In [29]:

    

%matplotlib inline


    

In [30]:

    

from dipy.reconst.dti import fractional_anisotropy, color_fa
from argparse import ArgumentParser
from scipy import ndimage
import os
import re
import numpy as np
import nibabel as nb
import sys
import matplotlib

matplotlib.use('Agg')  # very important above pyplot import
import matplotlib.pyplot as plt


    

    




/usr/lib/python2.7/dist-packages/matplotlib/__init__.py:1352: UserWarning:  This call to matplotlib.use() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  warnings.warn(_use_error_msg)

In [2]:

    

cd


    

    




/root

In [3]:

    

ls


    

    




Aut1367.nii           pipeline.ipynb
TIFF_stack/           prototyping.ipynb
Untitled-Copy1.ipynb  sample0.tiff
Untitled-Copy2.ipynb  sample1.tiff
Untitled.ipynb        sample2.tiff
bigtiff/              sample3.tiff
final.ipynb           seelviz/
index.html            tmp/
miniTIFF/             v100_ch0_tensorfsl_dogsig1_gausig2.3.nii

In [4]:

    

from dipy.reconst.dti import from_lower_triangular


    

In [5]:

    

img = nb.load('v100_ch0_tensorfsl_dogsig1_gausig2.3.nii')


    

In [6]:

    

data = img.get_data()


    

In [7]:

    

output = from_lower_triangular(data)


    

In [8]:

    

output_ds = output[4250:4300, 250:300, :, :, :]


    

In [9]:

    

print output.shape
print output_ds.shape


    

    




(5000, 5000, 5, 3, 3)
(50, 50, 5, 3, 3)

In [10]:

    

FA = fractional_anisotropy(output_ds)


    

In [11]:

    

FA = np.clip(FA, 0, 1)


    

In [12]:

    

FA[np.isnan(FA)] = 0


    

In [13]:

    

print FA.shape


    

    




(50, 50, 5, 3)

In [14]:

    

from dipy.reconst.dti import decompose_tensor


    

In [15]:

    

evalues, evectors = decompose_tensor(output_ds)


    

In [16]:

    

print evectors[..., 0, 0].shape
print evectors.shape[-2:]


    

    




(50, 50, 5)
(3, 3)

In [17]:

    

print FA[:, :, :, 0].shape


    

    




(50, 50, 5)

In [18]:

    

RGB = color_fa(FA[:, :, :, 0], evectors)


    

In [19]:

    

nb.save(nb.Nifti1Image(np.array(255 * RGB, 'uint8'), img.get_affine()), 'tensor_rgb_upper.nii.gz')


    

    




/usr/local/lib/python2.7/dist-packages/ipykernel/__main__.py:1: DeprecationWarning: get_affine method is deprecated.
Please use the ``img.affine`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  if __name__ == '__main__':

In [20]:

    

def plot_rgb(im):
    plt.rcParams.update({'axes.labelsize': 'x-large',
                         'axes.titlesize': 'x-large'})

    if im.shape == (182, 218, 182):
        x = [78, 90, 100]
        y = [82, 107, 142]
        z = [88, 103, 107]
    else:
        shap = im.shape
        x = [int(shap[0]*0.35), int(shap[0]*0.51), int(shap[0]*0.65)]
        y = [int(shap[1]*0.35), int(shap[1]*0.51), int(shap[1]*0.65)]
        z = [int(shap[2]*0.35), int(shap[2]*0.51), int(shap[2]*0.65)]
    coords = (x, y, z)

    labs = ['Sagittal Slice (YZ fixed)',
            'Coronal Slice (XZ fixed)',
            'Axial Slice (XY fixed)']
    var = ['X', 'Y', 'Z']

    idx = 0
    for i, coord in enumerate(coords):
        for pos in coord:
            idx += 1
            ax = plt.subplot(3, 3, idx)
            ax.set_title(var[i] + " = " + str(pos))
            if i == 0:
                image = ndimage.rotate(im[pos, :, :], 90)
            elif i == 1:
                image = ndimage.rotate(im[:, pos, :], 90)
            else:
                image = im[:, :, pos]

            if idx % 3 == 1:
                ax.set_ylabel(labs[i])
                ax.yaxis.set_ticks([0, image.shape[0]/2, image.shape[0] - 1])
                ax.xaxis.set_ticks([0, image.shape[1]/2, image.shape[1] - 1])

            plt.imshow(image)

    fig = plt.gcf()
    fig.set_size_inches(12.5, 10.5, forward=True)
    return fig


    

In [21]:

    

affine = img.get_affine()

fa = nb.Nifti1Image(np.array(255 * RGB, 'uint8'), affine)
im = fa.get_data()


    

    




/usr/local/lib/python2.7/dist-packages/ipykernel/__main__.py:1: DeprecationWarning: get_affine method is deprecated.
Please use the ``img.affine`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  if __name__ == '__main__':

In [22]:

    

print np.asarray(fa)


    

    




<class 'nibabel.nifti1.Nifti1Image'>
data shape (50, 50, 5, 3)
affine: 
[[ 1.  0.  0.  1.]
 [ 0.  1.  0.  1.]
 [ 0.  0.  1.  1.]
 [ 0.  0.  0.  1.]]
metadata:
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr      : 348
data_type       : 
db_name         : 
extents         : 0
session_error   : 0
regular         : 
dim_info        : 0
dim             : [ 4 50 50  5  3  1  1  1]
intent_p1       : 0.0
intent_p2       : 0.0
intent_p3       : 0.0
intent_code     : none
datatype        : uint8
bitpix          : 8
slice_start     : 0
pixdim          : [ 1.  1.  1.  1.  1.  1.  1.  1.]
vox_offset      : 0.0
scl_slope       : nan
scl_inter       : nan
slice_end       : 0
slice_code      : unknown
xyzt_units      : 0
cal_max         : 0.0
cal_min         : 0.0
slice_duration  : 0.0
toffset         : 0.0
glmax           : 0
glmin           : 0
descrip         : 
aux_file        : 
qform_code      : unknown
sform_code      : aligned
quatern_b       : 0.0
quatern_c       : 0.0
quatern_d       : 0.0
qoffset_x       : 1.0
qoffset_y       : 1.0
qoffset_z       : 1.0
srow_x          : [ 1.  0.  0.  1.]
srow_y          : [ 0.  1.  0.  1.]
srow_z          : [ 0.  0.  1.  1.]
intent_name     : 
magic           : n+1

In [31]:

    

fig = plot_rgb(im)


    

In [32]:

    

import os


    

In [33]:

    

cd /root/seelviz/Tony/aut1367/aut1367_raw/v100/ch0


    

    




/root/seelviz/Tony/aut1367/aut1367_raw/v100/ch0

In [34]:

    

ls


    

    




RAWoutfileaut1367_0.tiff  RAWoutfileaut1367_2.tiff  RAWoutfileaut1367_4.tiff
RAWoutfileaut1367_1.tiff  RAWoutfileaut1367_3.tiff

In [42]:

    

from PIL import Image
im = plt.imread('RAWoutfileaut1367_3.tiff') 
plt.imshow(im)


    

    
Out[42]:





<matplotlib.image.AxesImage at 0x7ff50c300510>






    

In [ ]: