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 __init__(self, bgcolor=None, **kwargs):
""" Create a FosWindow. All parameters are optional.
Parameters
----------
`bgcolor` : tuple
Specify the background color as 4-tuple with values
between 0 and 1
`width` : int
Width of the window, in pixels. Defaults to 640, or the
screen width if `fullscreen` is True.
`height` : int
Height of the window, in pixels. Defaults to 480, or the
screen height if `fullscreen` is True.
`caption` : str or unicode
Initial caption (title) of the window. Defaults to
``sys.argv[0]``.
`fullscreen` : bool
If True, the window will cover the entire screen rather
than floating. Defaults to False.
`visible` : bool
Determines if the window is visible immediately after
creation. Defaults to True. Set this to False if you
would like to change attributes of the window before
having it appear to the user.
"""
self.update_dt = 1.0/60
if bgcolor == None:
self.bgcolor = color.black
else:
self.bgcolor = bgcolor
self.mouse_x, self.mouse_y = 0,0
# create an empty world by default
emptyworld = World("Zero-Point World")
self.attach(emptyworld)
# the frame rate display from fos.lib.pyglet
#self.fps_display = FPSDisplay(self)
#self.foslabel = WindowText(self, 'fos', x=10 , y=40)
self.show_logos = False
# pushing new event handlers
foswinhandlers = FosWinEventHandler(self)
self.push_handlers(foswinhandlers)
# log handler
# self.push_handlers(WindowEventLogger())
self.show_fps = True
self.fps_display = ClockDisplay()
super(SimpleWindow, self).__init__(**kwargs)
print "init simple window"
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()
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()
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()
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
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=load_pickle(fpkl)
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 ;-)')
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()
""" 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()
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()
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() """
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()
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)
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()
dpr.close()
#load initial QuickBundles with threshold 30mm
fpkl = 'data/subj_'+("%02d" % subject)+'/101_32/DTI/qb_gqi_'+str(seeds)+'M_linear_'+str(qb_dist)+'.pkl'
#qb=QuickBundles(T,30.,12)
qb=load_pickle(fpkl)
#create the interaction system for tracks
tl = TrackLabeler(qb,qb.downsampled_tracks(),vol_shape=data.shape,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 Spaghetti using Diffusion Imaging in Python (dipy.org) and Free On Shades (fos.me)",\
bgcolor=(0.3,0.3,0.6,1),width=1200,height=800)
#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 ;-)')
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()
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()
import numpy as np
from fos import World, Window, WindowManager
from fos.actor.network import AttributeNetwork
w = World("myworld")
# node positions
s = 1000
pos = np.random.random((s, 3)).astype(np.float32) * 100
col = np.random.random_integers(0, 255, (s, 4)).astype(np.ubyte)
col[:, 3] = 255
print pos.shape
print col.shape
size = np.array([1.0, 10.0], dtype=np.float32)
size = np.random.random((s, 1)).astype(np.float32)
print size.shape
ss = 500
edg = np.array([[0, 1]], dtype=np.uint8)
edg_weight = np.array([1.5], dtype=np.float32)
edg_col = np.array([[255, 0, 0, 255]], dtype=np.ubyte)
print edg.shape
print edg_weight.shape
print edg_col.shape
edg = np.random.random_integers(0, s - 1, (ss, 2)).astype(np.uint32)
edg_weight = np.random.random((ss, 1)).astype(np.float32)
edg_col = np.random.random_integers(0, 255 - 1, (ss, 4)).astype(np.ubyte)
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()
