Ejemplo n.º 1
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def viewImg2(img, spacing, contours):
    print("In viewImg2: (min,max)=(%f,%f)"%(img.min(),img.max()))
    print("contours=",contours)
    mlab.figure(bgcolor=(0, 0, 0), size=(400, 400))
    
    src = mlab.pipeline.scalar_field(img)
    # Our data is not equally spaced in all directions:
    src.spacing = [1, 1, 1]
    src.update_image_data = True
    
    
    # Extract some inner structures: the ventricles and the inter-hemisphere
    # fibers. We define a volume of interest (VOI) that restricts the
    # iso-surfaces to the inner of the brain. We do this with the ExtractGrid
    # filter.
    blur = mlab.pipeline.user_defined(src, filter='ImageGaussianSmooth')
    #mlab.pipeline.volume(blur, vmin=0.2, vmax=0.8)
    mlab.pipeline.iso_surface(src, contours=contours)
    #mlab.pipeline.image_plane_widget(blur,
    #                            plane_orientation='z_axes',
    #                            slice_index=img.shape[0]/2,
    #                        )
    #voi = mlab.pipeline.extract_grid(blur)
    #voi.set(x_min=125, x_max=193, y_min=92, y_max=125, z_min=34, z_max=75)
    
    #mlab.pipeline.iso_surface(src, contours=[1,2], colormap='Spectral')
    #mlab.pipeline.contour3d(blur)
        
    mlab.view(-125, 54, 'auto','auto')
    mlab.roll(-175)
    
    mlab.show()
Ejemplo n.º 2
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def viewImg(img, spacing, contours):
    mlab.figure(bgcolor=(0, 0, 0), size=(400, 400))
    
    src = mlab.pipeline.scalar_field(img)
    # Our data is not equally spaced in all directions:
    src.spacing = [1, 1, 1]
    src.update_image_data = True
    
    
    # Extract some inner structures: the ventricles and the inter-hemisphere
    # fibers. We define a volume of interest (VOI) that restricts the
    # iso-surfaces to the inner of the brain. We do this with the ExtractGrid
    # filter.
    blur = mlab.pipeline.user_defined(blur, filter='ImageGaussianSmooth')
    print("blur type is",type(blur),blur.max())
    #voi = mlab.pipeline.extract_grid(blur)
    #voi.set(x_min=125, x_max=193, y_min=92, y_max=125, z_min=34, z_max=75)
    
    #mlab.pipeline.iso_surface(src, contours=[1,2], colormap='Spectral')
    mlab.pipeline.contour3d(blur)
        
    mlab.view(-125, 54, 'auto','auto')
    mlab.roll(-175)
    
    mlab.show()
Ejemplo n.º 3
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def viewImgWithNodes(img, spacing, contours,g, title=''):

    mlab.figure(bgcolor=(0, 0, 0), size=(900, 900))
    
    #src = mlab.pipeline.scalar_field(img)
    ## Our data is not equally spaced in all directions:
    #src.spacing = [1, 1, 1]
    #src.update_image_data = True
    #
    #mlab.pipeline.iso_surface(src, contours=contours, opacity=0.2)
    nodes = np.array(g.nodes())
    dsize = 4*np.ones(nodes.shape[0],dtype='float32')
    print(dsize.shape,nodes.shape)
    #mlab.points3d(nodes[:,0],nodes[:,1],nodes[:,2],color=(0.0,1.0,0.0))
    mlab.points3d(nodes[:,2],nodes[:,1],nodes[:,0],dsize,color=(0.0,0.0,1.0), scale_factor=0.25)
    
    for n1, n2, edge in g.edges(data=True):
        path = [n1]+edge['path']+[n2]
        pa = np.array(path)
        #print pa
        mlab.plot3d(pa[:,2],pa[:,1],pa[:,0],color=(0,1,0),tube_radius=0.25)
    mlab.view(-125, 54, 'auto','auto')
    mlab.roll(-175)
    mlab.title(title, height=0.1)
    
    mlab.show()
Ejemplo n.º 4
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def autoPositionCamera():
    """
    Set camera position looking along the x-axis.
    """
    s = mlab.gcf().scene
    s.disable_render = True
    mlab.view(90,90,distance='auto',focalpoint='auto')
    mlab.roll(0)
    s.disable_render = False
Ejemplo n.º 5
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    def __view(self, viewargs=None, roll=None):
        """Wrapper for mlab.view()

        Parameters
        ----------
        viewargs: dict
            mapping with keys corresponding to mlab.view args
        roll: num
            int or float to set camera roll

        Returns
        -------
        camera settings: tuple
            view settings, roll setting

        """
        from enthought.mayavi import mlab
        if viewargs:
            viewargs['reset_roll'] = True
            mlab.view(**viewargs)
        if not roll is None:
            mlab.roll(roll)
        return mlab.view(), mlab.roll()
Ejemplo n.º 6
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def viewGraph(g, sub=3,title=''):

    mlab.figure(bgcolor=(0, 0, 0), size=(900, 900))
    nodes = g.nodes()
    random.shuffle(nodes)
    nodes = np.array(nodes[0:100])
    #mlab.points3d(nodes[:,2],nodes[:,1],nodes[:,0],color=(0.0,0.0,1.0))
    edges = g.edges(data=True)
    print(len(edges))
    input('continue')
    count = 0
    for n1, n2, edge in edges:
        count += 1
        if( count % 100 == 0 ):
            print(count)
        path = [n1]+edge['path']+[n2]
        pa = np.array(path)
        #print pa
        mlab.plot3d(pa[::sub,2],pa[::sub,1],pa[::sub,0],color=(0,1,0),tube_radius=0.75)
    mlab.view(-125, 54, 'auto','auto')
    mlab.roll(-175)
    mlab.title(title, height=0.1)
    
    mlab.show()
Ejemplo n.º 7
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connect_ = tvtk.PolyDataConnectivityFilter(extraction_mode=4)
connect = mlab.pipeline.user_defined(smooth, filter=connect_)

# Compute normals for shading the surface
compute_normals = mlab.pipeline.poly_data_normals(connect)
compute_normals.filter.feature_angle = 80

surf = mlab.pipeline.surface(compute_normals,
                                        color=(0.9, 0.72, 0.62))

#----------------------------------------------------------------------
# Display a cut plane of the raw data
ipw = mlab.pipeline.image_plane_widget(src, colormap='bone', 
                plane_orientation='z_axes',
                slice_index=55)

mlab.view(-165, 32, 350, [143, 133, 73])
mlab.roll(180)

fig.scene.disable_render = False

#----------------------------------------------------------------------
# To make the link between the Mayavi pipeline and the much more
# complex VTK pipeline, we display both:
mlab.show_pipeline(rich_view=False)
from enthought.tvtk.pipeline.browser import PipelineBrowser
browser = PipelineBrowser(fig.scene)
browser.show()

mlab.show()
Ejemplo n.º 8
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# Create the points
src = mlab.pipeline.scalar_scatter( x, y, z, s )

# Connect them
src.mlab_source.dataset.lines = connections

# The stripper filter cleans up connected lines
lines = mlab.pipeline.stripper( src )

# Finally, display the set of lines
mlab.pipeline.surface( mlab.pipeline.tube( lines, tube_sides=7, tube_radius=0.1 ), opacity=.4, colormap='Accent' )

# And choose a nice view
mlab.view( 33.6, 106, 5.5, [0, 0, .05] )
mlab.roll( 125 )
mlab.show()



from enthought.mayavi import mlab
import numpy as np

mlab.clf()

# Number of lines
n_lines = 200
# Number of points per line
n_points = 100

# Create Example Coordinates
Ejemplo n.º 9
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                       [np.arange(index,   index + N - 1.5),
                        np.arange(index+1, index + N - .5)]
                            ).T)    
    index += N

# Now collapse all positions, scalars and connections in big arrays
x = np.hstack(x)
y = np.hstack(y)
z = np.hstack(z)
s = np.hstack(s)
connections = np.vstack(connections)

# Create the points
src = mlab.pipeline.scalar_scatter(x, y, z, s)

# Connect them
src.mlab_source.dataset.lines = connections

# The stripper filter cleans up connected lines
lines = mlab.pipeline.stripper(src)

# Finally, display the set of lines
mlab.pipeline.surface(lines, colormap='Accent', line_width=1, opacity=.4)

# And choose a nice view
mlab.view(33.6, 106, 5.5, [0, 0, .05])
mlab.roll(125)
mlab.show()


Ejemplo n.º 10
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    s = m.surf(n_e_arr[1], n_e_arr[2], n_mu_q_arr[0, :, :])

    m.axes(
        s,
        color=(0.7, 0.7, 0.7),
        extent=(-1, 1, 0, 1, 0, 1),
        ranges=(-0.21, 0.21, 0.1, 20, 0, max_mu_q),
        xlabel="x",
        ylabel="Lr",
        zlabel="Force",
    )

    m.view(-60.0, 70.0, focalpoint=[0.0, 0.45, 0.45])
    # Store the information
    view = m.view()
    roll = m.roll()
    print "view", view
    print "roll", roll
    print n_mu_q_arr.shape[2]

    ms = s.mlab_source
    for i in range(1, n_mu_q_arr.shape[0]):
        ms.scalars = n_mu_q_arr[i, :, :]
        fname = "x%02d.jpg" % i
        print "saving", fname
        m.savefig(fname)
        sleep(0.1)
    #    m.surf( n_e_arr[0], n_e_arr[1], n_mu_q_arr + n_std_q_arr )
    #    m.surf( n_e_arr[0], n_e_arr[1], n_mu_q_arr - n_std_q_arr )

    m.show()
Ejemplo n.º 11
0
Archivo: mri.py Proyecto: sjl421/code-2
                                            vmax=2600)
cut_plane2.implicit_plane.origin = (136, 111.5, 82)
cut_plane2.implicit_plane.widget.enabled = False

# Extract two views of the outside surface. We need to define VOIs in
# order to leave out a cut in the head.
voi2 = mlab.pipeline.extract_grid(src)
voi2.set(y_min=112)
outer = mlab.pipeline.iso_surface(voi2,
                                  contours=[
                                      1776,
                                  ],
                                  color=(0.8, 0.7, 0.6))

voi3 = mlab.pipeline.extract_grid(src)
voi3.set(y_max=112, z_max=53)
outer3 = mlab.pipeline.iso_surface(voi3,
                                   contours=[
                                       1776,
                                   ],
                                   color=(0.8, 0.7, 0.6))

mlab.view(-125, 54, 326, (145.5, 138, 66.5))
mlab.roll(-175)

mlab.show()

import shutil

shutil.rmtree('mri_data')
Ejemplo n.º 12
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cut_plane.implicit_plane.widget.enabled = False

cut_plane2 = mlab.pipeline.scalar_cut_plane(thr,
                                plane_orientation='z_axes',
                                colormap='black-white',
                                vmin=1400,
                                vmax=2600)
cut_plane2.implicit_plane.origin = (136, 111.5, 82)
cut_plane2.implicit_plane.widget.enabled = False

# Extract two views of the outside surface. We need to define VOIs in
# order to leave out a cut in the head.
voi2 = mlab.pipeline.extract_grid(src)
voi2.set(y_min=112)
outer = mlab.pipeline.iso_surface(voi2, contours=[1776, ], 
                                        color=(0.8, 0.7, 0.6))

voi3 = mlab.pipeline.extract_grid(src)
voi3.set(y_max=112, z_max=53)
outer3 = mlab.pipeline.iso_surface(voi3, contours=[1776, ],
                                         color=(0.8, 0.7, 0.6))


mlab.view(-125, 54, 326, (145.5, 138, 66.5))
mlab.roll(-175)

mlab.show()

import shutil
shutil.rmtree('mri_data')
Ejemplo n.º 13
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#filter.filter.source = extract_vector_norm.outputs[0]
#filter.filter.source = surface.outputs[0]

print "vectors"
vectors = mlab.pipeline.vectors(filter, mode='2darrow')

print "polishing"
vectors.glyph.color_mode = 'no_coloring'
vectors.actor.property.color = (0, 0, 0)
vectors.glyph.glyph.scale_factor = 0.25
vectors.glyph.glyph_source.glyph_source.scale = 1.033
vectors.glyph.glyph_source.glyph_source.center = array([0.5, 0, 0])
print "done"

mlab.view(0.0, 0.0, 19.6, array([5, 5, 0]))
mlab.roll(0)

#mlab.show()

for i in range(max_frame_number + 1):
    print "doing:", i
    vtk_file_reader.timestep = i
    vectors.actor.property.color = (0, 0, 0)
    vectors.glyph.glyph.scale_factor = 0.25
    vectors.glyph.glyph_source.glyph_source.scale = 1.033 * 0.5
    vectors.glyph.glyph_source.glyph_source.center = array([0.5, 0, 0])
    mlab.savefig("output/frame_vec%04d.png" % i)

print "Files saved to output/*"
print """Create the video using:
ffmpeg -i output/frame_vec%04d.png -r 15 -vcodec copy output/output.avi
Ejemplo n.º 14
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#filter.filter.source = extract_vector_norm.outputs[0]
#filter.filter.source = surface.outputs[0]

print "vectors"
vectors = mlab.pipeline.vectors(filter, mode='2darrow')

print "polishing"
vectors.glyph.color_mode = 'no_coloring'
vectors.actor.property.color = (0, 0, 0)
vectors.glyph.glyph.scale_factor = 0.25
vectors.glyph.glyph_source.glyph_source.scale = 1.033
vectors.glyph.glyph_source.glyph_source.center = array([0.5, 0, 0])
print "done"

mlab.view(0.0, 0.0, 19.6, array([5, 5, 0]))
mlab.roll(0)

#mlab.show()

for i in range(max_frame_number+1):
    print "doing:", i
    vtk_file_reader.timestep = i
    vectors.actor.property.color = (0, 0, 0)
    vectors.glyph.glyph.scale_factor = 0.25
    vectors.glyph.glyph_source.glyph_source.scale = 1.033*0.5
    vectors.glyph.glyph_source.glyph_source.center = array([0.5, 0, 0])
    mlab.savefig("output/frame_vec%04d.png" % i)

print "Files saved to output/*"
print """Create the video using:
ffmpeg -i output/frame_vec%04d.png -r 15 -vcodec copy output/output.avi
Ejemplo n.º 15
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vtk_file_reader = engine.open(u'output/frame_scal0000.vtk')

warp_scalar = WarpScalar()
engine.add_filter(warp_scalar, vtk_file_reader)
surface = Surface()
engine.add_filter(surface, warp_scalar)
warp_scalar.filter.normal = array([ 0.,  0.,  1.])
warp_scalar.filter.scale_factor = 10.0

module_manager = engine.scenes[0].children[0].children[0].children[0]
module_manager.scalar_lut_manager.use_default_range = False
module_manager.scalar_lut_manager.data_range = array([-1.5, 1.5])
module_manager.scalar_lut_manager.show_scalar_bar = True

mlab.view(-122, 53, 26, array([7.5, 2.5, -0.11]))
mlab.roll(40)
print "  done."

for i in range(max_frame_number+1):
    print "doing:", i
    vtk_file_reader.timestep = i
    mlab.savefig("output/frame_scal%04d.png" % i)

print "Files saved to output/*"
print """Create the video using:
ffmpeg -i output/frame_scal%04d.png -r 15 -vcodec copy output/output.avi
ffmpeg2theora output/output.avi -o output.ogv

To produce a FLV video, use:
ffmpeg -b 3600k -i output/frame_scal%04d.png -r 15 video.flv
"""