On Thursday, we showed Greg the output of the first step of the CAPTURE pipeline - namely, after modifying the CAPTURE MATLAB pipeline to accept TIFF files (originally it only took TIFs), we were able to generate two structure tensors from a TIFF stack of Aut1367 originally for use in Ilastik analysis. The main steps for the generation of the structure tensors are explained in a separate viewer (we showed Greg this) on Thursday: http://nbviewer.jupyter.org/github/NeuroDataDesign/seelviz/blob/gh-pages/Tony/ipynb/Generating%20Structure%20Tensors.ipynb
There were two separate structure tensors generated by the CAPTURE pipeline - one was "DTK" (which could be used later in the Diffusion ToolKit process) and the other was "FSL" (an alternate file format). We realized at office hours that the structure tensors (which were 5000 x 5000 x 5 x 6) each were the "lower triangular" values from the structures.
From there, we first tried to use the DTK file directly inside Diffusion ToolKit, but were informed that the "file appeared to be corrupted/missing data". Only the FSL format seemed to have properly saved all the image data (likely because it was run first during the MATLAB script, and because generating the structure tensors froze Tony's computer, so the DTK file format was corrupted. Thus, all analysis was done on the FSL file.
From there, we followed the DiPy tutorial/ndmg code that was suitable for generating FA maps (as recommended by Greg).
In [1]:
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
In [2]:
import vtk
In [3]:
from dipy.reconst.dti import from_lower_triangular
In [4]:
img = nb.load('../../../../../Desktop/result/dogsig1_gausig2.3/v100_ch0_tensorfsl_dogsig1_gausig2.3.nii')
In [5]:
data = img.get_data()
In [6]:
# Output is the structure tensor generated from a lower triangular structure tensor (which data is)
output = from_lower_triangular(data)
We added this step because the calculation of RGB/eigenvalues/eigenvectors took much too long on the full file. Even still, with small sizes like 25x25, the last VTK rendering step took significant amounts of time. In the pipeline we'll have to think of a more optimal way to compute these, and we're guessing we're missing something (since why is this taking so long)?
In [31]:
output_ds = output[4250:4300, 250:300, :, :, :]
In [32]:
print output.shape
print output_ds.shape
(5000, 5000, 5, 3, 3)
(50, 50, 5, 3, 3)
In [33]:
FA = fractional_anisotropy(output_ds)
In [34]:
FA = np.clip(FA, 0, 1)
In [35]:
FA[np.isnan(FA)] = 0
In [36]:
print FA.shape
(50, 50, 5, 3)
In [37]:
from dipy.reconst.dti import decompose_tensor
In [38]:
evalues, evectors = decompose_tensor(output_ds)
In [39]:
print evectors[..., 0, 0].shape
print evectors.shape[-2:]
(50, 50, 5)
(3, 3)
In [40]:
print FA[:, :, :, 0].shape
(50, 50, 5)
In [41]:
## To satisfy requirements for RGB
RGB = color_fa(FA[:, :, :, 0], evectors)
In [42]:
nb.save(nb.Nifti1Image(np.array(255 * RGB, 'uint8'), img.get_affine()), 'tensor_rgb_upper.nii.gz')
/Users/Tony/anaconda/lib/python2.7/site-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 [43]:
print('Computing tensor ellipsoids in a random part')
from dipy.data import get_sphere
sphere = get_sphere('symmetric724')
from dipy.viz import fvtk
Computing tensor ellipsoids in a random part
In [44]:
ren = fvtk.ren()
evals = evalues[:, :, :]
evecs = evectors[:, :, :]
In [45]:
print "printing evals:"
print evals
printing evals:
[[[[ 3.59858673e+02 4.20508653e-01 0.00000000e+00]
[ 4.05917450e+02 5.61607122e-01 7.03589618e-02]
[ 4.25848846e+02 7.01524436e-01 5.80489457e-01]
[ 4.19685120e+02 1.13140678e+00 6.51538432e-01]
[ 3.81875427e+02 1.34272110e+00 5.77863395e-01]]
[[ 3.61585938e+02 4.56072748e-01 0.00000000e+00]
[ 4.07860229e+02 6.18554890e-01 0.00000000e+00]
[ 4.27822357e+02 7.35710680e-01 4.71231312e-01]
[ 4.21525391e+02 1.06481409e+00 7.47136772e-01]
[ 3.83449982e+02 1.35440505e+00 6.66064262e-01]]
[[ 3.62073059e+02 5.12886703e-01 0.00000000e+00]
[ 4.08605103e+02 7.03238547e-01 0.00000000e+00]
[ 4.28809692e+02 8.40516150e-01 3.31217498e-01]
[ 4.22663727e+02 1.05653214e+00 8.71012688e-01]
[ 3.84584076e+02 1.45561719e+00 7.78225422e-01]]
...,
[[ 3.56612427e+02 6.11936986e-01 0.00000000e+00]
[ 4.02752686e+02 7.30627954e-01 0.00000000e+00]
[ 4.23407196e+02 7.53842890e-01 0.00000000e+00]
[ 4.18378021e+02 6.73720360e-01 0.00000000e+00]
[ 3.81691772e+02 5.22040427e-01 0.00000000e+00]]
[[ 3.55404449e+02 6.03852987e-01 0.00000000e+00]
[ 4.01798859e+02 7.27090955e-01 0.00000000e+00]
[ 4.22981354e+02 7.56930351e-01 0.00000000e+00]
[ 4.18546326e+02 6.82632506e-01 0.00000000e+00]
[ 3.82286804e+02 5.33642113e-01 0.00000000e+00]]
[[ 3.55258240e+02 6.66312158e-01 0.00000000e+00]
[ 4.01925415e+02 8.15788031e-01 0.00000000e+00]
[ 4.23530853e+02 8.63975525e-01 0.00000000e+00]
[ 4.19518768e+02 7.92349696e-01 1.01134628e-01]
[ 3.83493286e+02 6.29126668e-01 1.89753234e-01]]]
[[[ 3.57809509e+02 4.67865318e-01 0.00000000e+00]
[ 4.03147339e+02 6.35834515e-01 5.17178833e-01]
[ 4.22396515e+02 1.36941564e+00 6.89541876e-01]
[ 4.15794373e+02 2.06682944e+00 6.91424310e-01]
[ 3.78013458e+02 2.34213400e+00 6.00293398e-01]]
[[ 3.59174744e+02 5.03585398e-01 0.00000000e+00]
[ 4.04815796e+02 6.71246946e-01 3.34904611e-01]
[ 4.24247070e+02 1.24392700e+00 7.66928792e-01]
[ 4.17664490e+02 2.03908420e+00 7.75722563e-01]
[ 3.79717468e+02 2.39070702e+00 6.76855505e-01]]
[[ 3.59536102e+02 5.52521169e-01 0.00000000e+00]
[ 4.05594604e+02 7.39884377e-01 2.40310207e-02]
[ 4.25470459e+02 1.01363420e+00 8.59910727e-01]
[ 4.19204742e+02 1.92192245e+00 8.74882281e-01]
[ 3.81319366e+02 2.37068915e+00 7.66683817e-01]]
...,
[[ 3.54965668e+02 6.24985516e-01 0.00000000e+00]
[ 4.01175751e+02 7.57918656e-01 0.00000000e+00]
[ 4.22137238e+02 7.93716490e-01 0.00000000e+00]
[ 4.17521332e+02 7.18600869e-01 0.00000000e+00]
[ 3.81217773e+02 5.62417030e-01 0.00000000e+00]]
[[ 3.53336121e+02 5.68827510e-01 0.00000000e+00]
[ 3.99692322e+02 6.93498492e-01 0.00000000e+00]
[ 4.21115997e+02 7.31282055e-01 0.00000000e+00]
[ 4.17092255e+02 6.67581856e-01 0.00000000e+00]
[ 3.81277832e+02 5.27325153e-01 0.00000000e+00]]
[[ 3.52928040e+02 5.89172125e-01 0.00000000e+00]
[ 3.99422119e+02 7.27557421e-01 0.00000000e+00]
[ 4.21160187e+02 7.77772427e-01 1.39714861e-02]
[ 4.17512421e+02 7.19972253e-01 1.31833702e-01]
[ 3.81965759e+02 5.76425135e-01 2.01552317e-01]]]
[[[ 3.54687195e+02 5.23833692e-01 2.28979141e-01]
[ 3.99250061e+02 9.21877742e-01 6.66712403e-01]
[ 4.17898773e+02 1.80461884e+00 7.45360851e-01]
[ 4.11027313e+02 2.54443383e+00 7.27124453e-01]
[ 3.73475494e+02 2.80957508e+00 6.16639137e-01]]
[[ 3.55649628e+02 5.60207129e-01 3.85872051e-02]
[ 4.00564575e+02 7.76476085e-01 7.16372252e-01]
[ 4.19508972e+02 1.73554039e+00 8.17232072e-01]
[ 4.12788177e+02 2.56988859e+00 8.03484023e-01]
[ 3.75169983e+02 2.90267086e+00 6.84504271e-01]]
[[ 3.55939392e+02 6.00708246e-01 0.00000000e+00]
[ 4.01382874e+02 7.84672678e-01 4.76545751e-01]
[ 4.20911316e+02 1.49159718e+00 8.90556574e-01]
[ 4.14621216e+02 2.39817405e+00 8.80785048e-01]
[ 3.77112793e+02 2.80250573e+00 7.53656507e-01]]
...,
[[ 3.55364838e+02 6.49586082e-01 0.00000000e+00]
[ 4.01954468e+02 7.97650516e-01 0.00000000e+00]
[ 4.23358368e+02 8.46089244e-01 0.00000000e+00]
[ 4.19102783e+02 7.76365280e-01 0.00000000e+00]
[ 3.82920593e+02 6.16245806e-01 0.00000000e+00]]
[[ 3.53148773e+02 5.50384104e-01 0.00000000e+00]
[ 3.99721344e+02 6.79358721e-01 0.00000000e+00]
[ 4.21475708e+02 7.26188004e-01 0.00000000e+00]
[ 4.17781372e+02 6.72849834e-01 0.00000000e+00]
[ 3.82162109e+02 5.40047467e-01 0.00000000e+00]]
[[ 3.52224335e+02 5.35329878e-01 1.39594942e-01]
[ 3.98760406e+02 6.67076051e-01 1.49549291e-01]
[ 4.20697632e+02 7.21261978e-01 1.48808077e-01]
[ 4.17333588e+02 6.76820755e-01 1.39819428e-01]
[ 3.82041626e+02 5.50456226e-01 1.23499222e-01]]]
...,
[[[ 3.39595276e+02 8.91354561e-01 1.88191742e-01]
[ 3.83573151e+02 1.15893364e+00 3.28132153e-01]
[ 4.02730835e+02 1.31307340e+00 5.18151283e-01]
[ 3.96921417e+02 1.29334760e+00 6.87276721e-01]
[ 3.60963989e+02 1.10404134e+00 7.46736228e-01]]
[[ 3.38109436e+02 1.11758637e+00 8.03707719e-01]
[ 3.82249817e+02 1.25719190e+00 1.00777853e+00]
[ 4.01792511e+02 1.32786107e+00 1.09425449e+00]
[ 3.96424683e+02 1.28438330e+00 1.06195295e+00]
[ 3.60813293e+02 1.11512697e+00 9.16927278e-01]]
[[ 3.36890594e+02 1.75537479e+00 7.45460153e-01]
[ 3.81107300e+02 1.80357027e+00 9.44469750e-01]
[ 4.00922913e+02 1.67370188e+00 1.04015744e+00]
[ 3.95913208e+02 1.44061208e+00 9.94572282e-01]
[ 3.60617035e+02 1.15425324e+00 8.26307476e-01]]
...,
[[ 3.58613037e+02 6.67148411e-01 6.20746017e-01]
[ 4.05173157e+02 9.09415662e-01 7.64757335e-01]
[ 4.25715851e+02 1.16543388e+00 8.17883253e-01]
[ 4.20050995e+02 1.34338450e+00 7.66263664e-01]
[ 3.82510895e+02 1.34672415e+00 6.27659917e-01]]
[[ 3.59222839e+02 1.49669194e+00 6.86491191e-01]
[ 4.06451874e+02 1.60874546e+00 8.36362541e-01]
[ 4.27659882e+02 1.57611930e+00 8.84308517e-01]
[ 4.22389435e+02 1.43170071e+00 8.13841283e-01]
[ 3.84808594e+02 1.19917500e+00 6.53930306e-01]]
[[ 3.58545837e+02 2.19511509e+00 7.50551939e-01]
[ 4.06261505e+02 2.21592736e+00 9.01456952e-01]
[ 4.28091949e+02 1.96338105e+00 9.41773057e-01]
[ 4.23305664e+02 1.56276453e+00 8.58080506e-01]
[ 3.85887115e+02 1.13685513e+00 6.82278574e-01]]]
[[[ 3.37472534e+02 8.95489395e-01 3.20493013e-01]
[ 3.81124512e+02 1.14060271e+00 2.40691379e-02]
[ 4.00172028e+02 1.27781463e+00 0.00000000e+00]
[ 3.94478149e+02 1.24771488e+00 0.00000000e+00]
[ 3.58846069e+02 1.05519652e+00 0.00000000e+00]]
[[ 3.36088074e+02 1.15798974e+00 7.89062619e-01]
[ 3.79846588e+02 1.14896333e+00 7.16417849e-01]
[ 3.99212158e+02 1.22976398e+00 2.30751172e-01]
[ 3.93907776e+02 1.17697525e+00 0.00000000e+00]
[ 3.58598145e+02 9.80149627e-01 0.00000000e+00]]
[[ 3.34898224e+02 1.72548282e+00 7.79910207e-01]
[ 3.78731384e+02 1.43651009e+00 9.55634773e-01]
[ 3.98380981e+02 1.15918291e+00 7.18668818e-01]
[ 3.93454132e+02 1.06966782e+00 1.10383190e-01]
[ 3.58474884e+02 8.77274871e-01 0.00000000e+00]]
...,
[[ 3.56688049e+02 7.27307320e-01 6.17908359e-01]
[ 4.02922424e+02 1.06938815e+00 7.70037293e-01]
[ 4.23375244e+02 1.43306768e+00 8.40002596e-01]
[ 4.17864716e+02 1.69489312e+00 8.00248146e-01]
[ 3.80675507e+02 1.72290349e+00 6.64050996e-01]]
[[ 3.57972687e+02 1.49410093e+00 6.92057431e-01]
[ 4.04777802e+02 1.60340416e+00 8.45311821e-01]
[ 4.25700043e+02 1.56405187e+00 8.89966309e-01]
[ 4.20374237e+02 1.40984714e+00 8.12678933e-01]
[ 3.82992615e+02 1.16639090e+00 6.50406718e-01]]
[[ 3.57749969e+02 2.09966874e+00 7.47228920e-01]
[ 4.04926086e+02 2.01527023e+00 9.01064038e-01]
[ 4.26279877e+02 1.63663888e+00 9.35122073e-01]
[ 4.21250885e+02 1.16387713e+00 8.09465885e-01]
[ 3.83913727e+02 8.06572080e-01 5.23650348e-01]]]
[[[ 3.36039642e+02 9.08809602e-01 1.55218571e-01]
[ 3.79592865e+02 1.13101709e+00 0.00000000e+00]
[ 3.98764404e+02 1.24603474e+00 0.00000000e+00]
[ 3.93364807e+02 1.19976115e+00 0.00000000e+00]
[ 3.58093872e+02 1.00263965e+00 0.00000000e+00]]
[[ 3.35001892e+02 9.79336202e-01 5.35142004e-01]
[ 3.78626221e+02 1.14718246e+00 0.00000000e+00]
[ 3.98035187e+02 1.23317134e+00 0.00000000e+00]
[ 3.92933868e+02 1.16422987e+00 0.00000000e+00]
[ 3.57910248e+02 9.55571949e-01 0.00000000e+00]]
[[ 3.34022339e+02 1.16307700e+00 7.58749306e-01]
[ 3.77712555e+02 1.12263942e+00 4.50433195e-01]
[ 3.97376038e+02 1.16877949e+00 0.00000000e+00]
[ 3.92613770e+02 1.08464432e+00 0.00000000e+00]
[ 3.57880829e+02 8.77141535e-01 0.00000000e+00]]
...,
[[ 3.55389343e+02 7.14470565e-01 5.28124392e-01]
[ 4.01246765e+02 1.13221836e+00 7.52724290e-01]
[ 4.21460205e+02 1.66352570e+00 8.52787852e-01]
[ 4.15919525e+02 2.08385944e+00 8.25496078e-01]
[ 3.78926758e+02 2.18585038e+00 6.90535605e-01]]
[[ 3.57592346e+02 1.30233502e+00 6.70190156e-01]
[ 4.03946594e+02 1.51516414e+00 8.14386785e-01]
[ 4.24436615e+02 1.61977875e+00 8.58548820e-01]
[ 4.18859589e+02 1.58638489e+00 7.95690060e-01]
[ 3.81494781e+02 1.40156376e+00 6.50276184e-01]]
[[ 3.58084473e+02 1.79286420e+00 7.11783409e-01]
[ 4.04743530e+02 1.75025380e+00 8.53484035e-01]
[ 4.25505768e+02 1.47778225e+00 8.58741522e-01]
[ 4.20045624e+02 1.14625728e+00 6.83443308e-01]
[ 3.82586060e+02 8.50818276e-01 4.11481380e-01]]]]
In [46]:
print "printing evecs"
print evecs
printing evecs
[[[[[ 1.24202820e-03 9.98928905e-01 4.62541170e-02]
[ -8.69421288e-04 -4.62530591e-02 9.98929381e-01]
[ 9.99998868e-01 -1.28091278e-03 8.11042497e-04]]
[[ 1.37818838e-03 9.95012462e-01 9.97410789e-02]
[ -1.53448002e-03 -9.97389480e-02 9.95012462e-01]
[ 9.99997854e-01 -1.52436527e-03 1.38936774e-03]]
[[ 1.45453122e-03 -7.51945853e-01 -6.59223318e-01]
[ -2.36948044e-03 6.59219563e-01 -7.51946807e-01]
[ 9.99996126e-01 2.65574688e-03 -8.22865521e-04]]
[[ 1.44273485e-03 -1.34770319e-01 9.90875840e-01]
[ -3.16984626e-03 9.90871251e-01 1.34774312e-01]
[ 9.99993920e-01 3.33536742e-03 -1.00236328e-03]]
[[ 1.35963270e-03 -7.72602037e-02 9.97010052e-01]
[ -3.75703746e-03 9.97003555e-01 7.72648230e-02]
[ 9.99992013e-01 3.85085586e-03 -1.06528914e-03]]]
[[[ -1.23419065e-03 9.99839664e-01 1.78640019e-02]
[ 1.70951500e-03 -1.78618804e-02 9.99839008e-01]
[ -9.99997795e-01 -1.26453082e-03 1.68719597e-03]]
[[ 1.35540089e-03 9.99358714e-01 3.57820243e-02]
[ -2.25171121e-03 -3.57789174e-02 9.99357164e-01]
[ 9.99996543e-01 -1.43510045e-03 2.20177229e-03]]
[[ 1.41584885e-03 9.90882337e-01 1.34722516e-01]
[ -2.89704255e-03 -1.34718016e-01 9.90879714e-01]
[ 9.99994814e-01 -1.79323286e-03 2.67988816e-03]]
[[ 1.39172655e-03 -1.21305786e-01 9.92614210e-01]
[ -3.48720886e-03 9.92608547e-01 1.21309981e-01]
[ 9.99992967e-01 3.63028352e-03 -9.58421035e-04]]
[[ 1.30233588e-03 -5.12934476e-02 9.98682797e-01]
[ -3.89758172e-03 9.98675764e-01 5.12981713e-02]
[ 9.99991536e-01 3.95925529e-03 -1.10069092e-03]]]
[[[ 1.30669668e-03 9.99955595e-01 -9.33431741e-03]
[ -3.17609310e-03 9.33842827e-03 9.99951363e-01]
[ 9.99994099e-01 -1.27698644e-03 3.18815466e-03]]
[[ -1.43117504e-03 -9.99949276e-01 9.96712316e-03]
[ 3.46249249e-03 -9.97202937e-03 -9.99944270e-01]
[ -9.99992967e-01 1.39658421e-03 -3.47658852e-03]]
[[ -1.48819678e-03 -9.99892950e-01 1.45547194e-02]
[ 3.74420546e-03 -1.45602049e-02 -9.99886990e-01]
[ -9.99991894e-01 1.43353280e-03 -3.76547314e-03]]
[[ 1.45457999e-03 1.93449836e-02 9.99811828e-01]
[ -3.94707546e-03 9.99805212e-01 -1.93391126e-02]
[ 9.99991179e-01 3.91820259e-03 -1.53065263e-03]]
[[ -1.35325431e-03 -1.53862208e-03 9.99997914e-01]
[ 4.03842377e-03 -9.99990642e-01 -1.53314602e-03]
[ -9.99990940e-01 -4.03634040e-03 -1.35945529e-03]]]
...,
[[[ 1.52567867e-03 9.98370826e-01 5.70387878e-02]
[ 3.03875119e-03 -5.70432208e-02 9.98367071e-01]
[ 9.99994218e-01 -1.34986069e-03 -3.12083005e-03]]
[[ 1.59377279e-03 9.97604549e-01 6.91565350e-02]
[ 1.64615235e-03 -6.91591427e-02 9.97604311e-01]
[ 9.99997377e-01 -1.47611229e-03 -1.75243302e-03]]
[[ 1.56539411e-03 9.96367574e-01 8.51425231e-02]
[ -8.32873775e-06 -8.51426125e-02 9.96368766e-01]
[ 9.99998748e-01 -1.56041898e-03 -1.24983271e-04]]
[[ 1.43688428e-03 9.94342327e-01 1.06213219e-01]
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[ 9.99997973e-01 -2.86102964e-04 -1.97802135e-03]]
[[ 1.91370095e-03 -1.80757448e-01 9.83525872e-01]
[ 1.65347836e-03 9.83526886e-01 1.80754423e-01]
[ 9.99996781e-01 -1.28032884e-03 -2.18105479e-03]]
[[ 1.80538115e-03 -1.57250211e-01 9.87557173e-01]
[ 2.65917834e-03 9.87556040e-01 1.57245174e-01]
[ 9.99994814e-01 -2.34220317e-03 -2.20107147e-03]]
[[ 1.62112503e-03 -1.34765342e-01 9.90876198e-01]
[ 3.44792334e-03 9.90872383e-01 1.34759188e-01]
[ 9.99992728e-01 -3.19800386e-03 -2.07098853e-03]]]
[[[ 1.71554659e-03 -5.20809600e-03 9.99984980e-01]
[ 2.46085599e-03 9.99983430e-01 5.20386593e-03]
[ 9.99995530e-01 -2.45189155e-03 -1.72833446e-03]]
[[ 1.84813363e-03 -3.91599871e-02 9.99231219e-01]
[ 3.35658155e-03 9.99227583e-01 3.91536355e-02]
[ 9.99992669e-01 -3.28164012e-03 -1.97814964e-03]]
[[ 1.87882991e-03 -8.70141685e-02 9.96205330e-01]
[ 4.43297811e-03 9.96197999e-01 8.70051682e-02]
[ 9.99988437e-01 -4.25268849e-03 -2.25741859e-03]]
[[ 1.78877846e-03 -1.31379321e-01 9.91330564e-01]
[ 5.45503199e-03 9.91318703e-01 1.31367907e-01]
[ 9.99983549e-01 -5.17275184e-03 -2.48992792e-03]]
[[ 1.62002142e-03 -1.53666362e-01 9.88121450e-01]
[ 6.22707559e-03 9.88105178e-01 1.53653622e-01]
[ 9.99979317e-01 -5.90418512e-03 -2.55764346e-03]]]
[[[ 1.69697637e-03 -8.85467697e-03 9.99959350e-01]
[ 4.35462082e-03 9.99951363e-01 8.84721708e-03]
[ 9.99989092e-01 -4.33943048e-03 -1.73545268e-03]]
[[ 1.83175900e-03 -2.27846820e-02 9.99738693e-01]
[ 4.99112066e-03 9.99728143e-01 2.27752961e-02]
[ 9.99985874e-01 -4.94809775e-03 -1.94498210e-03]]
[[ 1.86735054e-03 -4.62143160e-02 9.98929799e-01]
[ 5.73595893e-03 9.98915613e-01 4.62029390e-02]
[ 9.99981821e-01 -5.64354332e-03 -2.13040900e-03]]
[[ 1.78342743e-03 -8.08096379e-02 9.96727943e-01]
[ 6.41513569e-03 9.96709943e-01 8.07967037e-02]
[ 9.99977827e-01 -6.25004992e-03 -2.29596463e-03]]
[[ 1.61990197e-03 -1.20825715e-01 9.92672443e-01]
[ 6.89694379e-03 9.92651463e-01 1.20811909e-01]
[ 9.99974906e-01 -6.65070256e-03 -2.44132616e-03]]]]
[[[[ 1.84624922e-03 9.67879772e-01 2.51406759e-01]
[ 2.56769801e-03 -2.51410931e-01 9.67877030e-01]
[ 9.99994993e-01 -1.14140555e-03 -2.94939033e-03]]
[[ 2.00815569e-03 9.88565028e-01 1.50781840e-01]
[ 1.95937976e-03 -1.50785744e-01 9.88564551e-01]
[ 9.99996066e-01 -1.68975268e-03 -2.23977538e-03]]
[[ 2.05299724e-03 9.94685233e-01 1.02942355e-01]
[ 1.23457657e-03 -1.02945015e-01 9.94686306e-01]
[ 9.99997139e-01 -1.91499805e-03 -1.43936090e-03]]
[[ 1.95540837e-03 9.97144580e-01 7.54906312e-02]
[ 5.53989958e-04 -7.54918456e-02 9.97146249e-01]
[ 9.99997914e-01 -1.90800719e-03 -7.00025470e-04]]
[[ 1.76220224e-03 9.98324215e-01 5.78419417e-02]
[ 4.87983489e-05 -5.78421168e-02 9.98325765e-01]
[ 9.99998450e-01 -1.75642932e-03 -1.50646083e-04]]]
[[[ 1.85413880e-03 -3.82229418e-01 9.24065590e-01]
[ 2.26621400e-03 9.24066424e-01 3.82225215e-01]
[ 9.99995708e-01 -1.38543174e-03 -2.57956097e-03]]
[[ 2.00648815e-03 9.14780974e-01 4.03945267e-01]
[ 1.37290813e-03 -4.03948218e-01 9.14780855e-01]
[ 9.99997020e-01 -1.28091720e-03 -2.06642761e-03]]
[[ 2.03716173e-03 9.85284984e-01 1.70907363e-01]
[ 3.08688992e-04 -1.70908332e-01 9.85286891e-01]
[ 9.99997854e-01 -1.95443165e-03 -6.52314571e-04]]
[[ 1.92422979e-03 9.94449735e-01 1.05194904e-01]
[ -6.89586799e-04 -1.05193757e-01 9.94451523e-01]
[ 9.99997914e-01 -1.98609428e-03 4.83342446e-04]]
[[ 1.71837281e-03 9.97145414e-01 7.54852667e-02]
[ -1.42981170e-03 -7.54828528e-02 9.97146070e-01]
[ 9.99997497e-01 -1.82139839e-03 1.29602244e-03]]]
[[[ 1.78587262e-03 -1.17666915e-01 9.93051529e-01]
[ 2.30611884e-03 9.93050933e-01 1.17662698e-01]
[ 9.99995768e-01 -2.07996415e-03 -2.04481627e-03]]
[[ 1.93709158e-03 -3.05656850e-01 9.52139795e-01]
[ 1.20028551e-03 9.52141583e-01 3.05655003e-01]
[ 9.99997377e-01 -5.50757919e-04 -2.21126084e-03]]
[[ 1.96800637e-03 9.28825021e-01 3.70513439e-01]
[ -1.31558889e-04 -3.70513916e-01 9.28826928e-01]
[ 9.99998033e-01 -1.87668169e-03 -6.06978603e-04]]
[[ 1.85691379e-03 9.88903046e-01 1.48550734e-01]
[ -1.39031024e-03 -1.48548290e-01 9.88904178e-01]
[ 9.99997318e-01 -2.04284140e-03 1.09904062e-03]]
[[ 1.65394845e-03 9.95572209e-01 9.39855054e-02]
[ -2.32938351e-03 -9.39815417e-02 9.95571196e-01]
[ 9.99995947e-01 -1.86555181e-03 2.16362881e-03]]]
...,
[[[ 1.95984542e-03 -4.37618762e-01 8.99158478e-01]
[ 2.19282834e-03 8.99159908e-01 4.37614709e-01]
[ 9.99995649e-01 -1.11404294e-03 -2.72183726e-03]]
[[ 2.12094886e-03 -3.26880127e-01 9.45063412e-01]
[ 2.27200706e-03 9.45064723e-01 3.26875448e-01]
[ 9.99995172e-01 -1.45390467e-03 -2.74710776e-03]]
[[ 2.15691398e-03 -2.48042181e-01 9.68746841e-01]
[ 2.32335925e-03 9.68747735e-01 2.48037234e-01]
[ 9.99994993e-01 -1.71575183e-03 -2.66579655e-03]]
[[ 2.04483257e-03 -1.96052238e-01 9.80591297e-01]
[ 2.35241838e-03 9.80591595e-01 1.96047395e-01]
[ 9.99995172e-01 -1.90587679e-03 -2.46634264e-03]]
[[ 1.83680258e-03 -1.60904184e-01 9.86968338e-01]
[ 2.37552729e-03 9.86967921e-01 1.60899699e-01]
[ 9.99995470e-01 -2.04902911e-03 -2.19509751e-03]]]
[[[ 1.99589459e-03 -7.36267418e-02 9.97283876e-01]
[ 4.86218277e-03 9.97274756e-01 7.36163408e-02]
[ 9.99986172e-01 -4.70204605e-03 -2.34844210e-03]]
[[ 2.16948125e-03 -1.41154855e-01 9.89985168e-01]
[ 5.05630765e-03 9.89976346e-01 1.41142517e-01]
[ 9.99984860e-01 -4.69946349e-03 -2.86145741e-03]]
[[ 2.21593538e-03 -2.28049368e-01 9.73647058e-01]
[ 5.22807427e-03 9.73638773e-01 2.28035539e-01]
[ 9.99983907e-01 -4.58498672e-03 -3.34977964e-03]]
[[ 2.10889336e-03 -3.01139772e-01 9.53577697e-01]
[ 5.34479599e-03 9.53569591e-01 3.01125377e-01]
[ 9.99983490e-01 -4.46163723e-03 -3.62050720e-03]]
[[ 1.89979724e-03 -3.32591444e-01 9.43069100e-01]
[ 5.40243881e-03 9.43060458e-01 3.32577527e-01]
[ 9.99983609e-01 -4.46304353e-03 -3.58842872e-03]]]
[[[ 2.05175835e-03 -4.89438586e-02 9.98799443e-01]
[ 5.97117841e-03 9.98784304e-01 4.89308536e-02]
[ 9.99980092e-01 -5.86361531e-03 -2.34151655e-03]]
[[ 2.22707656e-03 -9.41821560e-02 9.95552480e-01]
[ 6.14807475e-03 9.95537460e-01 9.41669792e-02]
[ 9.99978602e-01 -5.91101404e-03 -2.79617705e-03]]
[[ 2.27228180e-03 -1.97676539e-01 9.80264664e-01]
[ 6.29279669e-03 9.80250597e-01 1.97659120e-01]
[ 9.99977648e-01 -5.71946893e-03 -3.47134378e-03]]
[[ 2.16048304e-03 -4.69576180e-01 8.82889330e-01]
[ 6.36464637e-03 8.82879972e-01 4.69555616e-01]
[ 9.99977410e-01 -4.60481131e-03 -4.89613367e-03]]
[[ 1.94427907e-03 -8.20936143e-01 -5.71016669e-01]
[ 6.36076834e-03 5.71016371e-01 -8.20914030e-01]
[ 9.99977887e-01 -2.03601876e-03 6.33199979e-03]]]]
[[[[ 1.71475101e-03 9.66982186e-01 2.54838169e-01]
[ 4.38826671e-03 -2.54843384e-01 9.66972411e-01]
[ 9.99988914e-01 -5.39819070e-04 -4.68036858e-03]]
[[ 1.86118239e-03 9.90474820e-01 1.37681291e-01]
[ 3.56395775e-03 -1.37687221e-01 9.90469337e-01]
[ 9.99991894e-01 -1.35275384e-03 -3.78627144e-03]]
[[ 1.89615705e-03 9.96266186e-01 8.63136426e-02]
[ 2.53199181e-03 -8.63183066e-02 9.96264398e-01]
[ 9.99994993e-01 -1.67052820e-03 -2.68621091e-03]]
[[ 1.79772160e-03 9.98274982e-01 5.86841181e-02]
[ 1.52087177e-03 -5.86868748e-02 9.98275280e-01]
[ 9.99997199e-01 -1.70537003e-03 -1.62375090e-03]]
[[ 1.61157537e-03 9.99115884e-01 4.20100354e-02]
[ 7.36502523e-04 -4.20112647e-02 9.99116838e-01]
[ 9.99998450e-01 -1.57921168e-03 -8.03555653e-04]]]
[[[ 1.74846349e-03 8.75681460e-01 4.82886016e-01]
[ 4.20330139e-03 -4.82888907e-01 8.75671506e-01]
[ 9.99989629e-01 4.98635811e-04 -4.52506682e-03]]
[[ 1.88761461e-03 9.80870664e-01 1.94651335e-01]
[ 3.15788249e-03 -1.94656566e-01 9.80866373e-01]
[ 9.99993205e-01 -1.23681163e-03 -3.46491090e-03]]
[[ 1.91029557e-03 9.94107783e-01 1.08379334e-01]
[ 1.86791702e-03 -1.08382896e-01 9.94107485e-01]
[ 9.99996424e-01 -1.69659546e-03 -2.06395425e-03]]
[[ 1.79739972e-03 9.97509122e-01 7.05146492e-02]
[ 6.20013918e-04 -7.05158561e-02 9.97510493e-01]
[ 9.99998212e-01 -1.74920494e-03 -7.45214755e-04]]
[[ 1.59844523e-03 9.98755157e-01 4.98558730e-02]
[ -3.35983437e-04 -4.98553962e-02 9.98756409e-01]
[ 9.99998689e-01 -1.61320809e-03 2.55874067e-04]]]
[[[ 1.70804025e-03 -4.73342955e-01 8.80876601e-01]
[ 3.62769607e-03 8.80874991e-01 4.73335057e-01]
[ 9.99991953e-01 -2.38707708e-03 -3.22171417e-03]]
[[ 1.84813992e-03 9.48989093e-01 3.15303475e-01]
[ 2.44942866e-03 -3.15307379e-01 9.48986411e-01]
[ 9.99995291e-01 -9.81546240e-04 -2.90721329e-03]]
[[ 1.87241507e-03 9.90613163e-01 1.36682153e-01]
[ 1.00456376e-03 -1.36684179e-01 9.90614176e-01]
[ 9.99997735e-01 -1.71753496e-03 -1.25106366e-03]]
[[ 1.76151888e-03 9.96636033e-01 8.19361955e-02]
[ -3.82399885e-04 -8.19356441e-02 9.96637523e-01]
[ 9.99998391e-01 -1.78692827e-03 2.36782318e-04]]
[[ 1.56459259e-03 9.98408318e-01 5.63774444e-02]
[ -1.43428531e-03 -5.63752130e-02 9.98408616e-01]
[ 9.99997735e-01 -1.64296408e-03 1.34379813e-03]]]
...,
[[[ 2.26605381e-03 -8.21931124e-01 -5.69582343e-01]
[ 4.51856805e-03 5.69586396e-01 -8.21919024e-01]
[ 9.99987245e-01 -7.11183820e-04 5.00466535e-03]]
[[ 2.46287836e-03 -4.44539487e-01 8.95755887e-01]
[ 3.67412483e-03 8.95756543e-01 4.44529712e-01]
[ 9.99990225e-01 -2.19629635e-03 -3.83943296e-03]]
[[ 2.50451593e-03 -2.67349213e-01 9.63596463e-01]
[ 2.54580588e-03 9.63598073e-01 2.67343044e-01]
[ 9.99993622e-01 -1.78356445e-03 -3.09396582e-03]]
[[ 2.36273324e-03 -1.91368878e-01 9.81515348e-01]
[ 1.40717102e-03 9.81517732e-01 1.91365972e-01]
[ 9.99996245e-01 -9.29013186e-04 -2.58835335e-03]]
[[ 2.10246979e-03 -1.50078326e-01 9.88671899e-01]
[ 5.23998518e-04 9.88674104e-01 1.50077537e-01]
[ 9.99997675e-01 -2.02529103e-04 -2.15729815e-03]]]
[[[ 2.39077467e-03 -1.82164147e-01 9.83265221e-01]
[ 7.03689735e-03 9.83246744e-01 1.82143614e-01]
[ 9.99972403e-01 -6.48367172e-03 -3.63259180e-03]]
[[ 2.60464498e-03 -2.63234466e-01 9.64728355e-01]
[ 6.34357193e-03 9.64716554e-01 2.63214141e-01]
[ 9.99976516e-01 -5.43424441e-03 -4.18259110e-03]]
[[ 2.65417527e-03 -3.20567846e-01 9.47221816e-01]
[ 5.38460212e-03 9.47216034e-01 3.20550799e-01]
[ 9.99981999e-01 -4.24961466e-03 -4.24020737e-03]]
[[ 2.50734738e-03 -3.36293876e-01 9.41753745e-01]
[ 4.38366737e-03 9.41751361e-01 3.36281359e-01]
[ 9.99987245e-01 -3.28516099e-03 -3.83549812e-03]]
[[ 2.23189918e-03 -3.19571286e-01 9.47559595e-01]
[ 3.57352104e-03 9.47558463e-01 3.19562495e-01]
[ 9.99991119e-01 -2.67289276e-03 -3.25684948e-03]]]
[[[ 2.50513060e-03 -1.12470053e-01 9.93651986e-01]
[ 7.26889679e-03 9.93630886e-01 1.12449341e-01]
[ 9.99970436e-01 -6.94105309e-03 -3.30670830e-03]]
[[ 2.72277440e-03 -2.02674836e-01 9.79242325e-01]
[ 6.85032690e-03 9.79226768e-01 2.02652559e-01]
[ 9.99972820e-01 -6.15635235e-03 -4.05460224e-03]]
[[ 2.76895077e-03 -3.85497570e-01 9.22704697e-01]
[ 6.23374013e-03 9.22696948e-01 3.85475636e-01]
[ 9.99976754e-01 -4.68453811e-03 -4.95799398e-03]]
[[ 2.61110486e-03 -6.60043120e-01 7.51223147e-01]
[ 5.55131724e-03 7.51223743e-01 6.60024285e-01]
[ 9.99981165e-01 -2.44688522e-03 -5.62563259e-03]]
[[ 2.32018367e-03 -8.35079253e-01 -5.50124764e-01]
[ 4.95995302e-03 5.50129116e-01 -8.35064888e-01]
[ 9.99984980e-01 -7.91089027e-04 5.41835465e-03]]]]]
In [47]:
cfa = RGB[:, :, :]
In [48]:
cfa = cfa / cfa.max()
In [49]:
print "printing cfa"
print cfa
printing cfa
[[[[ 9.48516536e-04 6.63962739e-04 7.63682663e-01]
[ 1.05907558e-03 1.17917871e-03 7.68453181e-01]
[ 1.12608611e-03 1.83443225e-03 7.74188817e-01]
[ 1.12518156e-03 2.47214711e-03 7.79890180e-01]
[ 1.06707367e-03 2.94861686e-03 7.84818709e-01]]
[[ 9.09874274e-04 1.26029446e-03 7.37221777e-01]
[ 1.00808835e-03 1.67472509e-03 7.43754089e-01]
[ 1.06387143e-03 2.17684289e-03 7.51397967e-01]
[ 1.05572050e-03 2.64528813e-03 7.58563519e-01]
[ 9.95318987e-04 2.97875307e-03 7.64250219e-01]]
[[ 9.03575972e-04 2.19625677e-03 6.91492260e-01]
[ 1.00644864e-03 2.43493705e-03 7.03227460e-01]
[ 1.06497563e-03 2.67940876e-03 7.15609014e-01]
[ 1.05680479e-03 2.86769238e-03 7.26529598e-01]
[ 9.94428527e-04 2.96760467e-03 7.34835625e-01]]
...,
[[ 1.27324078e-03 2.53596087e-03 8.34535718e-01]
[ 1.33825780e-03 1.38223974e-03 8.39676917e-01]
[ 1.31950260e-03 7.02046282e-06 8.42919350e-01]
[ 1.21273112e-03 1.30824326e-03 8.43998730e-01]
[ 1.05783681e-03 2.25800718e-03 8.43124509e-01]]
[[ 1.21419330e-03 3.27732856e-03 7.92787671e-01]
[ 1.30230980e-03 2.23521492e-03 8.00981581e-01]
[ 1.30918657e-03 9.42319923e-04 8.07208121e-01]
[ 1.22404587e-03 2.95634993e-04 8.11129153e-01]
[ 1.08255702e-03 1.21796154e-03 8.12867999e-01]]
[[ 1.19536358e-03 4.13254648e-03 7.66569912e-01]
[ 1.31279498e-03 3.13294632e-03 7.79596806e-01]
[ 1.34897733e-03 1.83276949e-03 7.89545715e-01]
[ 1.28541712e-03 5.49672171e-04 7.95955002e-01]
[ 1.15428725e-03 4.28954168e-04 7.98969269e-01]]]
[[[ 9.61241545e-04 9.53330135e-04 7.59303749e-01]
[ 1.06929545e-03 1.39845873e-03 7.68735826e-01]
[ 1.13186671e-03 1.95865147e-03 7.78417587e-01]
[ 1.12571975e-03 2.49839551e-03 7.87205637e-01]
[ 1.06299378e-03 2.89564393e-03 7.94400871e-01]]
[[ 9.35247052e-04 1.83441746e-03 7.43924737e-01]
[ 1.03580835e-03 2.13756948e-03 7.57292390e-01]
[ 1.08988385e-03 2.48003774e-03 7.70051122e-01]
[ 1.07637618e-03 2.77463463e-03 7.80657947e-01]
[ 1.00906112e-03 2.95923231e-03 7.88434088e-01]]
[[ 9.32199880e-04 2.84286775e-03 7.09331453e-01]
[ 1.03939744e-03 2.98348791e-03 7.30135143e-01]
[ 1.09680754e-03 3.06537445e-03 7.49069452e-01]
[ 1.08257169e-03 3.06317862e-03 7.64201760e-01]
[ 1.01189560e-03 2.99202534e-03 7.74890661e-01]]
...,
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...,
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...,
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...,
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...,
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In [50]:
fvtk.add(ren, fvtk.tensor(evals, evecs, cfa, sphere))
In [51]:
from IPython.display import Image
def vtk_show(renderer, width=400, height=300):
"""
Takes vtkRenderer instance and returns an IPython Image with the rendering.
"""
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetOffScreenRendering(1)
renderWindow.AddRenderer(renderer)
renderWindow.SetSize(width, height)
renderWindow.Render()
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renderWindow)
windowToImageFilter.Update()
writer = vtk.vtkPNGWriter()
writer.SetWriteToMemory(1)
writer.SetInputConnection(windowToImageFilter.GetOutputPort())
writer.Write()
data = str(buffer(writer.GetResult()))
return Image(data)
In [52]:
# x = 4250:4300, y = 250:300, z = : on Tony's computer (doesn't show anything)
# Thus, all results were displayed after running on Albert's computer
vtk_show(ren)
Out[52]:
Content source: NeuroDataDesign/seelviz
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