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MRG: Add support for hemi=split in time_viewer #7219

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Merged
larsoner merged 9 commits into from
Jan 17, 2020
Merged

MRG: Add support for hemi=split in time_viewer #7219

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c3fcbd7
Start with all controls on the first view
GuillaumeFavelier Jan 16, 2020
18d13d0
Fix show_view when hemi=split
GuillaumeFavelier Jan 16, 2020
681d199
Mitigate slider disappearing if shape(1+,2)
GuillaumeFavelier Jan 16, 2020
aeba28a
Dispatch an orientation slider per view
GuillaumeFavelier Jan 16, 2020
79562d2
Dispatch orientation slider to each view (not only row)
GuillaumeFavelier Jan 16, 2020
2da4216
Refactor brain entirely
GuillaumeFavelier Jan 16, 2020
64f53df
Fix default value for orientation slider
GuillaumeFavelier Jan 16, 2020
b304337
Improve coverage
GuillaumeFavelier Jan 17, 2020
06dd268
Merge branch 'master' into time_viewer_hemi_split
GuillaumeFavelier Jan 17, 2020
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230 changes: 120 additions & 110 deletions mne/viz/_brain/_brain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -184,6 +184,9 @@ def __init__(self, subject_id, hemi, surf, title=None,
# for now only one color bar can be added
# since it is the same for all figures
self._colorbar_added = False
# for now only one time label can be added
# since it is the same for all figures
self._time_label_added = False
# array of data used by TimeViewer
self._data = {}
self.geo, self._hemi_meshes, self._overlays = {}, {}, {}
Expand Down Expand Up @@ -395,8 +398,11 @@ def time_label(x):
self._data['time_idx'] = time_idx
self._data['transparent'] = transparent
# data specific for a hemi
self._data[hemi + '_array'] = array
self._data[hemi + '_vertices'] = vertices
self._data[hemi] = dict()
self._data[hemi]['actor'] = list()
self._data[hemi]['mesh'] = list()
self._data[hemi]['array'] = array
self._data[hemi]['vertices'] = vertices

self._data['alpha'] = alpha
self._data['colormap'] = colormap
Expand All @@ -416,7 +422,7 @@ def time_label(x):
adj_mat,
smoothing_steps)
act_data = smooth_mat.dot(act_data)
self._data[hemi + '_smooth_mat'] = smooth_mat
self._data[hemi]['smooth_mat'] = smooth_mat

dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
Expand Down Expand Up @@ -445,16 +451,18 @@ def time_label(x):
actor, mesh = mesh_data
else:
actor, mesh = mesh_data, None
self._data[hemi + '_actor'] = actor
self._data[hemi + '_mesh'] = mesh
self._data[hemi]['actor'].append(actor)
self._data[hemi]['mesh'].append(mesh)
if array.ndim >= 2 and callable(time_label):
time_actor = self._renderer.text2d(
x_window=0.95, y_window=y_txt,
size=time_label_size,
text=time_label(time[time_idx]),
justification='right'
)
self._data[hemi + '_time_actor'] = time_actor
if not self._time_label_added:
time_actor = self._renderer.text2d(
x_window=0.95, y_window=y_txt,
size=time_label_size,
text=time_label(time[time_idx]),
justification='right'
)
self._data['time_actor'] = time_actor
self._time_label_added = True
if colorbar and not self._colorbar_added:
self._renderer.scalarbar(source=actor, n_labels=8,
bgcolor=(0.5, 0.5, 0.5))
Expand Down Expand Up @@ -738,14 +746,17 @@ def close(self):
"""Close all figures and cleanup data structure."""
self._renderer.close()

def show_view(self, view=None, roll=None, distance=None):
def show_view(self, view=None, roll=None, distance=None, row=0, col=0,
hemi=None):
"""Orient camera to display view."""
views_dict = lh_views_dict if self._hemi == 'lh' else rh_views_dict
hemi = self._hemi if hemi is None else hemi
views_dict = lh_views_dict if hemi == 'lh' else rh_views_dict
if isinstance(view, str):
view = views_dict.get(view)
elif isinstance(view, dict):
view = View(azim=view['azimuth'],
elev=view['elevation'])
self._renderer.subplot(row, col)
self._renderer.set_camera(azimuth=view.azim,
elevation=view.elev)

Expand Down Expand Up @@ -817,152 +828,151 @@ def set_data_smoothing(self, n_steps):
"""
from ..backends._pyvista import _set_mesh_scalars
from scipy.interpolate import interp1d
time_idx = self._data['time_idx']
for hemi in ['lh', 'rh']:
pd = self._data.get(hemi + '_mesh')
if pd is not None:
array = self._data[hemi + '_array']
vertices = self._data[hemi + '_vertices']
if pd is not None:
time_idx = self._data['time_idx']
act_data = array
if self._data['array'].ndim == 2:
hemi_data = self._data.get(hemi)
if hemi_data is not None:
array = hemi_data['array']
vertices = hemi_data['vertices']
for mesh in hemi_data['mesh']:
if array.ndim == 2:
if isinstance(time_idx, int):
act_data = act_data[:, time_idx]
act_data = array[:, time_idx]
else:
times = np.arange(self._n_times)
act_data = interp1d(
times, act_data, 'linear', axis=1,
times, array, 'linear', axis=1,
assume_sorted=True)(time_idx)

adj_mat = mesh_edges(self.geo[hemi].faces)
smooth_mat = smoothing_matrix(vertices,
adj_mat, int(n_steps),
verbose=False)
act_data = smooth_mat.dot(act_data)
_set_mesh_scalars(pd, act_data, 'Data')
self._data[hemi + '_smooth_mat'] = smooth_mat
_set_mesh_scalars(mesh, act_data, 'Data')
self._data[hemi]['smooth_mat'] = smooth_mat

def set_time_point(self, time_idx):
"""Set the time point shown."""
from ..backends._pyvista import _set_mesh_scalars
from scipy.interpolate import interp1d
time = self._data['time']
time_label = self._data['time_label']
time_actor = self._data.get('time_actor')
for hemi in ['lh', 'rh']:
pd = self._data.get(hemi + '_mesh')
if pd is not None:
array = self._data[hemi + '_array']
time = self._data['time']
time_label = self._data['time_label']
time_actor = self._data.get(hemi + '_time_actor')
if array.ndim == 1:
continue # skip data without time axis
# interpolation
if array.ndim == 2:
act_data = array

if isinstance(time_idx, int):
act_data = act_data[:, time_idx]
else:
times = np.arange(self._n_times)
act_data = interp1d(times, act_data, 'linear', axis=1,
assume_sorted=True)(time_idx)

smooth_mat = self._data[hemi + '_smooth_mat']
if smooth_mat is not None:
act_data = smooth_mat.dot(act_data)
_set_mesh_scalars(pd, act_data, 'Data')
if callable(time_label) and time_actor is not None:
if isinstance(time_idx, int):
self._current_time = time[time_idx]
time_actor.SetInput(time_label(self._current_time))
else:
ifunc = interp1d(times, self._data['time'])
self._current_time = ifunc(time_idx)
time_actor.SetInput(time_label(self._current_time))
self._data['time_idx'] = time_idx
hemi_data = self._data.get(hemi)
if hemi_data is not None:
array = hemi_data['array']
for mesh in hemi_data['mesh']:
# interpolation
if array.ndim == 2:
if isinstance(time_idx, int):
act_data = array[:, time_idx]
else:
times = np.arange(self._n_times)
act_data = interp1d(times, array, 'linear', axis=1,
assume_sorted=True)(time_idx)

smooth_mat = hemi_data['smooth_mat']
if smooth_mat is not None:
act_data = smooth_mat.dot(act_data)
_set_mesh_scalars(mesh, act_data, 'Data')
if callable(time_label) and time_actor is not None:
if isinstance(time_idx, int):
self._current_time = time[time_idx]
time_actor.SetInput(time_label(self._current_time))
else:
ifunc = interp1d(times, self._data['time'])
self._current_time = ifunc(time_idx)
time_actor.SetInput(time_label(self._current_time))
self._data['time_idx'] = time_idx

def update_fmax(self, fmax):
"""Set the colorbar max point."""
from ..backends._pyvista import _set_colormap_range
ctable = self.update_lut(fmax=fmax)
ctable = (ctable * 255).astype(np.uint8)
center = self._data['center']
fmin = self._data['fmin']
for hemi in ['lh', 'rh']:
actor = self._data.get(hemi + '_actor')
if actor is not None:
fmin = self._data['fmin']
center = self._data['center']
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['fmax'] = fmax
self._data['ctable'] = ctable
hemi_data = self._data.get(hemi)
if hemi_data is not None:
for actor in hemi_data['actor']:
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['fmax'] = fmax
self._data['ctable'] = ctable

def update_fmid(self, fmid):
"""Set the colorbar mid point."""
from ..backends._pyvista import _set_colormap_range
ctable = self.update_lut(fmid=fmid)
ctable = (ctable * 255).astype(np.uint8)
for hemi in ['lh', 'rh']:
actor = self._data.get(hemi + '_actor')
if actor is not None:
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar)
self._data['fmid'] = fmid
self._data['ctable'] = ctable
hemi_data = self._data.get(hemi)
if hemi_data is not None:
for actor in hemi_data['actor']:
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar)
self._data['fmid'] = fmid
self._data['ctable'] = ctable

def update_fmin(self, fmin):
"""Set the colorbar min point."""
from ..backends._pyvista import _set_colormap_range
ctable = self.update_lut(fmin=fmin)
ctable = (ctable * 255).astype(np.uint8)
center = self._data['center']
fmax = self._data['fmax']
for hemi in ['lh', 'rh']:
actor = self._data.get(hemi + '_actor')
if actor is not None:
fmax = self._data['fmax']
center = self._data['center']
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['fmin'] = fmin
self._data['ctable'] = ctable
hemi_data = self._data.get(hemi)
if hemi_data is not None:
for actor in hemi_data['actor']:
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['fmin'] = fmin
self._data['ctable'] = ctable

def update_fscale(self, fscale):
"""Scale the colorbar points."""
from ..backends._pyvista import _set_colormap_range
center = self._data['center']
fmin = self._data['fmin'] * fscale
fmid = self._data['fmid'] * fscale
fmax = self._data['fmax'] * fscale
ctable = self.update_lut(fmin=fmin, fmid=fmid, fmax=fmax)
ctable = (ctable * 255).astype(np.uint8)
for hemi in ['lh', 'rh']:
actor = self._data.get(hemi + '_actor')
if actor is not None:
center = self._data['center']
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['ctable'] = ctable
self._data['fmin'] = fmin
self._data['fmid'] = fmid
self._data['fmax'] = fmax
hemi_data = self._data.get(hemi)
if hemi_data is not None:
for actor in hemi_data['actor']:
dt_max = fmax
dt_min = fmin if center is None else -1 * fmax
rng = [dt_min, dt_max]
if self._colorbar_added:
scalar_bar = self._renderer.plotter.scalar_bar
else:
scalar_bar = None
_set_colormap_range(actor, ctable, scalar_bar, rng)
self._data['ctable'] = ctable
self._data['fmin'] = fmin
self._data['fmid'] = fmid
self._data['fmax'] = fmax

@property
def data(self):
Expand Down
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