their facets.

Parameters:

Name	Type	Description	Default
new_index	Union[ndarray, Index, Series]	Index of nodes to keep in the new layer.	required
new_nodes	Optional[DataFrame]	Pre-filtered nodes DataFrame. If None, nodes will be filtered automatically based on new_index.	None

Returns:

Type	Description
	A new layer instance containing only the specified nodes and facets that reference those nodes.

Notes

Only facets that reference exclusively the nodes in new_index are kept.

mask_nodes(mask)

Mask the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
mask	ndarray	A boolean mask array to filter the nodes DataFrame. This masking is applied in positional indexing (i.e. order, not key matters).	required

Returns:

Type	Description
	A new layer with the masked nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

query_nodes(query_str)

Query the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
query_str	str	A query string to pass to pd.DataFrame.query on the nodes DataFrame.	required

Returns:

Type	Description
	A new layer with the queried nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

to_adjacency(return_as='csr', weights=None, symmetrize=False)

Convert the graph to an adjacency matrix.

Parameters:

Name	Type	Description	Default
return_as	str	Format to return the adjacency matrix. Currently only "csr" is supported.	'csr'
weights	Optional[str]	Column name in facets to use as edge weights. If None, uses unit weights.	None
symmetrize	bool	If True, add reverse edges to make the graph symmetric.	False

Returns:

Type	Description
	Sparse adjacency matrix of shape (n_nodes, n_nodes).

morphsync.Mesh

Bases: Layer

Methods:

Name	Description
__repr__	Return a string representation of the Mesh.
from_dict	Create a Mesh from a dictionary containing vertices and faces.
get_params	Get the parameters used to initialize this layer.
mask_by_node_index	Create a new layer containing only the specified nodes and their facets.
mask_nodes	Mask the nodes DataFrame and return a new layer with the
query_nodes	Query the nodes DataFrame and return a new layer with the

Attributes:

Name	Type	Description
edge_index	Index	Index of the edges. Alias for facets_index.
faces	ndarray	Faces as a numpy array in positional indexing.
facets_index	Index	Index of the facets DataFrame.
facets_positional	ndarray	Array of the facets in positional indexing, such that 0 corresponds to the
is_spatially_valid	bool	Check if the mesh has valid spatial structure.
layer_type	str	String identifier of the layer type (e.g., 'mesh', 'points', 'graph').
mesh	tuple[ndarray, ndarray]	Get the mesh as a tuple of (vertices, faces).
n_facets	int	Number of facets (edges/faces) in the layer.
n_nodes	int	Number of nodes in the layer.
n_points	int	Number of points in the layer. Alias for n_nodes.
n_vertices	int	Number of vertices in the layer. Alias for n_nodes.
nodes_index	Index	Index of the nodes DataFrame.
points	ndarray	Alias for vertices
points_index	Index	Index of the points. Alias for nodes_index.
vertices	ndarray	Array of the spatial coordinates of the vertices
vertices_df	DataFrame	DataFrame of the spatial coordinates of the vertices
vertices_index	Index	Index of the vertices. Alias for nodes_index.

edge_index property

Index of the edges. Alias for facets_index.

faces property

Faces as a numpy array in positional indexing.

facets_index property

Index of the facets DataFrame.

facets_positional property

Array of the facets in positional indexing, such that 0 corresponds to the first node in its current node index ordering

is_spatially_valid property

Check if the mesh has valid spatial structure.

Returns:

Type	Description
bool	True if vertices are 3D, faces are triangular, and both are non-empty.

layer_type property

String identifier of the layer type (e.g., 'mesh', 'points', 'graph').

mesh property

Get the mesh as a tuple of (vertices, faces).

n_facets property

Number of facets (edges/faces) in the layer.

n_nodes property

Number of nodes in the layer.

n_points property

Number of points in the layer. Alias for n_nodes.

n_vertices property

Number of vertices in the layer. Alias for n_nodes.

nodes_index property

Index of the nodes DataFrame.

points property

Alias for vertices

points_index property

Index of the points. Alias for nodes_index.

vertices property

Array of the spatial coordinates of the vertices

vertices_df property

DataFrame of the spatial coordinates of the vertices

vertices_index property

Index of the vertices. Alias for nodes_index.

__repr__()

Return a string representation of the Mesh.

from_dict(data) classmethod

Create a Mesh from a dictionary containing vertices and faces.

Parameters:

Name	Type	Description	Default
data	dict	Dictionary with 'vertices' and 'faces' keys.	required

Returns:

Type	Description
Mesh	A new Mesh instance.

get_params()

Get the parameters used to initialize this layer.

Returns:

Type	Description
dict	Dictionary containing layer initialization parameters.

mask_by_node_index(new_index, new_nodes=None)

Create a new layer containing only the specified nodes and their facets.

Parameters:

Name	Type	Description	Default
new_index	Union[ndarray, Index, Series]	Index of nodes to keep in the new layer.	required
new_nodes	Optional[DataFrame]	Pre-filtered nodes DataFrame. If None, nodes will be filtered automatically based on new_index.	None

Returns:

Type	Description
	A new layer instance containing only the specified nodes and facets that reference those nodes.

Notes

Only facets that reference exclusively the nodes in new_index are kept.

mask_nodes(mask)

Mask the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
mask	ndarray	A boolean mask array to filter the nodes DataFrame. This masking is applied in positional indexing (i.e. order, not key matters).	required

Returns:

Type	Description
	A new layer with the masked nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.

query_nodes(query_str)

Query the nodes DataFrame and return a new layer with the corresponding nodes and facets.

Parameters:

Name	Type	Description	Default
query_str	str	A query string to pass to pd.DataFrame.query on the nodes DataFrame.	required

Returns:

Type	Description
	A new layer with the queried nodes and corresponding facets.

Notes

When masking by nodes, only relationships that reference exclusively the remaining nodes are kept.