コード例 #1
0
ファイル: atlas_combined.py プロジェクト: Garyfallidis/trn
def show():    

    #brains=[(1,1),(1,2),(2,1),(3,1),(3,2)]
    brains=[(1,1),(2,1),(3,1)]

    ids=tl.emi_atlas()    
    
    #print ids.keys()
    
    for (b,s) in brains:
        
        ids2 = pbc.load_pickle(path+'/Relabelling_8_sc1_'+str(b)+'_'+str(s)+'.pkl')
        #'/Relabelling_8_sc1_'+str(b)+'_'+str(s)+'.pkl'
        print b,s, ids2.keys()
        tracks = pbc.load_approximate_tracks(path,b,s)
        
        for i in ids:
            
            if i >0:
                
                r=fos.ren()
                
                color=np.array(ids[i]['color'])                
                indices=ids2[i]['indices']                
                
                bundle=[tracks[ind] for ind in indices]      
                fos.add(r,fos.line(bundle,color,opacity=0.9))      
                
                print 'Bundle_name',i,ids[i]['bundle_name']            
                
                fos.show(r,title=ids[i]['bundle_name'][0])
コード例 #2
0
ファイル: atlas_combined.py プロジェクト: Garyfallidis/trn
import pbc
import numpy as np
import pbc1109
from pbc1109 import track_volumes as tv
from dipy.viz import fos
from dipy.core import track_metrics as tm
from dipy.core import track_learning as tl
from dipy.core import performance as pf
from itertools import combinations

#---------------------------------------------------------------------------------------------------------------------------------------------

path='/home/eg01/Data/PBC/pbc2009icdm'

#---------------------------------------------------------------------------------------------------------------------------------------------
ids=tl.emi_atlas()

#---------------------------------------------------------------------------------------------------------------------------------------------
def load_template_tes_and_tracks(path,brain,scan):
    
    volpath=path+'/ICBM_WMPM_tweaked_'+str(brain) +'_'+str(scan)+'.nii'    
    print volpath    
    template,voxsz,aff=pbc.loadvol(volpath)    
    tracks=pbc.load_approximate_tracks(path,brain,scan)
    print 'template shape', template.shape    
    tcs,tes = tv.track_counts(tracks, template.shape, vox_sizes=(1,1,1), return_elements=True)
    print 'tcs shape', tcs.shape    
    return template,tcs,tes,tracks

#---------------------------------------------------------------------------------------------------------------------------------------------
def for_a_value_in_template(template,value,tes,tracks):