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"""Evaluation frame-bank workflow for manual annotation.
This pathway is intentionally outside the core library pipeline.
"""
from __future__ import annotations
import argparse
import hashlib
import json
import os
import sys
import tempfile
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from typing import Any
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.backend_bases import MouseButton
from matplotlib.lines import Line2D
from matplotlib.widgets import Button, RadioButtons, Slider
ROOT = Path(__file__).resolve().parents[2]
if str(ROOT) not in sys.path:
sys.path.insert(0, str(ROOT))
from deepivus.io.dicom import read_dicom
GROUPS = ("bifurcation", "paul")
@dataclass
class FrameState:
frame: int
lumen_x: list[float]
lumen_y: list[float]
lumen_confidence: float | None
bifurcation: bool
def _now_iso() -> str:
return datetime.now().isoformat(timespec="seconds")
def _safe_float(value: Any) -> float | None:
if value is None:
return None
try:
out = float(value)
except (TypeError, ValueError):
return None
if np.isnan(out):
return None
return out
def _video_id(group: str, dicom_path: Path) -> str:
return f"{group}/{dicom_path.stem}"
def _stable_video_seed(video_id: str, base_seed: int) -> int:
digest = hashlib.sha256(video_id.encode("utf-8")).hexdigest()[:16]
return (int(digest, 16) ^ int(base_seed)) & 0xFFFFFFFF
def _read_jsonl(path: Path) -> list[dict[str, Any]]:
rows: list[dict[str, Any]] = []
if not path.exists():
return rows
with path.open("r", encoding="utf-8") as fp:
for raw in fp:
line = raw.strip()
if not line:
continue
rows.append(json.loads(line))
return rows
def _write_jsonl_atomic(path: Path, rows: list[dict[str, Any]]) -> None:
path.parent.mkdir(parents=True, exist_ok=True)
with tempfile.NamedTemporaryFile("w", encoding="utf-8", dir=path.parent, delete=False) as tmp:
tmp_path = Path(tmp.name)
for rec in rows:
tmp.write(json.dumps(rec) + "\n")
tmp.flush()
os.fsync(tmp.fileno())
os.replace(tmp_path, path)
def _choose_frames(num_frames: int, frames_per_video: int, seed: int) -> list[int]:
k = min(frames_per_video, num_frames)
rng = np.random.default_rng(seed)
picks = rng.choice(num_frames, size=k, replace=False)
return sorted(int(v) for v in picks)
def _build_bank_file(
dicom_path: Path,
group: str,
out_root: Path,
frames_per_video: int,
base_seed: int,
force: bool,
) -> Path:
video_id = _video_id(group, dicom_path)
out_dir = out_root / group
out_dir.mkdir(parents=True, exist_ok=True)
out_file = out_dir / f"{dicom_path.stem}.jsonl"
if out_file.exists() and not force:
return out_file
_, images = read_dicom(str(dicom_path))
seed = _stable_video_seed(video_id, base_seed)
sampled = _choose_frames(images.shape[0], frames_per_video, seed)
default_bif = group == "bifurcation"
with out_file.open("w", encoding="utf-8") as fp:
meta = {
"record_type": "meta",
"schema": "deepivus_eval_frame_bank_v1",
"created_at": _now_iso(),
"video_id": video_id,
"group": group,
"dicom_path": str(dicom_path.resolve()),
"seed": seed,
"requested_frames_per_video": int(frames_per_video),
"sampled_frames": sampled,
"num_sampled_frames": len(sampled),
"default_bifurcation": default_bif,
}
fp.write(json.dumps(meta) + "\n")
for i, frame_idx in enumerate(sampled):
rec = {
"record_type": "frame",
"sample_order": i,
"frame": int(frame_idx),
"bifurcation": default_bif,
"lumen_confidence": None,
"lumen": {"x": [], "y": []},
"annotated_at": None,
"updated_at": None,
}
fp.write(json.dumps(rec) + "\n")
return out_file
def build_all_banks(data_root: Path, out_root: Path, frames_per_video: int, seed: int, force: bool) -> list[Path]:
out_files: list[Path] = []
for group in GROUPS:
group_dir = data_root / group
if not group_dir.exists():
continue
for dicom_path in sorted(group_dir.glob("*.dcm")):
out_files.append(_build_bank_file(dicom_path, group, out_root, frames_per_video, seed, force))
return out_files
def _load_bank_states(bank_path: Path) -> tuple[dict[str, Any], list[FrameState]]:
rows = _read_jsonl(bank_path)
if not rows:
raise ValueError(f"Empty bank file: {bank_path}")
meta = rows[0]
if meta.get("record_type") != "meta":
raise ValueError(f"Missing meta header in {bank_path}")
base: dict[int, FrameState] = {}
for rec in rows:
rtype = rec.get("record_type")
if rtype == "frame":
frame_idx = int(rec["frame"])
base[frame_idx] = FrameState(
frame=frame_idx,
lumen_x=[float(v) for v in rec.get("lumen", {}).get("x", [])],
lumen_y=[float(v) for v in rec.get("lumen", {}).get("y", [])],
lumen_confidence=_safe_float(rec.get("lumen_confidence")),
bifurcation=bool(rec.get("bifurcation", False)),
)
sampled = [int(v) for v in meta.get("sampled_frames", [])]
states = [base[idx] for idx in sampled if idx in base]
return meta, states
def _list_bank_entries(out_root: Path) -> list[dict[str, Any]]:
entries: list[dict[str, Any]] = []
for group in GROUPS:
group_dir = out_root / group
if not group_dir.exists():
continue
for bank_path in sorted(group_dir.glob("*.jsonl")):
rows = _read_jsonl(bank_path)
if not rows:
continue
meta = rows[0] if rows[0].get("record_type") == "meta" else {}
sampled = [r for r in rows if r.get("record_type") == "frame"]
edited_frames = {
int(r["frame"])
for r in sampled
if r.get("annotated_at") is not None or len(r.get("lumen", {}).get("x", [])) > 0
}
dicom_path = Path(meta.get("dicom_path", ""))
if not dicom_path.exists():
# Fallback from filename/group when absolute path changed.
dicom_path = Path("data") / group / f"{bank_path.stem}.dcm"
label = f"{group}/{bank_path.stem} [{len(edited_frames)}/{len(sampled)}]"
entries.append(
{
"label": label,
"group": group,
"stem": bank_path.stem,
"bank_path": bank_path,
"dicom_path": dicom_path,
}
)
return entries
class BankPicker:
"""Small GUI chooser for selecting a video bank to annotate."""
def __init__(self, entries: list[dict[str, Any]]) -> None:
self.entries = entries
self.selected_idx = 0
self.selected: dict[str, Any] | None = None
self.fig = None
self.radio = None
self.info_text = None
def _on_pick(self, label: str) -> None:
for i, entry in enumerate(self.entries):
if entry["label"] == label:
self.selected_idx = i
break
self._render_info()
def _on_open(self, _event: Any) -> None:
self.selected = self.entries[self.selected_idx]
plt.close(self.fig)
def _on_cancel(self, _event: Any) -> None:
self.selected = None
plt.close(self.fig)
def _render_info(self) -> None:
entry = self.entries[self.selected_idx]
self.info_text.set_text(
f"Selected: {entry['group']}/{entry['stem']}\n"
f"DICOM: {entry['dicom_path']}\n"
f"Bank: {entry['bank_path']}"
)
self.fig.canvas.draw_idle()
def show(self) -> dict[str, Any] | None:
if not self.entries:
raise ValueError("No bank files found to pick from.")
labels = [e["label"] for e in self.entries]
self.fig = plt.figure(figsize=(10, 8))
self.fig.canvas.manager.set_window_title("DeepIVUS Eval Bank Picker")
ax_radio = self.fig.add_axes([0.05, 0.2, 0.9, 0.74])
self.radio = RadioButtons(ax_radio, labels, active=0)
self.radio.on_clicked(self._on_pick)
ax_open = self.fig.add_axes([0.2, 0.06, 0.25, 0.08])
ax_cancel = self.fig.add_axes([0.55, 0.06, 0.25, 0.08])
open_btn = Button(ax_open, "Open Selected", color="#D6F5D6", hovercolor="#BFF0BF")
cancel_btn = Button(ax_cancel, "Cancel", color="#F5D6D6", hovercolor="#F0BFBF")
open_btn.on_clicked(self._on_open)
cancel_btn.on_clicked(self._on_cancel)
self.info_text = self.fig.text(0.05, 0.01, "", fontsize=9)
self._render_info()
plt.show()
return self.selected
class EvalFrameBankEditor:
def __init__(self, dicom_path: Path, bank_path: Path) -> None:
self.dicom_path = dicom_path
self.bank_path = bank_path
_, self.images = read_dicom(str(dicom_path))
self.meta, self.states = _load_bank_states(bank_path)
if not self.states:
raise ValueError(f"No sampled frame records found in {bank_path}")
self.current = 0
self.drag_target: int | None = None
self.drag_threshold_px = 10.0
self.dirty = False
self.is_updating_slider = False
self.fig = None
self.ax_image = None
self.image_artist = None
self.lumen_line: Line2D | None = None
self.lumen_points = None
self.slider: Slider | None = None
self.status_text = None
self.bif_button = None
self.clear_button = None
def _state(self) -> FrameState:
return self.states[self.current]
def _autosave_frame(self, reason: str) -> None:
s = self._state()
rows = _read_jsonl(self.bank_path)
if not rows:
raise ValueError(f"Bank file is empty: {self.bank_path}")
meta = rows[0]
sampled = [int(v) for v in meta.get("sampled_frames", [])]
frame_records: dict[int, dict[str, Any]] = {
int(r["frame"]): dict(r) for r in rows if r.get("record_type") == "frame"
}
now = _now_iso()
existing = frame_records.get(s.frame, {})
frame_records[s.frame] = {
"record_type": "frame",
"sample_order": existing.get("sample_order", self.current),
"frame": int(s.frame),
"bifurcation": bool(s.bifurcation),
"lumen_confidence": s.lumen_confidence,
"lumen": {"x": [float(v) for v in s.lumen_x], "y": [float(v) for v in s.lumen_y]},
"annotated_at": existing.get("annotated_at") or now,
"updated_at": now,
"last_save_reason": reason,
}
ordered_frames: list[dict[str, Any]] = []
for i, frame_idx in enumerate(sampled):
rec = frame_records.get(frame_idx)
if rec is None:
rec = {
"record_type": "frame",
"sample_order": i,
"frame": int(frame_idx),
"bifurcation": bool(meta.get("default_bifurcation", False)),
"lumen_confidence": None,
"lumen": {"x": [], "y": []},
"annotated_at": None,
"updated_at": None,
}
rec["sample_order"] = i
ordered_frames.append(rec)
_write_jsonl_atomic(self.bank_path, [meta] + ordered_frames)
self.dirty = False
def _build_ui(self) -> None:
self.fig = plt.figure(figsize=(13, 9))
self.fig.canvas.manager.set_window_title("DeepIVUS Eval Frame-Bank Editor")
self.ax_image = self.fig.add_axes([0.05, 0.22, 0.9, 0.74])
self.ax_image.set_title("DeepIVUS Eval Frame-Bank Editor", fontsize=14, weight="bold")
self.ax_image.set_axis_off()
slider_ax = self.fig.add_axes([0.12, 0.13, 0.76, 0.035])
self.slider = Slider(
ax=slider_ax,
label="Sample",
valmin=0,
valmax=len(self.states) - 1,
valinit=0,
valstep=1,
color="#1f77b4",
)
prev_ax = self.fig.add_axes([0.12, 0.05, 0.1, 0.055])
next_ax = self.fig.add_axes([0.24, 0.05, 0.1, 0.055])
save_ax = self.fig.add_axes([0.38, 0.05, 0.14, 0.055])
clear_ax = self.fig.add_axes([0.54, 0.05, 0.14, 0.055])
bif_ax = self.fig.add_axes([0.72, 0.05, 0.16, 0.055])
prev_button = Button(prev_ax, "Prev Frame", color="#E0E0E0", hovercolor="#D0D0D0")
next_button = Button(next_ax, "Next Frame", color="#E0E0E0", hovercolor="#D0D0D0")
save_button = Button(save_ax, "Save Frame", color="#D6F5D6", hovercolor="#BFF0BF")
self.clear_button = Button(clear_ax, "Clear Lumen", color="#F9E6CC", hovercolor="#F4DDB8")
self.bif_button = Button(bif_ax, "Bifurcation: No", color="#F5D6D6", hovercolor="#F0BFBF")
self.status_text = self.fig.text(0.05, 0.18, "", fontsize=10)
self.slider.on_changed(self._on_slider)
prev_button.on_clicked(self._on_prev)
next_button.on_clicked(self._on_next)
save_button.on_clicked(self._on_save)
self.clear_button.on_clicked(self._on_clear_lumen)
self.bif_button.on_clicked(self._on_toggle_bifurcation)
self.fig.canvas.mpl_connect("button_press_event", self._on_press)
self.fig.canvas.mpl_connect("motion_notify_event", self._on_motion)
self.fig.canvas.mpl_connect("button_release_event", self._on_release)
self.fig.canvas.mpl_connect("key_press_event", self._on_key)
self.fig.canvas.mpl_connect("close_event", self._on_close)
def _render(self) -> None:
s = self._state()
image = self.images[s.frame]
if self.image_artist is None:
self.image_artist = self.ax_image.imshow(image, cmap="gray")
self.lumen_line = self.ax_image.plot([], [], color="#1db954", lw=2)[0]
self.lumen_points = self.ax_image.scatter([], [], c="#1db954", s=28, edgecolors="black", linewidths=0.4)
else:
self.image_artist.set_data(image)
self.lumen_line.set_data(s.lumen_x + s.lumen_x[:1], s.lumen_y + s.lumen_y[:1])
lumen_offsets = np.c_[s.lumen_x, s.lumen_y] if s.lumen_x and s.lumen_y else np.empty((0, 2))
self.lumen_points.set_offsets(lumen_offsets)
bif_text = "Yes" if s.bifurcation else "No"
bif_color = "#D6F5D6" if s.bifurcation else "#F5D6D6"
self.bif_button.label.set_text(f"Bifurcation: {bif_text}")
self.bif_button.ax.set_facecolor(bif_color)
self.status_text.set_text(
f"Video: {self.meta.get('video_id')} Sample {self.current + 1}/{len(self.states)}"
f" DICOM frame: {s.frame} Lumen pts: {len(s.lumen_x)}"
f" Add: right/middle/double-left/shift-left"
)
self.fig.canvas.draw_idle()
def _set_current(self, idx: int) -> None:
idx = int(np.clip(idx, 0, len(self.states) - 1))
if idx == self.current:
return
if self.dirty:
self._autosave_frame("sample_change")
self.current = idx
self.is_updating_slider = True
self.slider.set_val(idx)
self.is_updating_slider = False
self._render()
def _nearest_point(self, x: float, y: float) -> int | None:
s = self._state()
if not s.lumen_x:
return None
pts = np.column_stack((np.asarray(s.lumen_x), np.asarray(s.lumen_y)))
d = np.linalg.norm(pts - np.asarray([x, y]), axis=1)
i = int(np.argmin(d))
if float(d[i]) > self.drag_threshold_px:
return None
return i
def _on_slider(self, val: float) -> None:
if self.is_updating_slider:
return
self._set_current(int(val))
def _on_prev(self, _event: Any) -> None:
self._set_current(self.current - 1)
def _on_next(self, _event: Any) -> None:
self._set_current(self.current + 1)
def _on_save(self, _event: Any) -> None:
self._autosave_frame("manual_save")
self._render()
def _on_toggle_bifurcation(self, _event: Any) -> None:
s = self._state()
s.bifurcation = not s.bifurcation
self.dirty = True
self._autosave_frame("bifurcation_toggle")
self._render()
def _on_clear_lumen(self, _event: Any) -> None:
s = self._state()
s.lumen_x = []
s.lumen_y = []
self.dirty = True
self._autosave_frame("clear_lumen")
self._render()
def _on_key(self, event: Any) -> None:
if event.key in {"left", "a"}:
self._set_current(self.current - 1)
elif event.key in {"right", "d"}:
self._set_current(self.current + 1)
elif event.key == "s":
self._on_save(event)
elif event.key == "b":
self._on_toggle_bifurcation(event)
elif event.key in {"x", "delete"}:
self._on_clear_lumen(event)
def _on_press(self, event: Any) -> None:
if event.inaxes != self.ax_image:
return
if event.xdata is None or event.ydata is None:
return
s = self._state()
h, w = self.images[s.frame].shape
x = float(np.clip(event.xdata, 0, w - 1))
y = float(np.clip(event.ydata, 0, h - 1))
is_left = event.button in (1, MouseButton.LEFT)
is_add_click = (
event.button in (3, 2, MouseButton.RIGHT, MouseButton.MIDDLE)
or (is_left and bool(getattr(event, "dblclick", False)))
or (is_left and str(getattr(event, "key", "")).lower() == "shift")
)
# Left-click: drag nearest existing point.
if is_left and not is_add_click:
self.drag_target = self._nearest_point(x, y)
return
# Right/middle/double-left/shift-left: add lumen point.
if is_add_click:
s.lumen_x.append(x)
s.lumen_y.append(y)
self.dirty = True
self._autosave_frame("point_add")
self._render()
def _on_motion(self, event: Any) -> None:
if self.drag_target is None:
return
if event.inaxes != self.ax_image or event.xdata is None or event.ydata is None:
return
s = self._state()
idx = self.drag_target
h, w = self.images[s.frame].shape
x = float(np.clip(event.xdata, 0, w - 1))
y = float(np.clip(event.ydata, 0, h - 1))
s.lumen_x[idx] = x
s.lumen_y[idx] = y
self.dirty = True
self._render()
def _on_release(self, _event: Any) -> None:
if self.drag_target is None:
return
self.drag_target = None
if self.dirty:
self._autosave_frame("point_drag")
self._render()
def _on_close(self, _event: Any) -> None:
if self.dirty:
self._autosave_frame("window_close")
def show(self) -> None:
self._build_ui()
self._render()
plt.show()
def _resolve_group_from_dicom(dicom_path: Path) -> str:
group = dicom_path.parent.name
if group not in GROUPS:
raise ValueError(f"Expected DICOM under data/{{bifurcation,paul}}, got: {dicom_path}")
return group
def _cmd_build(args: argparse.Namespace) -> None:
files = build_all_banks(
data_root=Path(args.data_root),
out_root=Path(args.out_root),
frames_per_video=args.frames_per_video,
seed=args.seed,
force=args.force,
)
print(f"Prepared {len(files)} bank files under {args.out_root}")
def _cmd_annotate(args: argparse.Namespace) -> None:
data_root = Path(args.data_root)
out_root = Path(args.out_root)
if (args.group and not args.stem) or (args.stem and not args.group):
raise ValueError("Provide both --group and --stem together, or provide neither.")
if args.dicom_path:
dicom_path = Path(args.dicom_path)
group = _resolve_group_from_dicom(dicom_path)
elif args.group and args.stem:
group = args.group
dicom_path = data_root / group / f"{args.stem}.dcm"
else:
entries = _list_bank_entries(out_root)
if not entries:
# Build banks if none exist yet.
build_all_banks(
data_root=data_root,
out_root=out_root,
frames_per_video=args.frames_per_video,
seed=args.seed,
force=False,
)
entries = _list_bank_entries(out_root)
picked = BankPicker(entries).show()
if picked is None:
return
dicom_path = Path(picked["dicom_path"])
group = str(picked["group"])
if not dicom_path.exists():
raise FileNotFoundError(f"DICOM not found: {dicom_path}")
bank_path = _build_bank_file(
dicom_path=dicom_path,
group=group,
out_root=out_root,
frames_per_video=args.frames_per_video,
base_seed=args.seed,
force=False,
)
editor = EvalFrameBankEditor(dicom_path=dicom_path, bank_path=bank_path)
editor.show()
def _cmd_status(args: argparse.Namespace) -> None:
out_root = Path(args.out_root)
total = 0
completed = 0
for group in GROUPS:
for bank_path in sorted((out_root / group).glob("*.jsonl")) if (out_root / group).exists() else []:
rows = _read_jsonl(bank_path)
sampled = [r for r in rows if r.get("record_type") == "frame"]
edited_frames = {
int(r["frame"])
for r in sampled
if r.get("annotated_at") is not None or len(r.get("lumen", {}).get("x", [])) > 0
}
total += 1
if sampled and len(edited_frames) >= len(sampled):
completed += 1
print(
f"{group}/{bank_path.stem}: {len(edited_frames)}/{len(sampled)} sampled frames edited"
)
print(f"Completed videos: {completed}/{total}")
def build_parser() -> argparse.ArgumentParser:
parser = argparse.ArgumentParser(description="Eval frame-bank annotation workflow")
sub = parser.add_subparsers(dest="command", required=True)
p_build = sub.add_parser("build", help="Create locked sampled-frame bank files for all videos")
p_build.add_argument("--data-root", default="data", help="Root data folder with bifurcation/ and paul/")
p_build.add_argument("--out-root", default="evals/frame_bank_merged", help="Output bank root")
p_build.add_argument("--frames-per-video", type=int, default=15)
p_build.add_argument("--seed", type=int, default=20260218)
p_build.add_argument("--force", action="store_true", help="Rebuild existing bank files")
p_build.set_defaults(func=_cmd_build)
p_annotate = sub.add_parser(
"annotate",
help="Open sampled-frame GUI for one video (or launch bank-picker GUI if no video is specified)",
)
p_annotate.add_argument("--data-root", default="data", help="Root data folder with bifurcation/ and paul/")
p_annotate.add_argument("--out-root", default="evals/frame_bank_merged", help="Output bank root")
p_annotate.add_argument("--frames-per-video", type=int, default=15)
p_annotate.add_argument("--seed", type=int, default=20260218)
p_annotate.add_argument("--dicom-path", default=None, help="Direct path to DICOM")
p_annotate.add_argument("--group", choices=GROUPS, default=None, help="Group when using --stem")
p_annotate.add_argument("--stem", default=None, help="File stem (e.g. FILE0003) when using --group")
p_annotate.set_defaults(func=_cmd_annotate)
p_status = sub.add_parser("status", help="Show annotation progress for bank files")
p_status.add_argument("--out-root", default="evals/frame_bank_merged", help="Output bank root")
p_status.set_defaults(func=_cmd_status)
return parser
def main() -> None:
parser = build_parser()
args = parser.parse_args()
args.func(args)
if __name__ == "__main__":
main()
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