def test_get_vertexcolor():
fsaverage = fetch_surf_fsaverage()
mesh = surface.load_surf_mesh(fsaverage['pial_left'])
surf_map = np.arange(len(mesh[0]))
colors = html_surface.colorscale('jet', surf_map, 10)
vertexcolors = html_surface._get_vertexcolor(
surf_map, colors['cmap'], colors['norm'], colors['abs_threshold'],
fsaverage['sulc_left'])
assert len(vertexcolors) == len(mesh[0])
vertexcolors = html_surface._get_vertexcolor(
surf_map, colors['cmap'], colors['norm'], colors['abs_threshold'])
assert len(vertexcolors) == len(mesh[0])
def test_get_vertexcolor():
fsaverage = fetch_surf_fsaverage()
mesh = surface.load_surf_mesh(fsaverage['pial_left'])
surf_map = np.arange(len(mesh[0]))
colors = html_surface.colorscale('jet', surf_map, 10)
vertexcolors = html_surface._get_vertexcolor(
surf_map, colors['cmap'], colors['norm'], colors['abs_threshold'],
fsaverage['sulc_left'])
assert len(vertexcolors) == len(mesh[0])
vertexcolors = html_surface._get_vertexcolor(
surf_map, colors['cmap'], colors['norm'], colors['abs_threshold'])
assert len(vertexcolors) == len(mesh[0])
def plot_surf(mesh, data, view="right", threshold="85%", output_file=None):
coords, triangles = surface.load_surf_mesh(mesh)
x, y, z = coords.T
i, j, k = triangles.T
colors = colorscale(cold_hot, data, threshold)
vertexcolor = _get_vertexcolor(
data,
colors["cmap"],
colors["norm"],
colors["abs_threshold"],
surface.load_surf_data(fsaverage["sulc_right"]),
)
mesh_3d = go.Mesh3d(x=x, y=y, z=z, i=i, j=j, k=k, vertexcolor=vertexcolor)
fig = go.Figure(data=[mesh_3d])
fig.update_layout(scene_camera=CAMERAS[view], **LAYOUT)
if output_file is not None:
fig.write_image(output_file)
return fig
def _plot_surf_plotly(coords, faces, surf_map=None, bg_map=None,
hemi='left', view='lateral', cmap=None,
symmetric_cmap=True, colorbar=False,
threshold=None, vmin=None, vmax=None,
cbar_vmin=None, cbar_vmax=None,
cbar_tick_format=".1f", title=None,
title_font_size=18, output_file=None):
"""Helper function for plot_surf.
.. versionadded:: 0.8.2
This function handles surface plotting when the selected
engine is plotly.
.. note::
This function assumes that plotly and kaleido are
installed.
.. warning::
This function is new and experimental. Please report
bugs that you may encounter.
"""
try:
import plotly.graph_objects as go
from nilearn.plotting.displays import PlotlySurfaceFigure
except ImportError:
msg = "Using engine='plotly' requires that ``plotly`` is installed."
raise ImportError(msg) # noqa
x, y, z = coords.T
i, j, k = faces.T
if cmap is None:
cmap = cold_hot
bg_data = None
if bg_map is not None:
bg_data = load_surf_data(bg_map)
if bg_data.shape[0] != coords.shape[0]:
raise ValueError('The bg_map does not have the same number '
'of vertices as the mesh.')
if surf_map is not None:
_check_surf_map(surf_map, coords.shape[0])
colors = colorscale(
cmap, surf_map, threshold, vmax=vmax, vmin=vmin,
symmetric_cmap=symmetric_cmap
)
vertexcolor = _get_vertexcolor(
surf_map, colors["cmap"], colors["norm"],
colors["abs_threshold"], bg_data
)
else:
if bg_data is None:
bg_data = np.zeros(coords.shape[0])
colors = colorscale('Greys', bg_data, symmetric_cmap=False)
vertexcolor = _get_vertexcolor(
bg_data, colors["cmap"], colors["norm"],
colors["abs_threshold"]
)
mesh_3d = go.Mesh3d(x=x, y=y, z=z, i=i, j=j, k=k, vertexcolor=vertexcolor)
fig_data = [mesh_3d]
if colorbar:
dummy = _get_cbar_plotly(
colors["colors"], float(colors["vmin"]), float(colors["vmax"]),
cbar_tick_format
)
fig_data.append(dummy)
cameras_view = _set_view_plot_surf_plotly(hemi, view)
fig = go.Figure(data=fig_data)
fig.update_layout(scene_camera=CAMERAS[cameras_view],
title=_configure_title_plotly(title, title_font_size),
**LAYOUT)
if output_file is not None:
try:
import kaleido # noqa: F401
except ImportError:
msg = ("Saving figures to file with engine='plotly' requires "
"that ``kaleido`` is installed.")
raise ImportError(msg) # noqa
plotly_figure = PlotlySurfaceFigure(figure=fig, output_file=output_file)
if output_file is not None:
plotly_figure.savefig()
return plotly_figure
