Exemple #1
0
    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()
Exemple #2
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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()
Exemple #3
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    """

    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()