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).

PSTH Plot

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

PSTH Plot

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