def init(self):
'''
global csurf
csurfr ='/home/eg01/Data_Backup/Data/Adam/multiple_transp_volumes/freesurfer_trich/rh.pial.vtk'
#csurf_fname ='/home/eg309/Desktop/rh.pial.vtk'
csurfl ='/home/eg01/Data_Backup/Data/Adam/multiple_transp_volumes/freesurfer_trich/lh.pial.vtk'
#csurfr = cortex.CorticalSurface(csurfr)
#csurfl = cortex.CorticalSurface(csurfl)
#csurfr.init()
#csurfl.init()
'''
global b1
#devel06
b1_fname='/home/ian/Data/dipy/brain2_scan1_fiber_track_mni.trk'
#devel07
#b1_fname='/home/eg01/Data_Backup/Data/PBC/pbc2009icdm/brain2/brain2_scan1_fiber_track_mni.trk'
#elfthin
#b1_fname='/home/eg309/Desktop/DataNew/garyfallidis/brain2/brain2_scan1_fiber_track_mni.trk'
b1=tracks.Tracks(b1_fname)
b1.angular_speed = 0.
b1.picking_example = True
b1.min_length = 0.
b1.init()
self.slots={0:{'actor':b1,'slot':( 0, 800*MS )}}
'''
def hidden_tracks(self,t1_fname,opacity,angle_table,many_colors=False,data_ext=None):
t1=tracks.Tracks(t1_fname,ang_table=angle_table,shrink=0.99,subset=[0,20000],data_ext=data_ext)
t1.angular_speed = 0.
t1.fade_demo = True
t1.opacity = opacity #0.1
#t1.opacity_rate = -0.01
#tb1.fadeout = True
#tb1.fadeout_speed = 0.001
t1.position = -tb1.mean
t1.position[0] += 5.
t1.position[2] += 10.
t1.manycolors = many_colors #False #True
#tb1.material_color = True
t1.orbit_demo = True#False
t1.orbit_anglez_rate = 0.#1.
t1.orbit_anglex_rate = 0.#-.1
t1.init()
return t1
def init(self):
tracks.angle_table_index=0
tracks.anglex = 0.
tracks.angley = 0.
tracks.anglez = 0.
empty = tracks.Empty()
empty.init()
ghost = tracks.Ghost()
ghost.init()
global csurf
#devel06
#csurfr ='/home/ian/Data/dipy/rh.pial.vtk'
#csurfl ='/home/ian/Data/dipy/lh.pial.vtk'
#devel07
csurfr ='/home/eg01/Data_Backup/Data/Adam/multiple_transp_volumes/freesurfer_trich/rh.pial.vtk'
csurfl ='/home/eg01/Data_Backup/Data/Adam/multiple_transp_volumes/freesurfer_trich/lh.pial.vtk'
csurfr = cortex.CorticalSurface(csurfr, angle_table=tracks.angle_table)
csurfl = cortex.CorticalSurface(csurfl, angle_table=tracks.angle_table)
csurfr.fadeout = True
csurfl.fadeout = True
csurfr.fadeout_speed = 0.001
csurfl.fadeout_speed = 0.001
csurfr.orbit_demo = True
csurfr.orbit_anglez_rate = 1.
csurfl.orbit_demo = True
csurfl.orbit_anglez_rate = 1.
csurfr.orbit_anglex_rate = -.1
csurfl.orbit_anglex_rate = -.1
csurfr.position[2]+=10
csurfl.position[2]+=10
csurfr.init()
csurfl.init()
#'''
import copy
global csurfR
global csurfL
csurfR = copy.copy(csurfr)
csurfL = copy.copy(csurfl)
csurfR.fadeout = False
csurfL.fadeout = False
csurfR.init()
csurfL.init()
global tb1
#devel06
#tb1_fname='/home/ian/Data/dipy/brain2_scan1_fiber_track_mni.trk'
#devel07
tb1_fname='/home/eg01/Data_Backup/Data/PBC/pbc2009icdm/brain2/brain2_scan1_fiber_track_mni.trk'
#tb1=tracks.ChromoTracks(tb1_fname,shrink=0.99)
tb1=tracks.Tracks(tb1_fname,ang_table=True,shrink=0.99,subset=[0,20000])
tb1.angular_speed = 0.
tb1.fade_demo = True
tb1.opacity = 0.1
tb1.opacity_rate = -0.01
#tb1.fadeout = True
#tb1.fadeout_speed = 0.001
tb1.position = -tb1.mean
tb1.position[0] += 5.
tb1.position[2] += 10.#20.
tb1.manycolors = False #True
#tb1.material_color = True
tb1.orbit_demo = True #False
tb1.orbit_anglez_rate = 1.
tb1.orbit_anglex_rate = -.1
tb1.init()
global t1; t1 = self.hidden_tracks(tb1_fname,0.1*0.1,angle_table=True, data_ext=tb1.data)
global ct1; ct1 = self.hidden_tracks(tb1_fname,0.1*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct6; ct6 = self.hidden_tracks(tb1_fname,1*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
#global ct7; ct7 = self.hidden_tracks(tb1_fname,0.7,angle_table=True,many_colors=True, data_ext=tb1.data)
'''
global t1; t1 = self.hidden_tracks(tb1_fname,1*0.1,angle_table=True, data_ext=tb1.data)
global t2; t2 = self.hidden_tracks(tb1_fname,.1*0.1,angle_table=True, data_ext=tb1.data)
global t3; t3 = self.hidden_tracks(tb1_fname,.05*0.1,angle_table=True, data_ext=tb1.data)
global t4; t4 = self.hidden_tracks(tb1_fname,.01*0.1,angle_table=True, data_ext=tb1.data)
#global t5; t5 = self.hidden_tracks(tb1_fname,.005*0.1,angle_table=True, data_ext=tb1.data)
#global ct1; ct1 = self.hidden_tracks(tb1_fname,.005*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct2; ct2 = self.hidden_tracks(tb1_fname,.01*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct3; ct3 = self.hidden_tracks(tb1_fname,.05*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct4; ct4 = self.hidden_tracks(tb1_fname,.1*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct5; ct5 = self.hidden_tracks(tb1_fname,.5*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
global ct6; ct6 = self.hidden_tracks(tb1_fname,1*0.1,angle_table=True,many_colors=True, data_ext=tb1.data)
'''
#'''
initial = 10*MS
delayt = 5*MS
delay = initial +delayt
self.slots={00:{'actor':empty, 'slot':(0, delayt)},
05:{'actor':ghost,'slot':( 0*MS+delayt, 800*MS+delayt )},
80:{'actor':csurfL,'slot':( 0*MS+delayt, 800*MS )},
90:{'actor':csurfR,'slot':( 0*MS+delayt, 800*MS )}}
'''
#05:{'actor':ghost,'slot':(39*MS+delay, 800*MS+delay )},
10:{'actor':tb1,'slot':( 0*MS+delay, 40*MS+delay )},
11:{'actor':csurfl,'slot':( 0*MS+delay, 40*MS+delay )},
12:{'actor':csurfr,'slot':( 0*MS+delay, 40*MS+delay )},
21:{'actor':t1,'slot':( 40*MS+delay, 41*MS+delay )},
22:{'actor':t1,'slot':( 40*MS+delay, 42*MS+delay )},
23:{'actor':t1,'slot':( 40*MS+delay, 43*MS+delay )},
31:{'actor':ct1,'slot':( 42*MS+delay, 47*MS+delay )},
32:{'actor':ct1,'slot':( 42*MS+delay, 46*MS+delay )},
33:{'actor':ct1,'slot':( 42*MS+delay, 45*MS+delay )},
34:{'actor':ct6,'slot':( 47*MS+delay, 800*MS+delay )}
#35:{'actor':ct7,'slot':( 48*MS, 800*MS )}
'''
'''
self.slots={00:{'actor':empty, 'slot':(0, delay)},
05:{'actor':ghost,'slot':( 0*MS+delay, 800*MS+delay )},
#05:{'actor':ghost,'slot':(39*MS+delay, 800*MS+delay )},
10:{'actor':tb1,'slot':( 0*MS+delay, 40*MS+delay )},
11:{'actor':csurfl,'slot':( 0*MS+delay, 40*MS+delay )},
12:{'actor':csurfr,'slot':( 0*MS+delay, 40*MS+delay )},
21:{'actor':t1,'slot':( 40*MS+delay, 41*MS+delay )},
22:{'actor':t1,'slot':( 40*MS+delay, 42*MS+delay )},
23:{'actor':t1,'slot':( 40*MS+delay, 43*MS+delay )},
31:{'actor':ct1,'slot':( 42*MS+delay, 47*MS+delay )},
32:{'actor':ct1,'slot':( 42*MS+delay, 46*MS+delay )},
33:{'actor':ct1,'slot':( 42*MS+delay, 45*MS+delay )},
34:{'actor':ct6,'slot':( 47*MS+delay, 800*MS+delay )}
#35:{'actor':ct7,'slot':( 48*MS, 800*MS )}
}
'''
'''
self.slots={10:{'actor':tb1,'slot':( 0, 3*40*MS )},
11:{'actor':csurfl,'slot':( 0,3*40*MS )},
12:{'actor':csurfr,'slot':( 0,3*40*MS )},
21:{'actor':t1,'slot':( 3*40*MS, 3*41*MS )},
22:{'actor':t1,'slot':( 3*40*MS, 3*42*MS )},
23:{'actor':t1,'slot':( 3*40*MS, 3*43*MS )},
31:{'actor':ct1,'slot':( 3*42*MS, 3*47*MS )},
32:{'actor':ct1,'slot':( 3*42*MS, 3*46*MS )},
33:{'actor':ct1,'slot':( 3*42*MS,3*45*MS )},
34:{'actor':ct6,'slot':( 3*47*MS, 3*48*MS )},
35:{'actor':ct7,'slot':( 3*48*MS, 800*MS )}
}
'''
global last_time
last_time = glut.glutGet(glut.GLUT_ELAPSED_TIME)
def init(self):
import pbc
G,hdr,R = pbc.load_approximate_training_set('/home/eg01/Data_Backup/Data/PBC/pbc2009icdm/')
tl=[]
self.slots={}
colors=np.array([[1.,1.,1.],
[0.5, 0, 0],
[0.29411765, 0., 0.50980392],
[0, 0.5, 0],
[0., 0.49, 1.],
[ 0.498, 1., 0.83 ],
[1. , 0.84, 0. ],
[0.74901961, 1., 0.],
[0.49803922, 1. , 0. ]])
data=G[0]['tracks']
d1z=np.concatenate(data).mean(axis=0)
for g in [0,1,2,3,4,5,6,7,8]:
data=G[g]['tracks']
print g, G[g]['label_name']
global t
#d1z=np.concatenate(data).mean(axis=0)
data=[t-d1z for t in data]
t=tracks.Tracks(None,data_ext=data)
t.angular_speed = 0.1
t.brain_color=colors[g]
t.manycolors = False
t.opacity = 0.1
t.orbit_demo = True
t.orbit_anglez_rate = 0.
t.orbit_anglex_rate = 0.
t.orbit_angley_rate = 1.
t.init()
t.position = np.array([0,0,10])
print 'tp', t.position
tl.append(t)
if g==0:
self.slots[g]={'actor':tl[g],'slot':( 0, 15*MS ) }
else:
self.slots[g]={'actor':tl[g],'slot':( 0, 25*MS ) }
#full arcuate
arcuate=G[1]['tracks']
#arcuate2=self.bloat_bundle(arcuate)
amean=np.concatenate(arcuate).mean(axis=0)
data=[t-amean for t in arcuate]
#data2=self.bloat_bundle(data)
t=tracks.Tracks(None,data_ext=data)
t.angular_speed = 0.1
t.brain_color=colors[1]
t.manycolors = False
t.opacity = 0.1
t.orbit_demo = True
t.orbit_anglez_rate = 0.
t.orbit_anglex_rate = 0.
t.orbit_angley_rate = -1.
t.init()
t.position = np.array([-40,0,60])
self.slots[g+1]={'actor':t,'slot':( 27*MS, 800*MS ) }
#broken arcuate - injury
dataa,datab=self.break_bundle(data, [-3000,3000,0], [-3000,-3000,0], [3000, -3000,0])
#dataa=[t+np.array([100,0,0],np.float32) for t in dataa]
#datab=[t+np.array([100,0,0],np.float32) for t in datab]
t1=tracks.Tracks(None,data_ext=dataa)
t1.angular_speed = 0.1
t1.brain_color=[1.,0.,0.]
t1.manycolors = False
t1.opacity = 0.1
t1.orbit_demo = True
t1.orbit_anglez_rate = 0.
t1.orbit_anglex_rate = 0.
t1.orbit_angley_rate = -1.
t1.init()
t1.position = np.array([0,0,60])
#datab=[t+np.array([0,20,0]) for t in datab]
t2=tracks.Tracks(None,data_ext=datab)
t2.angular_speed = 0.1
t2.brain_color=[1.,0.,0.]
t2.manycolors = False
t2.opacity = 0.1
t2.orbit_demo = True
t2.orbit_anglez_rate = 0.
t2.orbit_anglex_rate = 0.
t2.orbit_angley_rate = -1.
t2.init()
t2.position = np.array([0,0,60])
self.slots[g+2]={'actor':t1,'slot':( 27*MS, 800*MS ) }
self.slots[g+3]={'actor':t2,'slot':( 27*MS, 800*MS ) }
#bloated arcuate
data2=self.bloat_bundle(data)
t3=tracks.Tracks(None,data_ext=data2)
t3.angular_speed = 0.1
t3.brain_color=colors[1]
t3.manycolors = False
t3.opacity = 0.1
t3.orbit_demo = True
t3.orbit_anglez_rate = 0.
t3.orbit_anglex_rate = 0.
t3.orbit_angley_rate = -1.
t3.init()
t3.position = np.array([40,0,60])
self.slots[g+4]={'actor':t3,'slot':( 27*MS, 800*MS ) }
def init(self):
br1path='/home/eg01/Data_Backup/Data/Eleftherios/CBU090133_METHODS/20090227_145404/Series_003_CBU_DTI_64D_iso_1000/dtk_dti_out/dti_FACT.trk'
br2path='/home/eg01/Data_Backup/Data/Eleftherios/CBU090134_METHODS/20090227_154122/Series_003_CBU_DTI_64D_iso_1000/dtk_dti_out/dti_FACT.trk'
br3path='/home/eg01/Data_Backup/Data/Eleftherios/CBU090133_METHODS/20090227_145404/Series_003_CBU_DTI_64D_iso_1000/dtk_dti_out/dti_RK2.trk'
min_len=20
down=20
rand_tracks=-1 #default 10 min_search_len=70
min_search_len=70
max_search_len=140
corr_mat_demo=np.array([[ 1, 10560, 3609],[ 2, 17872, 15377],[ 3, 6447, 3897], [4, 18854, 6409], [ 5, 14416, 4515], [ 7, 9956, 13913], [8, 10853, 15572], [ 9, 13280, 8461], [ 0, 11275, 9224]])
print 'Minimum track length', min_len, 'mm'
print 'Number of segments for downsampling',down
print 'Number of tracks for detection',rand_tracks
print 'Minimum searched track length', min_search_len, 'mm'
print 'Maximum searched track length', max_search_len, 'mm'
tracks1,hdr1=tv.read(br1path)
tracks2,hdr2=tv.read(br2path)
tracks3,hdr3=tv.read(br3path)
#Load only track points, no scalars or parameters.
tracks1=[t[0] for t in tracks1]
tracks2=[t[0] for t in tracks2]
tracks3=[t[0] for t in tracks3]
print 'Before thresholding'
print len(tracks1)
print len(tracks2)
print len(tracks3)
print hdr1['dim']
print hdr2['dim']
print hdr3['dim']
#Apply thresholds
tracks1=[t for t in tracks1 if tm.length(t) > min_len]
tracks2=[t for t in tracks2 if tm.length(t) > min_len]
tracks3=[t for t in tracks3 if tm.length(t) > min_len]
print 'After thresholding'
print len(tracks1)
print len(tracks2)
print len(tracks3)
print 'Downsampling'
tracks1z=[tm.downsample(t,down) for t in tracks1]
tracks2z=[tm.downsample(t,down) for t in tracks2]
tracks3z=[tm.downsample(t,down) for t in tracks3]
print 'Detecting random tracks'
lt1=len(tracks1)
lt2=len(tracks2)
lt3=len(tracks3)
if rand_tracks==-1:
#use already stored indices
t_ind=corr_mat_demo[:,1]
t_ind=np.array(t_ind)
print 'Indices of tracks for detection', t_ind
print 'Finding corresponding tracks'
global track2track
track2track= self.corresponding_tracks(t_ind,tracks1z,tracks2z)
global track2track2
track2track2=self.corresponding_tracks(t_ind,tracks1z,tracks3z)
print 'First Correspondance Matrix'
print track2track
print 'Second Correspondance Matrix'
print track2track2
print 'first brain'
print track2track[:,1].T
print 'second brain'
print track2track[:,2].T
print 'third brain'
print track2track2[:,2].T
#fos.add(r,fos.line(tracks1,fos.red,opacity=0.01))
#fos.add(r,fos.line(tracks2,fos.cyan,opacity=0.01))
tracks1zshift = tracks1z
tracks2zshift = tracks2z
tracks3zshift = tracks3z
m1z=np.concatenate(tracks1zshift).mean(axis=0)
m2z=np.concatenate(tracks2zshift).mean(axis=0)
m3z=np.concatenate(tracks3zshift).mean(axis=0)
#tracks1zshift=[t+np.array([-70,0,0]) for t in tracks1z]
#tracks2zshift=[t+np.array([70,0,0]) for t in tracks2z]
tracks1zshift=[t-m1z for t in tracks1z]
tracks2zshift=[t-m2z for t in tracks2z]
tracks3zshift=[t-m3z for t in tracks3z]
global t1
#devel07
t1=tracks.Tracks(None,data_ext=tracks1zshift)
t1.angular_speed = 0.1
t1.brain_color=[1,0,0]
t1.manycolors=False
t1.opacity = 0.01
t1.orbit_demo=True
t1.orbit_anglez_rate = 0.
t1.orbit_anglex_rate = 0.
t1.orbit_angley_rate = .2
t1.init()
t1.position = np.array([-120,0,-30])
print 't1p',t1.position
global t2
#devel07
t2=tracks.Tracks(None,data_ext=tracks2zshift)
t2.angular_speed = 0.1
t2.brain_color=[0,1,1]
t2.manycolors=False
t2.opacity = 0.01
t2.orbit_demo=True
t2.orbit_anglez_rate = 0.
t2.orbit_anglex_rate = 0.
t2.orbit_angley_rate = .2
t2.init()
t2.position = np.array([0,0,-30])
print 't2p', t2.position
global t3
#devel07
t3=tracks.Tracks(None,data_ext=tracks3zshift)
t3.angular_speed = 0.1
t3.manycolors=False
t3.brain_color=[0,0,1]
t3.opacity = 0.01
t3.orbit_demo=True
t3.orbit_anglez_rate = 0.
t3.orbit_anglex_rate = 0.
t3.orbit_angley_rate = .2
t3.init()
#t3.position = -
#np.concatenate(tracks3zshift).mean(axis=0)+np.array([70,0,0])
t3.position = np.array([120,0,-30])
print 't3p', t3.position
self.slots={0:{'actor':t1,'slot':( 0, 800*MS ) },
1:{'actor':t2,'slot':( 0, 800*MS ) },
2:{'actor':t3,'slot':( 0, 800*MS ) }}
def init(self):
global b1
#devel06
b1_fname='/home/ian/Data/dipy/brain2_scan1_fiber_track_mni.trk'
#devel07
#b1_fname='/home/eg01/Data_Backup/Data/PBC/pbc2009icdm/brain2/brain2_scan1_fiber_track_mni.trk'
b1=tracks.Tracks(b1_fname,subset=[0,200])
b1.angular_speed = 0.
b1.picking_example = True
b1.min_length = 20.
b1.opacity = 0.8
b1.manycolors = False
b1.brain_color = [0, 0, 0]
b1.init()
global texim
#devel06
fname = '/home/ian/Data/dipy/Streaks4.bmp'
#devel07
#fname = '/home/eg01/Devel/Fos/fos/core/tests/data/Streaks4.bmp'
texim = texture.Texture_Demo(fname,red=False,green=False, blue=True)
#texim.orbit = b1.data[4246]
#print 'len(b1.data)', len(b1.data)
random_inx=np.trunc(len(b1.data)*np.random.rand(200)).astype(np.int)
#print random_inx
#texim.orbits = [b1.data[4246],b1.data[3000],b1.data[2000],b1.data[1000]]
texim.orbits =[]
for i in random_inx:
#print i
if tm.length(b1.data[i]) > 20.:
#print i
texim.orbits.append(b1.data[i])
texim.orbits_index = np.zeros((len(texim.orbits),),np.int)
texim.init()
self.slots={0:{'actor':texim,'slot':( 0, 800*MS )}}#,