pymaid.url_to_coordinates

pymaid.url_to_coordinates(coords, stack_id, active_skeleton_id=None, active_node_id=None, zoom=0, tool='tracingtool', open_browser=False, remote_instance=None)[source]

Generate URL to a location.

Parameters:

  • coords (list | np.ndarray | pandas.DataFrame) – x, y, z coordinates.

  • stack_id (int | list/array of ints) – ID of the image stack you want to link to. Depending on your setup this parameter might be overriden by local user settings.

  • active_skeleton_id (int | list/array of ints, optional) – Skeleton ID of the neuron that should be selected.

  • active_node_id (int | list/array of ints, optional) – Node/Connector ID of the node that should be active.

  • zoom (int, optional) –

  • tool (str, optional) –

  • open_browser (bool, optional) – If True will open all generated URLs as new tabs in the standard webbrowser.

  • remote_instance (CatmaidInstance, optional) – If not passed directly, will try using global.

Returns:

URL(s) to the coordinates provided.

Return type:

str | list of str

Examples

>>> # Get URL for a single coordinate
>>> url = pymaid.url_to_coordinates([1000, 1000, 1000], stack_id=5)
>>> # Get URLs for all low-confidence nodes of a neuron
>>> n = pymaid.get_neuron(27295)
>>> low_c = n.nodes.loc[n.nodes.confidence < 5]
>>> urls = pymaid.url_to_coordinates(low_c[['x', 'y', 'z']].values,
...                                  stack_id=5,
...                                  active_node_id=low_c.node_id.values)