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In [1]:



    


import numpy as np
import nibabel as nib
import dsiadapt as dsi
from dipy.viz import fvtk
import dipy.core.gradients as grad
from dipy.data import get_sphere
from dipy.direction import peaks_from_model

%pylab inline
np.set_printoptions(threshold=numpy.nan)



    


















    






Populating the interactive namespace from numpy and matplotlib

















In [2]:



    


# ODF sphere directions
sphere = get_sphere('symmetric724')
sphere = sphere.subdivide(2)



    











In [3]:



    


fnArr = np.array(['DSI11_exvivo', 'DSI11_invivo_b10k', 'DSI11_invivo_b7k'])
pdfwgtArr = np.array([0, 1, 2, 4, 8]);
rstartArr = np.array([0.0, 0.1, 0.2, 0.4, 0.8]);

qgridsz = 257; # Q-space grid size
qgridcenter = qgridsz//2;

for ii in np.arange(fnArr.shape[0]):
    fn = fnArr[ii];
    data = nib.load('data/' + fn + '_xfib.nii.gz').get_data();
    gtab = grad.gradient_table('data/' + fn + '_bvals.txt', 'data/' + fn + '_bvecs_dipy.txt');
    mdd = np.loadtxt('data/' + fn + '_stats.txt')[0];
    fov = np.loadtxt('data/' + fn + '_stats.txt')[1];
    rend = mdd / fov * qgridsz;
    
    for jj in np.arange(pdfwgtArr.shape[0]):
        pdfwgt = pdfwgtArr[jj];  
        dsimodel = dsi.DiffusionSpectrumModel(gtab, qgrid_size=qgridsz, filter_width=np.inf, 
               filter_type='none', pdfwgt=pdfwgt, r_start=0, r_end=rend, r_step=0.2);
                    
        dsipeaks = peaks_from_model(dsimodel, data[2, 0, 0], sphere, relative_peak_threshold=.2,
                 min_separation_angle=25, normalize_peaks=True, return_odf=True)
        odfvox = dsipeaks.odf;
        
        # Save ODF
        r = fvtk.ren();
        fvtk.add(r, fvtk.sphere_funcs(odfvox, sphere));
        fvtk.camera(r, pos=(0, 1, 0), viewup=(0, 0, 1))
        odfname = 'figure4/' + fn + '_xfib_odf_wgt_' + str(pdfwgt) + '.png';
        fvtk.record(r, n_frames=1, out_path=odfname, size=(600,600))
        #fvtk.show(r)
    
    for kk in np.arange(rstartArr.shape[0]):
        rstart = rstartArr[kk];
        dsimodel = dsi.DiffusionSpectrumModel(gtab, qgrid_size=qgridsz, filter_width=np.inf, 
               filter_type='none', pdfwgt=2, r_start=rstart*rend, r_end=rend, r_step=0.2);
        
        dsipeaks = peaks_from_model(dsimodel, data[2, 0, 0], sphere, relative_peak_threshold=.2,
                 min_separation_angle=25, normalize_peaks=True, return_odf=True)
        odfvox = dsipeaks.odf;
        
        # Save ODF
        r = fvtk.ren();
        fvtk.add(r, fvtk.sphere_funcs(odfvox, sphere));
        fvtk.camera(r, pos=(0, 1, 0), viewup=(0, 0, 1))
        odfname = 'figure4/' + fn + '_xfib_odf_wgt2_rend' + str(rstart) + '.png';
        fvtk.record(r, n_frames=1, out_path=odfname, size=(600,600))
        #fvtk.show(r)



    


















    






Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
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Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)
Camera Position (0.00,0.00,1.00)
Camera Focal Point (0.00,0.00,0.00)
Camera View Up (0.00,1.00,0.00)
-------------------------------------
Camera New Position (0.00,1.00,0.00)
Camera New Focal Point (0.00,0.00,0.00)
Camera New View Up (0.00,0.00,1.00)

Content source: mcnablab/DSIQspace

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