PyBroMo - GUI Trajectory explorer

This notebook is part of [PyBroMo](http://tritemio.github.io/PyBroMo/) a python-based single-molecule Brownian motion diffusion simulator that simulates confocal [smFRET](http://en.wikipedia.org/wiki/Single-molecule_FRET) experiments. You can find the full list of notebooks in [Usage Examples](http://tritemio.github.io/PyBroMo/#usage-examples).

Overview

In this notebook implements an interactive 3-D trajectories visualizer. To visualize trajectories you need simulatte the trajectories first.

For more info see PyBroMo Homepage.

Simulation setup

Together with a few standard python libraries we import PyBroMo using the short name pbm. All PyBroMo functions will be available as pbm.something.



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%matplotlib inline
import numpy as np
import tables
import matplotlib.pyplot as plt
plt.rcParams['path.simplify_threshold'] = 1.0
import pybromo as pbm
print('Numpy version:', np.__version__)
print('Matplotlib version:', plt.matplotlib.__version__)
print('PyTables version:', tables.__version__)
print('PyBroMo version:', pbm.__version__)

Load trajectories



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#SIM_DIR = r'E:\Data\pybromo'



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S = pbm.ParticlesSimulation.from_datafile('016') #, path=SIM_DIR)

Plotting the emission



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%matplotlib qt



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p = pbm.plotter.EmissionPlotter(S, duration=0.1, decimate=100, color_pop=False)

For simulations using radial = False (i.e. the 3D trajectories saved):



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p = pbm.plotter.TrackEmPlotter(S, duration=0.005, decimate=20)

For simulations using radial = True (i.e. the z-r 2D trajectories saved):



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p = pbm.plotter.TrackEmPlotterR(S, duration=0.01, decimate=100)



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