.. AUTO-GENERATED FILE -- DO NOT EDIT!

.. _example_simulate_multi_tensor:


======================
MultiTensor Simulation
======================

In this example we show how someone can simulate the signal and the ODF of a
single voxel using a MultiTensor.

::
  
  import numpy as np
  from dipy.sims.voxel import multi_tensor, multi_tensor_odf
  from dipy.data import get_sphere
  

For the simulation we will need a GradientTable with the b-values and b-vectors
Here we use the one we created in :ref:`example_gradients_spheres`.

::
  
  from gradients_spheres import gtab
  

In ``mevals`` we save the eigenvalues of each tensor.

::
  
  mevals = np.array([[0.0015, 0.0003, 0.0003],
                     [0.0015, 0.0003, 0.0003]])
  

In ``angles`` we save in polar coordinates (:math:`\theta, \phi`) the principal
axis of each tensor.

::
  
  angles = [(0, 0), (60, 0)]
  

In ``fractions`` we save the percentage of the contribution of each tensor.

::
  
  fractions = [50, 50]
  

The function ``multi_tensor`` will return the simulated signal and an array
with the principal axes of the tensors in cartesian coordinates.

::
  
  signal, sticks = multi_tensor(gtab, mevals, S0=100, angles=angles,
                           fractions=fractions, snr=None)
  

We can also add Rician noise with a specific SNR.

::
  
  signal_noisy, sticks = multi_tensor(gtab, mevals, S0=100, angles=angles,
                           fractions=fractions, snr=20)
  
  
  import matplotlib.pyplot as plt
  
  plt.plot(signal, label='noiseless')
  
  plt.plot(signal_noisy, label='with noise')
  plt.legend()
  #plt.show()
  plt.savefig('simulated_signal.png')
  

.. figure:: simulated_signal.png
   :align: center

   **Simulated MultiTensor signal**

::
  

For the ODF simulation we will need a sphere. Because we are interested in a
simulation of only a single voxel, we can use a sphere with very high
resolution. We generate that by subdividing the triangles of one of DIPY_'s
cached spheres, which we can read in the following way.

::
  
  sphere = get_sphere('repulsion724')
  sphere = sphere.subdivide(2)
  
  odf = multi_tensor_odf(sphere.vertices, mevals, angles, fractions)
  
  from dipy.viz import window, actor
  
  # Enables/disables interactive visualization
  interactive = False
  
  ren = window.Renderer()
  
  odf_actor = actor.odf_slicer(odf[None, None, None, :], sphere=sphere, colormap='plasma')
  odf_actor.RotateX(90)
  
  ren.add(odf_actor)
  
  print('Saving illustration as multi_tensor_simulation')
  window.record(ren, out_path='multi_tensor_simulation.png', size=(300, 300))
  if interactive:
      window.show(ren)
  
  

.. figure:: multi_tensor_simulation.png
   :align: center

   Simulating a MultiTensor ODF.

.. include:: ../links_names.inc



.. admonition:: Example source code

   You can download :download:`the full source code of this example <./simulate_multi_tensor.py>`. This same script is also included in the dipy source distribution under the :file:`doc/examples/` directory.