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)
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()
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()
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)
""" 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()
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()
""" 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 = wi.get_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()
