def _script_default(self):
from mayavi.plugins.script import Script
from mayavi.core.off_screen_engine import OffScreenEngine
engine = OffScreenEngine()
engine.start()
s = Script(engine=engine)
return s
def _script_default(self):
from mayavi.plugins.script import Script
from mayavi.core.off_screen_engine import OffScreenEngine
engine = OffScreenEngine()
engine.start()
s = Script(engine=engine)
return s
def new_engine(self):
""" Creates a new engine, envisage or not depending on the
options.
"""
check_backend()
if options.backend == 'envisage':
from mayavi.plugins.app import Mayavi
m = Mayavi(start_gui_event_loop=False)
m.main()
process_ui_events()
window = m.application.workbench.active_window
engine = window.get_service(Engine)
elif options.backend == 'test':
engine = NullEngine(name='Null Mlab Engine')
engine.start()
else:
if options.offscreen:
engine = OffScreenEngine(name='Mlab offscreen Engine')
engine.start()
else:
engine = Engine(name='Mlab Engine')
engine.start()
self.current_engine = engine
return engine
def plot_map_3d(map, affine, cut_coords=None, anat=None, anat_affine=None,
threshold=None, offscreen=False, vmin=None, vmax=None, cmap=None,
view=(38.5, 70.5, 300, (-2.7, -12, 9.1)),
):
""" Plot a 3D volume rendering view of the activation, with an
outline of the brain.
Parameters
----------
map : 3D ndarray
The activation map, as a 3D image.
affine : 4x4 ndarray
The affine matrix going from image voxel space to MNI space.
cut_coords: 3-tuple of floats, optional
The MNI coordinates of a 3D cursor to indicate a feature
or a cut, in MNI coordinates and order.
anat : 3D ndarray, optional
The anatomical image to be used as a background. If None, the
MNI152 T1 1mm template is used. If False, no anatomical
image is used.
anat_affine : 4x4 ndarray, optional
The affine matrix going from the anatomical image voxel space to
MNI space. This parameter is not used when the default
anatomical is used, but it is compulsory when using an
explicite anatomical image.
threshold : float, optional
The lower threshold of the positive activation. This
parameter is used to threshold the activation map.
offscreen: boolean, optional
If True, Mayavi attempts to plot offscreen. Will work only
with VTK >= 5.2.
vmin : float, optional
The minimal value, for the colormap
vmax : float, optional
The maximum value, for the colormap
cmap : a callable, or a pylab colormap
A callable returning a (n, 4) array for n values between
0 and 1 for the colors. This can be for instance a pylab
colormap.
Notes
-----
If you are using a VTK version below 5.2, there is no way to
avoid opening a window during the rendering under Linux. This is
necessary to use the graphics card for the rendering. You must
maintain this window on top of others and on the screen.
"""
# Late import to avoid triggering wx imports before needed.
try:
from mayavi import mlab
except ImportError:
# Try out old install of Mayavi, with namespace packages
from enthought.mayavi import mlab
if offscreen:
global off_screen_engine
if off_screen_engine is None:
try:
from mayavi.core.off_screen_engine import OffScreenEngine
except ImportError:
# Try out old install of Mayavi, with namespace packages
from enthought.mayavi.core.off_screen_engine import OffScreenEngine
off_screen_engine = OffScreenEngine()
off_screen_engine.start()
fig = mlab.figure('__private_plot_map_3d__',
bgcolor=(1, 1, 1), fgcolor=(0, 0, 0),
size=(400, 330),
engine=off_screen_engine)
mlab.clf(figure=fig)
else:
fig = mlab.gcf()
fig = mlab.figure(fig, bgcolor=(1, 1, 1), fgcolor=(0, 0, 0),
size=(400, 350))
disable_render = fig.scene.disable_render
fig.scene.disable_render = True
if threshold is None:
threshold = stats.scoreatpercentile(
np.abs(map).ravel(), 80)
contours = []
lower_map = map[map <= -threshold]
if np.any(lower_map):
contours.append(lower_map.max())
upper_map = map[map >= threshold]
if np.any(upper_map):
contours.append(map[map > threshold].min())
###########################################################################
# Display the map using iso-surfaces
if len(contours) > 0:
map_src = affine_img_src(map, affine)
module = mlab.pipeline.iso_surface(map_src,
contours=contours,
vmin=vmin, vmax=vmax)
if hasattr(cmap, '__call__'):
# Stick the colormap in mayavi
module.module_manager.scalar_lut_manager.lut.table \
= (255*cmap(np.linspace(0, 1, 256))).astype(np.int)
else:
module = None
if not anat is False:
plot_anat_3d(anat=anat, anat_affine=anat_affine, scale=1.05,
outline_color=(.9, .9, .9),
gyri_opacity=.2)
###########################################################################
# Draw the cursor
if cut_coords is not None:
x0, y0, z0 = cut_coords
mlab.plot3d((-90, 90), (y0, y0), (z0, z0),
color=(.5, .5, .5), tube_radius=0.25)
mlab.plot3d((x0, x0), (-126, 91), (z0, z0),
color=(.5, .5, .5), tube_radius=0.25)
mlab.plot3d((x0, x0), (y0, y0), (-72, 109),
color=(.5, .5, .5), tube_radius=0.25)
mlab.view(*view)
fig.scene.disable_render = disable_render
return module
def plot_map_3d(
map,
affine,
cut_coords=None,
anat=None,
anat_affine=None,
threshold=None,
offscreen=False,
vmin=None,
vmax=None,
cmap=None,
view=(38.5, 70.5, 300, (-2.7, -12, 9.1)),
):
""" Plot a 3D volume rendering view of the activation, with an
outline of the brain.
Parameters
----------
map : 3D ndarray
The activation map, as a 3D image.
affine : 4x4 ndarray
The affine matrix going from image voxel space to MNI space.
cut_coords: 3-tuple of floats, optional
The MNI coordinates of a 3D cursor to indicate a feature
or a cut, in MNI coordinates and order.
anat : 3D ndarray, optional
The anatomical image to be used as a background. If None, the
MNI152 T1 1mm template is used. If False, no anatomical
image is used.
anat_affine : 4x4 ndarray, optional
The affine matrix going from the anatomical image voxel space to
MNI space. This parameter is not used when the default
anatomical is used, but it is compulsory when using an
explicite anatomical image.
threshold : float, optional
The lower threshold of the positive activation. This
parameter is used to threshold the activation map.
offscreen: boolean, optional
If True, Mayavi attempts to plot offscreen. Will work only
with VTK >= 5.2.
vmin : float, optional
The minimal value, for the colormap
vmax : float, optional
The maximum value, for the colormap
cmap : a callable, or a pylab colormap
A callable returning a (n, 4) array for n values between
0 and 1 for the colors. This can be for instance a pylab
colormap.
Notes
-----
If you are using a VTK version below 5.2, there is no way to
avoid opening a window during the rendering under Linux. This is
necessary to use the graphics card for the rendering. You must
maintain this window on top of others and on the screen.
"""
# Late import to avoid triggering wx imports before needed.
try:
from mayavi import mlab
except ImportError:
# Try out old install of Mayavi, with namespace packages
from enthought.mayavi import mlab
if offscreen:
global off_screen_engine
if off_screen_engine is None:
try:
from mayavi.core.off_screen_engine import OffScreenEngine
except ImportError:
# Try out old install of Mayavi, with namespace packages
from enthought.mayavi.core.off_screen_engine import OffScreenEngine
off_screen_engine = OffScreenEngine()
off_screen_engine.start()
fig = mlab.figure('__private_plot_map_3d__',
bgcolor=(1, 1, 1),
fgcolor=(0, 0, 0),
size=(400, 330),
engine=off_screen_engine)
mlab.clf(figure=fig)
else:
fig = mlab.gcf()
fig = mlab.figure(fig,
bgcolor=(1, 1, 1),
fgcolor=(0, 0, 0),
size=(400, 350))
disable_render = fig.scene.disable_render
fig.scene.disable_render = True
if threshold is None:
threshold = stats.scoreatpercentile(np.abs(map).ravel(), 80)
contours = []
lower_map = map[map <= -threshold]
if np.any(lower_map):
contours.append(lower_map.max())
upper_map = map[map >= threshold]
if np.any(upper_map):
contours.append(map[map > threshold].min())
###########################################################################
# Display the map using iso-surfaces
if len(contours) > 0:
map_src = affine_img_src(map, affine)
module = mlab.pipeline.iso_surface(map_src,
contours=contours,
vmin=vmin,
vmax=vmax)
if hasattr(cmap, '__call__'):
# Stick the colormap in mayavi
module.module_manager.scalar_lut_manager.lut.table \
= (255*cmap(np.linspace(0, 1, 256))).astype(np.int)
else:
module = None
if not anat is False:
plot_anat_3d(anat=anat,
anat_affine=anat_affine,
scale=1.05,
outline_color=(.9, .9, .9),
gyri_opacity=.2)
###########################################################################
# Draw the cursor
if cut_coords is not None:
x0, y0, z0 = cut_coords
mlab.plot3d((-90, 90), (y0, y0), (z0, z0),
color=(.5, .5, .5),
tube_radius=0.25)
mlab.plot3d((x0, x0), (-126, 91), (z0, z0),
color=(.5, .5, .5),
tube_radius=0.25)
mlab.plot3d((x0, x0), (y0, y0), (-72, 109),
color=(.5, .5, .5),
tube_radius=0.25)
mlab.view(*view)
fig.scene.disable_render = disable_render
return module
