old_contents: """
  Generate nice plots providing additional information
  """
  import sys
  
  import numpy as np
  import matplotlib.pylab as plt
  
  
  def neural_spike():
      """ Plot various neural spikes
      """
      def do_plot(cell_evo):
          """ Plot [cAMP] for single cell over time
          """
          plt.plot(range(len(cell_evo)), cell_evo)
  
          plt.title('cAMP concentration in single cell')
          plt.xlabel('t')
          plt.ylabel('cAMP concentration')
  
          #plt.savefig('images/neural_spike.png', bbox_inches='tight', dpi=300)
          plt.show()
  
      camp, pacemaker = np.load(sys.argv[1])
      camp = np.rollaxis(camp, 0, 3)
  
      width, height, depth = camp.shape
      for j in range(width):
          for i in range(height):
              do_plot(camp[i, j])
  
  
  if __name__ == '__main__':
      neural_spike()
  
new_contents: """
  Generate nice plots providing additional information
  """
  import sys
  
  import numpy as np
  import matplotlib.pylab as plt
  
  from singularity_finder import compute_tau
  
  
  def neural_spike():
      """ Plot various neural spikes
      """
      def do_plot(cell_evo):
          """ Plot [cAMP] for single cell over time
          """
          plt.plot(range(len(cell_evo)), cell_evo)
  
          plt.title('cAMP concentration in single cell')
          plt.xlabel('t')
          plt.ylabel('cAMP concentration')
  
          #plt.savefig('images/neural_spike.png', bbox_inches='tight', dpi=300)
          plt.show()
  
      camp, pacemaker = np.load(sys.argv[1])
      camp = np.rollaxis(camp, 0, 3)
  
      width, height, depth = camp.shape
      for j in range(width):
          for i in range(height):
              do_plot(camp[i, j])
  
  def lagged_phase_space():
      """ Plot phase space lagged by tau
      """
      def do_plot(cell_evo):
          x = []
          y = []
          for t in range(len(cell_evo) - tau):
              x.append(cell_evo[t + tau])
              y.append(cell_evo[t])
  
          plt.plot(x, y)
  
          plt.title(r'Lagged phase space of neural spike ($\tau = %d$)' % tau)
          plt.xlabel(r'$x_{ij}(t - \tau)$')
          plt.ylabel(r'$x_{ij}(t)$')
  
          #plt.savefig('images/lagged_phase_space.png', bbox_inches='tight', dpi=300)
          plt.show()
  
      camp, pacemaker = np.load(sys.argv[1])
      camp = np.rollaxis(camp, 0, 3)
  
      tau = compute_tau(camp)
  
      width, height, depth = camp.shape
      for j in range(width):
          for i in range(height):
              do_plot(camp[i, j])
  
  
  if __name__ == '__main__':
      #neural_spike()
      lagged_phase_space()
  
subject: Add lagged phase space plot