io

load_json(filename, key=None)

Load a point cloud or skeleton file from a json file.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the point cloud or skeleton file to parse.	required
key	str	The key of the JSON dictionary containing the point cloud or skeleton coordinates to load.	None

Returns:

Type	Description
ndarray	The XYZ coordinates of the point cloud or skeleton.

Source code in skeleton_refinement/io.py

def load_json(filename, key=None):
    """Load a point cloud or skeleton file from a json file.
    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the point cloud or skeleton file to parse.
    key : str, optional
        The key of the JSON dictionary containing the point cloud or skeleton coordinates to load.

    Returns
    -------
    numpy.ndarray
        The XYZ coordinates of the point cloud or skeleton.
    """
    import json
    with open(filename, mode='rb') as f:
        X = json.load(f)

    if key is not None:
        X = X[key]
    return np.array(X)

load_nx(filename, key='position')

Load a tree graph from a pickled networkx file.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the tree graph file to parse.	required

Returns:

Type	Description
ndarray	The XYZ coordinates of the point cloud or skeleton.

Source code in skeleton_refinement/io.py

def load_nx(filename, key='position'):
    """Load a tree graph from a pickled networkx file.
    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the tree graph file to parse.

    Returns
    -------
    numpy.ndarray
        The XYZ coordinates of the point cloud or skeleton.
    """
    import pickle
    with open(filename, mode='rb') as f:
        G = pickle.load(f)

    X = []
    for node in G.nodes:
        X.append(G.nodes[node][key])

    return np.array(X)

load_ply(filename)

Load a point cloud coordinates.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the point cloud ofile to parse.	required

Returns:

Type	Description
ndarray	The XYZ coordinates of the point cloud or skeleton.

Source code in skeleton_refinement/io.py

def load_ply(filename):
    """Load a point cloud coordinates.

    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the point cloud ofile to parse.

    Returns
    -------
    numpy.ndarray
        The XYZ coordinates of the point cloud or skeleton.
    """
    from plyfile import PlyData
    plydata = PlyData.read(filename)
    X = np.array([plydata['vertex']['x'], plydata['vertex']['y'], plydata['vertex']['z']]).T
    return X

load_xyz(filename)

Load a point cloud or skeleton file saved as a series of space-separated XYZ coordinates.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the point cloud or skeleton file to parse.	required

Returns:

Type	Description
ndarray	The XYZ coordinates of the point cloud or skeleton.

Source code in skeleton_refinement/io.py

def load_xyz(filename):
    """Load a point cloud or skeleton file saved as a series of space-separated XYZ coordinates.

    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the point cloud or skeleton file to parse.

    Returns
    -------
    numpy.ndarray
        The XYZ coordinates of the point cloud or skeleton.
    """
    f = open(filename, "r")
    lines = f.readlines()
    org_x = []
    org_y = []
    org_z = []
    for l in lines:
        org_x.append(float(l.split(' ')[0]))
        org_y.append(float(l.split(' ')[1]))
        org_z.append(float(l.split(' ')[2]))
    f.close()
    X = np.column_stack((org_x, org_y, org_z))
    return X

save_json(filename, G, **kwargs)

Save a tree graph to a JSON file.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the JSON file to write.	required
G	Graph	Graph to write.	required

Source code in skeleton_refinement/io.py

def save_json(filename, G, **kwargs):
    """Save a tree graph to a JSON file.

    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the JSON file to write.
    G : networkx.Graph
        Graph to write.
    """
    import json
    data = {
        "points": [G.nodes[node]['position'] for node in G.nodes],
        "lines": list(G.edges),
    }
    if 'indent' not in kwargs:
        kwargs.update({'indent': 2})
    with open(filename, 'w') as f:
        f.writelines(json.dumps(data, **kwargs))
    return

save_nx(filename, G, **kwargs)

Save a tree graph to a pickle file.

Parameters:

Name	Type	Description	Default
filename	str or Path	Path to the pickle file to write.	required
G	Graph	Graph to write.	required

Source code in skeleton_refinement/io.py

def save_nx(filename, G, **kwargs):
    """Save a tree graph to a pickle file.

    Parameters
    ----------
    filename : str or pathlib.Path
        Path to the pickle file to write.
    G : networkx.Graph
        Graph to write.
    """
    import pickle
    if 'protocol' not in kwargs:
        kwargs['protocol'] = pickle.HIGHEST_PROTOCOL
    if isinstance(filename, str):
        filename = Path(filename)
    with filename.open(mode='wb') as f:
        pickle.dump(G, f, **kwargs)
    return