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 visualize(pos, parents, offset, colors):
wi = Window()
w = wi.get_world()
act = NeuronRegion(vertices=pos, connectivity=parents, offset=offset, colors=colors, force_centering=True)
w.add(act)
return act
def visualize(pos, parents, offset, colors):
wi = Window()
w = wi.get_world()
act = NeuronRegion(vertices=pos,
connectivity=parents,
offset=offset,
colors=colors,
force_centering=True)
w.add(act)
return act
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)
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)
"..", "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.random.rand(np.sum(lentra),4)
#colors[:,3]=0.9
"""
streamlines = Line('fornix', tracks, colors, line_width=2)
from fos import Window, Region
from fos.actor.axes import Axes
from fos.actor.text import Text3D
title = 'Bundle Picker'
w = Window(caption=title, width=1200, height=800, bgcolor=(0., 0., 0.2))
region = Region(regionname='Main',
extent_min=np.array([-5.0, -5, -5]),
extent_max=np.array([5, 5, 5]))
ax = Axes(name="3 axes", linewidth=2.0)
vert = np.array([[2.0, 3.0, 0.0]], dtype=np.float32)
ptr = np.array([[.2, .2, .2]], dtype=np.float32)
tex = Text3D("Text3D", vert, "Reg", 10, 2, ptr)
region.add_actor(ax)
region.add_actor(tex)
region.add_actor(streamlines)
#w.screenshot( 'red.png' )
w.add_region(region)
import numpy as np from fos import Window 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 = wi.get_world() w.add(sc)
parents = f["neurons/localtopology"].value
labeling = f["neurons/labeling"].value
colors = f["neurons/segmentcolors"].value
f.close()
print pos
print parents
print labeling
print colors
mycpt = "Treedemo - Fos.me"
try:
# Try and create a window with multisampling (antialiasing)
config = Config(sample_buffers=1, samples=4, depth_size=16, double_buffer=True)
window = Window(
resizable=True, config=config, vsync=False, width=1000, height=800, caption=mycpt
) # "vsync=False" to check the framerate
except fos.lib.pyglet.window.NoSuchConfigException:
# Fall back to no multisampling for old hardware
print "fallback"
window = Window(resizable=True, caption=mycpt)
ac = []
s = 500
# tune it up
# this is very inefficient, because it copies the position arrays
for i in range(1000):
pos2 = pos.copy()
pos2[:, 0] = pos2[:, 0] + (randn() - 0.5) * s
pos2[:, 1] = pos2[:, 1] + (randn() - 0.5) * s
# random width array
print parents
print labeling
print colors
mycpt = "Treedemo - Fos.me"
try:
# Try and create a window with multisampling (antialiasing)
config = Config(
sample_buffers=1,
samples=4,
depth_size=16,
double_buffer=True,
)
window = Window(resizable=True,
config=config,
vsync=False,
width=1000,
height=800,
caption=mycpt) # "vsync=False" to check the framerate
except fos.lib.pyglet.window.NoSuchConfigException:
# Fall back to no multisampling for old hardware
print "fallback"
window = Window(resizable=True, caption=mycpt)
ac = []
# spread factor
s = 500
# duplicator
d = 30
# tune it up
# this is very inefficient, because it copies the position arrays
import numpy as np
from fos import Window, WindowManager
from fos.actor.network import DynamicNetwork
#import fos.lib.pyglet
#fos.lib.pyglet.options['debug_gl'] = True
wi = Window(caption = "Dynamic Network with Fos")
w = wi.get_world()
# time steps
ts = 200
# node positions
s = 1000
pos = np.zeros( (s,3,ts)).astype(np.float32)
pos[:,:,0] = np.random.random( (s,3)).astype(np.float32) * 200 - 100
for i in xrange(1,ts):
pos[:,:,i] = pos[:,:,i-1] + np.random.random( (s,3)).astype(np.float32) * 4 - 2
col = np.random.random_integers( 0, 255-1, (s,4,ts) ).astype(np.ubyte)
#col[:, 3, :] = 255
size = np.random.random( (s ,ts) ).astype(np.float32)
ss = 500
edg = np.random.random_integers(0, s-1, (ss, 2,ts)).astype(np.uint32)
edg_weight = np.random.random( (ss,1,ts)).astype(np.float32)
edg_col = np.random.random_integers( 0, 255-1, (ss,4,ts) ).astype(np.ubyte)
""" 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()
if __name__ == '__main__':
import nibabel as nib
dname = '/usr/share/fsl/data/standard/'
fname = dname + 'FMRIB58_FA_1mm.nii.gz'
fname = '/home/eg309/Data/trento_processed/subj_01/MPRAGE_32/rawbet.nii.gz'
img=nib.load(fname)
data = img.get_data()
data = np.interp(data, [data.min(), data.max()], [0, 255])
from fos import Init, Run
Init()
window = Window(caption="[F]OS", bgcolor=(0.4, 0.4, 0.9))
scene = Scene(activate_aabb=False)
guil = Guillotine('VolumeSlicer', data)
scene.add_actor(guil)
window.add_scene(scene)
window.refocus_camera()
#window = Window()
window.show()
#print get_ipython()
Run()
import nibabel as nib
from fos import Window, Scene, Init, Run
#dname='/home/eg309/Data/trento_processed/subj_03/MPRAGE_32/'
#fname = dname + 'T1_flirt_out.nii.gz'
#dname = '/home/eg309/Data/111104/subj_05/'
#fname = dname + '101_32/DTI/fa.nii.gz'
dname = '/usr/share/fsl/data/standard/'
fname = dname + 'FMRIB58_FA_1mm.nii.gz'
#fname = '/home/eleftherios/Data/trento_processed/subj_01/MPRAGE_32/raw.nii'
img = nib.load(fname)
data = img.get_data()
data[np.isnan(data)] = 0
data = np.interp(data, [data.min(), data.max()], [0, 255])
data = data.astype(np.ubyte)
affine = img.get_affine()
print data.shape
Init()
window = Window(caption='[F]OS', bgcolor=(0.1, 0.2, 0.6))
scene = Scene(activate_aabb=False)
sli = Slicer('Volume Slicer', data, affine, convention='RAS')
scene.add_actor(sli)
window.add_scene(scene)
window.refocus_camera()
Run()
"""
affine = None
data = np.zeros((256, 128, 32), np.uint8)
volume = np.zeros(data.shape + (3, ))
volume[..., 0] = data.copy()
volume[..., 1] = data.copy()
volume[..., 2] = data.copy()
volume = volume.astype(np.ubyte)
volume[..., :] = (255, 0, 0)
#volume[] =
print volume.shape, volume.min(), volume.max()
window = Window()
region = Region()
#volume = data
tex = Texture3D('Buzz', volume, affine)
w, h, d = volume.shape[:-1]
depindex = 100
dep = (0.5 + depindex) / np.float(d)
texcoords = np.array([[dep, 0, 0], [dep, 0, 1], [dep, 1, 1], [dep, 1, 0]])
vertcoords = np.array([[-w / 2., -h / 2., 0.], [-w / 2., h / 2., 0.],
[w / 2., h / 2., 0.], [w / 2, -h / 2., 0]])
tex.update_quad(texcoords, vertcoords)
ax = Axes(name="3 axes", linewidth=2.0)
vert = np.array([[2.0, 3.0, 0.0]], dtype=np.float32)
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()
"""
affine = None
data = np.zeros((256, 128, 32), np.uint8)
volume = np.zeros(data.shape+(3,))
volume[...,0] = data.copy()
volume[...,1] = data.copy()
volume[...,2] = data.copy()
volume = volume.astype(np.ubyte)
volume[..., :] = (255, 0 , 0)
#volume[] =
print volume.shape, volume.min(), volume.max()
window = Window()
region = Region()
#volume = data
tex = Texture3D('Buzz', volume, affine)
w, h, d = volume.shape[:-1]
depindex = 100
dep = (0.5 + depindex) / np.float(d)
texcoords = np.array([ [dep, 0, 0],
[dep, 0, 1],
[dep, 1, 1],
[dep, 1, 0] ])
vertcoords = np.array( [ [-w/2., -h/2., 0.],
[-w/2., h/2., 0.],
[w/2., h/2., 0.],
[w/2, -h/2., 0] ])
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)
#!/usr/bin/env python
import numpy as np
import pyglet as pyglet
from pyglet.gl import *
from fos import World, Window, WindowManager
from fos.actor.treeregion import TreeRegion
from fos.actor.axes import Axes
mycpt = "TreeRegion Demo - Fos.me"
try:
# Try and create a window with multisampling (antialiasing)
config = Config(sample_buffers=1, samples=4,depth_size=16, double_buffer=True,)
window = Window(resizable=True, config=config, vsync=False, width=1000, height=800, 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],
""" 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()
from euclid import *
import fos.lib.pyglet as pyglet
from fos.lib.pyglet.gl import *
from fos.lib.pyglet.window import key
from fos.actor.tree import Tree
import numpy as np
from fos import Window
try:
# Try and create a window with multisampling (antialiasing)
config = Config(sample_buffers=1, samples=4,depth_size=16, double_buffer=True,)
window = Window(resizable=True, config=config, vsync=False, width=1000, height=800) # "vsync=False" to check the framerate
except pyglet.window.NoSuchConfigException:
# Fall back to no multisampling for old hardware
window = Window(resizable=True)
fps_display = pyglet.clock.ClockDisplay() # see programming guide pg 48
@window.event
def on_resize(width, height):
print "newsize ", width, height
if height==0: height=1
# Override the default on_resize handler to create a 3D projection
glViewport(0, 0, width, height)
glMatrixMode(GL_PROJECTION)
glLoadIdentity()
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.random.rand(np.sum(lentra),4)
#colors[:,3]=0.9
"""
streamlines = Line('fornix',tracks,colors,line_width=2)
from fos import Window, Scene
from fos.actor.axes import Axes
from fos.actor.text import Text3D
title='Bundle Picker'
w = Window(caption = title,
width = 1200,
height = 800,
bgcolor = (0.,0.,0.2) )
scene = Scene( scenename = 'Main',
extent_min = np.array([-5.0, -5, -5]),
extent_max = np.array([5, 5 ,5]))
ax = Axes(name = "3 axes", linewidth=2.0)
vert = np.array( [[2.0,3.0,0.0]], dtype = np.float32 )
ptr = np.array( [[.2,.2,.2]], dtype = np.float32 )
tex = Text3D( "Text3D", vert, "Reg", 10, 2, ptr)
scene.add_actor(ax)
scene.add_actor(tex)
scene.add_actor(streamlines)
#w.screenshot( 'red.png' )
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()
""" 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()
