"""
===========================
Calculate SHORE scalar maps
===========================

We show how to calculate two SHORE-based scalar maps: return to origin
probability (RTOP) [Descoteaux2011]_ and mean square displacement (MSD)
[Wu2007]_, [Wu2008]_ on your data. SHORE can be used with any multiple b-value
dataset like multi-shell or DSI.

First import the necessary modules:
"""

import numpy as np
import matplotlib.pyplot as plt
from dipy.core.gradients import gradient_table
from dipy.data import get_fnames
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.image import load_nifti
from dipy.reconst.shore import ShoreModel

"""
Download and get the data filenames for this tutorial.
"""

fraw, fbval, fbvec = get_fnames('taiwan_ntu_dsi')

"""
img contains a nibabel Nifti1Image object (data) and gtab contains a
GradientTable object (gradient information e.g. b-values). For example, to
read the b-values it is possible to write print(gtab.bvals).

Load the raw diffusion data and the affine.
"""

data, affine = load_nifti(fraw)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
bvecs[1:] = (bvecs[1:] /
             np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
gtab = gradient_table(bvals, bvecs)
print('data.shape (%d, %d, %d, %d)' % data.shape)

"""
Instantiate the Model.
"""

asm = ShoreModel(gtab)

"""
Let's just use only one slice only from the data.
"""

dataslice = data[30:70, 20:80, data.shape[2] // 2]

"""
Fit the signal with the model and calculate the SHORE coefficients.
"""

asmfit = asm.fit(dataslice)

"""
Calculate the analytical RTOP on the signal
that corresponds to the integral of the signal.
"""

print('Calculating... rtop_signal')
rtop_signal = asmfit.rtop_signal()

"""
Now we calculate the analytical RTOP on the propagator,
that corresponds to its central value.
"""

print('Calculating... rtop_pdf')
rtop_pdf = asmfit.rtop_pdf()
"""
In theory, these two measures must be equal,
to show that we calculate the mean square error on this two measures.
"""

mse = np.sum((rtop_signal - rtop_pdf) ** 2) / rtop_signal.size
print("MSE = %f" % mse)

"""
MSE = 0.000000

Let's calculate the analytical mean square displacement on the propagator.
"""

print('Calculating... msd')
msd = asmfit.msd()

"""
Show the maps and save them to a file.
"""

fig = plt.figure(figsize=(6, 6))
ax1 = fig.add_subplot(2, 2, 1, title='rtop_signal')
ax1.set_axis_off()
ind = ax1.imshow(rtop_signal.T, interpolation='nearest', origin='lower')
plt.colorbar(ind)
ax2 = fig.add_subplot(2, 2, 2, title='rtop_pdf')
ax2.set_axis_off()
ind = ax2.imshow(rtop_pdf.T, interpolation='nearest', origin='lower')
plt.colorbar(ind)
ax3 = fig.add_subplot(2, 2, 3, title='msd')
ax3.set_axis_off()
ind = ax3.imshow(msd.T, interpolation='nearest', origin='lower', vmin=0)
plt.colorbar(ind)
plt.savefig('SHORE_maps.png')

"""
.. figure:: SHORE_maps.png
   :align: center

   RTOP and MSD calculated using the SHORE model.

References
----------

.. [Descoteaux2011] Descoteaux M. et al., "Multiple q-shell diffusion
   propagator imaging", Medical Image Analysis, vol 15, No. 4, p. 603-621,
   2011.

.. [Wu2007] Wu Y. et al., "Hybrid diffusion imaging", NeuroImage, vol 36, p.
   617-629, 2007.

.. [Wu2008] Wu Y. et al., "Computation of Diffusion Function Measures in
   q-Space Using Magnetic Resonance Hybrid Diffusion Imaging", IEEE
   TRANSACTIONS ON MEDICAL IMAGING, vol. 27, No. 6, p. 858-865, 2008.

.. include:: ../links_names.inc

"""