4

I wrote a script for modeling the evolution of a pandemic (with graphs and scatter plots). I tried several libraries to display results in real-time (8 countries x 500 particles):

  • Matplotlib (not fast enough)
  • PyQtGraph (better but still not fast enough)
  • OpenGL (good, but I did not find how to use it in 2D efficiently, using subplots, titles, legends...)
  • Bokeh (good, but the scatter plots "blink" each time their particles turn color. Code is here if you are interested)

That is why I am turning now to VisPy.

I am using a class Visualizer to display the results, with the method app.Timer().connect to manage the real-time side. Pandemic code is here.

from Pandemic import *
from vispy.plot import Fig
from vispy import app

class Visualizer:
    def __init__(self, world):
        self.fig = Fig()
        self.world = world
        self.traces = {}

        #Scatter plots
        for idx, c in world.countries.items():
            pos_x = idx % self.world.nb_cols
            pos_y = idx // self.world.nb_cols
            subplot = self.fig[pos_y, pos_x]
            data = np.array([c.x_coord, c.y_coord]).reshape(-1,2)
            self.traces[idx] = subplot.plot(data, symbol='o', width=0, face_color=c.p_colors, title='Country {}'.format(idx+1))

    def display(self): 
        for idx, c in self.world.countries.items():
            data = np.array([c.x_coord, c.y_coord]).reshape(-1,2)
            self.traces[idx].set_data(data, face_color=c.p_colors)

    def update(self, event):
        self.world.update(quarantine=False)
        self.display()

    def animation(self):
        self.timer = app.Timer()
        self.timer.connect(self.update)
        self.timer.start(0)
        self.start()

    def start(self):
        if (sys.flags.interactive != 1):
            self.status = app.run()


if __name__ == '__main__':
    w = World(move=0.001)
    for i in range(8):
        w.add_country(nb_S=500)
    v = Visualizer(w)
    v.animation()

The scatter plots "blink" each time their particles turn color, as with Bokeh. Am I doing something wrong?

Is there a more efficient way for real-time display, maybe using vispy.gloo or vispy.scene? (It is slower than pyqtgraph.opengl for the moment)

Skryge
  • 81
  • 1
  • 9

1 Answers1

2

We can efficiently plot in real time by using vispy.gloo module to leverage the power of GPU. Here is one way of doing it :

1) Build a class that inherits vispy.app.Canvas class.

2) Create an OpenGL Program whose inputs are shaders. This object allows us to link our data to shader variables. Each dot on the canvas depends on these variable values (describing its coordinate, color, etc). For example, it is way harder for displaying text (titles, labels, etc) than with Matplotlib library. Here is a deeper explanation of the process.

3) Set a timer connected to the function we want to call repeatedly (real-time side).

The vispy.scene module, dedicated to the high-level visualization interfaces for scientists, is still experimental. Maybe this is the reason why my first code got some bugs.

Here is my new code.

Skryge
  • 81
  • 1
  • 9