def setup(self):
print('running setup')
self.generate_color_and_size()
self.fig = mlab.figure(figure=mlab.gcf())
self.fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain(
)
self.update_plot()
# The general mouse based clicker - which reveals point information
# of the known and labelled datapoints
self.info_picker = self.fig.on_mouse_pick(self.view_point_information)
self.info_picker.tolerance = 0.01
# picker which allows to re-assign the point trajectory number
self.reassign_picker = self.fig.on_mouse_pick(self.reassign_callback,
type='point',
button='Right')
self.reassign_picker.tolerance = 0.01
# outline which indicates which point has been clicked on
self.outline = mlab.outline(line_width=3, color=(0.9, 0.9, 0.9))
self.outline.outline_mode = 'cornered'
self.outline.bounds = (0.05, 0.05, 0.05, 0.05, 0.05, 0.05)
self.click_text = mlab.text(0.8, 0.8, 'STARTING INFO')
self.traj_text = mlab.text(0.8, 0.6, 'Trajectory number')
self.pointtype_text = mlab.text(0.8, 0.87, 'Point Type')
self.pointtype_info = mlab.text(0.8, 0.82, '')
mlab.axes()
def display_vscene3d(self):
"""
"""
self.vscene3d.mlab.view(10, 70)
self.vscene3d.scene.background = (0.925, 0.925, 0.925)
self.vscene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def show_surf(subject, hemi, type, patch=None, curv=True, freesurfer_subject_dir=None):
"""Show a surface from a Freesurfer subject directory
Parameters
----------
subject : str
Freesurfer subject name
hemi : str ['lh' | 'rh']
Left or right hemisphere
type :
patch :
curv : bool
freesurfer_subject_dir :
"""
warnings.warn(('Deprecated and probably broken! Try `cortex.segment.show_surf()`\n'
'which uses a third-party program (meshlab, available for linux & mac\n'
'instead of buggy mayavi code!'))
from mayavi import mlab
from tvtk.api import tvtk
pts, polys, idx = get_surf(subject, hemi, type, patch, freesurfer_subject_dir=freesurfer_subject_dir)
if curv:
curv = get_curv(subject, hemi, freesurfer_subject_dir=freesurfer_subject_dir)
else:
curv = idx
fig = mlab.figure()
src = mlab.pipeline.triangular_mesh_source(pts[:,0], pts[:,1], pts[:,2], polys, scalars=curv, figure=fig)
norms = mlab.pipeline.poly_data_normals(src, figure=fig)
norms.filter.splitting = False
surf = mlab.pipeline.surface(norms, figure=fig)
surf.parent.scalar_lut_manager.set(lut_mode='RdBu', data_range=[-1,1], use_default_range=False)
cursors = mlab.pipeline.scalar_scatter([0], [0], [0])
glyphs = mlab.pipeline.glyph(cursors, figure=fig)
glyphs.glyph.glyph_source.glyph_source = glyphs.glyph.glyph_source.glyph_dict['axes']
fig.scene.background = (0,0,0)
fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
path = os.path.join(os.environ['SUBJECTS_DIR'], subject)
def picker_callback(picker):
if picker.actor in surf.actor.actors:
npts = np.append(cursors.data.points.to_array(), [pts[picker.point_id]], axis=0)
cursors.data.points = npts
print(picker.point_id)
x, y, z = pts[picker.point_id]
with open(os.path.join(path, 'tmp', 'edit.dat'), 'w') as fp:
fp.write('%f %f %f\n'%(x, y, z))
picker = fig.on_mouse_pick(picker_callback)
picker.tolerance = 0.01
mlab.show()
return fig, surf
def display_scene3d(self):
if self.scene3d_inited: return
self.scene3d.mlab.view(40, 50)
self.scene3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
#self.scene3d.mayavi_scene.scene.light_manager.light_mode = "vtk"
self.scene3d_inited = True
def UpdatedSceneSettings(self):
self.updatedScene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
# The distance value is set in such a way that the entire surface should be visible without need to zoom out.
self.updatedScene.scene.mlab.view(30, 60, distance=2.5 * 512)
mlab.surf(np.zeros([2, 2]),
figure=self.updatedScene.mayavi_scene,
opacity=0) # Dummy surface
mlab.text(0.6, 0.9, 'Eroded', width=0.4)
def on_set_interaction(self, _, interaction):
if self.scene is None or self.scene.interactor is None:
return
# Ensure we're in the correct orientation for the
# InteractorStyleTerrain to have the correct "up"
self.on_set_view('front', '')
self.scene.mlab.draw()
self.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain() if interaction == 'terrain' else \
tvtk.InteractorStyleTrackballCamera()
# self.scene.interactor.interactor_style.
self.on_set_view('front', '')
self.scene.mlab.draw()
def display_scene3d(self):
outline = mlab.pipeline.outline(self.data_src3d,
figure=self.scene3d.mayavi_scene,
)
self.scene3d.mlab.view(40, 50)
# Interaction properties can only be changed after the scene
# has been created, and thus the interactor exists
for ipw in (self.ipw_3d_x, self.ipw_3d_y, self.ipw_3d_z):
# Turn the interaction off
ipw.ipw.interaction = 0
self.scene3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def show_surf(subject, hemi, type, patch=None, curv=True):
from mayavi import mlab
from tvtk.api import tvtk
pts, polys, idx = get_surf(subject, hemi, type, patch)
if curv:
curv = get_curv(subject, hemi)
else:
curv = idx
fig = mlab.figure()
src = mlab.pipeline.triangular_mesh_source(pts[:, 0],
pts[:, 1],
pts[:, 2],
polys,
scalars=curv,
figure=fig)
norms = mlab.pipeline.poly_data_normals(src, figure=fig)
norms.filter.splitting = False
surf = mlab.pipeline.surface(norms, figure=fig)
surf.parent.scalar_lut_manager.set(lut_mode='RdBu',
data_range=[-1, 1],
use_default_range=False)
cursors = mlab.pipeline.scalar_scatter([0], [0], [0])
glyphs = mlab.pipeline.glyph(cursors, figure=fig)
glyphs.glyph.glyph_source.glyph_source = glyphs.glyph.glyph_source.glyph_dict[
'axes']
fig.scene.background = (0, 0, 0)
fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
path = os.path.join(os.environ['SUBJECTS_DIR'], subject)
def picker_callback(picker):
if picker.actor in surf.actor.actors:
npts = np.append(cursors.data.points.to_array(),
[pts[picker.point_id]],
axis=0)
cursors.data.points = npts
print(picker.point_id)
x, y, z = pts[picker.point_id]
with open(os.path.join(path, 'tmp', 'edit.dat'), 'w') as fp:
fp.write('%f %f %f\n' % (x, y, z))
picker = fig.on_mouse_pick(picker_callback)
picker.tolerance = 0.01
mlab.show()
return fig, surf
def draw_groundtrack_surface(scene):
"""Load the Earth Texture image as the surface
"""
# set scene to have simple interactor
scene.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
surface_image = ndimage.imread('./data/earthmap1k.jpg')
surface_image = np.rot90(surface_image[:, :, 0], -1)
surface = mlab.imshow(surface_image,
figure=scene.mayavi_scene,
extent=[-180, 180, -90, 90, 0, 0])
mlab.axes(surface,
extent=[-180, 180, -90, 90, 0, 0],
z_axis_visibility=False)
return surface
def display_scene3d(self):
"""
"""
# outline = mlab.pipeline.outline(
# self.dataSource.mlab_source.dataset,
# figure = self.scene3d.mayavi_scene
# )
self.scene3d.mlab.view(10, 70)
for ipw in (self.ipw3dX, self.ipw3dY, self.ipw3dZ):
ipw.ipw.interaction = 0
#self.scene3d.scene.background = ( 0, 0, 0 )
self.scene3d.scene.background = (0.925, 0.925, 0.925)
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def on_set_interaction(self, _, interaction):
if self.scene is None:
return
if interaction == 'Terrain':
# Ensure we're in the correct orientatino for the
# InteractorStyleTerrain to have the correct "up"
if self._trackball_interactor is None:
self._trackball_interactor = \
self.scene.interactor.interactor_style
self.on_set_view('front', '')
self.scene.mlab.draw()
self.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
self.on_set_view('front', '')
self.scene.mlab.draw()
else: # interaction == 'trackball'
self.scene.interactor.interactor_style = self._trackball_interactor
def display_scene_3d(self):
self.scene_3d.mlab.view(40, 50)
self.scene_3d.scene.renderer.use_depth_peeling = True
self.scene_3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene_3d.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain(
)
self.scene_3d.scene_editor.aligner = self
self.opacity = float(options.config.get("mayavi_aligner", "opacity"))
self.xfm.widget.enabled = False
self.colormap = options.config.get("mayavi_aligner", "colormap")
self.disable_render = True
for ax in [self.x_axis, self.y_axis, self.z_axis]:
ax.update_position()
ax.reset_view()
self.disable_render = False
def display_model(self):
# Add the volume to the scene
self.volume_renderer.add_volume_to_scene(self.model)
# Add the other members to the scene
volume_actor = self.volume_renderer.actor
for member in self.scene_members.values():
member.add_actors_to_scene(self.model, volume_actor)
self._setup_camera()
self.model.scene.background = (0, 0, 0)
# Keep the view always pointing up
interactor = self.model.scene.interactor
interactor.interactor_style = tvtk.InteractorStyleTerrain()
# Let other code know that the scene is ready.
self.scene_initialized = True
def display_scene3d(self):
outline = mlab.pipeline.outline(
self.data_src,
colormap='gray',
opacity=0,
figure=self.scene3d.mayavi_scene,
)
# self.scene3d.mlab.view(40, 50)
self.scene3d.mlab.view(-30, -50)
# Interaction properties can only be changed after the scene
# has been created, and thus the interactor exists
for ipw in (self.ipw_3d_x, self.ipw_3d_y, self.ipw_3d_z):
ipw.ipw.interaction = 0
self.scene3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
self.update_position()
def display_scene3d(self):
outline = mlab.pipeline.outline(
self.data_src3d,
figure=self.scene3d.mayavi_scene,
)
self.scene3d.mlab.view(40, 50)
# Interaction properties can only be changed after the scene
# has been created, and thus the interactor exists
for ipw in (self.ipw_3d_x, self.ipw_3d_y, self.ipw_3d_z):
# Turn the interaction off
ipw.ipw.interaction = 0
# choose the flag style lut and reverse it
# this makes it nice for segmentations
ipw.parent.scalar_lut_manager.lut_mode = 'flag'
ipw.parent.scalar_lut_manager.reverse_lut = True
self.scene3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def display_scene3d(self):
from numpy import array
outline = mlab.pipeline.outline(
self.data_src3d,
figure=self.scene3d.mayavi_scene,
)
self.scene3d.mlab.view(220, 50)
self.scene3d.mlab.xlabel('Longitude (deg)')
self.scene3d.mlab.ylabel('Latitude (deg)')
self.scene3d.mlab.zlabel('Depth (km)')
self.scene3d.mlab.axes(
ranges=[176.144, 176.249, -38.68, -38.493, 7., 0.], nb_labels=8)
# Interaction properties can only be changed after the scene
# has been created, and thus the interactor exists
for ipw in (self.ipw_3d_x, self.ipw_3d_y, self.ipw_3d_z):
# Turn the interaction off
ipw.ipw.interaction = 0
self.scene3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene3d.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def justPlotBoolArray(blob, figSize=(300, 300)):
'''Plots a 3D boolean array with points where array is True'''
Nx, Ny, Nz = blob.shape
indexX, indexY, indexZ = mgrid[0:Nx, 0:Ny, 0:Nz]
fig = mlab.figure(0, size=figSize)
mlab.clf(fig)
fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
idx = blob
print idx.sum(), 'points'
if idx.sum() > 0:
idxFlat = idx.flatten()
pts = points3d(
indexX.flatten()[idxFlat] + .5,
indexY.flatten()[idxFlat] + .5,
indexZ.flatten()[idxFlat] + .5,
ones(sum(idxFlat)) * .9,
#((blob-mn) / (mx-mn) * .9)[idx],
color=(1, 1, 1),
mode='cube',
scale_factor=1.0)
lut = pts.module_manager.scalar_lut_manager.lut.table.to_array()
tt = linspace(0, 255, 256)
lut[:, 0] = tt * 0 + 255
lut[:, 1] = tt * 0 + 255
lut[:, 2] = tt * 0 + 255
lut[:, 3] = tt
pts.module_manager.scalar_lut_manager.lut.table = lut
#mlab.view(57.15, 75.55, 50.35, (7.5, 7.5, 7.5)) # nice view
#mlab.view(24, 74, 33, (5, 5, 5)) # Default older RBM
mlab.view(24, 88, 45, (5, 5, 10)) # Good for EF
mlab.draw()
def set_interactive(self):
from tvtk.api import tvtk
if self.fig.scene is not None:
self.fig.scene.interactor.interactor_style = \
tvtk.InteractorStyleTerrain()
def plot3DShape(blob,
saveFilename=None,
smoothed=False,
visSimple=True,
plotThresh=0,
figSize=(300, 300),
plotEdges=True,
rotAngle=24):
'''Plots a 3D shape inside a frame.'''
Nx, Ny, Nz = blob.shape
indexX, indexY, indexZ = mgrid[0:Nx, 0:Ny, 0:Nz]
edges = (array([Nx, Ny, Nz]) * cubeEdges.T).T
fig = mlab.figure(0, size=figSize)
mlab.clf(fig)
fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
if plotEdges:
plot3d(edges[0, :],
edges[1, :],
edges[2, :],
color=(.5, .5, .5),
line_width=0,
representation='wireframe',
opacity=1)
# Convert from bool to real if necessary
if type(blob[0]) is numpy.bool_ or blob.dtype == numpy.dtype('bool'):
blob = blob * 1
if smoothed:
# Pad with zeros to close, large negative values to make edges sharp
bs1, bs2, bs3 = blob.shape
blob = numpy.pad(blob, 1, 'constant', constant_values=(-1000, ))
contour3d(blob,
extent=[0, bs1, 0, bs2, 0, bs3],
contours=[.1],
color=(1, 1, 1))
else:
mn = blob.min()
mx = blob.max()
idx = (blob > plotThresh).flatten()
#print ' plot3DShape:', mn, mx, sum(idx)
if sum(idx) > 0:
if visSimple:
pts = points3d(
indexX.flatten()[idx] + .5,
indexY.flatten()[idx] + .5,
indexZ.flatten()[idx] + .5,
ones(sum(idx)) * .9,
#((blob-mn) / (mx-mn) * .9)[idx],
color=(1, 1, 1),
mode='cube',
scale_factor=1.0)
else:
pts = points3d(
indexX.flatten()[idx] + .5,
indexY.flatten()[idx] + .5,
indexZ.flatten()[idx] + .5,
#ones(sum(idx)) * .9,
((blob - mn) / (mx - mn) * .9)[idx],
colormap='bone',
#color = (1,1,1),
mode='cube',
scale_factor=1.0)
lut = pts.module_manager.scalar_lut_manager.lut.table.to_array()
tt = linspace(0, 255, 256)
lut[:, 0] = tt * 0 + 255
lut[:, 1] = tt * 0 + 255
lut[:, 2] = tt * 0 + 255
lut[:, 3] = tt
pts.module_manager.scalar_lut_manager.lut.table = lut
#mlab.view(57.15, 75.55, 50.35, (7.5, 7.5, 7.5)) # nice view
#mlab.view(24, 74, 33, (5, 5, 5)) # Default older RBM
mlab.view(rotAngle, 88, 45, (5, 5, 10)) # Good for EF
mlab.draw()
if saveFilename:
print saveFilename
mlab.savefig(saveFilename)
# Constrain Mayavi mouse drag to rotating Earth around its axis from tvtk.api import tvtk fig = mlab.gcf() fig.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
def __init__(self, parent, brain, title, width, height, n_rows, n_columns,
surf, pos):
EelbrainFrame.__init__(self, parent, wx.ID_ANY, "Brain: %s" % title,
wx.DefaultPosition if pos is None else pos)
# toolbar
tb = self.CreateToolBar(wx.TB_HORIZONTAL)
tb.SetToolBitmapSize(size=(32, 32))
tb.AddLabelTool(wx.ID_SAVE, "Save",
Icon("tango/actions/document-save"))
self.Bind(wx.EVT_TOOL, self.OnSaveAs, id=wx.ID_SAVE)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateUISave, id=wx.ID_SAVE)
# color-bar
tb.AddLabelTool(ID.PLOT_COLORBAR, "Plot Colorbar",
Icon("plot/colorbar"))
tb.Bind(wx.EVT_TOOL, self.OnPlotColorBar, id=ID.PLOT_COLORBAR)
# surface
self._surf_selector = wx.Choice(
tb,
choices=[name.capitalize() for name in SURFACES],
name='Surface')
if surf in SURFACES:
self._surf_selector.SetSelection(SURFACES.index(surf))
tb.AddControl(self._surf_selector, "Surface")
self._surf_selector.Bind(wx.EVT_CHOICE,
self.OnChoiceSurface,
source=self._surf_selector)
# view
tb.AddLabelTool(ID.VIEW_LATERAL, "Lateral View", Icon('brain/lateral'))
self.Bind(wx.EVT_TOOL, self.OnSetView, id=ID.VIEW_LATERAL)
tb.AddLabelTool(ID.VIEW_MEDIAL, "Medial View", Icon('brain/medial'))
self.Bind(wx.EVT_TOOL, self.OnSetView, id=ID.VIEW_MEDIAL)
# attach
tb.AddStretchableSpace()
tb.AddLabelTool(ID.ATTACH, "Attach", Icon("actions/attach"))
self.Bind(wx.EVT_TOOL, self.OnAttach, id=ID.ATTACH)
tb.Realize()
self.mayavi_view = MayaviView(width, height, n_rows, n_columns)
self._n_rows = n_rows
self._n_columns = n_columns
# Use traits to create a panel, and use it as the content of this
# wx frame.
self.ui = self.mayavi_view.edit_traits(parent=self,
view=self.mayavi_view.view,
kind='subpanel')
self.panel = self.ui.control
# Hide the toolbar (the edit_traits command assigns scene_editor)
for scene in self.mayavi_view.scenes:
scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
self.SetImageSize(width, height)
self.figure = self.mayavi_view.figures
self._brain = brain
self.Bind(wx.EVT_CLOSE, self.OnClose) # remove circular reference
# replace key bindings
self.panel.Unbind(wx.EVT_KEY_DOWN)
for child in self.panel.Children[0].Children:
panel = child.Children[0]
panel.Unbind(wx.EVT_CHAR)
panel.Bind(wx.EVT_KEY_DOWN, self.OnKeyDown)