"""Diagnostic plotting helpers for branch pathfinding.
Interactive plotly overlays and tabular summaries for Dijkstra-based
branch reconstruction. All plotting functions import plotly lazily so
that the pathfinding subpackage (hot-path for
:class:`~phenotypic.detect.FilamentousFungiDetector`) does not pull in
plotly at import time.
The three public functions cover the common diagnostic cases:
- :func:`plot_paths_over_image` overlays fragment-to-colony paths on an
image background.
- :func:`plot_cost_distance_heatmap` renders the accumulated Dijkstra
cost surface with optional colony boundaries.
- :func:`paths_metrics_dataframe` summarizes paths (and optional
structure-quality metrics / filter results) as a per-path DataFrame.
Style follows the Okabe-Ito palette used throughout PhenoTypic
diagnostics (see ``_measure_radial_expansion.py`` for the reference
pattern). Many-path scatters are built as a single NaN-separated
``go.Scattergl`` trace to keep browsers responsive at 100+ paths.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
from ._dataclasses import DijkstraResult, FilterResult, FragmentPath, PathMetrics
if TYPE_CHECKING: # pragma: no cover - typing only
import pandas as pd
import plotly.graph_objects as go # noqa: F401
def _iter_paths(
paths: dict[int, FragmentPath] | list[FragmentPath],
):
"""Yield ``FragmentPath`` objects regardless of container type.
Args:
paths: Either a dict keyed by path id or an iterable list.
Yields:
Each :class:`FragmentPath` in the container.
"""
if isinstance(paths, dict):
yield from paths.values()
else:
yield from paths
def _colony_boundary_coords(colony_labels: np.ndarray) -> tuple[np.ndarray, np.ndarray]:
"""Return (xs, ys) of inner colony boundary pixels.
Args:
colony_labels: Integer label array (H, W). Non-zero labels denote
colonies; zero is background.
Returns:
Tuple ``(xs, ys)`` of column/row coordinates along the inner
boundary of ``colony_labels > 0``.
"""
from skimage.segmentation import find_boundaries
boundary = find_boundaries(colony_labels > 0, mode="inner", connectivity=2)
coords = np.argwhere(boundary)
if coords.size == 0:
return np.empty(0, dtype=np.float64), np.empty(0, dtype=np.float64)
return coords[:, 1].astype(np.float64), coords[:, 0].astype(np.float64)
[docs]
def plot_paths_over_image(
background: np.ndarray,
paths: dict[int, FragmentPath] | list[FragmentPath],
*,
colony_labels: np.ndarray | None = None,
title: str = "Dijkstra paths",
path_color: str = "#E69F00", # Okabe-Ito orange
colony_boundary_color: str = "#56B4E9", # Okabe-Ito sky
show_fragment_seeds: bool = True,
fig=None,
):
"""Overlay Dijkstra paths on a background image.
``background`` is rendered via ``go.Image`` if it is an RGB array
(H, W, 3) and via ``go.Heatmap`` if it is scalar (H, W). Paths are
drawn as a single NaN-separated ``go.Scattergl`` trace (keeps the
browser responsive at 100+ paths). When ``colony_labels`` is given,
inner colony boundaries are overlaid in ``colony_boundary_color``.
When ``show_fragment_seeds`` is True, the first coord of each path
(the fragment seed) is marked.
Args:
background: Either an (H, W, 3) RGB uint8 array or an (H, W)
scalar array (e.g. grayscale, PCT energy, cost surface).
paths: Fragment-to-colony paths, either as a dict keyed by
fragment id or a list of :class:`FragmentPath`.
colony_labels: Optional (H, W) integer label array. When given,
inner colony boundaries are drawn.
title: Figure title.
path_color: Hex colour for path lines (default Okabe-Ito orange).
colony_boundary_color: Hex colour for colony boundary markers
(default Okabe-Ito sky blue).
show_fragment_seeds: If True, mark the first coord of every path
(the fragment seed) with a distinct marker.
fig: Optional existing ``plotly.graph_objects.Figure`` to add the
traces to. When ``None`` a new figure is created.
Returns:
A ``plotly.graph_objects.Figure`` with the background, path
scatter, optional colony boundary, and optional fragment-seed
markers.
Raises:
ImportError: If plotly is not installed.
ValueError: If ``background`` is neither (H, W) nor (H, W, 3).
"""
from phenotypic.tools_._plotly_helpers import _require_plotly
_require_plotly()
import plotly.graph_objects as go
if fig is None:
fig = go.Figure()
# Background layer
if background.ndim == 3 and background.shape[-1] == 3:
fig.add_trace(
go.Image(
z=background,
name="Background",
hoverinfo="skip",
)
)
elif background.ndim == 2:
fig.add_trace(
go.Heatmap(
z=background,
colorscale="Gray",
showscale=False,
name="Background",
hoverinfo="skip",
)
)
else:
raise ValueError(
f"background must be (H, W) or (H, W, 3); got shape {background.shape}"
)
# Path polylines — single NaN-separated Scattergl trace
path_xs: list[float] = []
path_ys: list[float] = []
seed_xs: list[float] = []
seed_ys: list[float] = []
for path in _iter_paths(paths):
coords = path.coords
if coords is None or len(coords) == 0:
continue
path_xs.extend(coords[:, 1].astype(np.float64).tolist())
path_ys.extend(coords[:, 0].astype(np.float64).tolist())
path_xs.append(float("nan"))
path_ys.append(float("nan"))
if show_fragment_seeds:
seed_xs.append(float(coords[0, 1]))
seed_ys.append(float(coords[0, 0]))
if path_xs:
fig.add_trace(
go.Scattergl(
x=path_xs,
y=path_ys,
mode="lines",
line=dict(color=path_color, width=2),
name="Paths",
hoverinfo="skip",
)
)
# Colony boundary overlay (inner boundary as scatter of sparse pixels)
if colony_labels is not None:
bx, by = _colony_boundary_coords(colony_labels)
if bx.size > 0:
fig.add_trace(
go.Scattergl(
x=bx,
y=by,
mode="markers",
marker=dict(color=colony_boundary_color, size=2),
name="Colony boundary",
hoverinfo="skip",
)
)
# Fragment seed markers
if show_fragment_seeds and seed_xs:
fig.add_trace(
go.Scatter(
x=seed_xs,
y=seed_ys,
mode="markers",
marker=dict(
color=path_color,
size=7,
symbol="circle",
line=dict(color="white", width=0.5),
),
name="Fragment seeds",
hoverinfo="skip",
)
)
# Layout: image-style axes (y reversed so origin is top-left)
fig.update_layout(
title=title,
xaxis=dict(scaleanchor="y", constrain="domain"),
yaxis=dict(autorange="reversed"),
)
return fig
[docs]
def plot_cost_distance_heatmap(
dijkstra: DijkstraResult,
*,
colony_labels: np.ndarray | None = None,
log_scale: bool = True,
colorscale: str = "Viridis",
title: str = "Cost-distance map",
):
"""Render the Dijkstra cost-distance map as a heatmap.
Unreached pixels (``cost_distance == inf``) are masked to NaN so
plotly colours them transparently. When ``log_scale`` is True the
values are ``np.log1p``-transformed for visibility (colour-bar ticks
are left in the transformed scale — document this in the annotation).
When ``colony_labels`` is given, inner colony boundaries are overlaid.
Args:
dijkstra: :class:`DijkstraResult` produced by
:func:`run_multisource_dijkstra`.
colony_labels: Optional (H, W) integer label array. When given,
inner boundaries are overlaid in Okabe-Ito sky blue.
log_scale: If True, apply ``np.log1p`` to the finite cost values
before plotting (recommended — raw Dijkstra cost ranges are
typically long-tailed).
colorscale: Plotly colorscale name (default ``"Viridis"``).
title: Figure title.
Returns:
A ``plotly.graph_objects.Figure`` containing the heatmap and
optional colony-boundary overlay.
Raises:
ImportError: If plotly is not installed.
"""
from phenotypic.tools_._plotly_helpers import _require_plotly
_require_plotly()
import plotly.graph_objects as go
cost = np.asarray(dijkstra.cost_distance, dtype=np.float64).copy()
# Mask unreached pixels to NaN for transparent rendering.
cost[~np.isfinite(cost)] = np.nan
colorbar_title = "cost"
if log_scale:
# log1p handles zero safely; NaNs propagate.
with np.errstate(invalid="ignore"):
cost = np.log1p(cost)
colorbar_title = "log1p(cost)"
fig = go.Figure()
fig.add_trace(
go.Heatmap(
z=cost,
colorscale=colorscale,
colorbar=dict(title=colorbar_title),
name="Cost distance",
hoverinfo="z",
)
)
if colony_labels is not None:
bx, by = _colony_boundary_coords(colony_labels)
if bx.size > 0:
fig.add_trace(
go.Scattergl(
x=bx,
y=by,
mode="markers",
marker=dict(color="#56B4E9", size=2),
name="Colony boundary",
hoverinfo="skip",
)
)
annotation_text = (
"Values shown on log1p(cost) scale; colorbar ticks are in log1p units."
if log_scale
else "Unreached pixels rendered transparent (NaN)."
)
fig.update_layout(
title=title,
xaxis=dict(scaleanchor="y", constrain="domain"),
yaxis=dict(autorange="reversed"),
annotations=[
dict(
text=annotation_text,
xref="paper",
yref="paper",
x=0.0,
y=1.02,
showarrow=False,
font=dict(size=10),
)
],
)
return fig
[docs]
def paths_metrics_dataframe(
paths: dict[int, FragmentPath] | list[FragmentPath],
metrics: dict[int, PathMetrics] | None = None,
filter_result: FilterResult | None = None,
) -> pd.DataFrame:
"""Summarize paths as a per-path DataFrame.
Columns (always): path_id, colony_id, n_pixels, total_cost,
mean_cost_profile, max_cost_profile, min_cost_profile.
Additional columns when ``metrics`` is given: median_raw_cost,
max_window_cost, band_cost_variance, pct_energy_band_median,
gray_band_snr.
Additional column when ``filter_result`` is given: passed (bool).
Args:
paths: Fragment-to-colony paths, either as a dict keyed by
fragment id or a list of :class:`FragmentPath`.
metrics: Optional mapping ``fragment_id -> PathMetrics`` (e.g.
the ``metrics`` field of a :class:`FilterResult`). When
provided, per-path structure-quality columns are appended.
filter_result: Optional :class:`FilterResult`. When provided, a
``passed`` boolean column is appended (True if the fragment
id is in ``filter_result.passed_ids``).
Returns:
A :class:`pandas.DataFrame` with one row per input path.
"""
import pandas as pd
records: list[dict] = []
for path in _iter_paths(paths):
cost_profile = np.asarray(path.cost_profile, dtype=np.float64)
if cost_profile.size > 0:
mean_cost = float(np.mean(cost_profile))
max_cost = float(np.max(cost_profile))
min_cost = float(np.min(cost_profile))
else:
mean_cost = float("nan")
max_cost = float("nan")
min_cost = float("nan")
row: dict = {
"path_id": int(path.fragment_id),
"colony_id": int(path.colony_id),
"n_pixels": int(path.path_length),
"total_cost": float(path.total_cost),
"mean_cost_profile": mean_cost,
"max_cost_profile": max_cost,
"min_cost_profile": min_cost,
}
if metrics is not None:
pm = metrics.get(int(path.fragment_id))
if pm is not None:
row["median_raw_cost"] = float(pm.median_raw_cost)
row["max_window_cost"] = float(pm.max_window_cost)
row["band_cost_variance"] = float(pm.band_cost_variance)
row["pct_energy_band_median"] = float(pm.pct_energy_band_median)
row["gray_band_snr"] = float(pm.gray_band_snr)
else:
row["median_raw_cost"] = float("nan")
row["max_window_cost"] = float("nan")
row["band_cost_variance"] = float("nan")
row["pct_energy_band_median"] = float("nan")
row["gray_band_snr"] = float("nan")
if filter_result is not None:
row["passed"] = int(path.fragment_id) in filter_result.passed_ids
records.append(row)
return pd.DataFrame(records)
