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()
# if modifiers & key.MOD_SHIFT:
# print 'Shift'
if __name__ == '__main__':
import nibabel as nib
dname = '/usr/share/fsl/data/standard/'
fname = dname + 'FMRIB58_FA_1mm.nii.gz'
img=nib.load(fname)
data = img.get_data()
data = np.interp(data, [data.min(), data.max()], [0, 255])
#data = np.ones((156, 122, 96), dtype=np.ubyte)
#data = 255*data
#data[70:100, 70:90, 70:80 ] = 140
window = Window(caption="Interactive Slicer",
bgcolor=(0.4, 0.4, 0.9))
scene = Scene(activate_aabb=False)
slicer = Slicer('VolumeSlicer', data)
scene.add_actor(slicer)
window.add_scene(scene)
window.refocus_camera()
#ax = Axes(name="3 axes", scale=200, linewidth=10.0)
#scene.add_actor(ax)
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()
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' )
w.add_scene(scene)
w.refocus_camera()
#dname='/home/eg309/Data/trento_processed/subj_03/MPRAGE_32/'
#fname = dname + 'T1_flirt_out.nii.gz'
dname = '/usr/share/fsl/data/standard/'
fname = dname + 'FMRIB58_FA_1mm.nii.gz'
img=nib.load(fname)
data = img.get_data()
data = np.interp(data, [data.min(), data.max()], [0, 255])
#affine = img.get_affine()
affine = None
#volume = prepare_volume(data)
i, j, k = data.shape[:3]
window = Window(bgcolor=(0, 0, 0.6))
scene = Scene()
tex = Texture3D('Buzz', data, affine, type=GL_RGBA, interp=GL_LINEAR)
#texcoords, vertcoords = tex.slice_i(i/2)
#texcoords, vertcoords = tex.slice_j(j/2)
texcoords, vertcoords = tex.slice_k(k/2 - 5)
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)
ptr = np.array([[.2,.2,.2]], dtype = np.float32)
#text = Text3D("Text3D", vert, "Reg", 20, 6, ptr)
scene.add_actor(tex)
tl = TrackLabeler('Bundle Picker',
qb,qb.downsampled_tracks(),
vol_shape=(182, 218, 182),tracks_alpha=1)
#add a interactive slicing/masking tool
#sl = Slicer(affine,data)
#add one way communication between tl and sl
#tl.slicer=sl
title = 'Bundle Picking'
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", scale= 10, 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, "(0,0,0)", 10*2.5, 10*.5, ptr)
#scene.add_actor(ax)
#scene.add_actor(tex)
scene.add_actor(tl)
#scene.add_actor(streamlines)
#w.screenshot( 'red.png' )
w.add_scene(scene)
w.refocus_camera()
#create the interaction system for tracks
tl = TrackLabeler('Bundle Picker',
qb,
qb.downsampled_tracks(),
vol_shape=(182, 218, 182),
tracks_alpha=1)
#add a interactive slicing/masking tool
#sl = Slicer(affine,data)
#add one way communication between tl and sl
#tl.slicer=sl
title = 'Bundle Picking'
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", scale=10, 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, "(0,0,0)", 10 * 2.5, 10 * .5, ptr)
#scene.add_actor(ax)
#scene.add_actor(tex)
scene.add_actor(tl)
#scene.add_actor(streamlines)
#w.screenshot( 'red.png' )
w.add_scene(scene)
w.refocus_camera()
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'
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
I, J, K = data.shape[:3]
window = Window(caption='[F]OS',bgcolor = (0, 0, 0.6))
scene = Scene(activate_aabb = False)
texi = Texture3D('i', data, affine=None, interp='linear')
texj = Texture3D('j', data, affine=None, interp='linear')
texk = Texture3D('k', data, affine=None, interp='linear')
container_size = texi.container.shape[0]
#centershift, _ = ijktoras(np.array([[I/2., J/2., K/2.]]), data.shape,
# affine, 3 * (container_size,), True)
#print centershift
centershift = img_to_ras_coords_container(np.array([[I/2., J/2., K/2.]]),
data.shape, affine)
centershift = ras_to_las_coords(centershift)
#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()
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'
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
I, J, K = data.shape[:3]
window = Window(caption='[F]OS', bgcolor=(0, 0, 0.6))
scene = Scene(activate_aabb=False)
texi = Texture3D('i', data, affine=None, interp='linear')
texj = Texture3D('j', data, affine=None, interp='linear')
texk = Texture3D('k', data, affine=None, interp='linear')
container_size = texi.container.shape[0]
#centershift, _ = ijktoras(np.array([[I/2., J/2., K/2.]]), data.shape,
# affine, 3 * (container_size,), True)
#print centershift
centershift = img_to_ras_coords_container(
np.array([[I / 2., J / 2., K / 2.]]), data.shape, affine)
centershift = ras_to_las_coords(centershift)
