def add_cortical_surf(self):
# lifted from Gael Varoquax
# this is fairly brittle-- don't know what will result if
# the brain is not skull-stripped
# brain_image is (currently) a copy of the integer indices
# (not the "real valued" scalars)
brain_image = self.master_src.blender.main.image_arr.copy()
np.putmask(brain_image, brain_image>255, 0)
# since this is skull stripped from BET, the boundary will be
# wherever the image drops off to 0
arr = ndimage.gaussian_filter(
(brain_image > 0).astype('d'), 6
)
mask = ndimage.binary_fill_holes(arr > .5)
# iterations x voxel size ~= erosion depth??
mask = ndimage.binary_erosion(mask, iterations=5)
arr_blurred = ndimage.gaussian_filter(
mask.astype('d'), 2
)
# This AA filter will rather dangle off the pipeline..
# it will be the "source" of the ProbeFilter, but we want
# to keep it pipeline-enabled so that we can dynamically
# change colors
point_scalars = surf_to_component[self.surface_component]
surf_colors = mlab.pipeline.set_active_attribute(
self.master_src, point_scalars=point_scalars
)
# Now, make a new ArraySource with the attributes copied
# from master_src
anat_blurred = ArraySource(transpose_input_array=False)
anat_blurred.scalar_data = arr_blurred
anat_blurred.scalar_name = 'blurred'
anat_blurred.origin = self.master_src.data.origin
anat_blurred.spacing = self.master_src.data.spacing
anat_blurred = mlab.pipeline.add_dataset(anat_blurred)
## anat_blurred.update_pipeline()
contour = mlab.pipeline.contour(anat_blurred)
decimated = mlab.pipeline.decimate_pro(contour)
extracted = mlab.pipeline.user_defined(
decimated, filter=self.poly_extractor
)
sampler = tvtk.ProbeFilter()
sampler.source = surf_colors.outputs[0]
surf_points = mlab.pipeline.user_defined(extracted, filter=sampler)
self.cortical_surf = mlab.pipeline.surface(
surf_points,
opacity=.95
)
self.cortical_surf.actor.property.backface_culling = True
self.bcontour = contour
self.surf_colors = surf_colors
