Пример #1
0
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)
Пример #2
0
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()
Пример #3
0
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()
Пример #4
0
    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"
Пример #5
0
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()
Пример #6
0
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)
Пример #7
0
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()
Пример #8
0
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()
Пример #9
0
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)
Пример #10
0
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()
Пример #11
0
        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()


    
Пример #12
0
    #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 ;-)')
Пример #13
0
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()
Пример #14
0
""" 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()
Пример #15
0
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()
Пример #16
0
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()

"""
Пример #17
0
                                 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()
        
Пример #18
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)
Пример #19
0
                    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()
Пример #20
0
    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 ;-)')
    
Пример #21
0
    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()
    



Пример #22
0
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()
Пример #23
0
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)
Пример #24
0
	

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()
    
Пример #25
0
    # 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()