neuror.cut_plane.viewer¶

App to find cut planes with arbitrary cut planes orientations with the help of a manual hint.

Functions

`create_plane`	Create a 3d plane using a center position and a quaternion for orientation.
`display_click_data`	Callback that redraw everything when sliders are changed.
`export`	Write the final file cut-plane.json to disk.
`optimize`	Optimize cut plane parameters.
`set_neuron`	Globally loads the neuron.
`update_output`	Update histo when sliders are changed.
`update_post_optim_x_rotate`	Dash callback.
`update_post_optim_x_translate`	Dash callback.
`update_post_optim_y_rotate`	Dash callback.
`update_post_optim_y_translate`	Dash callback.
`update_post_optim_z_rotate`	Dash callback.
`update_post_optim_z_translate`	Dash callback.

Classes

NumpyEncoder

JSON encoder that handles numpy types.

class neuror.cut_plane.viewer.NumpyEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]¶

Bases: JSONEncoder

JSON encoder that handles numpy types.

In python3, numpy types don’t serialize to correctly, so a custom converter is needed.

default(o)[source]¶

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

neuror.cut_plane.viewer.create_plane(pos, quat)[source]¶

Create a 3d plane using a center position and a quaternion for orientation.

Args :: pos: x,y,z position of the plane’s center (array([x,y,z])) quat: quaternion representing the orientations (Quaternion)
Returns :: dict: A square surface to the plotly format

neuror.cut_plane.viewer.display_click_data(rot_x, rot_y, rot_z, transl_x, transl_y, transl_z, hide, layout)[source]¶: Callback that redraw everything when sliders are changed.

neuror.cut_plane.viewer.export(n_clicks, rot_x, rot_y, rot_z, transl_x, transl_y, transl_z, output_path)[source]¶: Write the final file cut-plane.json to disk.

neuror.cut_plane.viewer.optimize(n_clicks, rot_x, rot_y, rot_z, transl_x, transl_y, transl_z)[source]¶: Optimize cut plane parameters.

neuror.cut_plane.viewer.set_neuron(filename)[source]¶: Globally loads the neuron.

neuror.cut_plane.viewer.update_output(rot_x, rot_y, rot_z, transl_x, transl_y, transl_z)[source]¶: Update histo when sliders are changed.

neuror.cut_plane.viewer.update_post_optim_x_rotate(params)[source]¶: Dash callback.

neuror.cut_plane.viewer.update_post_optim_x_translate(params)[source]¶: Dash callback.

neuror.cut_plane.viewer.update_post_optim_y_rotate(params)[source]¶: Dash callback.

neuror.cut_plane.viewer.update_post_optim_y_translate(params)[source]¶: Dash callback.

neuror.cut_plane.viewer.update_post_optim_z_rotate(params)[source]¶: Dash callback.

neuror.cut_plane.viewer.update_post_optim_z_translate(params)[source]¶: Dash callback.