def test_picking_trajectories():
curves=[100*np.random.rand(10,3),100*np.random.rand(5,3),100*np.random.rand(3,3)]
#curves=[100*np.array([[0,0,0],[1,0,0]]), 100*np.array([[0,1,0],[0,1,3]]),100*np.array([[0,2,0],[0,2,3]])]
'''
from nibabel import trackvis as tv
#fname='/home/eg309/Data/PROC_MR10032/subj_01/101/1312211075232351192010091419011391228126452ep2dadvdiffDSI25x25x25b4000s003a001_FA_warp.trk'
fname='/home/eg309/Data/fibers.trk'
streams,hdr=tv.read(fname)
T=[s[0] for s in streams]
curves=T[:200000]
fname='/home/eg309/Data/PROC_MR10032/subj_02/101/1312211075232351192010091708112071055601107ep2dadvdiffDSI10125x25x25STs002a001_QA_native.dpy'
from dipy.io.dpy import Dpy
dpr=Dpy(fname,'r')
T=dpr.read_indexed(range(20000))
from dipy.core.track_metrics import length
curves=[t for t in T if length(t) > 20]
dpr.close()
'''
#colors=np.random.rand(len(curves),4).astype('f4')
colors=0.5*np.ones((len(curves),4)).astype('f4')
for (i,c) in enumerate(curves):
orient=c[0]-c[-1]
orient=np.abs(orient/np.linalg.norm(orient))
colors[i,:3]=orient
c=InteractiveCurves(curves,colors=colors)
w=World()
w.add(c)
wi=Window()
wi.attach(w)
def show_tracks(tracks,alpha=1.,lw=2.,bg=(1.,1.,1.,1)):
colors=compute_colors(tracks,alpha=alpha)
ax = Line(tracks,colors,line_width=lw)
w=World()
w.add(ax)
wi = Window(caption=" Curve plotting (fos.me)",\
bgcolor=bg,width=1200,height=1000)
#(0,0.,0.2,1)
wi.attach(w)
wm = WindowManager()
wm.add(wi)
wm.run()
def load_tracks(method="pmt"):
from nibabel import trackvis as tv
dname = "/home/eg309/Data/orbital_phantoms/dwi_dir/subject1/"
if method == "pmt":
fname = "/home/eg309/Data/orbital_phantoms/dwi_dir/workflow/tractography/_subject_id_subject1/cam2trk_pico_twoten/data_fit_pdfs_tracked.trk"
streams, hdr = tv.read(fname, points_space="voxel")
tracks = [s[0] for s in streams]
if method == "dti":
fname = dname + "dti_tracks.dpy"
if method == "dsi":
fname = dname + "dsi_tracks.dpy"
if method == "gqs":
fname = dname + "gqi_tracks.dpy"
if method == "eit":
fname = dname + "eit_tracks.dpy"
if method in ["dti", "dsi", "gqs", "eit"]:
dpr_linear = Dpy(fname, "r")
tracks = dpr_linear.read_tracks()
dpr_linear.close()
if method != "pmt":
tracks = [t - np.array([96 / 2.0, 96 / 2.0, 55 / 2.0]) for t in tracks if track_range(t, 100 / 2.5, 150 / 2.5)]
tracks = [t for t in tracks if track_range(t, 100 / 2.5, 150 / 2.5)]
print "final no of tracks ", len(tracks)
qb = QuickBundles(tracks, 25.0 / 2.5, 18)
# from dipy.viz import fvtk
# r=fvtk.ren()
# fvtk.add(r,fvtk.line(qb.virtuals(),fvtk.red))
# fvtk.show(r)
# show_tracks(tracks)#qb.exemplars()[0])
# qb.remove_small_clusters(40)
del tracks
# load
tl = TrackLabeler(qb, qb.downsampled_tracks(), vol_shape=None, tracks_line_width=3.0, tracks_alpha=1)
# return tracks
w = World()
w.add(tl)
# create window
wi = Window(caption="Fos", bgcolor=(1.0, 1.0, 1.0, 1.0), width=1600, height=900)
wi.attach(w)
# create window manager
wm = WindowManager()
wm.add(wi)
wm.run()
def load_PX_tracks():
roi = "LH_premotor"
dn = "/home/hadron/from_John_mon12thmarch"
dname = "/extra_probtrackX_analyses/_subject_id_subj05_101_32/particle2trackvis_" + roi + "_native/"
fname = dn + dname + "tract_samples.trk"
from nibabel import trackvis as tv
points_space = [None, "voxel", "rasmm"]
streamlines, hdr = tv.read(fname, as_generator=True, points_space="voxel")
tracks = [s[0] for s in streamlines]
del streamlines
# return tracks
qb = QuickBundles(tracks, 25.0 / 2.5, 18)
# tl=Line(qb.exemplars()[0],line_width=1)
del tracks
qb.remove_small_clusters(20)
tl = TrackLabeler(qb, qb.downsampled_tracks(), vol_shape=None, tracks_line_width=3.0, tracks_alpha=1)
# put the seeds together
# seeds=np.vstack((seeds,seeds2))
# shif the seeds
# seeds=np.dot(mat[:3,:3],seeds.T).T + mat[:3,3]
# seeds=seeds-shift
# seeds2=np.dot(mat[:3,:3],seeds2.T).T + mat[:3,3]
# seeds2=seeds2-shift
# msk = Point(seeds,colors=(1,0,0,1.),pointsize=2.)
# msk2 = Point(seeds2,colors=(1,0,.ppppp2,1.),pointsize=2.)
w = World()
w.add(tl)
# w.add(msk)
# w.add(msk2)
# w.add(sl)
# create window
wi = Window(caption="Fos", bgcolor=(0.3, 0.3, 0.6, 1.0), width=1600, height=900)
wi.attach(w)
# create window manager
wm = WindowManager()
wm.add(wi)
wm.run()
def test_picking_trajectories():
curves = [
100 * np.random.rand(10, 3), 100 * np.random.rand(5, 3),
100 * np.random.rand(3, 3)
]
#curves=[100*np.array([[0,0,0],[1,0,0]]), 100*np.array([[0,1,0],[0,1,3]]),100*np.array([[0,2,0],[0,2,3]])]
'''
from nibabel import trackvis as tv
#fname='/home/eg309/Data/PROC_MR10032/subj_01/101/1312211075232351192010091419011391228126452ep2dadvdiffDSI25x25x25b4000s003a001_FA_warp.trk'
fname='/home/eg309/Data/fibers.trk'
streams,hdr=tv.read(fname)
T=[s[0] for s in streams]
curves=T[:200000]
fname='/home/eg309/Data/PROC_MR10032/subj_02/101/1312211075232351192010091708112071055601107ep2dadvdiffDSI10125x25x25STs002a001_QA_native.dpy'
from dipy.io.dpy import Dpy
dpr=Dpy(fname,'r')
T=dpr.read_indexed(range(20000))
from dipy.core.track_metrics import length
curves=[t for t in T if length(t) > 20]
dpr.close()
'''
#colors=np.random.rand(len(curves),4).astype('f4')
colors = 0.5 * np.ones((len(curves), 4)).astype('f4')
for (i, c) in enumerate(curves):
orient = c[0] - c[-1]
orient = np.abs(orient / np.linalg.norm(orient))
colors[i, :3] = orient
c = InteractiveCurves(curves, colors=colors)
w = World()
w.add(c)
wi = Window()
wi.attach(w)
except pyglet.window.NoSuchConfigException:
# Fall back to no multisampling for old hardware
window = Window(resizable=True, caption = mycpt)
# sample tree data
# ####
vert = np.array( [ [0,0,0],
[5,5,0],
[5,10,0],
[10,5,0]], dtype = np.float32 )
conn = np.array( [ 0, 1, 1, 2, 1, 3 ], dtype = np.uint32 )
cols = np.array( [ [0, 0, 1, 1],
[1, 0, 1, 1],
[0, 0, 1, 0.5] ] , dtype = np.float32 )
vert_width = np.array( [1, 5, 5, 1, 5, 1], dtype = np.float32 )
ax = Axes()
act = TreeRegion(vertices = vert, connectivity = conn, colors = cols, radius = vert_width)
w = World()
w.add(ax)
w.add(act)
window.attach(w)
wm = WindowManager()
wm.add(window)
wm.run()
edg_weight = np.random.random((ss, 1)).astype(np.float32)
edg_col = np.random.random_integers(0, 255 - 1, (ss, 4)).astype(np.ubyte)
#edg_col[:, 3] = np.random.random_integers(0,1, (ss,)).astype(np.ubyte).ravel()
print edg.shape
print edg_weight.shape
print edg_col.shape
aff = np.eye(4, dtype=np.float32)
aff[:3, 3] = [0, 0, 0]
cu = AttributeNetwork(affine=aff,
force_centering=True,
node_position=pos,
node_size=size,
node_color=col,
edge_connectivity=edg,
edge_weight=edg_weight,
edge_color=edg_col,
global_edge_width=3.5)
w.add(cu)
wi = Window()
wi.attach(w)
wm = WindowManager()
wm.add(wi)
wm.run()
cu.start()
import scipy.ndimage as nd import nibabel as ni from fos.actor.volslicer import ConnectedSlices from fos import World, Window # your nifti volume f1 = 'raw_t1_image.nii.gz' img = ni.load(f1) data = img.get_data() affine = img.get_affine() cds = ConnectedSlices(affine, data) w = World() w.add(cds) wi = Window() wi.attach(w)
import numpy as np import nibabel as nib import os.path as op from fos import World, Window, WindowManager from fos.actor.curve import InteractiveCurves from fos.core.data import get_track_filename # exmple track file streams,hdr = nib.trackvis.read(get_track_filename()) T=[s[0] for s in streams] Trk=np.array(T, dtype=np.object) print "loaded file" cu = InteractiveCurves(curves = T) w=World() w.add(cu) wi = Window(caption="Interactive Curves") wi.attach(w) wm = WindowManager() wm.add(wi) wm.run()
def unset_state(self):
glDisable(GL_BLEND)
glDisable(GL_DEPTH_TEST)
if __name__=='__main__':
pos1=100*np.random.rand(100,3) -50
cloud1 = Point(pos1,colors=(1,0,0,1.),pointsize=2.)
pos2=100*np.random.rand(100,3) -50
cloud2 = Point(pos2,colors=np.random.rand(100,4),pointsize=5.)
w=World()
w.add(cloud1)
w.add(cloud2)
wi = Window(caption="Fos",\
bgcolor=(.3,.3,.6,1.),\
width=1600,\
height=900)
wi.attach(w)
wm = WindowManager()
wm.add(wi)
wm.run()
qb.remove_small_clusters(1000)
print len(qb.clustering)
#create the interaction system for tracks
tl = TrackLabeler(qb,qb.downsampled_tracks(),vol_shape=data.shape,tracks_line_width=3.,tracks_alpha=1.)
#add a interactive slicing/masking tool
sl = Slicer(affine,data)
#add one way communication between tl and sl
tl.slicer=sl
#OpenGL coordinate system axes
ax = Axes(100)
x,y,z=data.shape
#add the actors to the world
w=World()
w.add(tl)
#w.add(sl)
#w.add(ax)
#create a window
#wi = Window(caption="Interactive bundle selection using fos and QB",\
# bgcolor=(0.3,0.3,0.6,1),width=1600,height=1000)
wi = Window(caption="Fos",bgcolor=(1.,1.,1.,1.),width=1600,height=900)
#attach the world to the window
wi.attach(w)
#create a manager which can handle multiple windows
wm = WindowManager()
wm.add(wi)
wm.run()
print('Everything is running ;-)')
#rotate camera
import numpy as np from fos import Window, WindowManager, World from fos.actor.spherecloud import SphereCloud n = 100 # the positions for the sphere positions = np.random.random( (n,3) ).astype( np.float32 ) * 500 # the radii for the spheres radii = np.random.random( (n,) ).astype( np.float32 ) * 10 # the color for the spheres colors = np.random.random( (n,4) ).astype( np.float32 ) * 10 colors[:,3] = 1.0 sc = SphereCloud( positions = positions, radii=radii, colors=colors ) wi = Window() w = World() w.add(sc) wi.attach(w) wm = WindowManager() wm.add(wi) wm.run()
aff[:3,3] = [0,0,0]
nlabs = {0 : { 'label' : 'Node 1',
'size' : 20,
'font' : 'Times New Roman',
'color' : ( 255, 0, 0, 255 ) },
1 : { 'label' : 'Node 2'}
}
class DynNet(DynamicNetwork):
def update(self, dt):
super(DynNet,self).update(dt)
dn = DynNet(affine = aff,
node_position = pos,
node_size = size,
node_color = col,
node_label = nlabs,
edge_connectivity = edg,
edge_color = edg_col,
global_edge_width = 3.5
)
w = World()
w.add(dn)
wi = Window(caption = "Dynamic Network with Fos")
wi.attach(w)
dn.start()
wm = WindowManager()
wm.add(wi)
wm.run()
font_size=26,
dpi=100,
# x=window.width//2, y=window.height//2,
anchor_x='center', anchor_y='center',
batch = self.batch)
def update(self, dt):
pass
def draw(self):
pass
glPushMatrix()
#glRotatef(5.0, 0, 1, 0)
glTranslatef(-100,0,0)
self.batch.draw()
glPopMatrix()
if __name__ == '__main__':
w = World()
wi = Window()
act = Dummy()
w.add(act)
wm = WindowManager()
wm.add(wi)
wm.run()
aff2=aff.copy() aff2[:3,3]=[250,0,0] l2=Light(position=np.array((1, 0, .5, 0),'f4'),ambient=(.0,.5,.5,1.),diffuse=(.5,.5,.5,1),specular=(.5,.5,.5,1)) m2=Material(diffuse=red,emissive=None,specular=(.9,.9,.9,1.),shininess=100,color=False) s2=Surface(vertices,faces,colors,normals, material = m2, light = l2, affine=aff2) aff3=aff.copy() aff3[:3,3]=[500,0,0] l3=Light(position=np.array((1, 0, .5, 0),'f4'),ambient=(.0,.5,.5,1.),diffuse=(.5,.5,.5,1),specular=(.5,.5,.5,1)) m3=Material(diffuse=blue,emissive=(.4,.4,.4,1.),specular=(.9,.9,.9,1.),shininess=100,color=False) s3=Surface(vertices,faces,colors,normals, material = m3, light = l3, affine=aff3) w=World() w.add(s) w.add(s2) w.add(s3) cam=DefaultCamera() w.add(cam) wi=Window() wi.attach(w) wm = WindowManager() wm.add(wi) wm.run() """ import os.path as op
caption=mycpt) # "vsync=False" to check the framerate
except pyglet.window.NoSuchConfigException:
# Fall back to no multisampling for old hardware
window = Window(resizable=True, caption=mycpt)
# sample tree data
# ####
vert = np.array([[0, 0, 0], [5, 5, 0], [5, 10, 0], [10, 5, 0]],
dtype=np.float32)
conn = np.array([0, 1, 1, 2, 1, 3], dtype=np.uint32)
cols = np.array([[0, 0, 1, 1], [1, 0, 1, 1], [0, 0, 1, 0.5]], dtype=np.float32)
vert_width = np.array([1, 5, 5, 1, 5, 1], dtype=np.float32)
ax = Axes()
act = TreeRegion(vertices=vert,
connectivity=conn,
colors=cols,
radius=vert_width)
w = World()
w.add(ax)
w.add(act)
window.attach(w)
wm = WindowManager()
wm.add(window)
wm.run()
def unset_state(self):
glDisable(GL_BLEND)
glDisable(GL_DEPTH_TEST)
def update(self,dt):
pass
if __name__ =='__main__':
ax = Axes(100)
data=np.round(255*np.random.rand(182,218,4)).astype(np.ubyte)
#data=np.round(255*np.ones((182,218,4))).astype(np.ubyte)
data[70:120,:,:3]=100
data[:,:,3]=150
data=data.astype(np.ubyte)
tex=Texture2D(data)
w=World()
w.add(ax)
w.add(tex)
wi = Window(caption="Texture by Free On Shades (fos.me)",\
bgcolor=(0,0.,0.2,1),width=800,height=600)
wi.attach(w)
wm = WindowManager()
wm.add(wi)
wm.run()
print normals.min(), normals.max(), normals.mean()
print vertices.dtype, faces.dtype, colors.dtype, normals.dtype
from fos.actor.surf import Surface
from fos import Window, World, DefaultCamera
aff = np.eye(4, dtype=np.float32)
#aff[0,3] = 30
s = Surface(vertices,
faces,
colors,
normals=normals,
affine=None,
force_centering=True,
add_lights=False)
#vertices2=vertices+np.array([10,0,0],dtype=vertices.dtype)
#s2=Surface(vertices2,faces,colors, affine = aff, normals=normals)
w = World()
w.add(s)
#w.add(s2)
cam = DefaultCamera()
w.add(cam)
wi = Window(bgcolor=(1., 0., 1., 1.), width=1000, height=1000)
wi.attach(w)
import scipy.ndimage as nd import nibabel as ni from fos.actor.volslicer import ConnectedSlices from fos import World,Window, WindowManager f1='/home/eg309/Data/regtest/fiac0/meanafunctional_01.nii' img=ni.load(f1) data =img.get_data() affine=img.get_affine() cds =ConnectedSlices(affine,data) #actors.append(cds) w=World() w.add(cds) wi=Window() wi.attach(w) wm = WindowManager() wm.add(wi) wm.run()
""" Create an empty Fos world and attach a window to it """ from fos import World, Window, DefaultCamera, WindowManager # create the first window wi = Window(caption = "My Window 1", bgcolor = (1,1,1,1) ) # return the default empty world of this window w = World() # add a new camera to this world cam2 = DefaultCamera() w.add(cam2) # create the second window wi2 = Window(caption = "My Window 2", bgcolor = (0,0,0,1) ) # we want to look at the same world as window 1, thus drop # the default world and attach the window to our world with the second camera wi2.attach(w) # set the camera for the second window to the second camera wi2.set_current_camera(cam2) # Create the window manager, add the windows, and go! wm = WindowManager() wm.add(wi) wm.add(wi2) wm.run()
if __name__ == '__main__':
tracks=[100*np.random.rand(100,3),100*np.random.rand(20,3)]
colors=np.ones((120,4))
colors[0:100,:3]=np.array([1,0,0.])
colors[100:120,:3]=np.array([0,1,0])
import nibabel as nib
from os import path as op
a=nib.trackvis.read( op.join(op.dirname(fos.__file__), "data", "tracks300.trk") )
g=np.array(a[0], dtype=np.object)
tracks = [tr[0] for tr in a[0]]
#tracks = tracks-np.concatenate(tracks,axis=0)
lentra = [len(t) for t in tracks]
colors = np.ones((np.sum(lentra),4))
#colors[:,3]=0.9
ax = Line(tracks,colors,line_width=2)
w=World()
w.add(ax)
wi = Window(caption=" Line plotting (fos.me)",\
bgcolor=(0,0.,0.2,1),width=800,height=600)
wi.attach(w)
wm = WindowManager()
wm.add(wi)
wm.run()
# fT1_ref = '/usr/share/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz'
img = nib.load(fT1)
# img = nib.load(fT1)
sl = Slicer(img.get_affine(), img.get_data())
tl.slicer = sl
luigi = Line([t - shift for t in lT], line_width=2)
# put the seeds together
seeds = np.vstack((seeds, seeds2))
# shif the seeds
seeds = np.dot(mat[:3, :3], seeds.T).T + mat[:3, 3]
seeds = seeds - shift
# seeds2=np.dot(mat[:3,:3],seeds2.T).T + mat[:3,3]
# seeds2=seeds2-shift
msk = Point(seeds, colors=(1, 0, 0, 1.0), pointsize=2.0)
# msk2 = Point(seeds2,colors=(1,0,.ppppp2,1.),pointsize=2.)
w = World()
w.add(tl)
w.add(msk)
# w.add(msk2)
w.add(sl)
w.add(luigi)
# create window
wi = Window(caption="subj_" + subject + ".png", bgcolor=(0.3, 0.3, 0.6, 1.0), width=1600, height=900)
wi.attach(w)
# create window manager
wm = WindowManager()
wm.add(wi)
wm.run()
