Giorgio Gilestro
2623df4172
Each annotation row now carries an `analyst` column. On first visit the web picker shows a small login modal asking for initials, persists them in localStorage, and shows the badge in the top-right. Click the badge to change identities. Submissions without initials are rejected by the backend (HTTP 400). Skip remains analyst-free. Backfill: every existing barrier_opening.csv row marked as `GG` since all current picks were done by Giorgio. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
349 lines
13 KiB
Python
349 lines
13 KiB
Python
"""FastAPI server for the web-based barrier-opening picker.
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Browse to http://<host>:8000/ and you'll see a video player loaded with
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the next un-annotated video from the queue. Use the arrow keys to
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scrub (←/→ ±5 s, Shift+←/→ ±1 s, Ctrl+←/→ ±0.1 s), space to pause/play,
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or click the seekbar. When the barrier opens, click one of:
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[All barriers open] every ROI is usable post-opening
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[Upper barriers open] only ROIs 1,3,5 are usable
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[Lower barriers open] only ROIs 2,4,6 are usable
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The current playhead time is recorded as the barrier-opening moment;
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ROI inclusion is set accordingly. There is also a Skip and a Mark
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unusable button.
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The queue is built from the merged TSV plus the inventory: every
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unique (machine, date, time) that has both a tracking DB and an mp4
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on disk and is not yet in barrier_opening.csv. Submissions persist
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to barrier_opening.csv after every click — refresh-safe.
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Configuration (environment variables):
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CUPIDO_DATA_VOLUME /mnt/data/projects/cupido (data volume)
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CUPIDO_INVENTORY_CSV /cupido/data/metadata/video_inventory.csv
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CUPIDO_OUTPUT_CSV /cupido/data/metadata/barrier_opening.csv
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"""
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from __future__ import annotations
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import os
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import re
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from dataclasses import dataclass
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from pathlib import Path
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import pandas as pd
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from fastapi import FastAPI, HTTPException, Request
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from fastapi.responses import FileResponse, HTMLResponse, JSONResponse, Response
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from fastapi.staticfiles import StaticFiles
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from pydantic import BaseModel
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# ─── Config ──────────────────────────────────────────────────────────────
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DATA_VOLUME = Path(os.environ.get("CUPIDO_DATA_VOLUME", "/mnt/data/projects/cupido"))
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INVENTORY_CSV = Path(os.environ.get(
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"CUPIDO_INVENTORY_CSV", "/cupido/data/metadata/video_inventory.csv"
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))
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OUTPUT_CSV = Path(os.environ.get(
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"CUPIDO_OUTPUT_CSV", "/cupido/data/metadata/barrier_opening.csv"
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))
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TSV_PATH = DATA_VOLUME / "all_video_info_merged.tsv"
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# Reason: the (date, time, machine_uuid) prefix encoded in every tracking
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# DB filename and every inventory mp4 filename.
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DB_NAME_RE = re.compile(
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r"^(\d{4}-\d{2}-\d{2})_(\d{2}-\d{2}-\d{2})_([0-9a-f]{32})__"
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)
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OUT_COLS = ["machine_name", "session_date", "session_time",
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"opening_s", "trim_first_s", "bad_rois", "analyst", "notes"]
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# ROI numbering in the HD mating arena (verified via tracking_geometry):
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# upper row = ROIs 1, 3, 5 (y ≈ 0.125)
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# lower row = ROIs 2, 4, 6 (y ≈ 0.795)
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ROIS_UPPER = "1,3,5"
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ROIS_LOWER = "2,4,6"
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@dataclass(frozen=True)
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class QueueItem:
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idx: int
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machine_name: str
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session_date: str
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session_time: str
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mp4_path: str
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duration_s: float | None
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done: bool
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metadata: dict # experimental fields aggregated from the merged TSV
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# ─── Queue building ─────────────────────────────────────────────────────
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_META_FIELDS = (
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"species", "training_length_hr", "consolidation_length_hr",
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"memory", "age", "training_date_time", "testing_date_time",
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)
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def _aggregate_metadata(rows: pd.DataFrame, db_filename: str) -> dict:
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"""Pull the experimental metadata for one video from its TSV rows.
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Most fields are uniform across the 6 ROIs of a video so the first-row
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value is representative. `male` is a per-fly label, so we summarise
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counts. `session_role` flags whether this video was the training or
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testing session for the flies in it.
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"""
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if rows.empty:
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return {}
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# Reason: the merged xlsx/TSV currently has duplicate rows per
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# (date, machine, ROI). De-dup on those keys so the male counts and
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# any per-ROI fields aren't doubled.
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if {"date", "machine_name", "roi"}.issubset(rows.columns):
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rows = rows.drop_duplicates(subset=["date", "machine_name", "roi"])
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r0 = rows.iloc[0]
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meta = {}
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for f in _META_FIELDS:
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v = r0.get(f)
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if pd.isna(v):
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meta[f] = None
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else:
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meta[f] = v if isinstance(v, str) else (
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int(v) if isinstance(v, float) and v.is_integer() else v
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)
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# Per-ROI tally.
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if "male" in rows.columns:
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m = rows["male"].dropna()
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meta["n_trained"] = int((m == "trained").sum())
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meta["n_naive"] = int((m == "naive").sum())
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# Was this the training session, the testing session, or both?
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is_training = rows["training_db_path"].astype(str).str.endswith(db_filename).any()
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is_testing = rows["testing_db_path"].astype(str).str.endswith(db_filename).any()
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if is_training and is_testing:
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meta["session_role"] = "training+testing"
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elif is_training:
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meta["session_role"] = "training"
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elif is_testing:
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meta["session_role"] = "testing"
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else:
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meta["session_role"] = "?"
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return meta
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def _build_queue() -> list[QueueItem]:
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"""Build the ordered queue of pickable videos."""
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if not TSV_PATH.exists():
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raise RuntimeError(f"merged TSV not found at {TSV_PATH}")
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if not INVENTORY_CSV.exists():
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raise RuntimeError(f"inventory not found at {INVENTORY_CSV}")
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tsv = pd.read_csv(TSV_PATH, sep="\t")
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inv = pd.read_csv(INVENTORY_CSV)
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inv_by_key: dict[tuple[str, str, str], dict] = {}
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for r in inv.itertuples(index=False):
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inv_by_key[(r.machine_name, r.session_date, r.session_time)] = {
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"mp4_path": r.mp4_path,
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"duration_s": float(r.duration_s) if pd.notna(r.duration_s) else None,
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}
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if OUTPUT_CSV.exists():
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out = pd.read_csv(OUTPUT_CSV)
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done_keys = set(zip(out["machine_name"],
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out["session_date"],
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out["session_time"]))
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else:
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done_keys = set()
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seen: set[tuple[str, str, str]] = set()
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items: list[QueueItem] = []
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for col in ("training_db_path", "testing_db_path"):
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for row in tsv.itertuples(index=False):
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db = getattr(row, col)
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if not isinstance(db, str) or not db:
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continue
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db_path = Path(db)
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if not db_path.exists():
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continue
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m = DB_NAME_RE.match(db_path.name)
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if not m:
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continue
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session_date, session_time = m.group(1), m.group(2)
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key = (row.machine_name, session_date, session_time)
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if key in seen:
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continue
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seen.add(key)
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inv_row = inv_by_key.get(key)
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if inv_row is None or not Path(inv_row["mp4_path"]).exists():
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continue
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# Reason: gather all TSV rows that reference this video — there
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# are typically 6 ROI-rows per session, sometimes also rows
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# using it as both training AND testing.
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db_filename = db_path.name
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related = tsv[
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tsv["training_db_path"].astype(str).str.endswith(db_filename)
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| tsv["testing_db_path"].astype(str).str.endswith(db_filename)
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]
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metadata = _aggregate_metadata(related, db_filename)
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items.append(QueueItem(
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idx=len(items),
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machine_name=row.machine_name,
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session_date=session_date,
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session_time=session_time,
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mp4_path=inv_row["mp4_path"],
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duration_s=inv_row["duration_s"],
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done=key in done_keys,
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metadata=metadata,
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))
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return items
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# ─── App ───────────────────────────────────────────────────────────────
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app = FastAPI(title="Cupido barrier-opening picker")
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STATIC_DIR = Path(__file__).parent / "static"
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app.mount("/static", StaticFiles(directory=STATIC_DIR), name="static")
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@app.get("/")
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async def index() -> FileResponse:
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return FileResponse(STATIC_DIR / "index.html")
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@app.get("/api/queue")
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async def get_queue() -> JSONResponse:
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queue = _build_queue()
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return JSONResponse([
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{
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"idx": q.idx,
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"machine_name": q.machine_name,
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"session_date": q.session_date,
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"session_time": q.session_time,
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"duration_s": q.duration_s,
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"done": q.done,
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"metadata": q.metadata,
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}
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for q in queue
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])
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def _stream_video(file_path: Path, request: Request) -> Response:
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"""HTTP Range-aware video streaming."""
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file_size = file_path.stat().st_size
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range_header = request.headers.get("range")
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if range_header is None:
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return FileResponse(file_path, media_type="video/mp4",
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headers={"Accept-Ranges": "bytes"})
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# Parse "bytes=START-END" (END optional)
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m = re.match(r"bytes=(\d+)-(\d*)", range_header)
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if not m:
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raise HTTPException(status_code=416, detail="bad Range header")
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start = int(m.group(1))
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end = int(m.group(2)) if m.group(2) else file_size - 1
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end = min(end, file_size - 1)
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if start > end:
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raise HTTPException(status_code=416, detail="range not satisfiable")
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chunk_size = end - start + 1
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def iterfile():
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with open(file_path, "rb") as f:
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f.seek(start)
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remaining = chunk_size
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while remaining > 0:
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buf = f.read(min(64 * 1024, remaining))
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if not buf:
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break
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yield buf
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remaining -= len(buf)
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return Response(
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content=b"".join(iterfile()),
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status_code=206,
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media_type="video/mp4",
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headers={
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"Content-Range": f"bytes {start}-{end}/{file_size}",
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"Accept-Ranges": "bytes",
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"Content-Length": str(chunk_size),
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},
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)
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@app.get("/api/video/{idx}")
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async def get_video(idx: int, request: Request) -> Response:
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queue = _build_queue()
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if not 0 <= idx < len(queue):
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raise HTTPException(status_code=404, detail="idx out of range")
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return _stream_video(Path(queue[idx].mp4_path), request)
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class Submission(BaseModel):
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idx: int
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time_s: float | None # None when marking unusable
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mode: str # "all" | "upper" | "lower" | "unusable" | "skip"
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analyst: str = "" # initials of the human picker (required, non-skip)
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notes: str = ""
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@app.post("/api/submit")
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async def submit(payload: Submission) -> dict:
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queue = _build_queue()
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if not 0 <= payload.idx < len(queue):
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raise HTTPException(status_code=404, detail="idx out of range")
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item = queue[payload.idx]
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if payload.mode == "skip":
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return {"status": "skipped"}
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analyst = payload.analyst.strip().upper()
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if not analyst:
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raise HTTPException(status_code=400, detail="analyst initials required")
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if payload.mode == "unusable":
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row = {
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"machine_name": item.machine_name,
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"session_date": item.session_date,
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"session_time": item.session_time,
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"opening_s": float("nan"),
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"trim_first_s": 0,
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"bad_rois": "",
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"analyst": analyst,
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"notes": payload.notes or "unusable",
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}
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else:
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if payload.time_s is None:
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raise HTTPException(status_code=400, detail="time_s required")
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bad_rois = {
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"all": "",
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"upper": ROIS_LOWER, # upper-only opens → lower row is bad
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"lower": ROIS_UPPER, # lower-only opens → upper row is bad
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}.get(payload.mode)
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if bad_rois is None:
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raise HTTPException(status_code=400, detail=f"unknown mode: {payload.mode}")
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row = {
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"machine_name": item.machine_name,
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"session_date": item.session_date,
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"session_time": item.session_time,
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"opening_s": round(payload.time_s, 1),
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"trim_first_s": 0,
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"bad_rois": bad_rois,
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"analyst": analyst,
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"notes": payload.notes,
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}
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OUTPUT_CSV.parent.mkdir(parents=True, exist_ok=True)
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if OUTPUT_CSV.exists():
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out = pd.read_csv(OUTPUT_CSV)
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else:
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out = pd.DataFrame(columns=OUT_COLS)
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for col in OUT_COLS:
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if col not in out.columns:
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out[col] = ""
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# Replace any existing row for this key.
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mask = ~((out["machine_name"] == row["machine_name"])
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& (out["session_date"] == row["session_date"])
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& (out["session_time"] == row["session_time"]))
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out = pd.concat([out[mask], pd.DataFrame([row])], ignore_index=True)
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out[OUT_COLS].to_csv(OUTPUT_CSV, index=False)
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return {"status": "saved", "row": row}
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if __name__ == "__main__":
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import uvicorn
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host = os.environ.get("HOST", "0.0.0.0")
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port = int(os.environ.get("PORT", "8000"))
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uvicorn.run("app:app", host=host, port=port, reload=False)
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