**MOVED** Adding Custom Plugins for Phy

Where to put customization code

• The phy user directory is ~/.phy/, where ~ is your home directory. On Linux, it is typically /home/username/.phy/.
• The phy user config file is ~/.phy/phy_config.py. It is a Python file. A default file is automatically created if needed. This file is used to add functionality to existing Phy user interface.

You can write the code either:

• In your phy user config file ~/.phy/phy_config.py
• Or in a separate Python file saved in ~/.phy/plugins/myplugin.py

How to load the plugins:

Add the following lines to ~/.phy/phy_config.py:

c = get_config()
c.Plugins.dirs = [r'path/to/your/plugins/folder']
c.TemplateGUI.plugins= ['MyPlugin1','MyPlugin2','MyPlugin3'] #names of python classes that defines different plugins 

Below are few examples of plugins

• Change the number of waveforms and other features

save the code below in the plugins director with some name e.g. ExampleNspikesViews.py.

"""Show how to change the number of displayed spikes in each view."""

from phy import IPlugin

class ExampleNspikesViewsPlugin(IPlugin):
    def attach_to_controller(self, controller):
        """Feel free to keep below just the values you need to change."""
        controller.n_spikes_waveforms = 100 # the number of waveforms displayed in the waveformview 
        controller.batch_size_waveforms = 1000 # 
        controller.n_spikes_features = 30000 #number of spikes shown in the featureview 
        controller.n_spikes_features_background = 1 # number of spikes shown (gray color) from other clusters in featureview (can not be zero)
        controller.n_spikes_amplitudes = 5000 # number of spikes in the amplitudeview
        controller.n_spikes_correlograms = 100000 # number of spikes used for calculating the correlograms

        # Number of "best" channels kept for displaying the waveforms.
        controller.model.n_closest_channels = 12

        # The best channels are selected among the N closest to the best (peak) channel if their
        # mean amplitude is greater than this fraction of the peak amplitude on the best channel.
        # If zero, just the N closest channels are kept as the best channels.
        controller.model.amplitude_threshold = 0

Then add the name of the class ExampleNspikesViewsPlugin to your ~/.phy/phy_config.py as below:

c.TemplateGUI.plugins = ['ExampleNspikesViewsPlugin']

• Customize the feature view

save the code below in the plugins director with some name, e.g. ExampleCustomFeatureView.py.

"""Show how to customize the subplot grid specifiction in the feature view."""

import re
from phy import IPlugin, connect
from phy.cluster.views import FeatureView


def my_grid():
    """In the grid specification, 0 corresponds to the best channel, 1
    to the second best, and so on. A, B, C refer to the PC components."""
    s = """
    0A,1A   0B,1A   0C,1A   time,1A 1A,1B
    0A,1B   0B,1B   0C,1B   time,1B 1B,1C
    0A,1C   0B,1C   0C,1C   time,1C 1C,1A
    time,0A time,0B time,0C 0A,2A   0A,2B
    0A,0B   0B,0C   0C,0A   1A,2A   1A,2B
    """.strip()
    return [[_ for _ in re.split(" +", line.strip())] for line in s.splitlines()]


class ExampleCustomFeatureViewPlugin(IPlugin):
    def attach_to_controller(self, controller):
        @connect
        def on_view_attached(view, gui):
            if isinstance(view, FeatureView):
                # We change the specification of the subplots here.
                view.set_grid_dim(my_grid())

Then add the name of the class ExampleCustomFeatureViewPlugin to your ~/.phy/phy_config.py as below:

c.TemplateGUI.plugins = ['ExampleCustomFeatureViewPlugin']

• Change colors of clusters in clusterview

save the code below in the plugins directory with some name ExampleClusterViewStyling.py.

"""Show how to customize the styling of the cluster view with CSS."""

from phy import IPlugin
from phy.cluster.supervisor import ClusterView


class ExampleClusterViewStylingPlugin(IPlugin):
    def attach_to_controller(self, controller):
        # We add a custom CSS style to the ClusterView.
        ClusterView._styles += """

            /* This CSS selector represents all rows for good clusters. */
            table tr[data-group='mua'] {

                /* We change the text color. Many other CSS attributes can be changed,
                such as background-color, the font weight, etc. */
                color: orange;
            }
            table tr[data-group='noise'] {

                /* We change the text color. Many other CSS attributes can be changed,
                such as background-color, the font weight, etc. */
                color: red;
            }
            table tr[data-group='good'] {

                /* We change the text color. Many other CSS attributes can be changed,
                such as background-color, the font weight, etc. */
                color: pink;
            }

        """

Then add the name of the class ExampleClusterViewStylingPlugin to your ~/.phy/phy_config.py as below:

c.TemplateGUI.plugins = ['ExampleClusterViewStylingPlugin']