{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# [PyBroMo](http://tritemio.github.io/PyBroMo/) - GUI Trajectory explorer"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<small><i>\n",
    "This notebook is part of [PyBroMo](http://tritemio.github.io/PyBroMo/) a \n",
    "python-based single-molecule Brownian motion diffusion simulator \n",
    "that simulates confocal [smFRET](http://en.wikipedia.org/wiki/Single-molecule_FRET)\n",
    "experiments. You can find the full list of notebooks in \n",
    "[Usage Examples](http://tritemio.github.io/PyBroMo/#usage-examples).\n",
    "</i></small>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## *Overview*\n",
    "\n",
    "*In this notebook implements an interactive 3-D trajectories visualizer. To visualize trajectories you need simulatte the trajectories first.*\n",
    "\n",
    "*For more info see [PyBroMo Homepage](http://tritemio.github.io/PyBroMo/)*."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Simulation setup"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Together with a few standard python libraries we import **PyBroMo** using the short name `pbm`. \n",
    "All **PyBroMo** functions will be available as `pbm.`*something*."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "import numpy as np\n",
    "import tables\n",
    "import matplotlib.pyplot as plt\n",
    "plt.rcParams['path.simplify_threshold'] = 1.0\n",
    "import pybromo as pbm\n",
    "print('Numpy version:', np.__version__)\n",
    "print('Matplotlib version:', plt.matplotlib.__version__)\n",
    "print('PyTables version:', tables.__version__)\n",
    "print('PyBroMo version:', pbm.__version__)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load trajectories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#SIM_DIR = r'E:\\Data\\pybromo'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "S = pbm.ParticlesSimulation.from_datafile('016') #, path=SIM_DIR)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plotting the emission"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib qt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "p = pbm.plotter.EmissionPlotter(S, duration=0.1, decimate=100, color_pop=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For simulations using `radial = False` (i.e. the 3D trajectories saved):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "p = pbm.plotter.TrackEmPlotter(S, duration=0.005, decimate=20)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For simulations using `radial = True` (i.e. the z-r 2D trajectories saved):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "p = pbm.plotter.TrackEmPlotterR(S, duration=0.01, decimate=100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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