plotting.py

This module contains functions to create nice plots.

class neurons.plotting.CurrentPlot(neurons)

A plot of the current of neurons.

Create the plot by adding the values of the currents at one timestep with CurrentPlot,add(values).

Example

The image above was created by following code:

c = CurrentPlot(3)
c.add(np.array([1, 5, 4]))
c.add(np.array([2, 4, 4]))
c.add(np.array([3, 5, 4]))
c.add(np.array([4, 3, 4]))
c.show_plot()
plt.show()

save_plot(filename='plot.png')

Saves the plot.

Parameters:filename (String) – Name of the file. Default: ‘plot.png’

class neurons.plotting.CurrentsHeatmapAnimation(fps=30)

Example

The video above was created by following code:

cha = CurrentsHeatmapAnimation()
for i in range(300):
    cha.add(np.random.randn(1, 20))
cha.show_animation()
plt.show()

Initialize the Currents Animation :param fps: How many frames-per-second the animation should be played. Default: 30 :return: None

add(currents)

Adds currents to the end of the animation :param currents: :return: None

class neurons.plotting.PSTH(spiketrain, binsize=20)

Peri-Stimulus Time Histogram

Example

The image above was created by following code:

spikes = np.random.randint(0, 2, size=(2, 200))
a = PSTH(spikes)
a.show_plot()
a.save_plot()
plt.show()

Initialize the PSTH plot with a spiketrain

Parameters:

• spiketrain (Numpy array) – The spiketrain to be plotted
• binsize – The size of the bins

Returns:

None

save_plot(filename=None)

Saves the plot.

Parameters:filename (String) – Name of the file. Default: ‘plot.png’

show_plot(neuron_indices=None)

Shows the PSTH plot.

Parameters:neuron_indices (List or Tuple) – The indices of the neurons to be plotted

class neurons.plotting.WeightHeatmapAnimation(fps=30)

Show an animation of the weights (as a heatmap).

Example

The video above was created by following code:

w = WeightHeatmapAnimation()
for i in range(300):
    w.add(np.array([[i/300, 1], [1, 3]]))
w.show_animation()
plt.show()

Initialize the Weight Animation

Parameters:fps – How many frames-per-second the animation should be played. Default: 30 Returns:None

add(weights)

Add weights to the end of animation.

Parameters:weights (Numpy array) – The weight matrix to be shown. Returns:None