"""
===========================================
Reconstruct with Diffusion Spectrum Imaging
===========================================

We show how to apply Diffusion Spectrum Imaging [Wedeen08]_ to
diffusion MRI datasets of Cartesian keyhole diffusion gradients.

First import the necessary modules:
"""

import numpy as np
from dipy.core.gradients import gradient_table
from dipy.data import get_fnames, get_sphere
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.image import load_nifti
from dipy.reconst.dsi import DiffusionSpectrumModel

"""
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, voxel_size = load_nifti(fraw, return_voxsize=True)
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)

"""
data.shape ``(96, 96, 60, 203)``

This dataset has anisotropic voxel sizes, therefore reslicing is necessary.

Instantiate the Model and apply it to the data.
"""

dsmodel = DiffusionSpectrumModel(gtab)

"""
Lets just use one slice only from the data.
"""

dataslice = data[:, :, data.shape[2] // 2]

dsfit = dsmodel.fit(dataslice)

"""
Load an odf reconstruction sphere
"""

sphere = get_sphere('repulsion724')

"""
Calculate the ODFs with this specific sphere
"""

ODF = dsfit.odf(sphere)

print('ODF.shape (%d, %d, %d)' % ODF.shape)

"""
ODF.shape ``(96, 96, 724)``

In a similar fashion it is possible to calculate the PDFs of all voxels
in one call with the following way
"""

PDF = dsfit.pdf()

print('PDF.shape (%d, %d, %d, %d, %d)' % PDF.shape)

"""
PDF.shape ``(96, 96, 17, 17, 17)``

We see that even for a single slice this PDF array is close to 345 MBytes so we
really have to be careful with memory usage when use this function with a full
dataset.

The simple solution is to generate/analyze the ODFs/PDFs by iterating through
each voxel and not store them in memory if that is not necessary.
"""

from dipy.core.ndindex import ndindex

for index in ndindex(dataslice.shape[:2]):
    pdf = dsmodel.fit(dataslice[index]).pdf()

"""
If you really want to save the PDFs of a full dataset on the disc we recommend
using memory maps (``numpy.memmap``) but still have in mind that even if you do
that for example for a dataset of volume size ``(96, 96, 60)`` you will need
about 2.5 GBytes which can take less space when reasonable spheres
(with < 1000 vertices) are used.

Let's now calculate a map of Generalized Fractional Anisotropy (GFA) [Tuch04]_
using the DSI ODFs.
"""

from dipy.reconst.odf import gfa

GFA = gfa(ODF)

import matplotlib.pyplot as plt

fig_hist, ax = plt.subplots(1)
ax.set_axis_off()
plt.imshow(GFA.T)
plt.savefig('dsi_gfa.png', bbox_inches='tight', origin='lower', cmap='gray')

"""
.. figure:: dsi_gfa.png
   :align: center

See also :ref:`example_reconst_dsi_metrics` for calculating different types
of DSI maps.


.. [Wedeen08] Wedeen et al., Diffusion spectrum magnetic resonance imaging
              (DSI) tractography of crossing fibers, Neuroimage, vol 41, no 4,
              1267-1277, 2008.

.. [Tuch04] Tuch, D.S, Q-ball imaging, MRM, vol 52, no 6, 1358-1372, 2004.

.. include:: ../links_names.inc

"""
