def show_plane_segmentation_2d(plane_seg: PlaneSegmentation,
color_wheel=color_wheel,
color_by=None,
threshold=.01,
fig=None):
"""
Parameters
----------
plane_seg: PlaneSegmentation
color_wheel: list
color_by: str, optional
threshold: float
fig: plotly.graph_objects.Figure, optional
Returns
-------
"""
layout_kwargs = dict()
if color_by:
if color_by not in plane_seg:
raise ValueError(
'specified color_by parameter, {}, not in plane_seg object'.
format(color_by))
cats = np.unique(plane_seg[color_by][:])
else:
layout_kwargs.update(title=color_by)
data = plane_seg['image_mask'].data
nUnits = data.shape[0]
if fig is None:
fig = go.FigureWidget()
aux_leg = []
all_hover = df_to_hover_text(plane_seg.to_dataframe())
for i in range(nUnits):
if plane_seg[color_by][i] not in aux_leg:
show_leg = True
aux_leg.append(plane_seg[color_by][i])
else:
show_leg = False
kwargs = dict()
if color_by:
c = color_wheel[np.where(cats == plane_seg[color_by][i])[0][0]]
kwargs.update(
line_color=c,
name=str(plane_seg[color_by][i]),
legendgroup=str(plane_seg[color_by][i]),
showlegend=show_leg,
)
# form cell borders
x, y = compute_outline(plane_seg['image_mask'][i], threshold)
fig.add_trace(
go.Scatter(x=x,
y=y,
fill='toself',
mode='lines',
text=all_hover[i],
hovertext='text',
line=dict(width=.5),
**kwargs))
width = 600
fig.update_layout(width=width,
yaxis=dict(mirror=True,
scaleanchor="x",
scaleratio=1,
range=[0, plane_seg['image_mask'].shape[2]],
constrain='domain'),
xaxis=dict(mirror=True,
range=[0, plane_seg['image_mask'].shape[1]],
constrain='domain'),
margin=dict(t=10, b=10),
**layout_kwargs)
return fig
def show_plane_segmentation_2d(plane_seg: PlaneSegmentation,
color_wheel: list = color_wheel,
color_by: str = None,
threshold: float = .01,
fig: go.Figure = None,
width: int = 600,
ref_image=None):
"""
Parameters
----------
plane_seg: PlaneSegmentation
color_wheel: list, optional
color_by: str, optional
threshold: float, optional
fig: plotly.graph_objects.Figure, optional
width: int, optional
width of image in pixels. Height is automatically determined
to be proportional
ref_image: image, optional
Returns
-------
"""
layout_kwargs = dict()
if color_by:
if color_by not in plane_seg:
raise ValueError(
'specified color_by parameter, {}, not in plane_seg object'.
format(color_by))
cats = np.unique(plane_seg[color_by][:])
layout_kwargs.update(title=color_by)
data = plane_seg['image_mask'].data
nUnits = data.shape[0]
if fig is None:
fig = go.FigureWidget()
if ref_image is not None:
fig.add_trace(
go.Heatmap(z=ref_image,
hoverinfo='skip',
showscale=False,
colorscale='gray'))
aux_leg = []
all_hover = df_to_hover_text(plane_seg.to_dataframe())
for i in range(nUnits):
kwargs = dict(showlegend=False)
if color_by is not None:
if plane_seg[color_by][i] not in aux_leg:
kwargs.update(showlegend=True)
aux_leg.append(plane_seg[color_by][i])
c = color_wheel[np.where(cats == plane_seg[color_by][i])[0][0]]
kwargs.update(
line_color=c,
name=str(plane_seg[color_by][i]),
legendgroup=str(plane_seg[color_by][i]),
)
# form cell borders
x, y = compute_outline(plane_seg['image_mask'][i], threshold)
fig.add_trace(
go.Scatter(x=x,
y=y,
fill='toself',
mode='lines',
text=all_hover[i],
hovertext='text',
line=dict(width=.5),
**kwargs))
fig.update_layout(width=width,
yaxis=dict(mirror=True,
scaleanchor="x",
scaleratio=1,
range=[0, plane_seg['image_mask'].shape[2]],
constrain='domain'),
xaxis=dict(mirror=True,
range=[0, plane_seg['image_mask'].shape[1]],
constrain='domain'),
margin=dict(t=30, b=10),
**layout_kwargs)
return fig
