How to add your own plot

This guide shows you how to add a plot to the Image Plots, Line Plots or Probe Plots menu, computed from the data the GUI has loaded. The example adds a line plot of the number of spikes along the probe.

How plots are found

Each shank has a plot loader, an instance of PlotLoader. When the plots are built, the loader calls every one of its methods whose name starts with image_, scatter_, line_, probe_ or feature_. Each returns a dict of {menu name: plot data}, where the plot data is an ImageData, ScatterData, LineData or ProbeData from the same module. A plugin adds a plot by attaching such a method to each shank’s loader, before the plots are built.

Steps

  1. Create ibl_alignment_gui/plugins/my_plots.py:

    from types import MethodType

import numpy as np

from ibl_alignment_gui.loaders.plot_loader import LineData, skip_missing
from ibl_alignment_gui.utils.helpers import shank_loop
from iblutil.util import Bunch

PLUGIN_NAME = 'My Plots'


def setup(controller):
    """Register the plugin, and the function that adds its plots when data is loaded."""
    controller.plugins[PLUGIN_NAME] = Bunch()
    controller.plugins[PLUGIN_NAME]['activated'] = True
    controller.plugins[PLUGIN_NAME]['load_data'] = add_plots


@shank_loop
def add_plots(_, items, **kwargs):
    """Attach the plot methods to the plot loader of every shank."""
    plots = items.model.loaders['plots']
    plots.line_spike_count = MethodType(line_spike_count, plots)


@skip_missing(['spikes'])
def line_spike_count(self):
    """Line plot of the number of spikes in 20 µm bins along the probe."""
    bins = np.arange(self.chn_min, self.chn_max + 20, 20)
    counts, _ = np.histogram(self.spike_depths, bins)
    depths = bins[:-1] + 10

    line = LineData(
        x=counts,
        y=depths,
        xrange=np.array([0, np.max(counts)]),
        levels=np.array([0, np.max(counts)]),
        default_levels=np.array([0, np.max(counts)]),
        xaxis='Number of spikes',
    )
    return {'Spike count': line}

    • load_data is called each time a session is loaded, after the shanks are created and before the plots are built.

    • shank_loop calls add_plots once for every shank and configuration.

    • skip_missing(['spikes']) skips the plot when the session has no spike sorting.

    • Inside the method, self is the plot loader. self.data holds the loaded data, and properties such as self.spike_depths give the spikes of the units selected by the current filter, so the plot follows the Filter Plots menu.

  2. Register the plugin in ibl_alignment_gui/plugins/add_plugins.py. Import its setup, and call it in Plugins.__init__ with the other plugins:

    from ibl_alignment_gui.plugins.my_plots import setup as setup_my_plots

class Plugins:
    def __init__(self, controller):
        ...
        setup_my_plots(controller)

  3. Start the GUI and load a session. Spike count is in the Line Plots menu.

For an image or probe plot, return an ImageData or ProbeData and start the method name with image_ or probe_. The built-in plots in plot_loader.py are worked examples of each.