Perception Benchmark Live Viewer
-
+
Connecting...
- 
+
`;
// Also get embryoId and groundTruth from stored data if not provided
embryoId = embryoId || imgData.embryoId;
@@ -628,10 +630,13 @@ async def broadcast(message: Dict):
// Update header
document.querySelector('.trace-section h2').innerHTML =
- `Reasoning Trace - T${timepoint} `;
+ `Reasoning Trace - T${timepoint} `;
if (traceSteps.length === 0) {
- list.innerHTML = 'THREE-VIEW (XY | YZ / XZ)
-
+
+ THREE-VIEW (XY | YZ / XZ)
+
No trace recorded for T' + timepoint + '
';
+ list.innerHTML = 'No trace recorded for T'
+ + timepoint + '
';
return;
}
@@ -685,12 +690,16 @@ async def broadcast(message: Dict):
'verified' : '';
html += `
-
+
`;
}
@@ -749,10 +758,14 @@ async def websocket_endpoint(websocket: WebSocket):
connected_clients.append(websocket)
# Send current state
- await websocket.send_text(json.dumps({
- "type": "status",
- "status": benchmark_state["status"],
- }))
+ await websocket.send_text(
+ json.dumps(
+ {
+ "type": "status",
+ "status": benchmark_state["status"],
+ }
+ )
+ )
try:
while True:
@@ -789,8 +802,8 @@ def __init__(
embryo_id: str,
enable_verification: bool = True,
start_timepoint: int = 0,
- max_timepoints: Optional[int] = None,
- trace_dir: Optional[Path] = None,
+ max_timepoints: int | None = None,
+ trace_dir: Path | None = None,
):
self.testset = testset
self.embryo_id = embryo_id
@@ -798,7 +811,7 @@ def __init__(
self.start_timepoint = start_timepoint
self.max_timepoints = max_timepoints
- self.predictions: List[Dict] = []
+ self.predictions: list[dict] = []
self.correct_count = 0
self.adjacent_count = 0
self.verified_count = 0
@@ -808,7 +821,7 @@ def __init__(
self.trace_dir = trace_dir or Path("benchmarks/results/traces")
self.run_dir = self.trace_dir / f"{self.run_id}_{embryo_id}"
self.run_dir.mkdir(parents=True, exist_ok=True)
- self.traces: Dict[int, List[Dict]] = {} # timepoint -> trace steps
+ self.traces: dict[int, list[dict]] = {} # timepoint -> trace steps
logger.info(f"Trace persistence enabled: {self.run_dir}")
@@ -861,23 +874,23 @@ async def run(self):
benchmark_state["current_timepoint"] = test_case.timepoint
# Send image(s)
- await broadcast({
- "type": "image",
- "embryo_id": self.embryo_id,
- "timepoint": test_case.timepoint,
- "ground_truth": test_case.ground_truth_stage,
- "image": test_case.image_b64, # Combined for backward compat
- "top_image": test_case.top_image_b64,
- "side_image": test_case.side_image_b64,
- })
+ await broadcast(
+ {
+ "type": "image",
+ "embryo_id": self.embryo_id,
+ "timepoint": test_case.timepoint,
+ "ground_truth": test_case.ground_truth_stage,
+ "image": test_case.image_b64, # Combined for backward compat
+ "top_image": test_case.top_image_b64,
+ "side_image": test_case.side_image_b64,
+ }
+ )
# Clear trace for new prediction
await broadcast({"type": "clear_trace"})
# Run perception with trace streaming
- result = await self._run_perception_with_streaming(
- engine, session, test_case
- )
+ result = await self._run_perception_with_streaming(engine, session, test_case)
# Check accuracy
is_correct = result.stage == test_case.ground_truth_stage
@@ -915,23 +928,29 @@ async def run(self):
await broadcast(pred_msg)
# Save trace for this timepoint
- self._save_timepoint_trace(test_case.timepoint, result, test_case, is_correct, is_adjacent)
+ self._save_timepoint_trace(
+ test_case.timepoint, result, test_case, is_correct, is_adjacent
+ )
# Send updated stats
total = len(self.predictions)
- await broadcast({
- "type": "stats",
- "accuracy": self.correct_count / total if total > 0 else None,
- "adjacent": self.adjacent_count / total if total > 0 else None,
- "total": total,
- "verified": self.verified_count,
- })
+ await broadcast(
+ {
+ "type": "stats",
+ "accuracy": self.correct_count / total if total > 0 else None,
+ "adjacent": self.adjacent_count / total if total > 0 else None,
+ "total": total,
+ "verified": self.verified_count,
+ }
+ )
# Add observation to session with simulated timestamp
# Typical diSPIM acquisition interval is ~4 minutes per timepoint
- simulated_timestamp = datetime.now() - timedelta(
- minutes=(self.max_timepoints or 100) * 4
- ) + timedelta(minutes=test_case.timepoint * 4)
+ simulated_timestamp = (
+ datetime.now()
+ - timedelta(minutes=(self.max_timepoints or 100) * 4)
+ + timedelta(minutes=test_case.timepoint * 4)
+ )
session.add_observation(
timepoint=test_case.timepoint,
@@ -953,7 +972,6 @@ async def run(self):
async def _run_perception_with_streaming(self, engine, session, test_case):
"""Run perception and stream trace steps."""
- from gently.harness.perception.session import ReasoningStep
# We need to hook into the reasoning trace
# For now, run perception and stream the trace after
@@ -985,7 +1003,9 @@ async def _run_perception_with_streaming(self, engine, session, test_case):
return result
- def _save_timepoint_trace(self, timepoint: int, result, test_case, is_correct: bool, is_adjacent: bool):
+ def _save_timepoint_trace(
+ self, timepoint: int, result, test_case, is_correct: bool, is_adjacent: bool
+ ):
"""Save trace for a single timepoint to disk."""
trace_data = {
"timepoint": timepoint,
@@ -1035,7 +1055,7 @@ async def run_benchmark_background(
embryo_id: str,
enable_verification: bool,
start_timepoint: int = 0,
- max_timepoints: Optional[int] = None,
+ max_timepoints: int | None = None,
):
"""Run benchmark in background after server starts."""
print("[DEBUG] run_benchmark_background starting", flush=True)
@@ -1049,7 +1069,10 @@ async def run_benchmark_background(
# Load data
ground_truth = GroundTruth.from_json(ground_truth_path)
- print(f"[DEBUG] Loaded ground truth: {len(ground_truth.transitions)} embryos", flush=True)
+ print(
+ f"[DEBUG] Loaded ground truth: {len(ground_truth.transitions)} embryos",
+ flush=True,
+ )
testset = OfflineTestset(
session_path=session_path,
ground_truth=ground_truth,
@@ -1071,6 +1094,7 @@ async def run_benchmark_background(
except Exception as e:
print(f"[DEBUG] ERROR in run_benchmark_background: {e}", flush=True)
import traceback
+
traceback.print_exc()
@@ -1142,9 +1166,9 @@ def main():
trace_dir = Path("benchmarks/results/traces")
run_id = datetime.now().strftime("%Y%m%d_%H%M%S")
- print(f"\n{'='*60}")
+ print(f"\n{'=' * 60}")
print("Perception Benchmark Live Viewer")
- print(f"{'='*60}")
+ print(f"{'=' * 60}")
print(f"Session: {session_path}")
print(f"Embryo: {args.embryo}")
print(f"Start timepoint: T{args.start_timepoint}")
@@ -1152,7 +1176,7 @@ def main():
print(f"Verification: {'disabled' if args.no_verification else 'enabled'}")
print(f"Traces: {trace_dir / f'{run_id}_{args.embryo}'}")
print(f"URL: http://localhost:{args.port}")
- print(f"{'='*60}\n")
+ print(f"{'=' * 60}\n")
# Open browser
if not args.no_browser:
@@ -1162,14 +1186,16 @@ def main():
@app.on_event("startup")
async def startup_event():
print("[DEBUG] Startup event fired", flush=True)
- asyncio.create_task(run_benchmark_background(
- session_path=session_path,
- ground_truth_path=gt_path,
- embryo_id=args.embryo,
- enable_verification=not args.no_verification,
- start_timepoint=args.start_timepoint,
- max_timepoints=args.max_timepoints,
- ))
+ asyncio.create_task(
+ run_benchmark_background(
+ session_path=session_path,
+ ground_truth_path=gt_path,
+ embryo_id=args.embryo,
+ enable_verification=not args.no_verification,
+ start_timepoint=args.start_timepoint,
+ max_timepoints=args.max_timepoints,
+ )
+ )
print("[DEBUG] Background task created", flush=True)
# Run server
diff --git a/benchmarks/perception/metrics.py b/benchmarks/perception/metrics.py
index f69c054f..97d5c0f9 100644
--- a/benchmarks/perception/metrics.py
+++ b/benchmarks/perception/metrics.py
@@ -6,14 +6,23 @@
from collections import defaultdict
from dataclasses import dataclass, field
-from typing import Any, Dict, List, Optional, Tuple, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
if TYPE_CHECKING:
from .runner import BenchmarkReport
# Stage order for metrics
-STAGE_ORDER = ["early", "bean", "comma", "1.5fold", "2fold", "pretzel", "hatching", "hatched"]
+STAGE_ORDER = [
+ "early",
+ "bean",
+ "comma",
+ "1.5fold",
+ "2fold",
+ "pretzel",
+ "hatching",
+ "hatched",
+]
@dataclass
@@ -25,30 +34,30 @@ class PerceptionMetrics:
adjacent_accuracy: float = 0.0 # Within 1 stage
# Per-stage accuracy
- stage_accuracy: Dict[str, float] = field(default_factory=dict)
- stage_counts: Dict[str, int] = field(default_factory=dict)
+ stage_accuracy: dict[str, float] = field(default_factory=dict)
+ stage_counts: dict[str, int] = field(default_factory=dict)
# Confusion matrix: confusion[gt_stage][pred_stage] = count
- confusion_matrix: Dict[str, Dict[str, int]] = field(default_factory=dict)
+ confusion_matrix: dict[str, dict[str, int]] = field(default_factory=dict)
# Confidence calibration
mean_confidence: float = 0.0
confidence_when_correct: float = 0.0
confidence_when_wrong: float = 0.0
- calibration_bins: List[Tuple[float, float, int]] = field(default_factory=list)
+ calibration_bins: list[tuple[float, float, int]] = field(default_factory=list)
# (confidence_bin_center, accuracy_in_bin, count)
expected_calibration_error: float = 0.0 # ECE
# Temporal metrics
backward_transitions: int = 0 # Errors where stage went backward
- stage_transition_delay: Dict[str, float] = field(default_factory=dict)
+ stage_transition_delay: dict[str, float] = field(default_factory=dict)
# How many timepoints after GT transition until prediction caught up
# Tool usage
total_tool_calls: int = 0
tool_call_rate: float = 0.0 # Avg tool calls per prediction
- tool_use_by_stage: Dict[str, float] = field(default_factory=dict)
+ tool_use_by_stage: dict[str, float] = field(default_factory=dict)
# When tools were used vs not
accuracy_with_tools: float = 0.0
@@ -59,7 +68,7 @@ class PerceptionMetrics:
transitional_rate: float = 0.0
transitional_accuracy: float = 0.0 # Accuracy when marked transitional
- def to_dict(self) -> Dict[str, Any]:
+ def to_dict(self) -> dict[str, Any]:
return {
"accuracy": self.accuracy,
"adjacent_accuracy": self.adjacent_accuracy,
@@ -102,8 +111,7 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
# Collect all predictions
all_preds = [
- p for r in report.embryo_results for p in r.predictions
- if p.ground_truth_stage is not None
+ p for r in report.embryo_results for p in r.predictions if p.ground_truth_stage is not None
]
if not all_preds:
@@ -116,8 +124,8 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
metrics.adjacent_accuracy = adjacent_correct / len(all_preds)
# Per-stage accuracy
- stage_correct = defaultdict(int)
- stage_total = defaultdict(int)
+ stage_correct: dict = defaultdict(int)
+ stage_total: dict = defaultdict(int)
for p in all_preds:
gt = p.ground_truth_stage
@@ -130,13 +138,11 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
metrics.stage_accuracy[stage] = stage_correct[stage] / stage_total[stage]
# Confusion matrix
- confusion = defaultdict(lambda: defaultdict(int))
+ confusion: dict = defaultdict(lambda: defaultdict(int))
for p in all_preds:
confusion[p.ground_truth_stage][p.predicted_stage] += 1
- metrics.confusion_matrix = {
- gt: dict(preds) for gt, preds in confusion.items()
- }
+ metrics.confusion_matrix = {gt: dict(preds) for gt, preds in confusion.items()}
# Confidence statistics
confidences = [p.confidence for p in all_preds]
@@ -156,10 +162,7 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
bin_high = (i + 1) / num_bins
bin_center = (bin_low + bin_high) / 2
- bin_preds = [
- p for p in all_preds
- if bin_low <= p.confidence < bin_high
- ]
+ bin_preds = [p for p in all_preds if bin_low <= p.confidence < bin_high]
if bin_preds:
bin_accuracy = sum(1 for p in bin_preds if p.is_correct) / len(bin_preds)
@@ -198,6 +201,8 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
stage_tool_calls[p.ground_truth_stage].append(p.tool_calls)
for stage, calls in stage_tool_calls.items():
+ if stage is None:
+ continue
metrics.tool_use_by_stage[stage] = sum(calls) / len(calls)
# Accuracy with vs without tools
@@ -207,7 +212,9 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
if with_tools:
metrics.accuracy_with_tools = sum(1 for p in with_tools if p.is_correct) / len(with_tools)
if without_tools:
- metrics.accuracy_without_tools = sum(1 for p in without_tools if p.is_correct) / len(without_tools)
+ metrics.accuracy_without_tools = sum(1 for p in without_tools if p.is_correct) / len(
+ without_tools
+ )
# Transitional observations
transitional_preds = [p for p in all_preds if p.is_transitional]
@@ -215,16 +222,16 @@ def compute_metrics(report: "BenchmarkReport") -> PerceptionMetrics:
metrics.transitional_rate = len(transitional_preds) / len(all_preds)
if transitional_preds:
- metrics.transitional_accuracy = sum(
- 1 for p in transitional_preds if p.is_correct
- ) / len(transitional_preds)
+ metrics.transitional_accuracy = sum(1 for p in transitional_preds if p.is_correct) / len(
+ transitional_preds
+ )
return metrics
def format_confusion_matrix(
- confusion: Dict[str, Dict[str, int]],
- stages: Optional[List[str]] = None,
+ confusion: dict[str, dict[str, int]],
+ stages: list[str] | None = None,
) -> str:
"""Format confusion matrix as ASCII table."""
if stages is None:
@@ -278,34 +285,38 @@ def format_metrics_summary(metrics: PerceptionMetrics) -> str:
count = metrics.stage_counts[stage]
lines.append(f" {stage:>10}: {acc:.1%} (n={count})")
- lines.extend([
- "",
- "CONFIDENCE CALIBRATION",
- f" Mean confidence: {metrics.mean_confidence:.2f}",
- f" Confidence (correct): {metrics.confidence_when_correct:.2f}",
- f" Confidence (wrong): {metrics.confidence_when_wrong:.2f}",
- f" Expected Cal. Error: {metrics.expected_calibration_error:.3f}",
- "",
- "TOOL USAGE",
- f" Total tool calls: {metrics.total_tool_calls}",
- f" Avg calls per pred: {metrics.tool_call_rate:.2f}",
- f" Accuracy with tools: {metrics.accuracy_with_tools:.1%}",
- f" Accuracy without tools: {metrics.accuracy_without_tools:.1%}",
- "",
- "TEMPORAL",
- f" Backward transitions: {metrics.backward_transitions}",
- "",
- "TRANSITIONAL OBSERVATIONS",
- f" Count: {metrics.transitional_count}",
- f" Rate: {metrics.transitional_rate:.1%}",
- f" Accuracy: {metrics.transitional_accuracy:.1%}",
- ])
+ lines.extend(
+ [
+ "",
+ "CONFIDENCE CALIBRATION",
+ f" Mean confidence: {metrics.mean_confidence:.2f}",
+ f" Confidence (correct): {metrics.confidence_when_correct:.2f}",
+ f" Confidence (wrong): {metrics.confidence_when_wrong:.2f}",
+ f" Expected Cal. Error: {metrics.expected_calibration_error:.3f}",
+ "",
+ "TOOL USAGE",
+ f" Total tool calls: {metrics.total_tool_calls}",
+ f" Avg calls per pred: {metrics.tool_call_rate:.2f}",
+ f" Accuracy with tools: {metrics.accuracy_with_tools:.1%}",
+ f" Accuracy without tools: {metrics.accuracy_without_tools:.1%}",
+ "",
+ "TEMPORAL",
+ f" Backward transitions: {metrics.backward_transitions}",
+ "",
+ "TRANSITIONAL OBSERVATIONS",
+ f" Count: {metrics.transitional_count}",
+ f" Rate: {metrics.transitional_rate:.1%}",
+ f" Accuracy: {metrics.transitional_accuracy:.1%}",
+ ]
+ )
if metrics.confusion_matrix:
- lines.extend([
- "",
- "CONFUSION MATRIX",
- format_confusion_matrix(metrics.confusion_matrix),
- ])
+ lines.extend(
+ [
+ "",
+ "CONFUSION MATRIX",
+ format_confusion_matrix(metrics.confusion_matrix),
+ ]
+ )
return "\n".join(lines)
diff --git a/benchmarks/perception/runner.py b/benchmarks/perception/runner.py
index 33d93fe3..70ac32fd 100644
--- a/benchmarks/perception/runner.py
+++ b/benchmarks/perception/runner.py
@@ -12,11 +12,11 @@
from dataclasses import dataclass, field
from datetime import datetime
from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import Any
from .ground_truth import GroundTruth
-from .testset import OfflineTestset, TestCase
from .metrics import PerceptionMetrics, compute_metrics
+from .testset import OfflineTestset
logger = logging.getLogger(__name__)
@@ -39,20 +39,20 @@ class BenchmarkConfig:
# Test settings
start_timepoint: int = 0
- max_timepoints_per_embryo: Optional[int] = None
- embryo_ids: Optional[List[str]] = None # None = all
+ max_timepoints_per_embryo: int | None = None
+ embryo_ids: list[str] | None = None # None = all
# Ablation toggles
include_temporal_context: bool = True
include_previous_observations: bool = True
# Custom system prompt override
- system_prompt_override: Optional[str] = None
+ system_prompt_override: str | None = None
# Metadata
description: str = ""
- def to_dict(self) -> Dict[str, Any]:
+ def to_dict(self) -> dict[str, Any]:
return {
"model": self.model,
"temperature": self.temperature,
@@ -78,20 +78,20 @@ class PredictionResult:
timepoint: int
predicted_stage: str
- ground_truth_stage: Optional[str]
+ ground_truth_stage: str | None
confidence: float
is_transitional: bool
- transition_between: Optional[List[str]]
+ transition_between: list[str] | None
reasoning: str
- reasoning_trace: Optional[Dict[str, Any]] # Serialized ReasoningTrace
+ reasoning_trace: dict[str, Any] | None # Serialized ReasoningTrace
tool_calls: int
- tools_used: List[str]
+ tools_used: list[str]
# Multi-phase verification fields
verification_triggered: bool = False
phase_count: int = 1
- verification_result: Optional[Dict[str, Any]] = None
- candidate_stages: Optional[List[Dict[str, Any]]] = None
+ verification_result: dict[str, Any] | None = None
+ candidate_stages: list[dict[str, Any]] | None = None
@property
def is_correct(self) -> bool:
@@ -113,7 +113,7 @@ def is_adjacent_correct(self) -> bool:
except ValueError:
return False
- def to_dict(self) -> Dict[str, Any]:
+ def to_dict(self) -> dict[str, Any]:
return {
"timepoint": self.timepoint,
"predicted_stage": self.predicted_stage,
@@ -139,9 +139,9 @@ class EmbryoResult:
"""Results for a single embryo run."""
embryo_id: str
- predictions: List[PredictionResult] = field(default_factory=list)
+ predictions: list[PredictionResult] = field(default_factory=list)
duration_seconds: float = 0.0
- error: Optional[str] = None
+ error: str | None = None
@property
def accuracy(self) -> float:
@@ -159,7 +159,7 @@ def adjacent_accuracy(self) -> float:
correct = sum(1 for p in self.predictions if p.is_adjacent_correct)
return correct / len(self.predictions)
- def to_dict(self) -> Dict[str, Any]:
+ def to_dict(self) -> dict[str, Any]:
return {
"embryo_id": self.embryo_id,
"predictions": [p.to_dict() for p in self.predictions],
@@ -175,11 +175,11 @@ class BenchmarkReport:
"""Complete benchmark report."""
config: BenchmarkConfig
- embryo_results: List[EmbryoResult] = field(default_factory=list)
- metrics: Optional[PerceptionMetrics] = None
+ embryo_results: list[EmbryoResult] = field(default_factory=list)
+ metrics: PerceptionMetrics | None = None
started_at: datetime = field(default_factory=datetime.now)
- completed_at: Optional[datetime] = None
- session_id: Optional[str] = None
+ completed_at: datetime | None = None
+ session_id: str | None = None
@property
def total_predictions(self) -> int:
@@ -192,7 +192,7 @@ def overall_accuracy(self) -> float:
return 0.0
return sum(1 for p in all_preds if p.is_correct) / len(all_preds)
- def to_dict(self) -> Dict[str, Any]:
+ def to_dict(self) -> dict[str, Any]:
return {
"config": self.config.to_dict(),
"embryo_results": [r.to_dict() for r in self.embryo_results],
@@ -222,7 +222,7 @@ def __init__(
self,
testset: OfflineTestset,
config: BenchmarkConfig,
- engine: Optional[Any] = None, # PerceptionEngine
+ engine: Any | None = None, # PerceptionEngine
):
"""
Parameters
@@ -246,7 +246,6 @@ async def _get_engine(self):
# Lazy import to avoid circular dependencies
import anthropic
from gently.harness.perception.engine import PerceptionEngine
- from gently.harness.perception.example_store import ExampleStore
client = anthropic.Anthropic()
@@ -465,7 +464,8 @@ async def main():
help="Description for this benchmark run",
)
parser.add_argument(
- "-v", "--verbose",
+ "-v",
+ "--verbose",
action="store_true",
help="Verbose logging",
)
@@ -481,6 +481,7 @@ async def main():
# The perception engine reads stage definitions etc. from the active
# organism module, which is normally loaded by launch_gently.py.
from gently.organisms import load_organism
+
load_organism("celegans")
# Find session path
diff --git a/benchmarks/perception/testset.py b/benchmarks/perception/testset.py
index 658cc011..c3514ffe 100644
--- a/benchmarks/perception/testset.py
+++ b/benchmarks/perception/testset.py
@@ -6,18 +6,19 @@
import base64
import io
+from collections.abc import Iterator
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
-from typing import Iterator, List, Optional, Tuple, Dict
+from typing import Any
import numpy as np
from .ground_truth import GroundTruth
# Lazy imports
-tifffile = None
-PIL_Image = None
+tifffile: Any = None
+PIL_Image: Any = None
def _ensure_dependencies():
@@ -26,10 +27,12 @@ def _ensure_dependencies():
if tifffile is None:
import tifffile as _tifffile
+
tifffile = _tifffile
if PIL_Image is None:
from PIL import Image as _Image
+
PIL_Image = _Image
@@ -40,27 +43,29 @@ class TestCase:
embryo_id: str
timepoint: int
image_b64: str # Combined view (for backward compatibility)
- top_image_b64: Optional[str] # TOP view only
- side_image_b64: Optional[str] # SIDE view only
- volume: Optional[np.ndarray]
- ground_truth_stage: Optional[str]
- acquired_at: Optional[datetime] = None
+ top_image_b64: str | None # TOP view only
+ side_image_b64: str | None # SIDE view only
+ volume: np.ndarray | None
+ ground_truth_stage: str | None
+ acquired_at: datetime | None = None
def _discover_volumes(
- session_dir: Path, embryo_id: Optional[str] = None
-) -> Dict[str, List[Tuple[datetime, Path]]]:
+ session_dir: Path, embryo_id: str | None = None
+) -> dict[str, list[tuple[datetime, Path]]]:
"""Discover volume files (with parsed acquisition timestamps) in a session directory."""
if not session_dir.exists():
return {}
tif_files = (
- list(session_dir.glob("*.tif")) + list(session_dir.glob("*.tiff"))
- + list(session_dir.glob("**/*.tif")) + list(session_dir.glob("**/*.tiff"))
+ list(session_dir.glob("*.tif"))
+ + list(session_dir.glob("*.tiff"))
+ + list(session_dir.glob("**/*.tif"))
+ + list(session_dir.glob("**/*.tiff"))
)
# Deduplicate (flat + recursive may overlap)
tif_files = list({f.resolve(): f for f in tif_files}.values())
- embryo_volumes = {}
+ embryo_volumes: dict = {}
for f in tif_files:
parts = f.stem.split("_")
@@ -89,6 +94,7 @@ def _discover_volumes(
def _load_volume(path: Path) -> np.ndarray:
"""Load a volume from TIFF file."""
from gently.core.imaging import load_volume
+
return load_volume(path)
@@ -122,9 +128,9 @@ def _create_three_view_image(volume: np.ndarray, max_dim: int = 1500) -> str:
_ensure_dependencies()
from gently.core.imaging import (
- projection_three_view,
- compute_crop_bounds,
apply_crop_bounds,
+ compute_crop_bounds,
+ projection_three_view,
)
# Auto-crop to embryo region
@@ -150,7 +156,7 @@ def _create_three_view_image(volume: np.ndarray, max_dim: int = 1500) -> str:
return base64.b64encode(buffer.getvalue()).decode("utf-8")
-def _create_separate_view_images(volume: np.ndarray, max_dim: int = 1000) -> Tuple[str, str]:
+def _create_separate_view_images(volume: np.ndarray, max_dim: int = 1000) -> tuple[str, str]:
"""Create separate TOP and SIDE view images from volume, return base64 tuple.
Parameters
@@ -244,7 +250,7 @@ def __init__(
self._embryo_volumes = _discover_volumes(self.session_path)
@property
- def embryo_ids(self) -> List[str]:
+ def embryo_ids(self) -> list[str]:
"""Get list of embryo IDs with both volumes and ground truth."""
gt_embryos = set(self.ground_truth.embryo_ids)
vol_embryos = set(self._embryo_volumes.keys())
@@ -258,7 +264,7 @@ def iter_embryo(
self,
embryo_id: str,
start_timepoint: int = 0,
- end_timepoint: Optional[int] = None,
+ end_timepoint: int | None = None,
) -> Iterator[TestCase]:
"""
Iterate through timepoints for an embryo sequentially.
@@ -318,7 +324,7 @@ def iter_embryo(
acquired_at=acquired_at,
)
- def iter_all(self) -> Iterator[Tuple[str, Iterator[TestCase]]]:
+ def iter_all(self) -> Iterator[tuple[str, Iterator[TestCase]]]:
"""
Iterate through all embryos in the testset.
diff --git a/benchmarks/perception/trace_viewer.py b/benchmarks/perception/trace_viewer.py
index 5a3ced2d..69ea5fa6 100644
--- a/benchmarks/perception/trace_viewer.py
+++ b/benchmarks/perception/trace_viewer.py
@@ -7,12 +7,9 @@
import argparse
import json
import sys
-from datetime import datetime
from pathlib import Path
-from typing import Any, Dict, List, Optional
-
-from .metrics import format_metrics_summary, PerceptionMetrics
+from .metrics import PerceptionMetrics, format_metrics_summary
HTML_TEMPLATE = """
@@ -293,16 +290,16 @@
"""
-def generate_embryo_section(embryo_id: str, predictions: List[Dict]) -> str:
+def generate_embryo_section(embryo_id: str, predictions: list[dict]) -> str:
"""Generate HTML for one embryo's predictions."""
rows = [
'
",
]
for i, pred in enumerate(predictions):
@@ -320,15 +317,15 @@ def generate_embryo_section(embryo_id: str, predictions: List[Dict]) -> str:
row_id = f"{embryo_id}-{timepoint}"
rows.append(f'T${pred.timepoint}
- ${pred.predicted}
- ${pred.ground_truth}
+ ${pred.predicted}
+ ${pred.ground_truth}
${(pred.confidence * 100).toFixed(0)}%
- ${pred.phase_count > 1 ? pred.phase_count + '-phase' : ''}${verifiedBadge}
+ ${pred.phase_count > 1
+ ? pred.phase_count + '-phase' : ''}${verifiedBadge}
',
- '
',
+ "Timepoint
',
- 'Predicted
',
- 'Ground Truth
',
- 'Confidence
',
- 'Details
',
- 'Timepoint
",
+ "Predicted
",
+ "Ground Truth
",
+ "Confidence
",
+ "Details
",
+ "')
- rows.append(f'
""")
+ rows.append("")
# Reasoning trace (hidden by default)
trace_html = format_reasoning_trace(pred.get("reasoning_trace"))
- rows.append(f'''T{timepoint}
')
+ rows.append(f"T{timepoint}
")
rows.append(f'{pred_stage}
')
rows.append(f'{gt_stage}
')
- rows.append(f'''
+ rows.append(f"""
""")
# Details column with expand button
tool_calls = pred.get("tool_calls", 0)
@@ -351,31 +348,31 @@ def generate_embryo_section(embryo_id: str, predictions: List[Dict]) -> str:
if phase_count > 1:
badges += f'{phase_count}-phase'
- rows.append(f'''
{confidence:.0%}
-
''')
+
+ rows.append(f"""
')
+
{details_str}
{badges}
-
''')
- rows.append('
+ rows.append(f"""
""")
- return f'''
+ return f"""
Reasoning: {reasoning}
{trace_html}
-
''')
+ {embryo_id}
{"".join(rows)}
Tool Call: {tool_name}
Input: {json.dumps(tool_input, indent=2)}
- ''')
+ """)
elif step_type == "tool_result":
summary = step.get("tool_result_summary", content)
- html_parts.append(f'''
+ html_parts.append(f"""
Input: {json.dumps(tool_input, indent=2)}
Tool Result: {summary}
- ''')
+ """)
elif step_type == "final_decision":
- html_parts.append(f'''
+ html_parts.append(f"""
Final Decision:
{content[:500]}...
- ''')
+ """)
elif step_type == "verification_requested":
- html_parts.append(f'''
+ html_parts.append(f"""
{content[:500]}...
Verification Requested:
{content}
- ''')
+ """)
elif step_type == "verification_subagent":
tool_input = step.get("tool_input", {})
summary = step.get("tool_result_summary", content)
- html_parts.append(f'''
+ html_parts.append(f"""
{content}
- Subagent: {tool_input.get("stage_a", "?")} vs {tool_input.get("stage_b", "?")}
+ Subagent: {tool_input.get("stage_a", "?")} vs + {tool_input.get("stage_b", "?")}
Result: {summary}
- ''')
+ """)
elif step_type == "verification_result":
- html_parts.append(f'''
+ html_parts.append(f"""
+ Subagent: {tool_input.get("stage_a", "?")} vs + {tool_input.get("stage_b", "?")}
Result: {summary}
Verification Result:
{content}
- ''')
+ """)
return "".join(html_parts)
-def generate_confusion_matrix_html(confusion: Dict[str, Dict[str, int]]) -> str:
+def generate_confusion_matrix_html(confusion: dict[str, dict[str, int]]) -> str:
"""Generate HTML table for confusion matrix."""
- stages = ["early", "bean", "comma", "1.5fold", "2fold", "pretzel", "hatching", "hatched"]
+ stages = [
+ "early",
+ "bean",
+ "comma",
+ "1.5fold",
+ "2fold",
+ "pretzel",
+ "hatching",
+ "hatched",
+ ]
# Filter to stages present in data
present = set()
@@ -478,7 +485,7 @@ def generate_confusion_matrix_html(confusion: Dict[str, Dict[str, int]]) -> str:
return "".join(rows)
-def generate_html_report(report_data: Dict) -> str:
+def generate_html_report(report_data: dict) -> str:
"""Generate complete HTML report from benchmark data."""
# Extract summary metrics
metrics = report_data.get("metrics", {})
@@ -493,9 +500,7 @@ def generate_html_report(report_data: Dict) -> str:
# Generate embryo sections
embryo_sections = []
for er in embryo_results:
- embryo_sections.append(
- generate_embryo_section(er["embryo_id"], er["predictions"])
- )
+ embryo_sections.append(generate_embryo_section(er["embryo_id"], er["predictions"]))
# Generate confusion matrix
confusion = metrics.get("confusion_matrix", {})
@@ -569,8 +574,7 @@ def main():
# Filter embryo if specified
if args.embryo:
report_data["embryo_results"] = [
- er for er in report_data.get("embryo_results", [])
- if er["embryo_id"] == args.embryo
+ er for er in report_data.get("embryo_results", []) if er["embryo_id"] == args.embryo
]
# Generate HTML
diff --git a/benchmarks/runner.py b/benchmarks/runner.py
index 4d6d847a..7dd31236 100644
--- a/benchmarks/runner.py
+++ b/benchmarks/runner.py
@@ -13,8 +13,6 @@
import json
import logging
import sys
-from datetime import datetime
-from pathlib import Path
logging.basicConfig(level=logging.INFO, format="%(message)s")
logger = logging.getLogger(__name__)
@@ -66,7 +64,6 @@ async def run_agent_benchmark(args):
def compare_reports(args):
"""Compare two benchmark reports"""
- from .agent.evaluator import BenchmarkReport, compare_reports as _compare
with open(args.before) as f:
before_data = json.load(f)
@@ -101,7 +98,10 @@ def compare_reports(args):
delta_str = f"+{fmt.format(delta)}" if delta > 0 else fmt.format(delta)
status = "improved" if delta > 0 else ("regressed" if delta < 0 else "unchanged")
- logger.info(f" {name}: {fmt.format(before_val)} -> {fmt.format(after_val)} ({delta_str}) [{status}]")
+ logger.info(
+ f" {name}: {fmt.format(before_val)} -> {fmt.format(after_val)}"
+ f" ({delta_str}) [{status}]"
+ )
# Token comparison
before_tokens = before_data.get("tokens", {})
@@ -111,7 +111,7 @@ def compare_reports(args):
after_total = after_tokens.get("total_input", 0) + after_tokens.get("total_output", 0)
token_delta = after_total - before_total
- logger.info(f"\nTokens:")
+ logger.info("\nTokens:")
logger.info(f" Total: {before_total:,} -> {after_total:,} ({token_delta:+,})")
return 0
diff --git a/config/config.yml b/config/config.yml
index e59e9f6d..9c05c274 100644
--- a/config/config.yml
+++ b/config/config.yml
@@ -1,4 +1,38 @@
organism: "celegans"
hardware: "dispim"
mmconfig: "MMConfig_tracking_screening.cfg"
-mmdirectory: "C:/Program Files/Micro-Manager-1.4"
\ No newline at end of file
+mmdirectory: "C:/Program Files/Micro-Manager-1.4"
+
+# SwitchBot Bot — physical button-pusher mounted on the diSPIM room light
+# switch. Talks BLE direct (no SwitchBot Hub / cloud). Plans address it by
+# name, e.g. `bps.mv(room_light, 'on')`. Remove this block to skip
+# registration; the device layer is tolerant of either state.
+switchbot:
+ name: room_light
+ address: "EC:6F:04:06:5B:23"
+ timeout: 20.0
+
+# ACUITYnano Precision Thermal Controller (Peltier/TEC, 0.0–99.9 °C). When this
+# block is present the device layer registers a `temperature` device and the
+# Devices tab shows a setpoint control; plans can also block on it via
+# `bps.mv(temperature, 20.0)`. Remove/comment the block to skip registration.
+#
+# backend: mqtt talks to the controller over the vendor's MQTT bridge
+# (acuitynano_precision_thermalizer_api). With no broker/port/user/password
+# keys it uses the vendor package's embedded HiveMQ Cloud defaults — set them
+# here only to point at a different broker. The vendor package must be
+# installed on the device-layer machine (not on PyPI).
+temperature:
+ name: temperature
+ backend: serial # serial | mqtt | mock — USB serial is the working
+ # link on this machine (MQTT cloud is firewalled)
+ com_port: "COM8"
+ baud_rate: 115200
+ stabilize_timeout: 600 # seconds to wait for "[ SYSTEM LOCKED ]" on a blocking set
+ feedback_peltier: false # true = control off the peltier sensor instead of water
+ # MQTT alternative (vendor HiveMQ Cloud defaults; needs outbound TLS :8883):
+ # backend: mqtt
+ # broker: "your-broker.example.com" # optional — overrides the embedded default
+ # port: 8883
+ # user: "username"
+ # password: "secret"
\ No newline at end of file
diff --git a/desktop/.gitignore b/desktop/.gitignore
new file mode 100644
index 00000000..6b3daa59
--- /dev/null
+++ b/desktop/.gitignore
@@ -0,0 +1,14 @@
+# Node / Tauri CLI
+node_modules/
+
+# Rust / Tauri build output
+src-tauri/target/
+src-tauri/gen/
+
+# Generated mobile / MS-Store icon variants (regenerate with `tauri icon`).
+# The desktop icons referenced by tauri.conf.json (32x32, 128x128, 128x128@2x,
+# icon.ico, icon.icns, icon.png) ARE committed so a clean checkout builds.
+src-tauri/icons/android/
+src-tauri/icons/ios/
+src-tauri/icons/Square*Logo.png
+src-tauri/icons/StoreLogo.png
diff --git a/desktop/README.md b/desktop/README.md
new file mode 100644
index 00000000..a18e4c44
--- /dev/null
+++ b/desktop/README.md
@@ -0,0 +1,159 @@
+# Gently Desktop (Tauri shell)
+
+A thin [Tauri](https://v2.tauri.app) desktop wrapper that turns gently into a
+double-click Windows app. It **owns** the Python backend: on launch it spawns
+`launch_gently.py --no-browser`, shows a splash while the server boots, then
+renders the existing web UI in a native WebView2 window. No application logic
+lives here — the web UI served by Python stays the single source of truth.
+
+This is the desktop-packaging fold-in described in RFC #78
+(`docs/superpowers/specs/2026-07-02-unified-launcher-design.md`).
+
+## Why Tauri (and what it does / doesn't solve)
+
+- **Tiny footprint** — uses the OS WebView2 (already present on Win 11), not a
+ bundled Chromium.
+- **Robust process ownership** — the shell puts the spawned Python into a
+ Windows **Job Object** with `KILL_ON_JOB_CLOSE`. Python's own device-layer
+ grandchild (via `DeviceLayerSupervisor`) inherits the job, so when the app
+ quits *or crashes* the OS reaps the **entire** process tree — no orphaned
+ device layer holding COM ports.
+- **Not solved here:** bundling the Python environment (torch, anthropic,
+ perception) into a redistributable installer. This build launches the repo's
+ existing `.venv`. Shipping a self-contained `.msi`/`.exe` to another machine
+ needs an embeddable-Python / PyInstaller sidecar — see *Bundling* below.
+
+## Architecture
+
+```
+Tauri shell (Rust, WebView2 window)
+ └─ spawns: python launch_gently.py --no-browser [in a kill-on-close Job]
+ └─ spawns: start_device_layer.py (DeviceLayerSupervisor)
+ ├─ shows splash/index.html while uvicorn boots
+ └─ navigate() → http://localhost:8080 (the live gently UI)
+```
+
+- `src-tauri/src/main.rs` — spawn + Job Object teardown + wait-for-server + navigate.
+- `splash/index.html` — boot splash (Rust updates its status line via `window.__gentlyStatus`).
+- `src-tauri/tauri.conf.json` — one window, `frontendDist: ../splash`, NSIS bundle.
+
+## Quitting (graceful handshake, issue #85)
+
+Closing the window does **not** kill the backend outright. The shell first runs
+a graceful handshake: it intercepts the close and `POST`s the backend's
+loopback-only `/api/shutdown`, which stops a managed device layer via its clean
+SIGTERM path and lets the backend drain state (e.g. session-replay final
+batches) before exiting on its own; the shell waits a few seconds for the port
+to go down, then quits. If an acquisition is running the backend answers `409`
+and the shell asks for confirmation first — cancel and the window stays open.
+If the backend is dead or hung, the shell just exits. Either way the Job-Object
+kill-on-close (and best-effort `child.kill()`) remains the unchanged crash-safe
+floor underneath.
+
+## Prerequisites
+
+- **Rust** (MSVC toolchain) — `rustup default stable-x86_64-pc-windows-msvc`
+- **MSVC C++ build tools** (Visual Studio 2022 / Build Tools)
+- **WebView2 runtime** (inbox on Windows 11)
+- **Node** (only for the Tauri CLI: `npm install` in this folder)
+- A working gently checkout with its Python **`.venv`** at the repo root
+
+### Linux (dev machines)
+
+The shell is cross-platform — the Job-Object code is `#[cfg(windows)]`, so on
+Linux teardown is the best-effort `child.kill()` only (fine for dev; the
+kill-on-close guarantee is a Windows-production feature). Verified on Manjaro
+(KDE/Wayland, webkit2gtk 2.52):
+
+- **Rust** — `rustup default stable`
+- **WebKitGTK + GTK3** — `webkit2gtk-4.1` and `gtk3` dev packages
+ (Arch/Manjaro: `pacman -S webkit2gtk-4.1`; Debian/Ubuntu:
+ `apt install libwebkit2gtk-4.1-dev build-essential`)
+- **Node** — as above
+- The venv is found at **`.venv/bin/python`** (Unix layout) automatically;
+ `GENTLY_PYTHON` overrides as usual
+
+Same commands, bash syntax:
+
+```bash
+cd desktop && npm install
+GENTLY_LAUNCH_ARGS="--no-api --offline --no-auth" npm run dev
+```
+
+`npm run build` is Windows-only as configured (`bundle.targets: ["nsis"]`) —
+on Linux use `npm run dev`, or override targets if a Linux bundle is ever needed.
+
+## Run (dev)
+
+```powershell
+cd desktop
+npm install # once — restores the Tauri CLI
+npm run dev # build + launch the shell (spawns the backend for you)
+```
+
+`npm run dev` (= `tauri dev`) compiles the shell, opens the window, spawns
+`launch_gently.py --no-browser`, and navigates to the live UI once it's up.
+
+UI-only (no hardware / API key / login) — handy for pure UI work:
+
+```powershell
+$env:GENTLY_LAUNCH_ARGS="--no-api --offline --no-auth"; npm run dev
+```
+
+## Making code changes — what reflects, and how
+
+The window is just a WebView pointed at the Python server, so it splits in three:
+
+| You edit… | Reflects by… | Rebuild? |
+|---|---|---|
+| **Web UI** (`gently/ui/web/templates`, `static/js`, `static/css`) | **Refresh the window** (Ctrl+R) | no — served live by Python |
+| **Python backend** (`gently/**/*.py`, `launch_gently.py`) | restart the backend — or run with **`--reload`** (below), then Ctrl+R | process restart |
+| **Rust shell / config** (`src-tauri/`, `splash/`) | `npm run dev` **auto-rebuilds + relaunches** | automatic (watched) |
+
+**Python hot-reload.** Pass `--reload` and the backend auto-restarts whenever a
+`gently/*.py` file changes (watchfiles) — then just Ctrl+R the window:
+
+```powershell
+$env:GENTLY_LAUNCH_ARGS="--reload --no-api --offline --no-auth"; npm run dev
+# or, iterating in a plain browser instead of the shell:
+uv run python launch_gently.py --reload
+```
+
+It restarts the *whole* backend (a few seconds), so use it for UI / backend dev,
+not live hardware sessions.
+
+## Build (installer)
+
+```powershell
+cd desktop
+npm run build # = tauri build — NSIS installer under src-tauri/target/release/bundle/
+```
+
+Then Gently installs like any Windows app (Start-Menu entry, double-click — no
+terminal). The built app launches the **repo's** `.venv` + `launch_gently.py`
+(paths baked at compile time / overridable — see env vars); it's a single-machine
+build until Python bundling lands.
+
+## Configuration (env vars read by the shell)
+
+| Var | Default | Purpose |
+|---|---|---|
+| `GENTLY_HOME` | compile-time repo root | Directory to run the backend from |
+| `GENTLY_PYTHON` | `{content}
Gently
+
+ Starting the backend…
+ microscopy agent · desktop
+
+
+
diff --git a/desktop/src-tauri/Cargo.lock b/desktop/src-tauri/Cargo.lock
new file mode 100644
index 00000000..27a8fbb4
--- /dev/null
+++ b/desktop/src-tauri/Cargo.lock
@@ -0,0 +1,4433 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 4
+
+[[package]]
+name = "adler2"
+version = "2.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "320119579fcad9c21884f5c4861d16174d0e06250625266f50fe6898340abefa"
+
+[[package]]
+name = "aho-corasick"
+version = "1.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ddd31a130427c27518df266943a5308ed92d4b226cc639f5a8f1002816174301"
+dependencies = [
+ "memchr",
+]
+
+[[package]]
+name = "alloc-no-stdlib"
+version = "2.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3"
+
+[[package]]
+name = "alloc-stdlib"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0e76a019e91224d279006ff972f1e984179a6e9feb050adba6ce8274aef23195"
+dependencies = [
+ "alloc-no-stdlib",
+]
+
+[[package]]
+name = "android_system_properties"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311"
+dependencies = [
+ "libc",
+]
+
+[[package]]
+name = "anyhow"
+version = "1.0.103"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2a4385e2e34eb35d6b3efe798b9eb88096925d87726c0798709bf56d9ed84af3"
+
+[[package]]
+name = "atk"
+version = "0.18.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "241b621213072e993be4f6f3a9e4b45f65b7e6faad43001be957184b7bb1824b"
+dependencies = [
+ "atk-sys",
+ "glib",
+ "libc",
+]
+
+[[package]]
+name = "atk-sys"
+version = "0.18.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5e48b684b0ca77d2bbadeef17424c2ea3c897d44d566a1617e7e8f30614d086"
+dependencies = [
+ "glib-sys",
+ "gobject-sys",
+ "libc",
+ "system-deps",
+]
+
+[[package]]
+name = "atomic-waker"
+version = "1.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1505bd5d3d116872e7271a6d4e16d81d0c8570876c8de68093a09ac269d8aac0"
+
+[[package]]
+name = "autocfg"
+version = "1.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2032f911046de80f0a198e0901378627c33f59ea0ac00e363d481118bd70a53"
+
+[[package]]
+name = "base64"
+version = "0.21.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9d297deb1925b89f2ccc13d7635fa0714f12c87adce1c75356b39ca9b7178567"
+
+[[package]]
+name = "base64"
+version = "0.22.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
+
+[[package]]
+name = "bit-set"
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+checksum = "b8848ee67ecc8aedbaf3e4122217aff892639231befc6a1b58d29fff4c2cabaa"
diff --git a/desktop/src-tauri/Cargo.toml b/desktop/src-tauri/Cargo.toml
new file mode 100644
index 00000000..6d85d560
--- /dev/null
+++ b/desktop/src-tauri/Cargo.toml
@@ -0,0 +1,29 @@
+[package]
+name = "gently-desktop"
+version = "0.1.0"
+edition = "2021"
+description = "Gently desktop shell — owns the Python backend + device layer"
+authors = ["gently"]
+default-run = "gently-desktop"
+
+[build-dependencies]
+tauri-build = { version = "2", features = [] }
+
+[dependencies]
+tauri = { version = "2" }
+
+# Windows Job Object: put the spawned Python (and its device-layer grandchild)
+# in a kill-on-close job so the whole tree dies when the shell exits or crashes.
+[target.'cfg(windows)'.dependencies]
+windows = { version = "0.62", features = [
+ "Win32_Foundation",
+ "Win32_System_JobObjects",
+ "Win32_System_Threading",
+ "Win32_Security",
+] }
+
+[profile.release]
+codegen-units = 1
+lto = true
+opt-level = "s"
+strip = true
diff --git a/desktop/src-tauri/build.rs b/desktop/src-tauri/build.rs
new file mode 100644
index 00000000..d860e1e6
--- /dev/null
+++ b/desktop/src-tauri/build.rs
@@ -0,0 +1,3 @@
+fn main() {
+ tauri_build::build()
+}
diff --git a/desktop/src-tauri/capabilities/default.json b/desktop/src-tauri/capabilities/default.json
new file mode 100644
index 00000000..c1da0cbb
--- /dev/null
+++ b/desktop/src-tauri/capabilities/default.json
@@ -0,0 +1,7 @@
+{
+ "$schema": "../gen/schemas/desktop-schema.json",
+ "identifier": "default",
+ "description": "Thin shell — the UI is served by the Python backend and makes no Tauri IPC calls. Navigation is driven from Rust, so no window/shell permissions are needed.",
+ "windows": ["main"],
+ "permissions": ["core:default"]
+}
diff --git a/desktop/src-tauri/icons/128x128.png b/desktop/src-tauri/icons/128x128.png
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diff --git a/desktop/src-tauri/icons/icon.ico b/desktop/src-tauri/icons/icon.ico
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diff --git a/desktop/src-tauri/src/main.rs b/desktop/src-tauri/src/main.rs
new file mode 100644
index 00000000..7e7ace4c
--- /dev/null
+++ b/desktop/src-tauri/src/main.rs
@@ -0,0 +1,366 @@
+// Gently desktop shell.
+//
+// A thin Tauri (WebView2) window that OWNS the Python backend. On launch it
+// spawns `launch_gently.py --no-browser`, shows a splash while uvicorn boots,
+// then navigates the window to the live UI (http://localhost:
+
+
+"""
+
+
+def main():
+ ap = argparse.ArgumentParser(description="Temporary SwitchBot room-light web GUI")
+ ap.add_argument("--address", default=DEFAULT_ADDRESS, help="Bot BLE MAC address")
+ ap.add_argument("--port", type=int, default=8765)
+ ap.add_argument("--host", default="127.0.0.1", help="bind host (default: localhost only)")
+ args = ap.parse_args()
+
+ logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
+ global BOT
+ BOT = Bot(args.address)
+ print(f"\n diSPIM Room Light GUI → http://{args.host}:{args.port}\n Bot: {args.address}\n")
+ uvicorn.run(app, host=args.host, port=args.port, log_level="warning")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
new file mode 100644
index 00000000..cd2621f9
--- /dev/null
+++ b/docs/ARCHITECTURE.md
@@ -0,0 +1,171 @@
+# Gently — Concurrency & Runtime Architecture
+
+How the system runs temperature telemetry, device-state polling, experiments,
+image acquisition, and perception/VLM "at the same time" without stepping on
+itself. The short version: **almost nothing runs truly in parallel — the design
+quarantines the blocking work and serializes the hardware, then keeps both event
+loops responsive by offloading and decoupling everything slow.**
+
+> Scope: the concurrency model. For storage layout see `CLAUDE.md`; for the
+> device/hardware plugin model see `docs/asi-plugin-architecture.md`.
+
+## 1. Two processes, bridged by HTTP + a shared filesystem
+
+This split is the load-bearing fact of the whole design.
+
+```
+┌────────────────────────────────────────┐ ┌────────────────────────────────────────┐
+│ APP / VIZ process (FastAPI :8080) │ │ DEVICE-LAYER process (aiohttp :60610) │
+│ gently/app/agent.py │ │ gently/hardware/dispim/device_layer.py │
+│ │ HTTP │ │
+│ • agent + TimelapseOrchestrator │◄──────►│ • the ONLY code touching hardware: │
+│ • Perceiver (gently_perception, VLM) │ (DiSPIM│ MMCore/pymmcore, Ophyd, Bluesky RE │
+│ • AsyncAnthropic clients │ Client)│ • plan queue + single executor │
+│ • EventBus + WebSocket ConnectionMgr │ │ • 3 state pollers + camera/LS streamers │
+│ • TemperatureSampler, DeviceStateMonitor│ │ │
+└──────────────┬──────────────────────────┘ └───────────────┬──────────────────────────┘
+ │ shared filesystem (incoming/ TIFF staging, session store)
+ └──────────────────────────────────────────────────┘
+```
+
+- The **device-layer process** (`device_layer.py`) is the *only* code that ever
+ touches the microscope: MMCore/pymmcore, the Ophyd devices, and a Bluesky
+ `RunEngine`. All truly blocking hardware work is quarantined here.
+- The **app/viz process** (`app/agent.py`, FastAPI+uvicorn) owns everything
+ cognitive and user-facing: the agent, the `TimelapseOrchestrator`, the
+ `Perceiver` (external `gently_perception` VLM package), the Anthropic clients,
+ the in-process `EventBus`, the WebSocket `ConnectionManager`, and the pollers.
+- The app reaches hardware **only** through `DiSPIMClient` (`client.py`), over a
+ single shared `aiohttp.ClientSession`. It never imports MMCore.
+
+Because blocking hardware calls live in a separate process, the app-side loop
+stays a light cooperative-asyncio world.
+
+## 2. One asyncio event loop per process
+
+- **Device loop:** HTTP routes + the RunEngine driver + the plan queue/executor +
+ three state pollers (XY ~5 Hz, piezo/galvo ~1 Hz, full property cache ~15 s) +
+ subscriber-gated camera/lightsheet SSE streamers.
+- **App loop:** FastAPI + the `TimelapseOrchestrator` acquisition loop +
+ `TemperatureSampler` (1 Hz) + `DeviceStateMonitor` + `Perceiver` calls + one
+ coroutine per open browser WebSocket.
+
+## 3. The core trick: hardware is serialized, not parallelized
+
+Every Bluesky plan — a move, a snap, a volume/burst acquisition, a focus/calibration
+sweep — is submitted as a `PlanRequest` onto **one `asyncio.Queue`
+(`self._plan_queue`), drained by one `_plan_executor` task**. Only one plan owns
+the hardware at a time.
+
+- `submit_plan` enqueues and `await`s a per-request `asyncio.Future`; the executor
+ sets the result/exception, which flows back to the awaiting HTTP handler. On
+ failure the executor records it in `_plan_execution_log` and continues to the
+ next queued plan.
+- Underneath, **pymmcore's internal `g_core_lock` is the real mutex** serializing
+ every actual core call across pollers *and* plans. The `DiSPIMSystem` facade is
+ the single place the process touches MMCore.
+
+A microscope has one stage and one camera; single-file execution is correct, not
+a limitation.
+
+## 4. How constant polling coexists with long experiments
+
+Four cooperating mechanisms keep the loops responsive while a plan runs:
+
+1. **Offload blocking reads.** Every MMCore read, camera grab, SAM call, and
+ transient temperature probe goes through `asyncio.to_thread`; the camera
+ sequence runs on its own `threading.Thread` returning an Ophyd `Status`. The
+ loop itself never sits on I/O.
+2. **Split pollers by cadence.** The three device-state pollers are independent
+ tasks so a slow (~1.5 s) full-state-cache read cannot stall the ~5 Hz XY path.
+3. **`pause_state_updates()` — a reference-counted async context manager.** Heavy
+ plans (a `frozenset` of names) wrap execution in it, incrementing a counter;
+ every poller/streamer checks `if self._state_pause_counter > 0` and *skips its
+ MMCore read*, emitting only ~2 s heartbeats. The plan gets full serial/camera
+ bandwidth instead of the pollers fighting it for `g_core_lock`. Nested heavy
+ sections stack and unwind cleanly.
+4. **Telemetry bypasses the plan queue.** `GET /api/temperature/status` reads the
+ temperature Ophyd device directly (`temp.read()` over serial/MQTT — a device
+ wholly separate from MMCore); `GET /api/devices/state` returns the cached
+ `_state_latest` snapshot. Neither sits behind a running experiment, so status
+ polls are never blocked by a long acquisition. (MMCore push callbacks also
+ mirror joystick/property changes into `_state_latest` via
+ `loop.call_soon_threadsafe` with ~50 ms debouncing.)
+
+### Temperature specifically
+The vendor SDK backend (serial or MQTT) runs its own **background daemon thread**
+that ingests the controller's 500 ms telemetry broadcast into a cache
+(`self.telemetry`); `get_water_temp()`/`get_system_state()` return the cached
+value (non-blocking). `TemperatureController.read()` returns that cache, and
+`TemperatureSampler` (`interval_sec=1.0`) polls it at 1 Hz → persists + emits
+`TEMPERATURE_UPDATE`. So we ride the telemetry indirectly, resampled at 1 Hz.
+
+## 5. Image data travels via the filesystem, not JSON
+
+Arrays over ~1 MB are written as **TIFF into the shared `incoming/` staging dir**;
+only a small `{__file_ref__, path, shape, dtype}` dict crosses HTTP (`serialize_value`).
+The client resolves the ref with `tifffile` and hands the decoded array to
+`register_volume`, which renames the file into the session store and stamps it
+with the latest temperature sample — avoiding a multi-GB JSON blob and a double
+decode.
+
+## 6. Perception / VLM / events are decoupled (fire-and-forget)
+
+- **Perception never gates acquisition.** The `TimelapseOrchestrator` does
+ `asyncio.create_task(self._run_perception(...))` rather than awaiting it inline,
+ so a slow VLM call doesn't hold up the next embryo. Inside the task the
+ `Perceiver` and the Claude client are awaited cooperatively, and every Claude
+ call is wrapped in `asyncio.wait_for(timeout=30)` returning a safe fallback
+ instead of raising into the loop.
+- **The `EventBus` publishes without awaiting handlers** (`event_bus.py`): sync
+ handlers run inline, async handlers are scheduled via `asyncio.ensure_future` /
+ `loop.call_soon_threadsafe`; high-volume telemetry types skip the bounded
+ history deque, so one slow WebSocket client delays only its own broadcast.
+
+## 7. Backpressure & failure isolation
+
+- **SSE streams** use per-subscriber queues bounded at `maxsize=4`; device-state
+ broadcasts drop slow subscribers, camera/lightsheet streams drop the *oldest*
+ frame and push the newest so steady clients keep fresh frames.
+- **WebSocket fan-out** (`ConnectionManager.broadcast`) sends per client under an
+ `asyncio.Lock` and drops clients that error.
+- **Failure = a gap, not a crash.** A failed temperature poll logs once and backs
+ off (`1.0 s → min(interval*10, 30 s)`); a stalled SSE forces a watchdog
+ reconnect after 60 s (chosen to tolerate the quiet windows during heavy plans);
+ volume acquisition always disables lasers on error to protect the sample.
+- **Config safety.** `POST /api/temperature/config` refuses (`409`) while the
+ RunEngine is not idle or a ramp holds the controller lock; `health_check()` is
+ read-only and never flips the connected flag, so a transient status-poll timeout
+ can't disconnect an in-flight acquisition.
+
+## 8. Known limits & bottlenecks
+
+- **RunEngine on the loop.** `self.RE(plan)` is invoked synchronously on the
+ device-layer loop, so while a plan runs the loop is largely occupied — which is
+ exactly why heavy plans quiet the pollers and the app-side watchdog tolerates
+ 60 s of silence. Whether the telemetry HTTP handlers stay fully responsive
+ mid-acquisition depends on Bluesky's internal threading (external package) and
+ is not verified from repo code.
+- **Unbounded in-flight perception.** `_perception_tasks` is a plain set that
+ self-prunes; sustained fast acquisition against a slow VLM could grow concurrent
+ Claude calls without an explicit cap. A semaphore is the obvious guard if
+ cadence is ever pushed.
+- **~~Synchronous O(n) prediction writes~~ — FIXED.** `store_prediction` used to
+ re-parse the entire `predictions.jsonl` on every append to compute the next id.
+ Now O(1) via a bounded tail read (`_last_jsonl_record`, `file_store.py`). Other
+ `FileStore` JSONL writes remain synchronous on the app loop but are single-line
+ appends.
+- **External VLM internals.** How `gently_perception`'s `Perceiver` implements its
+ VLM call (async httpx vs sync-in-thread) is not inspectable from this repo; the
+ orchestrator awaits it, implying a coroutine.
+
+## The model in one line
+
+Two single-threaded event loops; hardware fenced into one process behind a
+one-at-a-time plan queue; everything blocking pushed into threads; and the
+slow/cognitive work (VLM, persistence, UI) decoupled with fire-and-forget tasks —
+so the system *feels* concurrent while the microscope itself stays strictly
+serialized.
+
+---
+*Generated from a code-grounded architecture pass (Claude Opus 4.8), 2026-07-01.*
diff --git a/docs/CLOSED_LOOP_PARADIGM.md b/docs/CLOSED_LOOP_PARADIGM.md
new file mode 100644
index 00000000..8f1cf80d
--- /dev/null
+++ b/docs/CLOSED_LOOP_PARADIGM.md
@@ -0,0 +1,536 @@
+# Closed-Loop Paradigm: Notes on the Discussion
+
+This document captures the design conversation that produced everything on the
+`paradigm/closed-loop` branch: the schema split, the Map-as-embryo-home work,
+the operator-action vocabulary, the eval substrate (capture / replay /
+decisions / shadow), and the trajectory the system is on. It is a
+distillation, not a transcript — a future-self / new-collaborator reference
+for *why* this code looks the way it does and *where it is going*.
+
+---
+
+## 1. The Original Friction
+
+The conversation started from a small, concrete observation by the operator:
+
+> "It feels awkward that the operator has to go between the chat in the TUI
+> and the viz server… or even to chat about detecting embryos."
+
+That awkwardness is a symptom, not a defect. It surfaces a deeper design
+question: **what is the orchestrator (the agent) actually for?** Today the
+orchestrator does at least four jobs at once, and one of them — *tool router*
+— is the one creating the friction.
+
+### The four orchestrator roles
+
+| Role | Description | Replaceable by a button? |
+| --- | --- | --- |
+| 1. Tool router | "Detect embryos" → `detect_embryos()` call | **Yes** — this is the friction surface |
+| 2. Workflow runner | Timelapses, multi-embryo plans, perception loops | No |
+| 3. Domain reasoner | Knows microscopy, embryos, safety constraints | No |
+| 4. Session memory | Coherent narrative of what happened and why | No |
+
+Routing a single click through chat for a routine action is the system
+fighting against its own users. Routing a multi-step scientific decision
+through Claude is using the right tool for the right job. The paradigm here
+is: **shrink role 1 to its essentials, keep roles 2–4 first-class, and let
+the UI carry the rest.**
+
+---
+
+## 2. Web ↔ Chat Reconciliation Patterns
+
+Four ways to relate the web UI and the chat orchestrator. Each has a
+distinct world model property:
+
+### A. Chat-only intent (the old default)
+
+Every action originates in chat. The web is observation + delegated subtasks
+(e.g. the marking canvas is a delegation the orchestrator triggers).
+
+* Cleanest record.
+* Worst friction.
+* Orchestrator's world model is "complete" because every change passes
+ through it.
+
+### B. Two parallel command surfaces
+
+Operator clicks in web, web acts directly; orchestrator finds out by polling
+state or doesn't find out at all.
+
+* Lowest friction.
+* Orchestrator's world model **drifts from reality** — fatal for role 4
+ (session memory) and dangerous for role 3 (safety reasoning).
+
+### C. Web acts, orchestrator subscribes *(the chosen direction)*
+
+Operator clicks → web performs the action **and** publishes an event
+(`OPERATOR_*`) → orchestrator's session memory ingests it.
+
+* Chat log shows only human conversation.
+* Orchestrator's working context shows chat + events as a single timeline.
+* Phase 7 (operator events vocabulary + reactive candidate) is the first
+ installment of this pattern.
+
+### D. Cross-pattern hybrid
+
+Different action classes use different patterns. Heavy / novel / composite
+actions use chat (A); routine / clickable / contextual actions use web (C).
+This is what the system actually drifts toward; pattern C is the substrate
+that makes it possible.
+
+The orchestrator's job shifts from being **a funnel for action** to being **a
+brain that knows what's happening on every surface**.
+
+---
+
+## 3. The "Turn" is Wrong; the "Decision Moment" is Right
+
+Chat-AI literature reasons in *turns* (user message → assistant response).
+That model imports an assumption that does not hold here: the human is at
+the keyboard continuously. In a microscopy experiment running 12+ hours, the
+human checks in once, twice, maybe ten times. The agent is autonomous in
+between.
+
+The right unit is a **decision moment**, triggered by:
+
+1. **User message** — rare, interrupting (classic chat turn).
+2. **Critical event** — error, safety violation, lost focus, perception
+ anomaly. Wake immediately; decide to act / abort / escalate.
+3. **Phase boundary** — between timepoints, between embryos. Built-in
+ checkpoint: review state, decide whether to continue.
+4. **Periodic checkpoint** — every N minutes if nothing else happened.
+ Catches slow drifts.
+
+Between moments the agent is asleep. Plans execute autonomously. Events
+accumulate on the bus and in the world model. When the next decision
+moment fires, the agent reads:
+
+* The trigger (why am I waking up?)
+* The world snapshot (NOW state)
+* The events digest (what happened since last wake)
+* The conversation history (which might be hours old and less relevant
+ than usual)
+
+This is closer to a **supervisory controller** than a chat partner. The
+conversation history matters less than usual; what matters more is the
+**flight log** (events) plus the **current state snapshot**.
+
+### Trigger model — concrete
+
+A small router (in code, not Claude) sits between the bus and the brain:
+
+```
+ user input ─┐
+ event bus ──┼─► wake-router ──► (compose context) ──► claude.messages.create
+ schedule ──┘
+```
+
+The router's responsibilities:
+* Subscribe to a whitelist of "wake-worthy" event types.
+* Hold a debounce / coalescing buffer (so a burst of events becomes one
+ wake).
+* Keep a heartbeat schedule (every N minutes if no other trigger fired).
+* On wake, package: trigger, world snapshot, events digest, recent
+ conversation tail.
+* Surface the package to the brain.
+
+The brain stays the brain (Claude). The router is cheap, deterministic,
+debuggable code. It's the **meta-orchestrator** the operator mentioned —
+**not as another LLM**, but as a control surface.
+
+### Phase boundaries: hand-back vs subscribe
+
+Two designs for letting the brain look in mid-plan:
+
+* **Plan hands control back** at well-known points (between embryos, every
+ 5 timepoints). Cheaper, predictable, slightly less reactive.
+* **Plan never pauses; brain subscribes to plan events** ("perception
+ complete for embryo 3"). More reactive, more plan-coupling.
+
+The first one composes better with the supervisory-controller framing and
+is the recommended starting point.
+
+### Idle ticks
+
+If 30 min pass with no event and no user, should the agent wake to verify
+everything's OK? Default to **yes — periodic ticks with a high action
+threshold.** Most ticks should result in the agent doing nothing. The
+purpose is catching slow drifts (focus, sample state, hardware
+degradation) that don't trigger their own events.
+
+---
+
+## 4. World Model — Tiered, Not Monolithic
+
+A common mistake is "summarise everything every turn." Better is a tiered
+model where different freshness/density tiers carry different cadence
+costs.
+
+### Tier 1 — World snapshot
+
+Structured, ~30 lines, computed from in-memory state (not events), every
+wake.
+
+Includes: live stage XY/Z, current session id, embryo list with
+calibration state, current plan, acquisition status, recent operator
+actions (one-line summary).
+
+Cheap to build, fresh every time. Already mostly present in the
+codebase — `agent.experiment.get_summary()` plus the cached
+`DEVICE_STATE_UPDATE` payload is 80% of this.
+
+### Tier 2 — Recent-events digest
+
+Hand-written formatter over the events bus, filtered to wake-worthy types,
+inserted as a system note at each wake.
+
+Shape: `"Since last response: operator added embryo 4 via Map at 14:32; calibration completed for embryo 2; one perception trace pending."`
+
+Hand-written because LLM summarisation here adds latency, cost, and
+non-determinism for low value. Events are already structured.
+
+### Tier 3 — Pull tools
+
+For when reasoning needs depth: `get_recent_perceptions(embryo_id, n=5)`,
+`get_session_timeline()`, `get_learnings(campaign_id)`, etc. The agent
+calls these when it wants the detail.
+
+### Tier 4 — Optional LLM summariser
+
+Reserved for genuinely natural-language streams that resist rule-based
+compression: accumulated CV reasoning chains, narrative observations,
+cross-session learnings. Use a smaller, faster Claude model (Haiku is the
+natural fit). Run lazily, when a tier-3 tool asks for "summarise the last
+30 min for embryo 3."
+
+### Why this shape
+
+Decision moments are **rare** in autonomous mode. Token budget per wake
+can be generous (it's mostly idle compute). What matters more than budget
+is **cadence of waking** — saving 200 tokens per turn doesn't help if
+you're waking up at the wrong moments.
+
+---
+
+## 5. Testing — Where Most Projects Fail
+
+You cannot iterate on agent architecture without a way to compare
+architectures. Microscopy makes this hard:
+
+* Physical, non-deterministic, non-replayable in the trivial sense.
+* "Correct" is fuzzy — biological judgements rarely have ground truth.
+* Slow feedback (a timelapse takes hours).
+* Can't always reset to a clean state (samples are consumed).
+
+Five testing primitives, ranked by payoff per unit work (this ordering
+informed Phase 6's build order):
+
+### 5.1 Event replay *(built — Phase 6a/6b)*
+
+Capture the full event stream during a real run. Offline, replay it
+through any candidate architecture. Diff its decisions against
+production's. **Foundation** — without it, every change to the
+orchestrator is a flight test.
+
+### 5.2 Shadow mode *(built — Phase 6d)*
+
+During a real experiment, candidate architectures run alongside
+production. They see the same events but their decisions are *logged,
+not enacted*. Unique value over pure replay: shadow agents experience
+real temporal cadence, so timing-sensitive things (drift, races) are
+caught.
+
+### 5.3 Synthetic event sequences
+
+Hand-crafted streams: cascading errors, ambiguous perception,
+contradictory operator actions, focus drift, network drop mid-acquisition.
+Stress / chaos testing. The orchestrator is correct if it doesn't do
+something catastrophic — much easier to score than biological
+correctness.
+
+Trivially built on top of 5.1 — write a `jsonl` by hand, replay it.
+
+### 5.4 Decision-level micro-benchmarks
+
+Specific judgements — "given this perception result and these recent
+observations, should the agent re-focus?" — captured as
+(input → expected decision) pairs labelled by a biologist. Regression
+suite. Cheap with biologist time, expensive to bootstrap, very valuable
+once you have a few hundred.
+
+### 5.5 Multi-agent A/B in production
+
+Two embryos in the same dish, one supervised by architecture A and one
+by B (both honouring the firmware fence). Compare biological outcomes.
+Slow (one timelapse per data point), but the **only thing that measures
+biological correctness end-to-end.**
+
+---
+
+## 6. Embryo Schema: Coarse vs Fine
+
+Foundational and quietly important. Each embryo carries:
+
+* `position_coarse` — set by bottom-camera detection or manual Map
+ placement. Always present.
+* `position_fine` — set later by SPIM-objective alignment (workflow not
+ yet built). Initially `{}`.
+* `stage_position` — a *derived property*: `fine if fine else coarse`.
+ Downstream motion / perception keeps reading this and stays agnostic
+ about which calibration stage we're in.
+
+This is the seed for a broader idea: **measurements have provenance and
+calibration state**. The same embryo at the same nominal XY can have
+different "true" positions depending on which sensor sighted it. Encode
+that explicitly so any downstream decision can ask *"how confident is
+this position?"* without needing to know the whole calibration history.
+
+When the operator drags an embryo on the Map, the PUT clears `fine` —
+overriding the sighting invalidates any SPIM-derived fine alignment
+derived from the old coarse. `OPERATOR_EDITED_EMBRYO` carries
+`fine_position_invalidated` so the candidate / future controller can
+schedule a re-alignment without inferring it.
+
+---
+
+## 7. The Map as Collaborative World Model
+
+The Devices > Map page is more than visualisation. It is the **first
+collaborative surface** between operator and orchestrator: both can read
+the embryo list; both can mutate it. The orchestrator subscribes; the
+operator clicks.
+
+Visual semantics matter:
+
+* Coarse-only embryo → outlined ring + number. *Provisional.*
+* SPIM-fine-calibrated → filled disc + number. *Committed.*
+
+Calibration state is then visible at a glance across the slide — the
+operator can scan and see "embryo 3 still needs alignment" without
+opening anything.
+
+The pick-up / drop interaction (Phase 5) deliberately rejects
+click-to-add: the Map is a schematic, not a satellite view. Adding a
+new sighting without a visual reference is guessing. New embryos go
+through the bottom-camera marking canvas. The Map is for **editing what
+already exists**.
+
+### Future arc
+
+* **Annotations beyond position**: operator marks "this is the control",
+ "this one is dead, skip", "I think this is in 2-cell stage". These
+ become first-class scientific observations through additional
+ `OPERATOR_*` events.
+* **Satellite tile**: render the live bottom-camera frame as an overlay
+ on the Map at the current stage XY, scaled by um_per_pixel. Inside
+ that tile, click-to-add becomes meaningful (you can see what you're
+ picking). Outside, the Map stays schematic.
+
+---
+
+## 8. Revolutionary Trajectories
+
+Some of these are reasonable extensions; some are genuinely new.
+
+### 8.1 Plans-as-goals, not scripts
+
+Operator specifies "characterise gut development for these four
+embryos." Orchestrator translates this into a continuously adapted
+imaging plan that changes based on what perception sees mid-run. The
+plan isn't a fixed script handed to Bluesky — it's a negotiation the
+orchestrator keeps in flight, with the world model as the substrate
+for adaptation.
+
+Requires: tier-1 + tier-2 world model, decent perception loop, a way
+to express goals as predicates over the world model.
+
+### 8.2 Compounding cross-session learning
+
+`agent/learnings/` already exists. Today it's barely used. With replay
++ shadow, an architecture that proposes priors ("embryos at 3-fold
+typically need slower piezo") becomes **A/B testable across sessions**.
+Improvement gets *measurable*, which is the unlock — most "smart
+microscopy" today is shallow because it has no measurement loop.
+
+The right framing: each session is a **trial**, the orchestrator is the
+**experimenter**, the world model is what carries learning between
+trials.
+
+### 8.3 Collaborative world model
+
+The Map (operator edits embryos) is the first instance. Extend
+everywhere:
+
+* Operator annotates morphology on the Map → orchestrator updates
+ hypothesis space.
+* Operator marks a focus failure → orchestrator marks the calibration
+ region as untrustworthy.
+* Operator confirms a perception → orchestrator increases confidence in
+ the perception predicate for similar inputs.
+
+The point is making the operator's tacit knowledge **first-class data**
+that the system can reason about, not just record.
+
+### 8.4 Reverse-mode microscopy
+
+"I want to know X — plan the imaging that answers X." The orchestrator
+translates scientific goals into imaging plans. This is the
+plans-as-goals idea taken to its conclusion: the operator describes
+intent in scientific terms, the orchestrator owns the imaging strategy.
+
+Tractable only once 8.1 and the goal language are built.
+
+### 8.5 Continuous shadow / always-on critic
+
+Run the production orchestrator + a shadow candidate continuously, and
+log all decision divergences. Over weeks, the divergence log becomes a
+**dataset of disagreements**. Each disagreement is either:
+
+* Production was right, candidate was wrong → candidate needs a fix.
+* Candidate was right, production was wrong → consider promotion or
+ investigate why production picked differently.
+* Both were defensible → annotate the case.
+
+Free with the eval substrate (Phase 6); the only addition is a
+divergence collator.
+
+---
+
+## 9. Concretely Built Today (`paradigm/closed-loop` branch)
+
+| # | Commit | What |
+| --- | --- | --- |
+| 1 | `3e410581` | Schema split: `position_coarse` / `position_fine` / derived `stage_position`. |
+| 2 | `617e54c9` | `ExperimentState.notify_embryos_changed()` observer → `EMBRYOS_UPDATE` broadcast. |
+| 3 | `144d9fc9` | Map render layer — lavender rings (coarse) / discs (fine) / numbers. |
+| 4 | `4fbb9edf` | `detect_embryos` flows through web Marking canvas; `auth.py` + `require_control`. |
+| 5 | `8f6553e1` | Map pick-up / drop / Delete to edit embryos in place (control-gated PUT/DELETE). |
+| 6 | `808fe813` | Side-fix: re-enable XY joystick at device-layer boot. |
+| 7 | `f7a13d69` | Side-fix: image-anchored crosshair + scroll-to-zoom in camera panel. |
+| 8 | `d69cc219` | `gently/eval/`: event capture / replay / shadow / decision log scaffolding. |
+| 9 | `75d7c9db` | Production decision capture wired through `ConversationManager.call_claude`. |
+| 10 | `0a97563e` | `OPERATOR_*` event vocabulary + `ReactiveCandidate` (first real shadow). |
+
+### Per-session disk shape now
+
+`D:\Gently3\sessions\{id}\`
+
+* `events.jsonl` — captured event bus, telemetry-filtered.
+* `decisions.jsonl` — every Claude turn (success + error).
+* `interaction_log.jsonl` — pre-existing chat-shaped interactions.
+* `timeline.jsonl` — pre-existing session timeline.
+* Plus everything from the legacy FileStore layout.
+
+### Eval CLI
+
+`python scripts/replay_session.py {session_id_prefix} [--histogram] [--candidate {name}] [--real-time] [--time-scale N]`
+
+---
+
+## 10. What is *Not* Done Yet
+
+These are the natural follow-ups; sketched as future-self breadcrumbs.
+
+### Near-term (days)
+
+* **Tier-1 world snapshot** as a system-prompt section the brain sees
+ on every wake. Build the snapshot from `agent.experiment` plus the
+ last cached `DEVICE_STATE_UPDATE`. ~30 lines of formatted prose, every
+ wake.
+* **Tier-2 events digest** — hand-written formatter that reads the
+ bus's recent meaningful events (or the captured jsonl tail) and
+ produces a one-paragraph "since last response" note.
+* **Snapshot ingest into the brain's prompt** — `_update_system_prompt`
+ already takes a `context_summary`; route tier-1 + tier-2 through it.
+
+### Medium-term (weeks)
+
+* **Wake-router** — the code-level scheduler from §3. Currently the
+ brain only wakes on user message. Add: event-driven wake (subscribe
+ to wake-worthy events), periodic-tick wake (heartbeat), debounce /
+ coalesce buffer.
+* **More operator events** — `OPERATOR_ANNOTATED_EMBRYO` ("this is the
+ control", "skip, looks dead"), `OPERATOR_STARTED_TIMELAPSE`,
+ `OPERATOR_INTERRUPTED_PLAN`, `OPERATOR_TOGGLED_CAMERA`. Whatever the
+ Map / web UI lets the operator do should publish a typed event.
+* **SPIM-fine alignment workflow** — populate `position_fine`. Tool +
+ per-embryo state transition. Triggers `EMBRYOS_UPDATE` and a new
+ `FINE_ALIGNMENT_COMPLETED` event the orchestrator can react to.
+* **Continuous-shadow harness** — extend `ShadowRunner` to run a
+ candidate alongside production in the live agent process (not just
+ during replay). Collect divergences into a per-session
+ `divergences.jsonl`.
+
+### Longer arc (months)
+
+* **A goal expression language** — predicates over the world model that
+ let the operator say "image until 4-fold" or "follow the cell
+ divisions in embryo 3 at high resolution." This is the substrate for
+ §8.1 (plans-as-goals).
+* **LLM-driven candidates** — once the rule-based `ReactiveCandidate`
+ proves the substrate, add Claude-driven candidates (Haiku for cheap,
+ Opus for thinking). Use the snapshot+digest as their input.
+* **Cross-session learning loop** — wire the `learnings/` store into
+ the world model as priors. Add a learning-write surface (a tool the
+ orchestrator can call when it notices a pattern). Use shadow A/B to
+ validate that learnings improve decisions.
+* **Goal-driven evaluation** — once goals exist, "did the experiment
+ achieve its goal" becomes a measurable end-to-end success rate. The
+ ultimate metric is this, not turn-level decision diffs.
+
+---
+
+## 11. Principles That Surface Throughout
+
+A few recurring design priors worth naming:
+
+1. **Distill, don't dump.** Structured summaries beat raw logs in
+ prompts. Hand-written formatters beat LLM summarisers for
+ structured data. LLMs for prose, code for structure.
+2. **Pull beats push when uncertain.** Default to tools the agent
+ queries on demand, not data shoved into every prompt. Push only
+ what's universally relevant (the world snapshot).
+3. **Same shape for production and shadow.** If production writes a
+ Decision with these fields, shadow candidates write Decisions with
+ the same fields. Diff is then trivial.
+4. **Events carry intent; state carries position.** `EMBRYOS_UPDATE`
+ is state (the embryo list now). `OPERATOR_EDITED_EMBRYO` is intent
+ (a human just did this). Both exist; they answer different
+ questions.
+5. **The brain doesn't move hardware.** All hardware action goes
+ through tools that go through the device layer that goes through
+ ophyd that goes through MMCore. Shadow candidates are constructively
+ prevented from acting. Layers are not negotiable.
+6. **No SaveCardSettings.** Firmware persistent state silently inherits
+ between sessions; if it ever gets out of sync with code it's a
+ debugging nightmare. Apply firmware config every boot, code wins.
+7. **Localhost is the diSPIM box. Remote is view-only by default.**
+ Auth surface stays tiny and explicit. Token upgrade is the seam,
+ not user accounts.
+
+---
+
+## 12. Open Questions (Worth Revisiting Later)
+
+* **Continuous vs episodic shadows.** Continuous always-on shadow
+ captures divergence over time but multiplies cost (multiple LLM
+ candidates running). Episodic shadow at decision moments is cheaper
+ but misses timing-sensitive cases. Hybrid?
+* **Is the conversation history the right substrate at all?** With
+ decision moments hours apart, prior chat may be more distracting
+ than useful. Maybe the brain shouldn't see chat history beyond N
+ hours; the world model + events digest are the durable memory and
+ chat is just for the active dialogue.
+* **How much should the operator know about the orchestrator's plan?**
+ Today the operator drives by asking. With autonomous mode, the
+ orchestrator runs experiments largely on its own. Should there be a
+ permanent "what is the orchestrator thinking right now" surface
+ visible on the Map? An always-on intent display?
+* **Failure semantics.** If a candidate would have made a different
+ decision than production, and production's decision led to a bad
+ outcome, the candidate "wins." How do we score? Define "bad outcome"
+ rigorously enough that it can be measured?
+
+These are not blockers. They are notes for the next iteration of this
+document, after a few weeks of running on the substrate built here.
diff --git a/docs/EVAL.md b/docs/EVAL.md
new file mode 100644
index 00000000..73f35b69
--- /dev/null
+++ b/docs/EVAL.md
@@ -0,0 +1,187 @@
+
+
+> **Status:** design + intended usage for the `gently/eval/` capture/replay substrate and the
+> proposed offline replay harness for testing agentic orchestrator patterns. Grounded in the
+> code as of the 0.22 epoch; the harness itself is a work-in-progress (see the incremental plan).
+
+# Testing agentic orchestrator patterns offline (replay harness)
+
+## Goal
+
+We want to iterate on the agent's design — its realtime reasoning and the wake-router that
+turns developmental events into autonomous turns — **without booking a live microscope run**.
+Concretely: take a recorded session, simulate the microscope conditions from its on-disk
+artifacts (captured events, recorded volumes, recorded perception traces), drive the *real*
+`WakeRouter -> run_wake_turn -> Claude` loop offline, and observe/diff what the agent decides.
+This lets us tune wake triggers, coalescing/throttling, prompt construction, and tool policy on
+a laptop, replayed at a controllable clock (e.g. 10x), instead of waiting hours for embryos to
+develop on a live rig.
+
+## What's already in place (reuse)
+
+A real, tested replay/eval substrate shipped in the 0.22 epoch (`gently/eval/`), plus production
+capture wiring. None of this is hypothetical — it's on disk and runnable today:
+
+- **`gently/eval/event_capture.py`** — `EventCapture` wildcard-subscribes the bus and appends every
+ `Event.to_dict()` to `{session_dir}/events.jsonl`. Auto-wired into **every** live session by
+ `gently/app/agent.py` `_init_event_capture()` (line ~506, called at agent init). Skips only
+ `_NO_HISTORY_TYPES` (`DEVICE_STATE_UPDATE`, `BOTTOM_CAMERA_FRAME`, `LOG_RECORD`); `DETECTOR_EVALUATED`
+ and lifecycle events are **not** skipped.
+- **`gently/eval/event_replay.py`** — `EventReplay(path).replay(target_bus, real_time=, time_scale=, on_event=)`
+ republishes each event via `target.publish_event(ev)`, **preserving the original `Event.timestamp`**
+ (not re-stamping `now()`). `real_time=True` sleeps `(ev.timestamp - prev)/time_scale` between events,
+ so cadence is reproducible. `event_types()` gives a pre-flight histogram.
+- **`gently/eval/shadow.py` + `candidates.py`** — `ShadowRunner` + `OrchestratorCandidate` host
+ sandboxed rule-based candidates (e.g. `ReactiveCandidate`) that may *only* write a `DecisionLog`.
+- **`gently/eval/decision_log.py`** — `Decision`/`DecisionLog` + `prompt_hash()` (sha256[:16] over
+ system prompt + messages) for apples-to-apples A/B diffing.
+- **`scripts/replay_session.py`** — working CLI: resolves a session by id-prefix via
+ `FileStore.list_sessions`, prints `--histogram`, or replays `events.jsonl` into a **fresh** `EventBus()`
+ with an optional `NoOpCandidate`.
+- **Recorded perception inputs/outputs** persist via `FileStore` (`gently/core/file_store.py`):
+ `embryos/{id}/volumes/t{NNNN}.tif` + `.meta.yaml`, `projections/t{NNNN}.jpg`,
+ `predictions.jsonl`, and `traces/t{NNNN}.json` (verbatim `predicted_stage`/`reasoning`/`raw_response`/`stability`).
+ Verified on disk: session `68e7dc33` has 9 embryos, 56 predictions on embryo_001, volume
+ `t0001.tif` shape `[50,512,2048]` uint16.
+- **`timeline.jsonl`** (durable, predates eval) carries 256 `detection/evaluated` records on `68e7dc33`
+ with exactly the fields `WakeRouter._is_wake_worthy` reads (`embryo_id`, `timepoint`,
+ `detector_name`, `stage`, `reasoning`) — a fallback event source for pre-eval-scaffold sessions.
+
+### The one central wiring gap
+
+The real agent subscribes its `WakeRouter` to the **global singleton** bus
+(`gently/app/agent.py:126` `self._event_bus = get_event_bus()`; WakeRouter built with that same bus).
+But `scripts/replay_session.py:124` replays into a **fresh** `EventBus()` that the agent never sees.
+**So today's replay reaches shadow candidates but never the real WakeRouter/agent.** Bridging this —
+either `set_event_bus(replay_bus)` before constructing the agent, or replaying into `get_event_bus()`
+directly — is the core seam to build.
+
+## Approaches, compared
+
+### (A) Event-stream replay into the agent's bus — *recommended first*
+Publish recorded `DETECTOR_EVALUATED` + critical events (`HATCHING_DETECTED`, `EMBRYO_TERMINATED`,
+`ERROR_OCCURRED`, …) onto the bus the agent's `WakeRouter` is subscribed to, on a controllable clock.
+
+- **Reuses:** `EventReplay`, `EventCapture` output, the entire real `WakeRouter` (`_is_wake_worthy`
+ filter at wake_router.py:129, coalesce `COALESCE_WINDOW=20s`, throttle `MIN_WAKE_INTERVAL=120s`,
+ `_flush -> agent.run_wake_turn`).
+- **Fidelity:** Exercises the *real* wake path end-to-end: filtering, transition gate, coalescing,
+ throttling, prompt build, and a real Claude turn (`run_wake_turn -> handle_message_stream`, gated on
+ `agent.mode=='run'`). Highest leverage for the least new code.
+- **Effort:** Medium. Needs (1) the bus bridge above; (2) a running asyncio loop so the async dispatch
+ + `loop.call_later` coalesce timers fire (`EventReplay.replay` is a blocking `time.sleep` loop — run it
+ in a thread or port it to `await asyncio.sleep`, and call `bus.set_event_loop(loop)`); (3) a stub
+ client so any tools the woken agent calls don't hit hardware (autonomous mode already refuses
+ irreversible tools via `_autonomous_active`).
+- **Can't catch:** Anything depending on *fresh* perception of new pixels — the wake note embeds
+ `build_perception_snapshot(agent.perceiver, ...)`, which reads **live** Perceiver state, so this
+ approach needs (B) to make that snapshot reflect the replayed timepoint rather than empty state.
+- **Blocker today:** No recorded session yet contains `DETECTOR_EVALUATED` (verified: all 20 captured
+ `events.jsonl` hold only `STATUS_CHANGED`/`EMBRYO_DETECTED`/`EMBRYOS_UPDATE`). Either capture one fresh
+ perception-driven session, or synthesize `DETECTOR_EVALUATED` events from `traces/`+`timeline.jsonl`.
+
+### (B) Perceiver stub — feed recorded traces
+Replace `agent.perceiver`/`orchestrator.perceiver` with a duck-typed stub whose `__call__(...)` returns
+`.stage`/`.reasoning` from `traces/t{NNNN}.json`, and whose `get_session(embryo_id)` returns an object
+with `.stability`/`.summary()` matching what `build_perception_snapshot` reads
+(`current_stage`/`stability`/`temporal`/`stage_sequence`).
+
+- **Reuses:** All downstream code in `_run_perception` (DETECTOR_EVALUATED emit, trace write,
+ `store_prediction`, `_check_interval_rules`) is pure local code; the Perceiver is the *only* external
+ VLM dependency. `perceiver` is already an optional ctor arg (timelapse.py:71).
+- **Fidelity:** Reproduces recorded perception verbatim — no VLM spend, deterministic. Makes (A)'s wake
+ snapshot reflect the replayed timepoint.
+- **Effort:** Low-medium (one stub class).
+- **Can't catch:** Perception on *new* conditions — it only echoes what the recorded run already saw.
+ Also the stub interface was inferred from call sites (`templates.py` `build_perception_snapshot`,
+ `timelapse.py` `_run_perception`), not from `gently_perception` source — **verify against the
+ installed package** before relying on it.
+
+### (C) Full offline re-feed through the timelapse loop
+Inject a fake `microscope_client` whose `acquire_volume(...)` returns
+`{'success': True, 'volume': diSPIM Room Light
+SwitchBot Bot · __ADDRESS__
+
+ —
+
+
+
+
+
+
+
+
+
+
+ fast
+
+ slow
+ 0.7s
+
+
+
+
+
+
+
+
+
diff --git a/docs/superpowers/notes/2026-06-28-lightsheet-fps-measurement.md b/docs/superpowers/notes/2026-06-28-lightsheet-fps-measurement.md
new file mode 100644
index 00000000..d1a4abd9
--- /dev/null
+++ b/docs/superpowers/notes/2026-06-28-lightsheet-fps-measurement.md
@@ -0,0 +1,57 @@
+# Lightsheet live-view FPS measurement + transport decision (B1 Task 7)
+
+Status: **deferred to the rig** — the numbers below must be filled in on the microscope
+(the streamer needs the real `pymmcore` core, SPIM camera, and rpyc transport; it cannot run
+on the Linux dev box). This file is the measurement protocol + the decision gate.
+
+## What to measure
+
+With the Manual view open and lightsheet live running, record three rates:
+
+| Metric | Where to read it |
+|---|---|
+| **device grab rate** (frames peeked/encoded /s) | device-layer log / instrument `_lightsheet_streamer` |
+| **delivered rate** (frames broadcast /s) | device-layer `_broadcast_lightsheet` |
+| **browser paint rate** | the Manual-view FPS readout (`computeLightsheetFps`) |
+
+Record at two resolution/quality settings:
+- default **512 px / JPEG q70** (`_ls_target_max_dim=512`, `_ls_jpeg_quality=70`)
+- reduced **384 px / q60**
+
+Note the exposure used (the peek floor is `max(exposure, 1/30 s)`).
+
+## Target
+
+**≥ ~15 fps usable for focus** (stretch 25–30), end-to-end latency < ~150 ms.
+
+## Diagnosis rule (the gate)
+
+- **device grab < target** → limiter is exposure / readout / rpyc, **not** transport. Tune
+ exposure, the 512 px size, and JPEG quality. A binary transport path will NOT help — stop here.
+- **device grab ≥ target but browser paint < target** → transport is the bottleneck → build the
+ **binary WebSocket path** (below).
+
+## Conditional escalation — binary WebSocket path
+
+Only if the diagnosis points to transport. The current path is base64-JPEG-in-JSON over SSE →
+EventBus → `ConnectionManager.broadcast` (`json.dumps` + `send_text`) — `connection_manager.py`
+has **no `send_bytes` path** (confirmed). Escalation, on the **agent→browser hop** (where cost
+multiplies per client):
+
+- push raw JPEG bytes via `websocket.send_bytes(prefix + jpeg)` (a 1-byte type tag identifies a
+ lightsheet frame), bypassing **base64 (+33%)**, the **per-client `json.dumps`**, and the
+ **EventBus fan-out**;
+- browser `onmessage` (binary) → `createImageBitmap(new Blob([buf]))` → `ctx.drawImage`;
+- the device→agent SSE stays as-is (single consumer = the monitor, so its base64 cost is paid
+ once, not per browser).
+
+Re-measure after building; record the before/after numbers here.
+
+## Results (fill in on the rig)
+
+| setting | device grab fps | delivered fps | browser paint fps | exposure | notes |
+|---|---|---|---|---|---|
+| 512px/q70 | _TBD_ | _TBD_ | _TBD_ | _TBD_ | |
+| 384px/q60 | _TBD_ | _TBD_ | _TBD_ | _TBD_ | |
+
+Decision: _TBD (transport bottleneck? build binary path Y/N)_
diff --git a/docs/superpowers/plans/2026-06-16-notebook-foundation.md b/docs/superpowers/plans/2026-06-16-notebook-foundation.md
new file mode 100644
index 00000000..4cb777e9
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-16-notebook-foundation.md
@@ -0,0 +1,661 @@
+# Notebook Foundation Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Build the unit-testable foundation of the shared lab notebook — the unified `Note` model and a file-backed `NotebookStore` (write / read / scope-query / rebuildable reverse-indexes / link & supersede) — with no UI, API, or agent wiring.
+
+**Architecture:** A new self-contained module `gently/harness/memory/notebook.py`. One `Note` dataclass (three kinds: observation/finding/question) with author, status, confidence, scope facets (strains/embryos/sessions/threads), typed links, basis, and artifact pointers — orthogonal fields, not subtypes. `NotebookStore` persists one YAML per note under `notebook/notes/{id}_{slug}.yaml` (atomic write, mirroring `FileContextStore`), maintains rebuildable reverse-indexes by strain/embryo/thread, and answers scope+kind+status queries. This is Increment 1's keystone from the design doc (`docs/superpowers/specs/2026-06-16-shared-lab-notebook-design.md`).
+
+**Tech Stack:** Python 3.11, dataclasses, `str`-Enums, PyYAML, pytest (fixtures in `tests/conftest.py`, flat `tests/` layout).
+
+**Follow-on plans (NOT in scope here):** producer wiring (`apply_updates` → notebook), `/api/notebook` + Notebook tab (UI), retrieval/embeddings + brainstorm. Each ships on top of this foundation.
+
+---
+
+### Task 1: The `Note` model
+
+**Files:**
+- Create: `gently/harness/memory/notebook.py`
+- Test: `tests/test_notebook_store.py`
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_notebook_store.py
+"""Tests for the shared lab notebook: Note model + NotebookStore."""
+
+from datetime import datetime
+
+from gently.harness.memory.model import Confidence
+from gently.harness.memory.notebook import (
+ Author,
+ Note,
+ NoteKind,
+ NoteStatus,
+ note_from_dict,
+ note_to_dict,
+)
+
+
+class TestNoteModel:
+ def test_round_trip_minimal(self):
+ n = Note(id="abc123", kind=NoteKind.OBSERVATION, body="dim rings at 10 ms")
+ d = note_to_dict(n)
+ assert d["kind"] == "observation"
+ assert d["author"] == "agent" # default
+ assert d["status"] == "confirmed" # default
+ back = note_from_dict(d)
+ assert back == n
+
+ def test_round_trip_full(self):
+ n = Note(
+ id="def456",
+ kind=NoteKind.FINDING,
+ body="temperature shifts timing ~12 min/degC",
+ author=Author.AGENT,
+ title="Temp shifts timing",
+ status=NoteStatus.PROPOSED,
+ confidence=Confidence.MEDIUM,
+ strains=["N2", "OH904"],
+ embryos=["emb_0007"],
+ sessions=["20260615_1432_x"],
+ threads=["q_division_temp"],
+ basis=["obs_1", "obs_2"],
+ links=[{"rel": "supports", "to": "q_division_temp"}],
+ artifacts=[{"kind": "projection", "session": "s1", "embryo": "emb_0007", "t": 42}],
+ created_at=datetime(2026, 6, 16, 11, 0, 0),
+ updated_at=datetime(2026, 6, 16, 11, 0, 0),
+ )
+ back = note_from_dict(note_to_dict(n))
+ assert back == n
+ assert note_to_dict(n)["confidence"] == "medium"
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNoteModel -v`
+Expected: FAIL — `ModuleNotFoundError: No module named 'gently.harness.memory.notebook'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+```python
+# gently/harness/memory/notebook.py
+"""
+The shared lab notebook — unified memory entry (Note) and file-backed store.
+
+One Note kind taxonomy (observation / finding / question); everything else
+(author, status, confidence, scope, links) is an orthogonal field. See
+docs/superpowers/specs/2026-06-16-shared-lab-notebook-design.md.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from datetime import datetime
+from enum import Enum
+from typing import Any
+
+from .model import Confidence
+
+
+class NoteKind(str, Enum):
+ OBSERVATION = "observation" # immutable record of what was seen/done/read/noted
+ FINDING = "finding" # revisable, supersedable believed claim
+ QUESTION = "question" # open inquiry; large ones are the thread spine
+
+
+class Author(str, Enum):
+ HUMAN = "human"
+ AGENT = "agent"
+ PERCEPTION = "perception"
+
+
+class NoteStatus(str, Enum):
+ OPEN = "open" # questions not yet answered
+ PROPOSED = "proposed" # agent-drafted finding awaiting human confirm
+ CONFIRMED = "confirmed" # accepted observation/finding (default)
+ ANSWERED = "answered" # question resolved
+ SUPERSEDED = "superseded" # replaced by a newer note
+
+
+@dataclass
+class Note:
+ id: str
+ kind: NoteKind
+ body: str
+ author: Author = Author.AGENT
+ title: str | None = None
+ status: NoteStatus = NoteStatus.CONFIRMED
+ confidence: Confidence | None = None
+ strains: list[str] = field(default_factory=list)
+ embryos: list[str] = field(default_factory=list)
+ sessions: list[str] = field(default_factory=list)
+ threads: list[str] = field(default_factory=list)
+ basis: list[str] = field(default_factory=list) # note ids this rests on
+ links: list[dict] = field(default_factory=list) # [{"rel": ..., "to": ...}]
+ artifacts: list[dict] = field(default_factory=list) # FileStore pointers
+ superseded_by: str | None = None
+ created_at: datetime = field(default_factory=datetime.now)
+ updated_at: datetime = field(default_factory=datetime.now)
+
+
+def note_to_dict(n: Note) -> dict[str, Any]:
+ return {
+ "id": n.id,
+ "kind": n.kind.value,
+ "body": n.body,
+ "author": n.author.value,
+ "title": n.title,
+ "status": n.status.value,
+ "confidence": n.confidence.value if n.confidence else None,
+ "strains": list(n.strains),
+ "embryos": list(n.embryos),
+ "sessions": list(n.sessions),
+ "threads": list(n.threads),
+ "basis": list(n.basis),
+ "links": list(n.links),
+ "artifacts": list(n.artifacts),
+ "superseded_by": n.superseded_by,
+ "created_at": n.created_at.isoformat(),
+ "updated_at": n.updated_at.isoformat(),
+ }
+
+
+def note_from_dict(d: dict[str, Any]) -> Note:
+ conf = d.get("confidence")
+ return Note(
+ id=d["id"],
+ kind=NoteKind(d["kind"]),
+ body=d.get("body", ""),
+ author=Author(d.get("author", "agent")),
+ title=d.get("title"),
+ status=NoteStatus(d.get("status", "confirmed")),
+ confidence=Confidence(conf) if conf else None,
+ strains=list(d.get("strains") or []),
+ embryos=list(d.get("embryos") or []),
+ sessions=list(d.get("sessions") or []),
+ threads=list(d.get("threads") or []),
+ basis=list(d.get("basis") or []),
+ links=list(d.get("links") or []),
+ artifacts=list(d.get("artifacts") or []),
+ superseded_by=d.get("superseded_by"),
+ created_at=datetime.fromisoformat(d["created_at"]),
+ updated_at=datetime.fromisoformat(d["updated_at"]),
+ )
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNoteModel -v`
+Expected: PASS (2 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): unified Note model + dict serialization"
+```
+
+---
+
+### Task 2: `NotebookStore` — write & read a note
+
+**Files:**
+- Modify: `gently/harness/memory/notebook.py` (append `NotebookStore`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+from gently.harness.memory.notebook import NotebookStore
+
+
+class TestNotebookStoreReadWrite:
+ def test_write_assigns_id_and_persists(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ n = Note(id="", kind=NoteKind.OBSERVATION, body="bean stage at t40")
+ note_id = store.write_note(n)
+ assert note_id # non-empty id assigned
+ files = list((tmp_path / "notebook" / "notes").glob("*.yaml"))
+ assert len(files) == 1
+ assert files[0].name.startswith(note_id + "_")
+
+ def test_get_note_round_trip(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ n = Note(id="", kind=NoteKind.FINDING, body="x", strains=["N2"], threads=["t1"])
+ note_id = store.write_note(n)
+ got = store.get_note(note_id)
+ assert got is not None
+ assert got.id == note_id
+ assert got.kind == NoteKind.FINDING
+ assert got.strains == ["N2"]
+
+ def test_get_missing_returns_none(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ assert store.get_note("nope") is None
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookStoreReadWrite -v`
+Expected: FAIL — `ImportError: cannot import name 'NotebookStore'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+```python
+# append to gently/harness/memory/notebook.py
+import copy
+import os
+import re
+import uuid
+from pathlib import Path
+
+import yaml
+
+
+class NotebookStore:
+ """File-backed store for notebook Notes. One YAML per note under notes/;
+ flat pool, rebuildable reverse-indexes (added in Task 3)."""
+
+ def __init__(self, notebook_dir: Path):
+ self.root = Path(notebook_dir)
+ self.notes_dir = self.root / "notes"
+ self.index_dir = self.root / "index"
+ self.notes_dir.mkdir(parents=True, exist_ok=True)
+ self.index_dir.mkdir(parents=True, exist_ok=True)
+
+ # ---- helpers (mirror FileContextStore conventions) ----
+ @staticmethod
+ def _gen_id() -> str:
+ return str(uuid.uuid4())[:8]
+
+ @staticmethod
+ def _slugify(text: str) -> str:
+ slug = re.sub(r"[^a-z0-9]+", "-", (text or "").lower()).strip("-")
+ return slug[:30]
+
+ def _write_yaml(self, path: Path, data: dict) -> None:
+ path.parent.mkdir(parents=True, exist_ok=True)
+ tmp = path.with_suffix(".tmp")
+ with open(tmp, "w", encoding="utf-8") as fh:
+ yaml.safe_dump(data, fh, default_flow_style=False, allow_unicode=True, sort_keys=False)
+ os.replace(str(tmp), str(path))
+
+ def _read_yaml(self, path: Path) -> dict | None:
+ try:
+ with open(path, encoding="utf-8") as fh:
+ return yaml.safe_load(fh)
+ except OSError:
+ return None
+
+ def _note_path(self, note_id: str) -> Path | None:
+ return next(self.notes_dir.glob(f"{note_id}_*.yaml"), None)
+
+ # ---- read/write ----
+ def write_note(self, note: Note) -> str:
+ if not note.id:
+ note.id = self._gen_id()
+ note.updated_at = datetime.now()
+ slug = self._slugify(note.title or note.body or note.kind.value)
+ # remove any stale file for this id (slug may have changed)
+ old = self._note_path(note.id)
+ if old is not None:
+ old.unlink()
+ self._write_yaml(self.notes_dir / f"{note.id}_{slug}.yaml", note_to_dict(note))
+ return note.id
+
+ def get_note(self, note_id: str) -> Note | None:
+ path = self._note_path(note_id)
+ if path is None:
+ return None
+ data = self._read_yaml(path)
+ return note_from_dict(data) if data else None
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookStoreReadWrite -v`
+Expected: PASS (3 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): NotebookStore write_note/get_note with atomic YAML"
+```
+
+---
+
+### Task 3: Reverse-indexes (by strain / embryo / thread) + rebuild
+
+**Files:**
+- Modify: `gently/harness/memory/notebook.py` (`NotebookStore`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+class TestNotebookIndex:
+ def test_index_updated_on_write(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ a = store.write_note(Note(id="", kind=NoteKind.OBSERVATION, body="a", strains=["N2"]))
+ b = store.write_note(
+ Note(id="", kind=NoteKind.OBSERVATION, body="b", strains=["N2", "OH904"])
+ )
+ assert set(store.ids_for_strain("N2")) == {a, b}
+ assert store.ids_for_strain("OH904") == [b]
+ assert store.ids_for_strain("missing") == []
+
+ def test_index_by_embryo_and_thread(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ a = store.write_note(
+ Note(id="", kind=NoteKind.FINDING, body="a", embryos=["e1"], threads=["t1"])
+ )
+ assert store.ids_for_embryo("e1") == [a]
+ assert store.ids_for_thread("t1") == [a]
+
+ def test_rebuild_index_from_disk(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ a = store.write_note(Note(id="", kind=NoteKind.OBSERVATION, body="a", strains=["N2"]))
+ # a fresh store over the same dir must rebuild the index by scanning notes/
+ store2 = NotebookStore(tmp_path / "notebook")
+ assert store2.ids_for_strain("N2") == [a]
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookIndex -v`
+Expected: FAIL — `AttributeError: 'NotebookStore' object has no attribute 'ids_for_strain'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+Modify `NotebookStore.__init__` to add index state + rebuild, extend `write_note` to update the index, and add the index methods. Replace the existing `__init__` and `write_note` with these versions and add the new methods:
+
+```python
+# --- replace __init__ ---
+def __init__(self, notebook_dir: Path):
+ self.root = Path(notebook_dir)
+ self.notes_dir = self.root / "notes"
+ self.index_dir = self.root / "index"
+ self.notes_dir.mkdir(parents=True, exist_ok=True)
+ self.index_dir.mkdir(parents=True, exist_ok=True)
+ # reverse indexes: facet -> {value: [note_id, ...]}
+ self._index: dict[str, dict[str, list[str]]] = {"strain": {}, "embryo": {}, "thread": {}}
+ self.rebuild_index()
+
+
+# --- add: facet extraction + index maintenance ---
+_FACETS = {"strain": "strains", "embryo": "embryos", "thread": "threads"}
+
+
+def _index_note(self, note: Note) -> None:
+ for facet, attr in self._FACETS.items():
+ for value in getattr(note, attr):
+ bucket = self._index[facet].setdefault(value, [])
+ if note.id not in bucket:
+ bucket.append(note.id)
+
+
+def rebuild_index(self) -> None:
+ """Rebuild reverse-indexes by scanning notes/ (the notes are authoritative;
+ indexes are disposable caches)."""
+ self._index = {"strain": {}, "embryo": {}, "thread": {}}
+ for f in sorted(self.notes_dir.glob("*.yaml")):
+ data = self._read_yaml(f)
+ if data:
+ self._index_note(note_from_dict(data))
+
+
+def ids_for_strain(self, strain: str) -> list[str]:
+ return list(self._index["strain"].get(strain, []))
+
+
+def ids_for_embryo(self, embryo: str) -> list[str]:
+ return list(self._index["embryo"].get(embryo, []))
+
+
+def ids_for_thread(self, thread: str) -> list[str]:
+ return list(self._index["thread"].get(thread, []))
+```
+
+Then add an index-update at the end of `write_note` (just before `return note.id`):
+
+```python
+ self._index_note(note)
+ return note.id
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookIndex -v`
+Expected: PASS (3 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): rebuildable reverse-indexes by strain/embryo/thread"
+```
+
+---
+
+### Task 4: `query_notes` — filter by kind / author / status / scope
+
+**Files:**
+- Modify: `gently/harness/memory/notebook.py` (`NotebookStore`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+class TestNotebookQuery:
+ def _seed(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ store.write_note(Note(id="o1", kind=NoteKind.OBSERVATION, body="o", strains=["N2"]))
+ store.write_note(
+ Note(
+ id="f1",
+ kind=NoteKind.FINDING,
+ body="f",
+ status=NoteStatus.PROPOSED,
+ strains=["N2"],
+ threads=["t1"],
+ )
+ )
+ store.write_note(
+ Note(id="q1", kind=NoteKind.QUESTION, body="q", status=NoteStatus.OPEN, threads=["t1"])
+ )
+ return store
+
+ def test_query_by_kind(self, tmp_path):
+ store = self._seed(tmp_path)
+ ids = {n.id for n in store.query_notes(kind=NoteKind.FINDING)}
+ assert ids == {"f1"}
+
+ def test_query_by_thread_scope(self, tmp_path):
+ store = self._seed(tmp_path)
+ ids = {n.id for n in store.query_notes(thread="t1")}
+ assert ids == {"f1", "q1"}
+
+ def test_query_by_thread_and_kind(self, tmp_path):
+ store = self._seed(tmp_path)
+ ids = {n.id for n in store.query_notes(thread="t1", kind=NoteKind.QUESTION)}
+ assert ids == {"q1"}
+
+ def test_query_by_status(self, tmp_path):
+ store = self._seed(tmp_path)
+ ids = {n.id for n in store.query_notes(status=NoteStatus.OPEN)}
+ assert ids == {"q1"}
+
+ def test_query_all_sorted_newest_first(self, tmp_path):
+ store = self._seed(tmp_path)
+ notes = store.query_notes()
+ assert len(notes) == 3
+ ts = [n.created_at for n in notes]
+ assert ts == sorted(ts, reverse=True)
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookQuery -v`
+Expected: FAIL — `AttributeError: 'NotebookStore' object has no attribute 'query_notes'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+```python
+# add to NotebookStore
+ def query_notes(
+ self,
+ *,
+ kind: NoteKind | None = None,
+ author: Author | None = None,
+ status: NoteStatus | None = None,
+ strain: str | None = None,
+ embryo: str | None = None,
+ thread: str | None = None,
+ ) -> list[Note]:
+ """Structural query: narrow by scope via the indexes, then filter by
+ kind/author/status. Returned newest-first. (No semantic ranking here —
+ that's a later increment.)"""
+ # 1. candidate ids — intersect any scope facets given, else all notes
+ scope_sets: list[set[str]] = []
+ if strain is not None:
+ scope_sets.append(set(self.ids_for_strain(strain)))
+ if embryo is not None:
+ scope_sets.append(set(self.ids_for_embryo(embryo)))
+ if thread is not None:
+ scope_sets.append(set(self.ids_for_thread(thread)))
+ if scope_sets:
+ candidate_ids: set[str] | None = set.intersection(*scope_sets)
+ else:
+ candidate_ids = None # means "all"
+
+ # 2. load + filter
+ results: list[Note] = []
+ if candidate_ids is not None:
+ notes = [n for n in (self.get_note(i) for i in candidate_ids) if n]
+ else:
+ notes = [
+ note_from_dict(d)
+ for d in (self._read_yaml(f) for f in self.notes_dir.glob("*.yaml"))
+ if d
+ ]
+ for n in notes:
+ if kind is not None and n.kind != kind:
+ continue
+ if author is not None and n.author != author:
+ continue
+ if status is not None and n.status != status:
+ continue
+ results.append(n)
+ results.sort(key=lambda n: n.created_at, reverse=True)
+ return results
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookQuery -v`
+Expected: PASS (5 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): query_notes by kind/author/status/scope"
+```
+
+---
+
+### Task 5: `link_notes` and `supersede_note`
+
+**Files:**
+- Modify: `gently/harness/memory/notebook.py` (`NotebookStore`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+class TestNotebookLinkSupersede:
+ def test_link_notes_adds_typed_edge(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ a = store.write_note(Note(id="", kind=NoteKind.FINDING, body="a"))
+ b = store.write_note(Note(id="", kind=NoteKind.QUESTION, body="b"))
+ store.link_notes(a, "supports", b)
+ got = store.get_note(a)
+ assert {"rel": "supports", "to": b} in got.links
+
+ def test_supersede_marks_old_and_points_new(self, tmp_path):
+ store = NotebookStore(tmp_path / "notebook")
+ old = store.write_note(Note(id="", kind=NoteKind.FINDING, body="old claim"))
+ new = store.write_note(Note(id="", kind=NoteKind.FINDING, body="better claim"))
+ store.supersede_note(old, new)
+ old_n = store.get_note(old)
+ new_n = store.get_note(new)
+ assert old_n.status == NoteStatus.SUPERSEDED
+ assert old_n.superseded_by == new
+ assert {"rel": "refines", "to": old} in new_n.links
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestNotebookLinkSupersede -v`
+Expected: FAIL — `AttributeError: 'NotebookStore' object has no attribute 'link_notes'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+```python
+# add to NotebookStore
+ def link_notes(self, from_id: str, rel: str, to_id: str) -> None:
+ """Add a typed edge from one note to another (append-only)."""
+ note = self.get_note(from_id)
+ if note is None:
+ raise KeyError(from_id)
+ edge = {"rel": rel, "to": to_id}
+ if edge not in note.links:
+ note.links.append(edge)
+ self.write_note(note)
+
+ def supersede_note(self, old_id: str, new_id: str) -> None:
+ """Mark old as superseded (kept, never deleted) and link the new note
+ back to it as a refinement — the chain is the intellectual history."""
+ old = self.get_note(old_id)
+ if old is None:
+ raise KeyError(old_id)
+ old.status = NoteStatus.SUPERSEDED
+ old.superseded_by = new_id
+ self.write_note(old)
+ self.link_notes(new_id, "refines", old_id)
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py -v`
+Expected: PASS (all tests across all classes pass)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): link_notes + supersede_note (append-only history)"
+```
+
+---
+
+## Self-Review
+
+**Spec coverage (against the design doc §2 data model):**
+- Three kinds (Observation/Finding/Question) → Task 1 `NoteKind`. ✓
+- Orthogonal fields (author/status/confidence/scope/links/artifacts) → Task 1 `Note`. ✓
+- Flat note pool + rebuildable reverse-indexes (strain/embryo/thread) → Tasks 2-3. ✓
+- "By question + by strain + links coexist over flat YAML, no DB" → Tasks 3-4 (indexes + scope-intersect query). ✓
+- Append-only / supersede-never-overwrite → Task 5 `supersede_note`. ✓
+- Typed links graph → Tasks 1 (`links`) + 5 (`link_notes`). ✓
+- *Deferred to follow-on plans (correctly out of scope):* inquiry-thread object, working-memory split, producer wiring, API/tab, embeddings/retrieval, consolidation. Noted in header.
+
+**Placeholder scan:** No TBD/TODO; every code step shows complete code; commands have expected output. ✓
+
+**Type consistency:** `Note`, `NoteKind`, `Author`, `NoteStatus`, `note_to_dict`/`note_from_dict`, and `NotebookStore.{write_note,get_note,rebuild_index,ids_for_strain,ids_for_embryo,ids_for_thread,query_notes,link_notes,supersede_note}` are named identically across all tasks and tests. `Confidence` is imported from `.model` (confirmed to exist). ✓
diff --git a/docs/superpowers/plans/2026-06-16-notebook-live-edge.md b/docs/superpowers/plans/2026-06-16-notebook-live-edge.md
new file mode 100644
index 00000000..9265d769
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-16-notebook-live-edge.md
@@ -0,0 +1,188 @@
+# Notebook Live Edge Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: superpowers:executing-plans. Steps use checkbox (`- [ ]`) syntax.
+
+**Goal:** Make the Home "Agent's view" panel surface recent notebook activity — the ambient "live edge" of the notebook (design §3, two-faced presentation), complementing the Notebook tab (the reading room).
+
+**Architecture:** Add an optional `limit` to the notes read API (TDD). Extend `context-surface.js` to also fetch recent notes and render a "From the notebook" section whose rows click through to the Notebook tab. Reuse the existing `cx-dot` colors (amber/blue/green) for kinds — no new CSS.
+
+**Tech Stack:** FastAPI, pytest + TestClient (venv), vanilla JS.
+
+**Out of scope:** retrieval/"Ask the notebook" (next increment); proactive surfacing.
+
+---
+
+### Task 1: `limit` param on `GET /api/notebook/notes`
+
+**Files:**
+- Modify: `gently/ui/web/routes/notebook.py`
+- Test: `tests/test_notebook_api.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_api.py
+class TestLimit:
+ def test_limit_returns_newest(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes?limit=1").json()
+ assert len(data["notes"]) == 1 # newest-first, capped
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_api.py::TestLimit -v`
+Expected: FAIL — returns 2 notes, not 1.
+
+- [ ] **Step 3: Write minimal implementation**
+
+In `gently/ui/web/routes/notebook.py`, add a `limit` param to `list_notes` and slice. Replace the `list_notes` signature and the final return:
+
+```python
+ @router.get("/api/notebook/notes")
+ async def list_notes(
+ kind: str | None = None,
+ author: str | None = None,
+ status: str | None = None,
+ strain: str | None = None,
+ embryo: str | None = None,
+ thread: str | None = None,
+ limit: int | None = None,
+ ):
+ nb = _nb()
+ if nb is None:
+ return {"available": False, "notes": []}
+ notes = nb.query_notes(
+ kind=_coerce(NoteKind, kind),
+ author=_coerce(Author, author),
+ status=_coerce(NoteStatus, status),
+ strain=strain,
+ embryo=embryo,
+ thread=thread,
+ )
+ if limit is not None and limit >= 0:
+ notes = notes[:limit]
+ return {"available": True, "notes": [note_to_dict(n) for n in notes]}
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_api.py -q`
+Expected: all pass
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/routes/notebook.py tests/test_notebook_api.py
+git commit -m "feat(notebook): limit param on GET /api/notebook/notes"
+```
+
+---
+
+### Task 2: "From the notebook" section in the Agent's-view panel
+
+**Files:**
+- Modify: `gently/ui/web/static/js/context-surface.js`
+
+Verification is browser-based (chrome-devtools), not pytest.
+
+- [ ] **Step 1: Extend `fetchAndRender` to also pull recent notes**
+
+Replace `fetchAndRender` with a version that fetches both endpoints and passes notes to `render`:
+
+```javascript
+ async function fetchAndRender() {
+ if (!el || loading) return;
+ loading = true;
+ try {
+ const [ctx, nb] = await Promise.all([
+ fetch('/api/context').then(r => r.json()).catch(() => ({})),
+ fetch('/api/notebook/notes?limit=5').then(r => r.json()).catch(() => ({})),
+ ]);
+ render(ctx || {}, (nb && nb.notes) || []);
+ } catch (e) { /* keep last render */ }
+ finally { loading = false; }
+ }
+```
+
+- [ ] **Step 2: Render the notebook section**
+
+Replace `render(data)` with `render(data, notes)`. Add the notebook section and include notes in the empty-state check. Replace the whole `render` function body:
+
+```javascript
+ function render(data, notes) {
+ if (!el) return;
+ notes = notes || [];
+ const hc = hasControl();
+ const questions = data.questions || [], watchpoints = data.watchpoints || [], expectations = data.expectations || [];
+ el.classList.remove('hidden');
+ if (!questions.length && !watchpoints.length && !expectations.length && !notes.length) {
+ el.innerHTML = 'Gently
+ What do you need today?
+ +
+
+
+
+
+
+
+
+
+ Microscope hardware
+ Start the device layer & connect to the rig · :60610
+
+
+
+
+
+
+
+
+
+
+ AI agent
+ Chat, perception & planning — uses your API key
+ Advanced options · remembers your choice
+ Agent’s view
' +
+ 'Nothing yet — the agent’s notes, expectations, and open questions appear here as it works.
';
+ return;
+ }
+
+ const qHtml = questions.map(it => `
+
+
+ ${esc(it.content)}
+ ${hc ? '' : ''}
+ ${hc ? '' : ''}
+
`).join('');
+ const wHtml = watchpoints.map(it => `
+
+
+ ${esc(it.target)}${it.condition ? ' — ' + esc(it.condition) : ''}
+ ${hc ? '' : ''}
+
`).join('');
+ const eHtml = expectations.map(it => `
+
+
+ ${esc(it.target)}${it.prediction ? ': ' + esc(it.prediction) : ''}
+ ${hc ? '' : ''}
+
`).join('');
+ // kind → existing cx-dot color: observation=blue, finding=green, question=amber
+ const dotFor = (k) => k === 'finding' ? 'cx-e' : (k === 'question' ? 'cx-q' : 'cx-w');
+ const nHtml = notes.map(n => `
+
+
+ ${esc(n.title || n.body)}
+
`).join('');
+
+ el.innerHTML = 'Agent’s view
' +
+ section('Open questions', qHtml) + section('Watching', wHtml) +
+ section('Expectations', eHtml) + section('From the notebook', nHtml);
+ wire();
+ }
+```
+
+- [ ] **Step 3: Make notebook rows click through to the Notebook tab**
+
+In `wire()`, after the existing `.cx-item` loop, add a handler for note rows (append inside `wire`, before its closing brace):
+
+```javascript
+ el.querySelectorAll('.cx-note').forEach(row => {
+ row.style.cursor = 'pointer';
+ row.addEventListener('click', () => {
+ if (typeof switchTab === 'function') switchTab('notebook');
+ });
+ });
+```
+
+- [ ] **Step 4: Verify in the browser**
+
+Restart the server, open `http://localhost:8080`, confirm the Home "Agent's view" panel shows a "From the notebook" section with recent notes, and clicking a row switches to the Notebook tab. Use chrome-devtools (navigate, evaluate_script to click, take_screenshot, list_console_messages → zero errors).
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/static/js/context-surface.js
+git commit -m "feat(notebook): Agent's-view live edge — recent notes section -> Notebook tab"
+```
+
+---
+
+## Self-Review
+**Spec coverage:** design §3 two-faced presentation — the ambient live edge now surfaces recent notebook notes on Home, clicking through to the tab. ✓ Reuses `/api/notebook/notes` (+ new `limit`) and existing `cx-dot` colors. ✓
+**Placeholder scan:** none. ✓
+**Type consistency:** `render(data, notes)`, `dotFor`, `limit` param, `switchTab('notebook')` all consistent; kinds map to existing cx classes. ✓
diff --git a/docs/superpowers/plans/2026-06-16-notebook-producer-bridge.md b/docs/superpowers/plans/2026-06-16-notebook-producer-bridge.md
new file mode 100644
index 00000000..27974225
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-16-notebook-producer-bridge.md
@@ -0,0 +1,261 @@
+# Notebook Producer Bridge Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax.
+
+**Goal:** Make the existing agent-memory write path actually populate the shared notebook — when `FileContextStore.apply_updates()` records observations and learnings, mirror them into the `NotebookStore` as Notes.
+
+**Architecture:** Pure converters (`observation_to_note`, `learning_to_note`) in `notebook.py`; a lazy `FileContextStore.notebook` property rooted at `agent_dir/notebook`; a guarded mirror step at the end of `apply_updates`. Builds on the foundation plan (`2026-06-16-notebook-foundation.md`). Backend-only, no UI/agent-loop changes. Transitional dual-write (legacy YAML + notebook) — legacy silos retire in a later increment.
+
+**Tech Stack:** Python 3.11, dataclasses, PyYAML, pytest (`file_context_store` fixture in `tests/conftest.py`).
+
+**Out of scope:** wiring the live loop to *call* `apply_updates` (separate increment); read API + Notebook tab; mapping expectations/watchpoints (they're working memory, not notebook entries — see design doc §2).
+
+---
+
+### Task 1: Converters — Observation/Learning → Note
+
+**Files:**
+- Modify: `gently/harness/memory/notebook.py`
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+from datetime import datetime as _dt
+
+from gently.harness.memory.model import Learning, Observation
+from gently.harness.memory.notebook import learning_to_note, observation_to_note
+
+
+class TestConverters:
+ def test_observation_to_note(self):
+ obs = Observation(
+ id="o1",
+ timestamp=_dt(2026, 6, 16, 9, 0, 0),
+ type="milestone",
+ content="nerve ring formed",
+ embryo_id="e1",
+ session_id="s1",
+ relates_to=["o0"],
+ gently_refs={"kind": "projection", "t": 42},
+ )
+ n = observation_to_note(obs)
+ assert n.id == "o1"
+ assert n.kind == NoteKind.OBSERVATION
+ assert n.body == "nerve ring formed"
+ assert n.author == Author.AGENT
+ assert n.embryos == ["e1"]
+ assert n.sessions == ["s1"]
+ assert {"rel": "relates_to", "to": "o0"} in n.links
+ assert n.artifacts == [{"kind": "projection", "t": 42}]
+ assert n.created_at == _dt(2026, 6, 16, 9, 0, 0)
+
+ def test_learning_to_note(self):
+ lrn = Learning(id="l1", content="rings form by comma", confidence=Confidence.HIGH)
+ n = learning_to_note(lrn)
+ assert n.id == "l1"
+ assert n.kind == NoteKind.FINDING
+ assert n.body == "rings form by comma"
+ assert n.status == NoteStatus.PROPOSED # agent-drafted, awaits confirm
+ assert n.confidence == Confidence.HIGH
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestConverters -v`
+Expected: FAIL — `ImportError: cannot import name 'observation_to_note'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+Add the model imports and converters to `notebook.py`. Extend the existing model import line:
+
+```python
+from .model import Confidence, Learning, Observation
+```
+
+Append at end of `notebook.py` (module-level functions, after `note_from_dict`):
+
+```python
+def observation_to_note(obs: Observation) -> Note:
+ """Bridge a legacy Observation into a notebook Note (kind=observation)."""
+ return Note(
+ id=obs.id,
+ kind=NoteKind.OBSERVATION,
+ body=obs.content,
+ author=Author.AGENT,
+ embryos=[obs.embryo_id] if obs.embryo_id else [],
+ sessions=[obs.session_id] if obs.session_id else [],
+ links=[{"rel": "relates_to", "to": r} for r in (obs.relates_to or [])],
+ artifacts=[obs.gently_refs] if obs.gently_refs else [],
+ created_at=obs.timestamp,
+ updated_at=obs.timestamp,
+ )
+
+
+def learning_to_note(learning: Learning) -> Note:
+ """Bridge a legacy Learning into a notebook Note (kind=finding, proposed)."""
+ return Note(
+ id=learning.id,
+ kind=NoteKind.FINDING,
+ body=learning.content,
+ author=Author.AGENT,
+ status=NoteStatus.PROPOSED,
+ confidence=learning.confidence,
+ created_at=learning.created_at,
+ updated_at=learning.created_at,
+ )
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestConverters -v`
+Expected: PASS (2 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook.py tests/test_notebook_store.py
+git commit -m "feat(notebook): Observation/Learning -> Note converters"
+```
+
+---
+
+### Task 2: `FileContextStore.notebook` property
+
+**Files:**
+- Modify: `gently/harness/memory/file_store.py` (add property near `apply_updates`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+class TestContextStoreNotebook:
+ def test_notebook_property_rooted_under_agent_dir(self, file_context_store):
+ nb = file_context_store.notebook
+ assert nb.root == file_context_store.agent_dir / "notebook"
+
+ def test_notebook_property_is_cached(self, file_context_store):
+ assert file_context_store.notebook is file_context_store.notebook
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestContextStoreNotebook -v`
+Expected: FAIL — `AttributeError: 'FileContextStore' object has no attribute 'notebook'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+In `gently/harness/memory/file_store.py`, add this property immediately **before** `def apply_updates(self, updates: ContextUpdates):` (line ~2178):
+
+```python
+@property
+def notebook(self):
+ """The shared lab notebook, rooted at agent_dir/notebook (lazy)."""
+ nb = getattr(self, "_notebook", None)
+ if nb is None:
+ from .notebook import NotebookStore
+
+ nb = NotebookStore(self.agent_dir / "notebook")
+ self._notebook = nb
+ return nb
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestContextStoreNotebook -v`
+Expected: PASS (2 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/file_store.py tests/test_notebook_store.py
+git commit -m "feat(notebook): FileContextStore.notebook lazy property"
+```
+
+---
+
+### Task 3: Mirror observations & learnings in `apply_updates`
+
+**Files:**
+- Modify: `gently/harness/memory/file_store.py` (`apply_updates`)
+- Test: `tests/test_notebook_store.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_store.py
+class TestApplyUpdatesMirror:
+ def test_apply_updates_mirrors_observations_and_learnings(self, file_context_store):
+ from gently.harness.memory.model import ContextUpdates
+
+ cs = file_context_store
+ obs = Observation(
+ id="o1",
+ timestamp=_dt(2026, 6, 16, 9, 0, 0),
+ type="milestone",
+ content="ring formed",
+ embryo_id="e1",
+ )
+ lrn = Learning(id="l1", content="rings form by comma", confidence=Confidence.HIGH)
+ cs.apply_updates(ContextUpdates(new_observations=[obs], new_learnings=[lrn]))
+
+ bodies = {n.body for n in cs.notebook.query_notes()}
+ assert "ring formed" in bodies
+ assert "rings form by comma" in bodies
+ assert cs.notebook.ids_for_embryo("e1") == ["o1"]
+
+ def test_apply_updates_empty_is_noop_for_notebook(self, file_context_store):
+ from gently.harness.memory.model import ContextUpdates
+
+ cs = file_context_store
+ cs.apply_updates(ContextUpdates())
+ assert cs.notebook.query_notes() == []
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestApplyUpdatesMirror -v`
+Expected: FAIL — `assert "ring formed" in set()` (notebook not populated yet)
+
+- [ ] **Step 3: Write minimal implementation**
+
+In `gently/harness/memory/file_store.py`, at the END of `apply_updates` (after the `if updates.new_focus is not None:` block), append:
+
+```python
+ # Mirror new observations & learnings into the shared notebook
+ # (best-effort — a notebook failure never breaks the legacy write).
+ from .notebook import learning_to_note, observation_to_note
+
+ try:
+ for obs in updates.new_observations:
+ self.notebook.write_note(observation_to_note(obs))
+ for learning in updates.new_learnings:
+ self.notebook.write_note(learning_to_note(learning))
+ except Exception:
+ logger.warning("notebook mirror failed", exc_info=True)
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_store.py::TestApplyUpdatesMirror -v`
+Expected: PASS (2 passed)
+
+- [ ] **Step 5: Run full notebook suite + commit**
+
+Run: `python -m pytest tests/test_notebook_store.py -q`
+Expected: all pass
+
+```bash
+git add gently/harness/memory/file_store.py tests/test_notebook_store.py
+git commit -m "feat(notebook): apply_updates mirrors observations & learnings into notebook"
+```
+
+---
+
+## Self-Review
+
+**Spec coverage:** Producer wiring (design doc increment 1b) — `apply_updates` now populates the notebook. ✓ Converters honor the model (Observation→observation note, Learning→finding/proposed). ✓ Working-memory types (expectation/watchpoint) intentionally not mirrored (design §2). ✓
+**Placeholder scan:** none; complete code + commands throughout. ✓
+**Type consistency:** `observation_to_note`/`learning_to_note`, `FileContextStore.notebook`, `NoteKind`/`Author`/`NoteStatus`/`Confidence` match the foundation module and `model.py` (`Observation`, `Learning`, `ContextUpdates` confirmed at `file_store.py:2178-2203`). ✓
diff --git a/docs/superpowers/plans/2026-06-16-notebook-read-api.md b/docs/superpowers/plans/2026-06-16-notebook-read-api.md
new file mode 100644
index 00000000..9bd42e20
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-16-notebook-read-api.md
@@ -0,0 +1,273 @@
+# Notebook Read API Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:executing-plans (or subagent-driven-development) to implement task-by-task. Steps use checkbox (`- [ ]`) syntax.
+
+**Goal:** Expose the shared notebook over HTTP so the frontend can read it — list/filter notes, fetch one note, and list inquiry-threads with counts.
+
+**Architecture:** A new route module `gently/ui/web/routes/notebook.py` exposing `create_router(server)` (the established pattern), reading `server.context_store.notebook` (the `NotebookStore` added in the producer-bridge plan) and serializing via `note_to_dict`. Registered in `routes/__init__.py`. Read-only; authoring/curation is a later increment.
+
+**Tech Stack:** FastAPI `APIRouter`, pytest + `fastapi.testclient.TestClient`, the `file_context_store` fixture (`tests/conftest.py`).
+
+**Out of scope:** the Notebook tab UI (next plan, browser-verified); the Agent's-View rewire; retrieval/embeddings.
+
+---
+
+### Task 1: Route module — list & get notes
+
+**Files:**
+- Create: `gently/ui/web/routes/notebook.py`
+- Modify: `gently/ui/web/routes/__init__.py`
+- Test: `tests/test_notebook_api.py`
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_notebook_api.py
+"""Tests for the notebook read API."""
+
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+
+from gently.harness.memory.notebook import Note, NoteKind, NoteStatus
+
+
+def _make_app(context_store):
+ from gently.ui.web.routes.notebook import create_router
+
+ app = FastAPI()
+
+ class _Server:
+ pass
+
+ server = _Server()
+ server.context_store = context_store
+ app.include_router(create_router(server))
+ return app
+
+
+def _seed(cs):
+ nb = cs.notebook
+ nb.write_note(Note(id="o1", kind=NoteKind.OBSERVATION, body="ring formed", strains=["N2"]))
+ nb.write_note(
+ Note(
+ id="f1",
+ kind=NoteKind.FINDING,
+ body="rings by comma",
+ status=NoteStatus.PROPOSED,
+ strains=["N2"],
+ threads=["t1"],
+ )
+ )
+ return cs
+
+
+class TestListNotes:
+ def test_no_store_available_false(self):
+ client = TestClient(_make_app(None))
+ data = client.get("/api/notebook/notes").json()
+ assert data == {"available": False, "notes": []}
+
+ def test_list_all(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes").json()
+ assert data["available"] is True
+ assert {n["id"] for n in data["notes"]} == {"o1", "f1"}
+
+ def test_filter_by_kind(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes?kind=finding").json()
+ assert {n["id"] for n in data["notes"]} == {"f1"}
+
+ def test_filter_by_strain(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes?strain=N2").json()
+ assert {n["id"] for n in data["notes"]} == {"o1", "f1"}
+
+ def test_invalid_kind_is_ignored(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes?kind=bogus").json()
+ assert {n["id"] for n in data["notes"]} == {"o1", "f1"}
+
+
+class TestGetNote:
+ def test_get_existing(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ data = client.get("/api/notebook/notes/o1").json()
+ assert data["id"] == "o1"
+ assert data["body"] == "ring formed"
+
+ def test_get_missing_404(self, file_context_store):
+ client = TestClient(_make_app(_seed(file_context_store)))
+ resp = client.get("/api/notebook/notes/nope")
+ assert resp.status_code == 404
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_api.py -v`
+Expected: FAIL — `ModuleNotFoundError: No module named 'gently.ui.web.routes.notebook'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+Create `gently/ui/web/routes/notebook.py`:
+
+```python
+"""Notebook (shared lab notebook) read routes.
+
+Exposes the notebook's Notes for the Notebook tab + Agent's-View live edge.
+Read-only here; authoring/curation come in a later increment.
+"""
+
+from fastapi import APIRouter, HTTPException
+
+from gently.harness.memory.notebook import Author, NoteKind, NoteStatus, note_to_dict
+
+
+def _coerce(enum_cls, value):
+ """Parse a query-param string into an enum; invalid/None → None (no filter)."""
+ if value is None:
+ return None
+ try:
+ return enum_cls(value)
+ except ValueError:
+ return None
+
+
+def create_router(server) -> APIRouter:
+ router = APIRouter()
+
+ def _nb():
+ cs = getattr(server, "context_store", None)
+ return cs.notebook if cs is not None else None
+
+ @router.get("/api/notebook/notes")
+ async def list_notes(
+ kind: str | None = None,
+ author: str | None = None,
+ status: str | None = None,
+ strain: str | None = None,
+ embryo: str | None = None,
+ thread: str | None = None,
+ ):
+ nb = _nb()
+ if nb is None:
+ return {"available": False, "notes": []}
+ notes = nb.query_notes(
+ kind=_coerce(NoteKind, kind),
+ author=_coerce(Author, author),
+ status=_coerce(NoteStatus, status),
+ strain=strain,
+ embryo=embryo,
+ thread=thread,
+ )
+ return {"available": True, "notes": [note_to_dict(n) for n in notes]}
+
+ @router.get("/api/notebook/notes/{note_id}")
+ async def get_note(note_id: str):
+ nb = _nb()
+ if nb is None:
+ raise HTTPException(status_code=404, detail="notebook unavailable")
+ note = nb.get_note(note_id)
+ if note is None:
+ raise HTTPException(status_code=404, detail="note not found")
+ return note_to_dict(note)
+
+ return router
+```
+
+Then register it in `gently/ui/web/routes/__init__.py`. Add the import after the `images` import line:
+
+```python
+from .notebook import create_router as create_notebook_router
+```
+
+And add `create_notebook_router,` to the factory tuple in `register_all_routes` (after `create_context_router,`):
+
+```python
+ create_context_router,
+ create_notebook_router,
+ ):
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_api.py -v`
+Expected: PASS (7 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/routes/notebook.py gently/ui/web/routes/__init__.py tests/test_notebook_api.py
+git commit -m "feat(notebook): read API — GET /api/notebook/notes + /notes/{id}"
+```
+
+---
+
+### Task 2: `GET /api/notebook/threads`
+
+**Files:**
+- Modify: `gently/ui/web/routes/notebook.py`
+- Test: `tests/test_notebook_api.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_api.py
+class TestThreads:
+ def test_no_store(self):
+ client = TestClient(_make_app(None))
+ assert client.get("/api/notebook/threads").json() == {"available": False, "threads": []}
+
+ def test_thread_counts(self, file_context_store):
+ cs = file_context_store
+ nb = cs.notebook
+ nb.write_note(Note(id="a", kind=NoteKind.QUESTION, body="q", threads=["t1"]))
+ nb.write_note(Note(id="b", kind=NoteKind.FINDING, body="f", threads=["t1", "t2"]))
+ client = TestClient(_make_app(cs))
+ data = client.get("/api/notebook/threads").json()
+ assert data["available"] is True
+ assert data["threads"] == [{"id": "t1", "count": 2}, {"id": "t2", "count": 1}]
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `python -m pytest tests/test_notebook_api.py::TestThreads -v`
+Expected: FAIL — 404 (route not defined)
+
+- [ ] **Step 3: Write minimal implementation**
+
+Add this endpoint inside `create_router`, just before `return router`:
+
+```python
+ @router.get("/api/notebook/threads")
+ async def list_threads():
+ nb = _nb()
+ if nb is None:
+ return {"available": False, "threads": []}
+ counts: dict[str, int] = {}
+ for n in nb.query_notes():
+ for t in n.threads:
+ counts[t] = counts.get(t, 0) + 1
+ threads = [{"id": t, "count": c} for t, c in sorted(counts.items())]
+ return {"available": True, "threads": threads}
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `python -m pytest tests/test_notebook_api.py -q`
+Expected: all pass
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/routes/notebook.py tests/test_notebook_api.py
+git commit -m "feat(notebook): read API — GET /api/notebook/threads with counts"
+```
+
+---
+
+## Self-Review
+
+**Spec coverage:** read surface API for the notebook (design increment 1c, backend half) — query notes by kind/author/status/scope, fetch one, list threads. ✓ Reuses `NotebookStore.query_notes` + `note_to_dict` from the foundation. ✓ Follows `create_router(server)` + `server.context_store` convention (`context.py`). ✓
+**Placeholder scan:** none — complete code + commands. ✓
+**Type consistency:** `create_router`, `note_to_dict`, `NoteKind`/`Author`/`NoteStatus`, `server.context_store.notebook`, `nb.query_notes`/`get_note` all match the foundation + producer-bridge modules. Registration matches the existing tuple in `routes/__init__.py`. ✓
diff --git a/docs/superpowers/plans/2026-06-17-notebook-ask.md b/docs/superpowers/plans/2026-06-17-notebook-ask.md
new file mode 100644
index 00000000..03d62f06
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-17-notebook-ask.md
@@ -0,0 +1,418 @@
+# "Ask the Notebook" Implementation Plan (Increment 2, backend)
+
+> **For agentic workers:** REQUIRED SUB-SKILL: superpowers:executing-plans. Steps use checkbox (`- [ ]`) syntax.
+
+**Goal:** Let the notebook be *reasoned with* — given a question (+ optional scope), retrieve relevant Notes, ask Claude to synthesize a **grounded, cited** answer, and return it as a validated structured object.
+
+**Architecture:** A new module `gently/harness/memory/notebook_ask.py`: structural retrieval (`select_notes`) + a forced-`tool_choice` synthesis call (`answer_question`) that reuses gently's conventions — `anthropic.AsyncAnthropic` (per `chat.py:198`), `settings.models.main` (Opus 4.8), structured output via a pinned tool (per `verifier.py`), and **no self-rated confidence** (per the lab rule). A `POST /api/notebook/ask` route wires retrieval → synthesis. The Claude client is injected so everything is unit-testable with a fake.
+
+**Tech Stack:** Python 3.11, `anthropic` SDK, FastAPI, pytest + TestClient (venv).
+
+**Out of scope (later plans):** embeddings/semantic recall (structural-only here); the "Ask" UI box on the Notebook tab; proactive surfacing.
+
+---
+
+### Task 1: Structural retrieval — `select_notes`
+
+**Files:**
+- Create: `gently/harness/memory/notebook_ask.py`
+- Test: `tests/test_notebook_ask.py`
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_notebook_ask.py
+"""Tests for 'Ask the notebook' — retrieval + grounded synthesis."""
+
+from gently.harness.memory.notebook import Note, NoteKind
+from gently.harness.memory.notebook_ask import select_notes
+
+
+def _seed(cs):
+ nb = cs.notebook
+ nb.write_note(
+ Note(id="o1", kind=NoteKind.OBSERVATION, body="ring formed", strains=["N2"], threads=["t1"])
+ )
+ nb.write_note(
+ Note(id="f1", kind=NoteKind.FINDING, body="12 min/degC", strains=["N2"], threads=["t1"])
+ )
+ nb.write_note(Note(id="x1", kind=NoteKind.OBSERVATION, body="unrelated", strains=["OH904"]))
+ return nb
+
+
+class TestSelectNotes:
+ def test_scope_by_thread(self, file_context_store):
+ nb = _seed(file_context_store)
+ ids = {n.id for n in select_notes(nb, thread="t1")}
+ assert ids == {"o1", "f1"}
+
+ def test_scope_by_strain(self, file_context_store):
+ nb = _seed(file_context_store)
+ ids = {n.id for n in select_notes(nb, strain="OH904")}
+ assert ids == {"x1"}
+
+ def test_no_scope_returns_recent_capped(self, file_context_store):
+ nb = _seed(file_context_store)
+ notes = select_notes(nb, limit=2)
+ assert len(notes) == 2 # newest-first, capped
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_ask.py::TestSelectNotes -v`
+Expected: FAIL — `ModuleNotFoundError: No module named 'gently.harness.memory.notebook_ask'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+```python
+# gently/harness/memory/notebook_ask.py
+"""Ask the notebook — retrieve relevant Notes and synthesize a grounded,
+cited answer with Claude. Structural retrieval only (semantic recall is a
+later increment). See docs/superpowers/specs/2026-06-16-shared-lab-notebook-design.md §4.
+"""
+
+from __future__ import annotations
+
+from .notebook import Note, NotebookStore
+
+
+def select_notes(
+ store: NotebookStore,
+ *,
+ thread: str | None = None,
+ strain: str | None = None,
+ limit: int = 12,
+) -> list[Note]:
+ """Structural narrowing: scope by thread/strain when given, else recent.
+ Returns newest-first, capped at `limit`."""
+ notes = store.query_notes(thread=thread, strain=strain)
+ return notes[:limit]
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_ask.py::TestSelectNotes -v`
+Expected: PASS (3 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook_ask.py tests/test_notebook_ask.py
+git commit -m "feat(notebook): select_notes — structural retrieval for ask"
+```
+
+---
+
+### Task 2: Grounded synthesis — `answer_question` (forced tool)
+
+**Files:**
+- Modify: `gently/harness/memory/notebook_ask.py`
+- Test: `tests/test_notebook_ask.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_ask.py
+import asyncio
+
+from gently.harness.memory.notebook_ask import ASK_TOOL, answer_question, build_ask_messages
+
+
+class _FakeBlock:
+ def __init__(self, inp):
+ self.type = "tool_use"
+ self.input = inp
+
+
+class _FakeResp:
+ def __init__(self, inp):
+ self.content = [_FakeBlock(inp)]
+ self.stop_reason = "tool_use"
+
+
+class _FakeMessages:
+ def __init__(self, captured, inp):
+ self._captured, self._inp = captured, inp
+
+ async def create(self, **kwargs):
+ self._captured.update(kwargs)
+ return _FakeResp(self._inp)
+
+
+class _FakeClient:
+ def __init__(self, inp):
+ self.captured = {}
+ self.messages = _FakeMessages(self.captured, inp)
+
+
+class TestAnswerQuestion:
+ def test_build_messages_embeds_note_ids(self):
+ notes = [Note(id="o1", kind=NoteKind.OBSERVATION, body="ring formed")]
+ msgs = build_ask_messages("what formed?", notes)
+ text = msgs[0]["content"]
+ assert "o1" in text and "ring formed" in text and "what formed?" in text
+
+ def test_answer_returns_structured_and_forces_tool(self):
+ canned = {
+ "answer": "A ring formed.",
+ "points": [{"text": "ring formed", "note_ids": ["o1"]}],
+ "suggested_next": [],
+ "coverage": "covered",
+ }
+ client = _FakeClient(canned)
+ notes = [Note(id="o1", kind=NoteKind.OBSERVATION, body="ring formed")]
+ out = asyncio.run(answer_question(client, "m", "what formed?", notes))
+ assert out == canned
+ # tool_choice is pinned to the ask tool (forced structured output)
+ assert client.captured["tool_choice"] == {"type": "tool", "name": ASK_TOOL["name"]}
+ assert client.captured["model"] == "m"
+
+ def test_answer_no_notes_short_circuits_without_api(self):
+ client = _FakeClient({"should": "not be used"})
+ out = asyncio.run(answer_question(client, "m", "anything?", []))
+ assert out["coverage"] == "not_in_notebook"
+ assert client.captured == {} # no API call when nothing to ground on
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_ask.py::TestAnswerQuestion -v`
+Expected: FAIL — `ImportError: cannot import name 'ASK_TOOL'`
+
+- [ ] **Step 3: Write minimal implementation**
+
+Append to `gently/harness/memory/notebook_ask.py`:
+
+```python
+# ASK_TOOL pins the structured output. No confidence field — we don't ask the
+# model to self-rate (lab rule); "coverage" is a factual grounding classification.
+ASK_TOOL = {
+ "name": "answer_from_notebook",
+ "description": "Return a grounded answer built ONLY from the provided notebook entries.",
+ "input_schema": {
+ "type": "object",
+ "properties": {
+ "answer": {"type": "string", "description": "Direct synthesis grounded in the notes."},
+ "points": {
+ "type": "array",
+ "description": "Supporting points, each citing the note ids it rests on.",
+ "items": {
+ "type": "object",
+ "properties": {
+ "text": {"type": "string"},
+ "note_ids": {"type": "array", "items": {"type": "string"}},
+ },
+ "required": ["text", "note_ids"],
+ },
+ },
+ "suggested_next": {
+ "type": "array",
+ "items": {"type": "string"},
+ "description": "Concrete next experiments/moves if the question asks what to do; else empty.",
+ },
+ "coverage": {
+ "type": "string",
+ "enum": ["covered", "partial", "not_in_notebook"],
+ "description": "How well the provided notes cover the question.",
+ },
+ },
+ "required": ["answer", "points", "coverage"],
+ },
+}
+
+_SYSTEM = (
+ "You reason over a shared lab notebook. Answer ONLY from the notebook entries "
+ "provided — every claim must cite the note id(s) it rests on. If the notes do "
+ "not contain the answer, say so plainly and set coverage to 'not_in_notebook'. "
+ "Never invent facts not in the notes. Call the answer_from_notebook tool."
+)
+
+
+def _render_notes(notes: list[Note]) -> str:
+ lines = []
+ for n in notes:
+ scope = []
+ if n.strains:
+ scope.append("strains=" + ",".join(n.strains))
+ if n.embryos:
+ scope.append("embryos=" + ",".join(n.embryos))
+ tag = f" [{'; '.join(scope)}]" if scope else ""
+ lines.append(f"[{n.id}] ({n.kind.value}){tag} {n.body}")
+ return "\n".join(lines)
+
+
+def build_ask_messages(question: str, notes: list[Note]) -> list[dict]:
+ body = (
+ "Notebook entries:\n" + _render_notes(notes) + f"\n\nQuestion: {question}\n\n"
+ "Answer using only these entries, citing note ids."
+ )
+ return [{"role": "user", "content": body}]
+
+
+async def answer_question(client, model: str, question: str, notes: list[Note]) -> dict:
+ """Force the ask tool and return its validated input dict. Short-circuits
+ (no API call) when there are no notes to ground on."""
+ if not notes:
+ return {
+ "answer": "The notebook doesn't cover this yet.",
+ "points": [],
+ "suggested_next": [],
+ "coverage": "not_in_notebook",
+ }
+ resp = await client.messages.create(
+ model=model,
+ max_tokens=2048,
+ system=_SYSTEM,
+ tools=[ASK_TOOL],
+ tool_choice={"type": "tool", "name": ASK_TOOL["name"]},
+ messages=build_ask_messages(question, notes),
+ )
+ for block in resp.content:
+ if getattr(block, "type", None) == "tool_use":
+ return block.input
+ return {"answer": "", "points": [], "suggested_next": [], "coverage": "not_in_notebook"}
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_ask.py -q`
+Expected: all pass
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/harness/memory/notebook_ask.py tests/test_notebook_ask.py
+git commit -m "feat(notebook): answer_question — forced-tool grounded synthesis"
+```
+
+---
+
+### Task 3: `POST /api/notebook/ask`
+
+**Files:**
+- Modify: `gently/ui/web/routes/notebook.py`
+- Test: `tests/test_notebook_api.py` (append)
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# append to tests/test_notebook_api.py
+class _AskBlock:
+ def __init__(self, inp):
+ self.type = "tool_use"
+ self.input = inp
+
+
+class _AskResp:
+ def __init__(self, inp):
+ self.content = [_AskBlock(inp)]
+ self.stop_reason = "tool_use"
+
+
+class _AskMessages:
+ def __init__(self, inp):
+ self._inp = inp
+
+ async def create(self, **kwargs):
+ return _AskResp(self._inp)
+
+
+class _AskClient:
+ def __init__(self, inp):
+ self.messages = _AskMessages(inp)
+
+
+def _make_app_with_client(context_store, client):
+ from gently.ui.web.routes.notebook import create_router
+
+ app = FastAPI()
+
+ class _Server:
+ pass
+
+ server = _Server()
+ server.context_store = context_store
+ server.claude_async = client
+ app.include_router(create_router(server))
+ return app
+
+
+class TestAsk:
+ def test_ask_returns_grounded_answer(self, file_context_store):
+ cs = _seed(file_context_store)
+ canned = {
+ "answer": "A ring formed.",
+ "points": [{"text": "ring", "note_ids": ["o1"]}],
+ "suggested_next": [],
+ "coverage": "covered",
+ }
+ client = TestClient(_make_app_with_client(cs, _AskClient(canned)))
+ resp = client.post("/api/notebook/ask", json={"question": "what happened?"})
+ assert resp.status_code == 200
+ assert resp.json()["coverage"] == "covered"
+
+ def test_ask_no_store(self):
+ client = TestClient(_make_app(None))
+ resp = client.post("/api/notebook/ask", json={"question": "x"})
+ assert resp.json() == {"available": False}
+```
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_api.py::TestAsk -v`
+Expected: FAIL — 404/405 (route not defined)
+
+- [ ] **Step 3: Write minimal implementation**
+
+In `gently/ui/web/routes/notebook.py`, add `Body` to the fastapi import and add the route inside `create_router`, before `return router`:
+
+```python
+ @router.post("/api/notebook/ask")
+ async def ask(
+ question: str = Body(..., embed=True),
+ thread: str | None = Body(None, embed=True),
+ strain: str | None = Body(None, embed=True),
+ ):
+ nb = _nb()
+ if nb is None:
+ return {"available": False}
+ from gently.harness.memory.notebook_ask import answer_question, select_notes
+ from gently.settings import settings
+
+ notes = select_notes(nb, thread=thread, strain=strain)
+ client = getattr(server, "claude_async", None)
+ if client is None:
+ import anthropic
+
+ client = anthropic.AsyncAnthropic()
+ result = await answer_question(client, settings.models.main, question, notes)
+ result["available"] = True
+ result["note_ids"] = [n.id for n in notes]
+ return result
+```
+
+Update the import line at the top of the file:
+
+```python
+from fastapi import APIRouter, Body, HTTPException
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `.venv/bin/python -m pytest tests/test_notebook_api.py -q`
+Expected: all pass
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/routes/notebook.py tests/test_notebook_api.py
+git commit -m "feat(notebook): POST /api/notebook/ask — grounded notebook Q&A"
+```
+
+---
+
+## Self-Review
+**Spec coverage (design §4):** structural retrieval (`select_notes`) → grounded synthesis (`answer_question`, forced tool, cited, "not_in_notebook" valid) → endpoint. ✓ No self-rated confidence (`coverage` is grounding, not correctness-confidence). ✓ Reuses `settings.models.main`, `anthropic.AsyncAnthropic`, the `verifier.py` forced-tool pattern. ✓ Client injected → unit-testable without real API. ✓
+**Deferred (correct):** embeddings/semantic recall; the "Ask" UI; proactive surfacing.
+**Placeholder scan:** none — complete code + commands. ✓
+**Type consistency:** `select_notes`, `answer_question`, `ASK_TOOL`, `build_ask_messages` named consistently across tasks/tests; route uses `server.claude_async` (tests inject) with a real `AsyncAnthropic` fallback. ✓
diff --git a/docs/superpowers/plans/2026-06-27-temperature-interface.md b/docs/superpowers/plans/2026-06-27-temperature-interface.md
new file mode 100644
index 00000000..025e8236
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-27-temperature-interface.md
@@ -0,0 +1,842 @@
+# Temperature Interface Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Persist live temperature into each imaging session and chart it, so bursts/volumes are correlatable to temperature and the rise/fall trajectory is visible during the temperature-strain experiments.
+
+**Architecture:** A `FileStore`-backed append-only `temperature.jsonl` per session (mirroring `predictions.jsonl`); a `TemperatureSampler(Service)` in the agent process — modeled on `DeviceStateMonitor` — that, while a session is active, polls the device layer at 1 Hz, appends each reading, holds the latest in memory, and publishes a `TEMPERATURE_UPDATE` event that the viz server already forwards to the browser; acquisition code stamps the latest reading into volume/burst metadata; a FastAPI history route backfills the graph; a hand-rolled SVG component renders water-temp + stepped-setpoint as a card on the Devices tab.
+
+**Tech Stack:** Python 3 + asyncio, FastAPI, the project's `EventBus`, `FileStore` (file-based YAML/JSONL), vanilla-JS + hand-rolled SVG frontend (no build step), pytest with `asyncio_mode = "auto"`.
+
+## Global Constraints
+
+- **No new dependency** — chart is hand-rolled SVG (`createElementNS`), matching `experiment-overview.js`. No charting library.
+- **Session-scoped capture only** — sampler persists/emits **only while a session is active**; no always-on facility daemon.
+- **Sample schema** (one JSONL line): `{"t": No temperature data yet
';
+ }
+
+ function render() {
+ if (!_samples.length) { renderEmpty(); return; }
+ const W = _root.clientWidth || 480, H = 160, pad = 24;
+ const xs = _samples.map((_, i) => i);
+ const ws = _samples.map(s => s.water_c).filter(v => v != null);
+ const sps = _samples.map(s => s.setpoint_c).filter(v => v != null);
+ const lo = Math.min(...ws, ...sps) - 1, hi = Math.max(...ws, ...sps) + 1;
+ const sx = i => pad + (i / Math.max(1, xs.length - 1)) * (W - 2 * pad);
+ const sy = v => H - pad - ((v - lo) / Math.max(0.001, hi - lo)) * (H - 2 * pad);
+
+ const svg = document.createElementNS(SVGNS, "svg");
+ svg.setAttribute("viewBox", `0 0 ${W} ${H}`); svg.setAttribute("width", "100%");
+
+ const line = (pts, cls) => {
+ const p = document.createElementNS(SVGNS, "polyline");
+ p.setAttribute("points", pts); p.setAttribute("class", cls);
+ p.setAttribute("fill", "none"); svg.appendChild(p);
+ };
+ line(_samples.map((s, i) => s.water_c != null ? `${sx(i)},${sy(s.water_c)}` : "").filter(Boolean).join(" "), "temp-water");
+ // Stepped setpoint: carry previous y until it changes.
+ let sp = []; _samples.forEach((s, i) => { if (s.setpoint_c != null) sp.push(`${sx(i)},${sy(s.setpoint_c)}`); });
+ line(sp.join(" "), "temp-setpoint");
+
+ const last = _samples[_samples.length - 1];
+ const readout = document.createElement("div");
+ readout.className = "temp-graph-readout";
+ readout.textContent = `${last.water_c?.toFixed?.(1) ?? "—"} °C → ${last.setpoint_c?.toFixed?.(1) ?? "—"} °C (${last.state ?? ""})`;
+
+ _root.innerHTML = ""; _root.appendChild(readout); _root.appendChild(svg);
+ }
+
+ function dispose() { ClientEventBus.off("TEMPERATURE_UPDATE", onEvent); }
+ return { init, dispose, _render: render, _samples: () => _samples };
+})();
+window.TemperatureGraph = TemperatureGraph;
+```
+
+Add minimal CSS (in the devices stylesheet) for `.temp-water` (stroke: water color), `.temp-setpoint` (dashed stroke), `.temp-graph-empty` (muted), matching existing palette.
+
+- [ ] **Step 2: Mount it**
+
+In `templates/index.html`, add inside `#devices-content` (under the map/details view):
+
+```html
+
+```
+
+Load the script (next to the other `static/js/*.js` includes for the devices tab).
+
+In `devices.js` `init()` (`:1556`), after existing setup:
+
+```javascript
+ const tg = document.getElementById('devices-temp-graph');
+ if (tg && window.TemperatureGraph) TemperatureGraph.init(tg, 'current');
+```
+
+(No extra subscription needed in `devices.js` — the component self-subscribes. Optionally also route the existing small readout off the new event.)
+
+- [ ] **Step 3: Add the script tag**
+
+Add `` in `index.html` alongside the other component scripts, **before** `devices.js` loads (so `window.TemperatureGraph` exists when `init()` runs).
+
+- [ ] **Step 4: Verify live in the app (Chrome DevTools MCP)**
+
+Use the `run` skill to launch the app with the mock temperature backend and an active session. Then with Chrome DevTools MCP:
+- navigate to the Devices tab, take a snapshot/screenshot;
+- confirm the empty state shows when no samples, then the water trace + stepped setpoint render and update live as the sampler emits;
+- run the UI audit (alignment/spacing/overflow/contrast) per the "UI audit before done" practice and fix any flaws;
+- trigger one burst and confirm (Task 6) that `burst.yaml` + a frame `.meta.yaml` carry a `temperature` block.
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/static/js/temperature-graph.js gently/ui/web/templates/index.html gently/ui/web/static/js/devices.js
+git commit -m "feat(temperature): live SVG temperature graph on the Devices tab"
+```
+
+---
+
+## Self-Review
+
+**Spec coverage:**
+- Persistence / `temperature.jsonl` → Task 1. ✓
+- Sampler (poll @1 Hz, session-gated, latest-in-memory, SSE) → Tasks 2–4. ✓
+- Per-acquisition stamp (burst + volume) → Task 6. ✓
+- History API (`current` resolution, `since`) → Task 5. ✓
+- Reusable SVG graph on Devices card (water trace + stepped setpoint + readout, backfill + live, empty state) → Task 7. ✓
+- Error/empty handling (gap-not-crash, no-device idle, empty state) → Tasks 3 & 7. ✓
+- Out-of-scope (setpoint control, choreography, always-on) → not implemented, by design. ✓
+
+**Open verification items folded into tasks (not placeholders):** session-creation API (Task 1/3/6), `EventBus.subscribe` shape (Task 2), the agent's FileStore attribute (Task 4), the volume-meta accessor + `create_embryo` signature (Task 6), the burst-acquisition construction site (Task 6). Each is an explicit "confirm from the real API" instruction with a concrete fallback, not a TODO.
+
+**Type consistency:** `temperature_stamp` returns `{water_c, setpoint_c, state, sampled_at}` everywhere; sample lines are `{t, water_c, setpoint_c, state}`; event payload is `{session_id, sample}`; history response is `{session_id, samples}`. Consistent across Tasks 1/3/5/6/7.
diff --git a/docs/superpowers/plans/2026-06-28-manual-mode-live-view.md b/docs/superpowers/plans/2026-06-28-manual-mode-live-view.md
new file mode 100644
index 00000000..abdd9fce
--- /dev/null
+++ b/docs/superpowers/plans/2026-06-28-manual-mode-live-view.md
@@ -0,0 +1,845 @@
+# Manual Mode — SPIM Live View (B1) Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** A Manual view in the Devices tab with a continuous SPIM single-slice brightfield live view (galvo/piezo/exposure controlled live), brightfield illumination, temperature, and by-hand burst/volume triggers — the hand-driven surface for next week's temperature-strain experiments.
+
+**Architecture:** A device-layer lightsheet live streamer (MMCore continuous sequence acquisition + peek-latest, parked galvo/piezo), bridged to the browser by a `LightSheetStreamMonitor` (EventBus `LIGHTSHEET_FRAME`) over the existing base64-JPEG/SSE→WS transport; `require_control` FastAPI proxy routes; a Manual view that mirrors the bottom-camera panel. FPS is measured on the rig; a binary transport path is a conditional follow-up.
+
+**Tech Stack:** Python asyncio + aiohttp (device layer), FastAPI (viz proxy), `pymmcore.CMMCore`, the project EventBus, vanilla-JS + canvas/SVG frontend (no build step), pytest (`asyncio_mode=auto`).
+
+## Global Constraints
+
+- **No new dependency.** Reuse `_encode_frame_for_stream` (OpenCV already present), the bottom-camera streamer pattern, A's portable temperature graph.
+- **Single SPIM camera** today: `self.devices.get("camera")` (`HamCam1`). No side-A/B selector in B1 (deferred to B2).
+- **Live = continuous sequence acquisition**, never a snap loop: `core.startContinuousSequenceAcquisition(0)` → peek `core.getLastImage()` (NEVER `popNextImage` — don't drain) → `stopSequenceAcquisition()` on exit. The core handle is `self.system.core` in the device layer; unwrap rpyc frames with `_safe_obtain`.
+- **Park** before/under live: `piezo.setPosition(z)`, `scanner.sa_offset_y.setPosition(deg)` (or `scanner.set_y_offset(deg)`), `scanner.set_spim_state("Idle")`, `piezo.set_spim_state("Idle")`. galvo/piezo updates apply live (no restart); exposure change → stop→`setExposure`→restart.
+- **Brightfield safety:** laser forced off in manual live (`setConfig(laser_group, "ALL OFF")` / `set_laser_power(...,0)`).
+- **Concurrency:** the streamer honors `self._state_pause_counter > 0` (heavy plan owns MMCore → back off / stop sequence). Only one live stream at a time.
+- **Lightsheet stream resolution/quality:** its own config — default `_ls_target_max_dim = 512`, `_ls_jpeg_quality = 70` (higher than the bottom-camera 360/55 thumbnail, for focus).
+- **Transport stays JSON/`send_text`** (no binary path exists); a binary hop is Task 8, conditional on the FPS measurement.
+- **Auth:** browser-facing writes are FastAPI proxy routes guarded by `Depends(require_control)`; device-layer aiohttp routes have no auth, so the browser must go through the proxy.
+- **Tests:** `pytest`; `file_store`-style fixtures; FastAPI `TestClient` + mock client for routes; a fake core for the streamer. Frontend has no JS unit harness → `node --check` + Chrome-MCP harness + UI audit. Much of B1 needs the real rig; off-rig we cover streamer (fake core), routes, client, frontend harness, and defer live/FPS verification.
+
+---
+
+### Task 1: `LIGHTSHEET_FRAME` event type + frontend exclusion
+
+**Files:**
+- Modify: `gently/core/event_bus.py` (enum near `:88`; `_NO_HISTORY_TYPES` near `:186-195`)
+- Modify: `gently/ui/web/static/js/websocket.js` (exclusion guard `:104-107`)
+- Test: `tests/test_lightsheet_event.py`
+
+**Interfaces:**
+- Produces: `EventType.LIGHTSHEET_FRAME` (declared with `auto()`, matching `BOTTOM_CAMERA_FRAME`), in `_NO_HISTORY_TYPES`. Wire serialization uses `.name` (so the browser receives `"LIGHTSHEET_FRAME"`).
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_lightsheet_event.py
+from gently.core.event_bus import EventType, EventBus, _NO_HISTORY_TYPES
+
+
+def test_lightsheet_frame_event_exists():
+ assert EventType.LIGHTSHEET_FRAME.name == "LIGHTSHEET_FRAME"
+
+
+def test_lightsheet_frame_excluded_from_history():
+ assert EventType.LIGHTSHEET_FRAME in _NO_HISTORY_TYPES
+
+
+def test_lightsheet_frame_publishes_to_subscriber():
+ bus = EventBus()
+ seen = []
+ bus.subscribe(EventType.LIGHTSHEET_FRAME, lambda e: seen.append(e.data))
+ bus.publish(event_type=EventType.LIGHTSHEET_FRAME, data={"jpeg_b64": "x"}, source="t")
+ assert seen == [{"jpeg_b64": "x"}]
+```
+
+> Confirm `EventBus.subscribe` signature / `_NO_HISTORY_TYPES` exportability against the real file; adapt the import/subscribe if needed, keep the assertions.
+
+- [ ] **Step 2: Run test to verify it fails**
+
+Run: `pytest tests/test_lightsheet_event.py -v`
+Expected: FAIL — `AttributeError: LIGHTSHEET_FRAME`
+
+- [ ] **Step 3: Write minimal implementation**
+
+In `gently/core/event_bus.py`, add the member next to `BOTTOM_CAMERA_FRAME` (`:88`):
+```python
+ LIGHTSHEET_FRAME = auto() # Live JPEG frame from the SPIM lightsheet live stream
+```
+Add to `_NO_HISTORY_TYPES` (next to `BOTTOM_CAMERA_FRAME`):
+```python
+(EventType.LIGHTSHEET_FRAME,) # high-volume live frames — keep out of history
+```
+In `gently/ui/web/static/js/websocket.js`, extend the exclusion guard (`:104-107`) so the frame skips the Events table but still reaches `ClientEventBus.emit`:
+```javascript
+ if (msg.event_type !== 'DEVICE_STATE_UPDATE' &&
+ msg.event_type !== 'BOTTOM_CAMERA_FRAME' &&
+ msg.event_type !== 'TEMPERATURE_UPDATE' &&
+ msg.event_type !== 'LIGHTSHEET_FRAME') {
+```
+
+- [ ] **Step 4: Run test to verify it passes**
+
+Run: `pytest tests/test_lightsheet_event.py -v` (3 passed) and `node --check gently/ui/web/static/js/websocket.js` (exit 0)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/core/event_bus.py gently/ui/web/static/js/websocket.js tests/test_lightsheet_event.py
+git commit -m "feat(manual-mode): add LIGHTSHEET_FRAME event type + frontend exclusion"
+```
+
+---
+
+### Task 2: Device-layer lightsheet live streamer (continuous sequence acquisition)
+
+**Files:**
+- Modify: `gently/hardware/dispim/device_layer.py` — add config attrs (near `:160-169`), `_park_lightsheet_sync`, `_grab_lightsheet_frame_sync`, `_lightsheet_streamer`, `_broadcast_lightsheet`, `handle_lightsheet_stream`, `handle_lightsheet_params`; register two routes (near `:2806`).
+- Test: `tests/test_lightsheet_streamer.py`
+- Reference (mirror): `_bottom_camera_streamer`/`_broadcast_camera`/`handle_bottom_camera_stream`/`_encode_frame_for_stream` (same file); sequence-acq calls in `devices/acquisition.py:186-254`.
+
+**Interfaces:**
+- Consumes: `self.system.core` (`pymmcore.CMMCore`), `self.devices["camera"]` / `["scanner"]` / `["piezo"]`, `self._state_pause_counter`, `self._encode_frame_for_stream` (reused verbatim), `_safe_obtain` (rpyc unwrap, imported as in `acquisition.py`).
+- Produces: SSE `GET /api/lightsheet/stream`; `POST /api/lightsheet/live/params` `{galvo, piezo, exposure}`; in-process live param state `self._ls_params`.
+
+> **Implementer confirmations (cannot be verified off-rig — confirm against the real code, do not guess silently):**
+> 1. The device-layer core handle (`self.system.core`) and that `pymmcore.CMMCore` exposes `startContinuousSequenceAcquisition(float)`, `getLastImage()`, `stopSequenceAcquisition()`, `isSequenceRunning()` (standard CMMCore API). If `getLastImage` is unavailable, use `getLastImageMD`/`getNBeforeLastImage`.
+> 2. The scanner/piezo park calls: `self.devices["scanner"].sa_offset_y.setPosition(deg)` and `self.devices["piezo"].setPosition(z)`, and `set_spim_state("Idle")` on both (from `devices/scanner.py:271`, `devices/piezo.py:226`, recon §3).
+> 3. Whether brightfield live needs the scanner/beam enabled or a static park — confirm against `../micro-manager/plugins/ASIdiSPIM/src/main/java/org/micromanager/asidispim/SetupPanel.java`. Default: static park, laser "ALL OFF".
+
+- [ ] **Step 1: Write the failing test (fake core + fake devices)**
+
+```python
+# tests/test_lightsheet_streamer.py
+import asyncio, numpy as np, pytest
+from gently.hardware.dispim.device_layer import DeviceLayer # confirm class name/import
+
+
+class FakeCore:
+ def __init__(self):
+ self.running = False
+ self.exposure = None
+ self.cam = None
+ self._frame = np.full((64, 64), 1000, dtype=np.uint16)
+ self.started = 0
+ self.stopped = 0
+
+ def setCameraDevice(self, n):
+ self.cam = n
+
+ def getCameraDevice(self):
+ return self.cam
+
+ def setExposure(self, n, ms):
+ self.exposure = ms
+
+ def startContinuousSequenceAcquisition(self, interval):
+ self.running = True
+ self.started += 1
+
+ def stopSequenceAcquisition(self):
+ self.running = False
+ self.stopped += 1
+
+ def isSequenceRunning(self):
+ return self.running
+
+ def getLastImage(self):
+ return self._frame
+
+
+class FakeAxis:
+ def __init__(self):
+ self.pos = None
+
+ def setPosition(self, v):
+ self.pos = v
+
+
+class FakeScanner:
+ def __init__(self):
+ self.sa_offset_y = FakeAxis()
+ self.name = "Scanner"
+ self.state = None
+
+ def set_spim_state(self, s):
+ self.state = s
+
+
+class FakePiezo(FakeAxis):
+ def __init__(self):
+ super().__init__()
+ self.name = "Piezo"
+ self.state = None
+
+ def set_spim_state(self, s):
+ self.state = s
+
+
+def _streamer(dl):
+ dl.system = type("S", (), {"core": FakeCore()})()
+ dl.devices = {
+ "camera": type("C", (), {"name": "HamCam1"})(),
+ "scanner": FakeScanner(),
+ "piezo": FakePiezo(),
+ }
+ return dl
+
+
+async def test_grab_parks_and_peeks(monkeypatch):
+ dl = _streamer(DeviceLayer.__new__(DeviceLayer))
+ dl._state_pause_counter = 0
+ dl._ls_target_max_dim = 512
+ dl._ls_jpeg_quality = 70
+ dl._ls_params = {"galvo": 1.5, "piezo": 40.0, "exposure": 20.0}
+ dl._ls_seq_started = False
+ dl._ls_applied = {}
+ img = await asyncio.to_thread(dl._grab_lightsheet_frame_sync)
+ assert img is not None and img.shape == (64, 64)
+ assert dl.system.core.running is True # sequence started
+ assert dl.devices["piezo"].pos == 40.0 # piezo parked
+ assert dl.devices["scanner"].sa_offset_y.pos == 1.5 # galvo parked
+
+
+async def test_exposure_change_restarts_sequence():
+ dl = _streamer(DeviceLayer.__new__(DeviceLayer))
+ dl._state_pause_counter = 0
+ dl._ls_target_max_dim = 512
+ dl._ls_jpeg_quality = 70
+ dl._ls_params = {"galvo": 0.0, "piezo": 50.0, "exposure": 10.0}
+ dl._ls_seq_started = False
+ dl._ls_applied = {}
+ await asyncio.to_thread(dl._grab_lightsheet_frame_sync)
+ starts = dl.system.core.started
+ dl._ls_params["exposure"] = 30.0 # exposure change
+ await asyncio.to_thread(dl._grab_lightsheet_frame_sync)
+ assert dl.system.core.stopped >= 1 and dl.system.core.started == starts + 1
+ assert dl.system.core.exposure == 30.0
+```
+
+- [ ] **Step 2: Run to verify it fails**
+
+Run: `pytest tests/test_lightsheet_streamer.py -v`
+Expected: FAIL — `AttributeError: _grab_lightsheet_frame_sync` (or import).
+
+- [ ] **Step 3: Implement the streamer**
+
+Add config attrs in `__init__` (near `:169`, after the `_cam_*` block):
+```python
+# Lightsheet (SPIM) live stream — continuous sequence acquisition.
+self._ls_subscribers: list[asyncio.Queue] = []
+self._ls_task: asyncio.Task | None = None
+self._ls_interval_sec: float = 0.0 # peek as fast as exposure allows
+self._ls_target_max_dim: int = 512
+self._ls_jpeg_quality: int = 70
+self._ls_params: dict = {"galvo": 0.0, "piezo": 50.0, "exposure": 20.0}
+self._ls_seq_started: bool = False
+self._ls_applied: dict = {} # last-applied galvo/piezo/exposure
+```
+
+Add the grab/park/peek (mirrors the sequence-acq calls from `acquisition.py`; uses `self.system.core`):
+```python
+def _park_lightsheet_sync(self) -> None:
+ """Park scanner galvo + imaging piezo at the current live params (static sheet)."""
+ p = self._ls_params
+ scanner = self.devices.get("scanner")
+ piezo = self.devices.get("piezo")
+ if scanner is not None:
+ try:
+ scanner.set_spim_state("Idle")
+ except Exception:
+ pass
+ scanner.sa_offset_y.setPosition(float(p["galvo"]))
+ if piezo is not None:
+ try:
+ piezo.set_spim_state("Idle")
+ except Exception:
+ pass
+ piezo.setPosition(float(p["piezo"]))
+
+
+def _ensure_lightsheet_sequence_sync(self) -> None:
+ """Start (or restart on exposure change) the continuous sequence on the SPIM camera."""
+ core = self.system.core
+ cam = self.devices.get("camera")
+ if cam is None:
+ raise RuntimeError("No lightsheet camera configured")
+ p = self._ls_params
+ need_restart = not self._ls_seq_started or self._ls_applied.get("exposure") != p["exposure"]
+ if need_restart:
+ if core.isSequenceRunning():
+ core.stopSequenceAcquisition()
+ if core.getCameraDevice() != cam.name:
+ core.setCameraDevice(cam.name)
+ core.setExposure(cam.name, float(p["exposure"]))
+ core.startContinuousSequenceAcquisition(self._ls_interval_sec * 1000.0)
+ self._ls_seq_started = True
+ self._ls_applied["exposure"] = p["exposure"]
+
+
+def _grab_lightsheet_frame_sync(self):
+ """Park → ensure sequence running → peek the latest frame (never drain)."""
+ try:
+ self._park_lightsheet_sync() # galvo/piezo applied live
+ self._ensure_lightsheet_sequence_sync() # start / restart on exposure
+ from gently.hardware.dispim.devices.acquisition import _safe_obtain
+
+ core = self.system.core
+ img = core.getLastImage()
+ try:
+ img = _safe_obtain(img)
+ except (ImportError, AttributeError):
+ pass
+ return np.asarray(img)
+ except Exception as exc:
+ logger.debug("Lightsheet grab failed: %s", exc)
+ return None
+
+
+def _stop_lightsheet_sequence_sync(self) -> None:
+ try:
+ if self.system.core.isSequenceRunning():
+ self.system.core.stopSequenceAcquisition()
+ except Exception:
+ logger.debug("stop lightsheet sequence failed", exc_info=True)
+ self._ls_seq_started = False
+ self._ls_applied = {}
+```
+
+Add the streamer loop + broadcast (mirror `_bottom_camera_streamer`/`_broadcast_camera`, reusing `_encode_frame_for_stream`):
+```python
+async def _lightsheet_streamer(self):
+ logger.info("Lightsheet streamer started")
+ try:
+ while self._ls_subscribers:
+ if self._state_pause_counter > 0:
+ # Heavy plan owns MMCore: release the sequence and back off.
+ if self._ls_seq_started:
+ await asyncio.to_thread(self._stop_lightsheet_sequence_sync)
+ await asyncio.sleep(0.1)
+ continue
+ tick = time.monotonic()
+ img = await asyncio.to_thread(self._grab_lightsheet_frame_sync)
+ payload = self._encode_frame_for_stream(img) if img is not None else None
+ if payload is not None:
+ await self._broadcast_lightsheet(payload)
+ elapsed = time.monotonic() - tick
+ # Pace to at least the exposure; peek-rate caps near the camera rate.
+ floor = max(self._ls_interval_sec, self._ls_params["exposure"] / 1000.0)
+ await asyncio.sleep(max(0.0, floor - elapsed))
+ except asyncio.CancelledError:
+ raise
+ except Exception:
+ logger.exception("Lightsheet streamer crashed")
+ finally:
+ await asyncio.to_thread(self._stop_lightsheet_sequence_sync)
+ logger.info("Lightsheet streamer exiting")
+
+
+async def _broadcast_lightsheet(self, payload):
+ if not self._ls_subscribers:
+ return
+ dead = []
+ for q in self._ls_subscribers:
+ try:
+ q.put_nowait(payload)
+ except asyncio.QueueFull:
+ try:
+ _ = q.get_nowait()
+ q.put_nowait(payload)
+ except Exception:
+ dead.append(q)
+ for q in dead:
+ try:
+ self._ls_subscribers.remove(q)
+ except ValueError:
+ pass
+```
+
+> `_encode_frame_for_stream` uses `self._cam_target_max_dim`/`self._cam_jpeg_quality`. To get the 512/70 lightsheet settings without duplicating the encoder, add an optional override: change its signature to `_encode_frame_for_stream(self, img, max_dim=None, quality=None)` defaulting to the `_cam_*` values, and call it `self._encode_frame_for_stream(img, self._ls_target_max_dim, self._ls_jpeg_quality)` from the lightsheet loop. (One-line change to the encoder; bottom-camera behavior unchanged.)
+
+Add the SSE handler + params handler (mirror `handle_bottom_camera_stream`; the params handler updates `self._ls_params` — galvo/piezo apply on the next grab, exposure triggers the restart path):
+```python
+async def handle_lightsheet_stream(self, request):
+ response = web.StreamResponse(
+ status=200,
+ reason="OK",
+ headers={
+ "Content-Type": "text/event-stream",
+ "Cache-Control": "no-cache",
+ "Connection": "keep-alive",
+ "X-Accel-Buffering": "no",
+ },
+ )
+ await response.prepare(request)
+ queue: asyncio.Queue = asyncio.Queue(maxsize=4)
+ self._ls_subscribers.append(queue)
+ if len(self._ls_subscribers) == 1 and (self._ls_task is None or self._ls_task.done()):
+ self._ls_task = asyncio.create_task(self._lightsheet_streamer(), name="lightsheet-streamer")
+ try:
+ await response.write(b": connected\n\n")
+ while True:
+ try:
+ payload = await asyncio.wait_for(queue.get(), timeout=10.0)
+ except asyncio.TimeoutError:
+ await response.write(b": keepalive\n\n")
+ continue
+ if payload is None:
+ break
+ await response.write(f"data: {json.dumps(payload)}\n\n".encode())
+ except (asyncio.CancelledError, ConnectionResetError, ConnectionAbortedError):
+ pass
+ except Exception:
+ logger.exception("Lightsheet SSE writer failed")
+ finally:
+ try:
+ self._ls_subscribers.remove(queue)
+ except ValueError:
+ pass
+ return response
+
+
+async def handle_lightsheet_params(self, request):
+ body = await request.json()
+ for k in ("galvo", "piezo", "exposure"):
+ if k in body and body[k] is not None:
+ self._ls_params[k] = float(body[k])
+ return web.json_response({"params": self._ls_params})
+```
+
+Register both routes near `:2806`:
+```python
+ self._app.router.add_get("/api/lightsheet/stream", self.handle_lightsheet_stream)
+ self._app.router.add_post("/api/lightsheet/live/params", self.handle_lightsheet_params)
+```
+
+- [ ] **Step 4: Run to verify it passes**
+
+Run: `pytest tests/test_lightsheet_streamer.py -v`
+Expected: PASS (2 passed). If `DeviceLayer.__new__` bypassing `__init__` leaves attrs unset, the test sets the needed ones explicitly (it does).
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/hardware/dispim/device_layer.py tests/test_lightsheet_streamer.py
+git commit -m "feat(manual-mode): device-layer lightsheet live streamer (continuous sequence acquisition)"
+```
+
+---
+
+### Task 3: Client methods — `stream_lightsheet` + `set_lightsheet_live_params`
+
+**Files:**
+- Modify: `gently/hardware/dispim/client.py` (add two methods on `DiSPIMMicroscope`, near `stream_bottom_camera` `:913`)
+- Test: `tests/test_lightsheet_client.py`
+
+**Interfaces:**
+- Produces: `async def stream_lightsheet(self, timeout=None)` (async generator over `GET /api/lightsheet/stream`, identical SSE parse to `stream_bottom_camera`); `async def set_lightsheet_live_params(self, galvo=None, piezo=None, exposure=None) -> dict` (`POST /api/lightsheet/live/params`).
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_lightsheet_client.py
+import pytest
+from gently.hardware.dispim.client import DiSPIMMicroscope
+
+
+async def test_set_params_posts_body(monkeypatch):
+ m = DiSPIMMicroscope.__new__(DiSPIMMicroscope)
+ sent = {}
+
+ async def fake_post(path, body):
+ sent["path"] = path
+ sent["body"] = body
+ return {"params": body}
+
+ m._api_post = fake_post # confirm the real low-level POST helper name
+ res = await m.set_lightsheet_live_params(galvo=1.0, piezo=42.0, exposure=15.0)
+ assert sent["path"] == "/api/lightsheet/live/params"
+ assert sent["body"] == {"galvo": 1.0, "piezo": 42.0, "exposure": 15.0}
+ assert res == {"params": {"galvo": 1.0, "piezo": 42.0, "exposure": 15.0}}
+
+
+def test_stream_lightsheet_is_async_generator():
+ m = DiSPIMMicroscope.__new__(DiSPIMMicroscope)
+ import inspect
+
+ assert inspect.isasyncgenfunction(m.stream_lightsheet)
+```
+
+> Confirm the real low-level POST helper (the recon shows `set_led` etc. POST via an internal helper — find whether it's `self._api_post(path, body)` or an inline `self._session.post`). Match it; if `set_lightsheet_live_params` should drop `None` keys, build the body from only the provided args (the test passes all three).
+
+- [ ] **Step 2: Run to verify it fails**
+
+Run: `pytest tests/test_lightsheet_client.py -v` → FAIL (no such methods).
+
+- [ ] **Step 3: Implement**
+
+```python
+async def stream_lightsheet(self, timeout: float | None = None):
+ """Async generator yielding JPEG frames from the lightsheet live SSE stream.
+
+ Mirrors :meth:`stream_bottom_camera`; subscriber-gated on the device layer.
+ """
+ self._ensure_connected()
+ client_timeout = aiohttp.ClientTimeout(total=None, sock_read=timeout, sock_connect=10.0)
+ url = f"{self.http_url}/api/lightsheet/stream"
+ async with self._session.get(url, timeout=client_timeout) as resp:
+ resp.raise_for_status()
+ buf = b""
+ async for chunk in resp.content.iter_any():
+ if not chunk:
+ continue
+ buf += chunk
+ while b"\n\n" in buf:
+ event_block, buf = buf.split(b"\n\n", 1)
+ data_lines = []
+ for line in event_block.splitlines():
+ if not line or line.startswith(b":"):
+ continue
+ if line.startswith(b"data:"):
+ data_lines.append(line[5:].lstrip())
+ if not data_lines:
+ continue
+ raw = b"\n".join(data_lines).decode("utf-8", errors="replace")
+ try:
+ import json as _json
+
+ yield _json.loads(raw)
+ except Exception as exc:
+ logger.warning("Malformed lightsheet SSE payload skipped: %s", exc)
+
+
+async def set_lightsheet_live_params(self, galvo=None, piezo=None, exposure=None) -> dict:
+ """POST live galvo/piezo/exposure to the device-layer lightsheet streamer."""
+ body = {}
+ if galvo is not None:
+ body["galvo"] = float(galvo)
+ if piezo is not None:
+ body["piezo"] = float(piezo)
+ if exposure is not None:
+ body["exposure"] = float(exposure)
+ return await self._api_post("/api/lightsheet/live/params", body)
+```
+
+> If the real POST helper isn't `_api_post`, adapt this one call site (and the test) to the real helper. `stream_lightsheet` copies `stream_bottom_camera` verbatim except the URL.
+
+- [ ] **Step 4: Run to verify it passes**
+
+Run: `pytest tests/test_lightsheet_client.py -v` (2 passed)
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/hardware/dispim/client.py tests/test_lightsheet_client.py
+git commit -m "feat(manual-mode): client stream_lightsheet + set_lightsheet_live_params"
+```
+
+---
+
+### Task 4: `LightSheetStreamMonitor` (agent Service) + agent wiring
+
+**Files:**
+- Create: `gently/app/lightsheet_monitor.py`
+- Modify: `gently/app/agent.py` (init attr; construct in `start_viz_server` near the bottom-camera monitor `:849-860`; stop in `stop_viz_server` near `:862-869`)
+- Test: `tests/test_lightsheet_monitor.py`
+- Reference (mirror verbatim, swapping names/event): `gently/app/bottom_camera_monitor.py`
+
+**Interfaces:**
+- Consumes: `microscope.stream_lightsheet()` (Task 3); `EventType.LIGHTSHEET_FRAME` (Task 1).
+- Produces: `LightSheetStreamMonitor(Service)` with `running` property, `on_start`/`on_stop`; publishes `LIGHTSHEET_FRAME`. `agent.lightsheet_monitor` (constructed, not started; started via proxy in Task 5).
+
+- [ ] **Step 1: Write the failing test**
+
+```python
+# tests/test_lightsheet_monitor.py
+import asyncio
+from gently.core.event_bus import EventType, get_event_bus
+from gently.app.lightsheet_monitor import LightSheetStreamMonitor
+
+
+class FakeScope:
+ async def stream_lightsheet(self):
+ for i in range(3):
+ yield {"t": float(i), "jpeg_b64": f"f{i}"}
+ await asyncio.sleep(0)
+
+
+async def test_monitor_publishes_frames():
+ bus = get_event_bus()
+ seen = []
+ bus.subscribe(EventType.LIGHTSHEET_FRAME, lambda e: seen.append(e.data))
+ mon = LightSheetStreamMonitor(FakeScope(), reconnect_delay_sec=0.01)
+ await mon.start()
+ await asyncio.sleep(0.05)
+ await mon.stop()
+ assert any(d.get("jpeg_b64") == "f0" for d in seen)
+ assert mon.running is False
+```
+
+- [ ] **Step 2: Run to verify it fails** — `pytest tests/test_lightsheet_monitor.py -v` → FAIL (no module).
+
+- [ ] **Step 3: Implement** — copy `gently/app/bottom_camera_monitor.py` to `gently/app/lightsheet_monitor.py` and change: class → `LightSheetStreamMonitor`; `name="lightsheet-monitor"`; the `_run` loop calls `self.microscope.stream_lightsheet()` and publishes `EventType.LIGHTSHEET_FRAME` with `source="lightsheet-monitor"`. (Everything else — Service base, on_start/on_stop, reconnect loop, `_last_frame_ts`, `running` — is identical.)
+
+Agent wiring in `gently/app/agent.py`: add `self.lightsheet_monitor = None` next to `self.bottom_camera_monitor = None`; in `start_viz_server` (after the bottom-camera monitor construction `:849-860`):
+```python
+if self.microscope is not None and self.lightsheet_monitor is None:
+ try:
+ from .lightsheet_monitor import LightSheetStreamMonitor
+
+ self.lightsheet_monitor = LightSheetStreamMonitor(self.microscope)
+ logger.info("Lightsheet monitor ready (not started)")
+ except Exception as e:
+ logger.warning(f"Failed to construct lightsheet monitor: {e}")
+ self.lightsheet_monitor = None
+```
+In `stop_viz_server` (near `:862`):
+```python
+ if self.lightsheet_monitor is not None:
+ try:
+ await self.lightsheet_monitor.stop()
+ except Exception:
+ logger.exception("Failed to stop lightsheet monitor")
+ self.lightsheet_monitor = None
+```
+
+- [ ] **Step 4: Run to verify it passes** — `pytest tests/test_lightsheet_monitor.py -v` (1 passed); `pytest -q` (no new failures).
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/app/lightsheet_monitor.py gently/app/agent.py tests/test_lightsheet_monitor.py
+git commit -m "feat(manual-mode): LightSheetStreamMonitor bridge + agent wiring"
+```
+
+---
+
+### Task 5: Browser proxy routes (`require_control`)
+
+**Files:**
+- Modify: `gently/ui/web/routes/data.py` (add routes in `create_router`, mirroring the bottom-camera + room-light routes)
+- Test: `tests/test_lightsheet_routes.py`
+- Reference: bottom-camera start/stop/status (`data.py:260-311`), room-light proxy (`data.py:335-355`), `_resolve_client` (`:313`), `require_control` (`:10`).
+
+**Interfaces:**
+- Consumes: `agent.lightsheet_monitor` (Task 4); `client.set_lightsheet_live_params`, `set_led`, `set_laser_power`, `set_camera_led_mode`, `move_to_position`, `acquire_burst`, `acquire_volume`.
+- Produces (all `Depends(require_control)` except GET status): `POST /api/devices/lightsheet/live/{start,stop}`, `GET /api/devices/lightsheet/live/status`, `POST /api/devices/lightsheet/live/params`, `POST /api/devices/led/set`, `POST /api/devices/laser/off`, `POST /api/devices/camera/led_mode`, `POST /api/devices/stage/move`, `POST /api/devices/acquire/{burst,volume}`.
+
+- [ ] **Step 1: Write the failing test (TestClient + mock client/monitor)**
+
+```python
+# tests/test_lightsheet_routes.py
+from unittest.mock import MagicMock, AsyncMock
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+from gently.ui.web.routes.data import create_router
+import gently.ui.web.auth as auth
+
+
+def _app(client=None, monitor=None):
+ server = MagicMock()
+ server.agent_bridge.agent.client = client
+ server.agent_bridge.agent.lightsheet_monitor = monitor
+ app = FastAPI()
+ app.include_router(create_router(server))
+ # legacy localhost = CONTROL; TestClient client.host is "testclient" → force CONTROL:
+ app.dependency_overrides[auth.require_control] = lambda: True
+ return TestClient(app)
+
+
+def test_live_params_forwards():
+ client = MagicMock()
+ client.set_lightsheet_live_params = AsyncMock(return_value={"params": {}})
+ r = _app(client=client).post(
+ "/api/devices/lightsheet/live/params", json={"galvo": 1.0, "piezo": 40.0, "exposure": 20.0}
+ )
+ assert r.status_code == 200
+ client.set_lightsheet_live_params.assert_awaited_once_with(galvo=1.0, piezo=40.0, exposure=20.0)
+
+
+def test_acquire_burst_forwards():
+ client = MagicMock()
+ client.acquire_burst = AsyncMock(return_value={"success": True, "request_id": "b1"})
+ r = _app(client=client).post(
+ "/api/devices/acquire/burst",
+ json={"frames": 60, "mode": "1hz", "num_slices": 1, "exposure_ms": 5.0},
+ )
+ assert r.status_code == 200 and r.json().get("request_id") == "b1"
+
+
+def test_live_start_requires_monitor():
+ r = _app(monitor=None).post("/api/devices/lightsheet/live/start")
+ assert r.status_code == 503
+```
+
+> Confirm the `require_control` override mechanism: in legacy mode `TestClient` requests are not localhost, so override the dependency (as above) to isolate route logic. A separate test can assert the gate by NOT overriding and expecting 403.
+
+- [ ] **Step 2: Run to verify it fails** — `pytest tests/test_lightsheet_routes.py -v` → FAIL (routes 404).
+
+- [ ] **Step 3: Implement** — in `create_router`, add (mirroring the referenced routes). Live start/stop/status copy the bottom-camera versions verbatim, swapping `bottom_camera_monitor` → `lightsheet_monitor`. Then:
+```python
+@router.post("/api/devices/lightsheet/live/params", dependencies=[Depends(require_control)])
+async def lightsheet_live_params(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ res = await client.set_lightsheet_live_params(
+ galvo=payload.get("galvo"), piezo=payload.get("piezo"), exposure=payload.get("exposure")
+ )
+ except Exception as exc:
+ logger.exception("lightsheet live params failed")
+ raise HTTPException(status_code=502, detail=f"params failed: {exc}") from exc
+ return res
+
+
+@router.post("/api/devices/led/set", dependencies=[Depends(require_control)])
+async def led_set(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.set_led(str(payload.get("state", "Closed")))
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"led failed: {exc}") from exc
+
+
+@router.post("/api/devices/laser/off", dependencies=[Depends(require_control)])
+async def laser_off():
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.set_laser_power(488, 0) # confirm signature; force off
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"laser off failed: {exc}") from exc
+
+
+@router.post("/api/devices/camera/led_mode", dependencies=[Depends(require_control)])
+async def camera_led_mode(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.set_camera_led_mode(bool(payload.get("use_led", False)))
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"camera led mode failed: {exc}") from exc
+
+
+@router.post("/api/devices/stage/move", dependencies=[Depends(require_control)])
+async def stage_move(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.move_to_position(float(payload["x"]), float(payload["y"]))
+ except KeyError:
+ raise HTTPException(status_code=400, detail="x and y required")
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"stage move failed: {exc}") from exc
+
+
+@router.post("/api/devices/acquire/burst", dependencies=[Depends(require_control)])
+async def acquire_burst(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.acquire_burst(
+ frames=int(payload.get("frames", 60)),
+ mode=str(payload.get("mode", "1hz")),
+ num_slices=int(payload.get("num_slices", 1)),
+ exposure_ms=float(payload.get("exposure_ms", 5.0)),
+ )
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"burst failed: {exc}") from exc
+
+
+@router.post("/api/devices/acquire/volume", dependencies=[Depends(require_control)])
+async def acquire_volume(payload: dict = Body(...)): # noqa: B008
+ client = _resolve_client()
+ if client is None:
+ raise HTTPException(status_code=503, detail="Microscope not connected")
+ try:
+ return await client.acquire_volume(
+ num_slices=int(payload.get("num_slices", 50)),
+ exposure_ms=float(payload.get("exposure_ms", 10.0)),
+ )
+ except Exception as exc:
+ raise HTTPException(status_code=502, detail=f"volume failed: {exc}") from exc
+```
+Add the live start/stop/status routes by copying `start_bottom_camera_stream`/`stop_bottom_camera_stream`/`get_bottom_camera_status` (`data.py:260-311`) under `/api/devices/lightsheet/live/...` with `getattr(agent, "lightsheet_monitor", None)`.
+
+- [ ] **Step 4: Run to verify it passes** — `pytest tests/test_lightsheet_routes.py -v` (3 passed); `pytest -q` (no new failures).
+
+- [ ] **Step 5: Commit**
+
+```bash
+git add gently/ui/web/routes/data.py tests/test_lightsheet_routes.py
+git commit -m "feat(manual-mode): require_control proxy routes for lightsheet live + illumination + acquire"
+```
+
+---
+
+### Task 6: Manual view (frontend)
+
+**Files:**
+- Modify: `gently/ui/web/templates/index.html` — add a `data-view="manual"` button to `#devices-view-switcher` (`:445-449`); add a `#devices-view-manual` container with the live canvas + control rail (model the camera panel `:569-608`); load A's `temperature-graph.js` if not already loaded on this page.
+- Modify: `gently/ui/web/static/js/devices.js` — add `'manual'` to `VIEWS` (`:17`); a `handleLightsheetFrame` (mirror `handleCameraFrame` `:1111`); live toggle (mirror `toggleCameraStream`); galvo/piezo/exposure controls (debounced POST `live/params`); illumination toggles; acquire buttons; FPS readout; embed `TemperatureGraph.init`; a `'v'`-style key handled only if not deferred — leave existing keys, add nothing conflicting.
+- Modify: the devices stylesheet for the manual panel (reuse `.devices-camera-*` styles where possible).
+
+**No JS unit harness** — verified by `node --check` + a Chrome-MCP harness (like A) + a UI audit.
+
+- [ ] **Step 1: Markup** — add to `#devices-view-switcher`:
+```html
+
+```
+Add the view container after `#devices-view-optical3d` (`:716`-ish), with: a live ``;
+ html += `
`;
html += `
${shortName}
${latestStage}
${reasoning.length} eval
+ ${isTerminated ? `${termBadge}` : ''}
`;
html += ``;
@@ -1000,7 +1097,7 @@ const EmbryosManager = {
intervalSeconds: embryoData.interval_seconds || this.state.baseInterval,
timepoints: embryoData.timepoints || 0,
isComplete: embryoData.is_complete || false,
- completionReason: null,
+ completionReason: embryoData.completion_reason || null,
firstAcquired: embryoData.first_acquired ? new Date(embryoData.first_acquired) : null,
lastAcquired: embryoData.last_acquired ? new Date(embryoData.last_acquired) : null,
detections: embryoData.detections || {},
@@ -2726,10 +2823,17 @@ const EmbryosManager = {
`;
}
- // Format confidence display
- const confDisplay = typeof item.confidence === 'number'
- ? `${Math.round(item.confidence * 100)}%`
- : (item.confidence || 'Unknown');
+ // Format confidence display. Hide entirely when the detector
+ // doesn't emit a probabilistic confidence (e.g. dopaminergic_signal
+ // returns structured intensity/structure findings instead) — the
+ // string "Unknown confidence" was actively confusing.
+ const hasNumericConf = typeof item.confidence === 'number';
+ const hasTextConf = typeof item.confidence === 'string' && item.confidence.trim() !== '';
+ const confHtml = hasNumericConf
+ ? `${Math.round(item.confidence * 100)}% confidence`
+ : hasTextConf
+ ? `${item.confidence}`
+ : '';
return `
`
- : '';
-
- tr.innerHTML = `
- ${formatEventTime(event.timestamp)}
- ${imageIndicator}${event.event_type}
- ${event.source || '-'}
- ${thumbnailHtml}
- `;
-
- // Click to expand data
- tr.addEventListener('click', () => {
- const dataDiv = tr.querySelector('.event-data');
- dataDiv.classList.toggle('expanded');
- if (dataDiv.classList.contains('expanded')) {
- dataDiv.innerHTML = `${formatEventTime(event.timestamp)}
+ ${label}
+ ${event.source || '-'}
+ ${formatEventTime(event.timestamp)}
+ ${imageIndicator}${event.event_type}
+ ${event.source || '-'}
+ ${thumbnailHtml}
+ `;
+
+ // Click to expand data
+ tr.addEventListener('click', () => {
+ const dataDiv = tr.querySelector('.event-data');
+ dataDiv.classList.toggle('expanded');
+ if (dataDiv.classList.contains('expanded')) {
+ dataDiv.innerHTML = ` is active
+ _subscribed: false, // guard: prevents double-registration across tab re-clicks
+ _planRefreshTimer: null, // debounce handle for tactic-event-driven refetch
+ _tempUpdateHandler: null,// stored handler ref so it can be off()'d if needed
+ _rosterEmbryos: [], // embryos from /api/embryos/positions (D2 roster lens)
+ _rolesMap: null, // Map(role name → registry obj) from /api/roles (D2 roster lens)
+ _currentSessionId: null, // session_id from /api/operation_plan/current (always, even idle)
+ _planPickerOpen: false, // whether the plan-link picker is visible
+ _pickerItems: null, // flat plan items for the picker (null=not loaded)
+ _expandedTacticIds: new Set(), // tactic expand-keys for click-to-expand (survives refresh)
async init() {
console.log('[ExperimentOverview] init() called, view=', this.activeView);
- const strategy = await this.loadStrategy();
+
+ // Scenario dev mode: ?scenario= renders a fixture with no fetch.
+ // Guard against double-registration when the tab is clicked repeatedly.
+ const scenarioParam = new URLSearchParams(location.search).get('scenario');
+ if (scenarioParam && window.OPERATIONS_SCENARIOS &&
+ Object.prototype.hasOwnProperty.call(window.OPERATIONS_SCENARIOS, scenarioParam)) {
+ this.scenarioMode = true;
+ this.activePlan = window.OPERATIONS_SCENARIOS[scenarioParam];
+ this.activeStrategy = null;
+ this.isLive = false;
+ this.render(null);
+ this.initialized = true;
+ return;
+ }
+
+ this.scenarioMode = false;
+ // Fetch plan (overview) and strategy (rules) in parallel so tab-switching
+ // between the two views doesn't require a second round-trip.
+ // D2: also fetch roster + roles for the roster lens.
+ const [plan, strategy, rosterEmbryos, rolesMap] = await Promise.all([
+ this.loadPlan(),
+ this.loadStrategy(),
+ this._loadRoster(),
+ this._loadRolesMap(),
+ ]);
+ this.activePlan = plan;
this.activeStrategy = strategy;
+ this._rosterEmbryos = rosterEmbryos;
+ this._rolesMap = rolesMap;
+ this.isLive = plan !== null || strategy !== null;
this.render(strategy);
this.initialized = true;
+
+ // Subscribe to tactic-state events once per page load.
+ // Guard: _subscribed prevents double-registration across tab re-clicks.
+ // Skip entirely in scenario mode — no live backend, no websocket.
+ if (!this._subscribed) {
+ this._subscribed = true;
+ const refresh = () => this._debouncedRefresh();
+ // Plan-changing events: re-fetch the whole plan after debounce.
+ // CONTEXT_UPDATED fires when OperationPlanUpdater patches the plan.
+ // The tactic-lifecycle events fire on transitions the updater also
+ // reacts to, so they all funnel into the same debounced refetch.
+ const TACTIC_EVENTS = [
+ 'CONTEXT_UPDATED',
+ 'TEMP_PROTOCOL_STARTED', 'TEMP_PROTOCOL_COMPLETED',
+ 'BURST_START', 'BURST_COMPLETE',
+ 'EMBRYO_CADENCE_CHANGED', 'TEMPERATURE_SETPOINT_CHANGED',
+ 'POWER_RAMP_STEP',
+ ];
+ TACTIC_EVENTS.forEach(ev => ClientEventBus.on(ev, refresh));
+
+ // High-frequency temperature binding (~1 Hz).
+ // Updates the active scripted_protocol tactic's temperature gauge
+ // IN PLACE — no plan refetch, no full re-render.
+ this._tempUpdateHandler = (data) => this._handleTempUpdate(data);
+ ClientEventBus.on('TEMPERATURE_UPDATE', this._tempUpdateHandler);
+ }
},
async loadStrategy() {
@@ -164,26 +94,98 @@ const ExperimentOverview = {
cache: 'no-store'
});
if (!resp.ok) {
- console.warn(
- '[ExperimentOverview] strategy fetch returned',
- resp.status, '- falling back to stub'
- );
- this.isLive = false;
- return STUB_STRATEGY;
+ // No active experiment / not ready yet — show the empty state,
+ // never stubbed data.
+ console.warn('[ExperimentOverview] strategy fetch returned', resp.status);
+ return null;
}
const data = await resp.json();
- this.isLive = true;
return data;
} catch (e) {
- console.warn(
- '[ExperimentOverview] strategy fetch error - falling back to stub:',
- e
- );
- this.isLive = false;
- return STUB_STRATEGY;
+ console.warn('[ExperimentOverview] strategy fetch error:', e);
+ return null;
}
},
+ // Fetch the agent-authored Operation Plan for the current session.
+ // Returns the plan object (plan.tactics etc.) or null when unavailable.
+ // Always captures data.session_id in _currentSessionId so the Linked-plans
+ // panel can work even when no operation plan is active.
+ async loadPlan() {
+ try {
+ const resp = await fetch('/api/operation_plan/current', { cache: 'no-store' });
+ if (!resp.ok) {
+ console.warn('[ExperimentOverview] plan fetch returned', resp.status);
+ return null;
+ }
+ const data = await resp.json();
+ // Capture session_id regardless of plan availability — used by the
+ // Linked-plans panel which is session-scoped, not plan-scoped.
+ this._currentSessionId = data.session_id || null;
+ if (!data.available) return null;
+ return data.plan || null;
+ } catch (e) {
+ console.warn('[ExperimentOverview] plan fetch error:', e);
+ return null;
+ }
+ },
+
+ // Debounced plan refetch — coalesces rapid tactic-event bursts into a single
+ // fetch+render. 500 ms window matches experiment-strip.js convention.
+ // D2: also re-fetches the embryo roster so the lens stays current.
+ _debouncedRefresh() {
+ if (this._planRefreshTimer) clearTimeout(this._planRefreshTimer);
+ this._planRefreshTimer = setTimeout(async () => {
+ this._planRefreshTimer = null;
+ const [plan, rosterEmbryos] = await Promise.all([
+ this.loadPlan(),
+ this._loadRoster(),
+ ]);
+ this.activePlan = plan;
+ this._rosterEmbryos = rosterEmbryos;
+ this.isLive = plan !== null;
+ this.render(this.activeStrategy);
+ }, 500);
+ },
+
+ // In-place temperature gauge update — called at ~1 Hz by TEMPERATURE_UPDATE.
+ // Finds the active scripted_protocol tactic's temperature readout in the DOM
+ // and rewrites only that element's value, never refetching the plan.
+ // No-op when there is no active scripted_protocol tactic with temperature binding.
+ _handleTempUpdate(data) {
+ if (!data || !data.sample) return;
+ const plan = this.activePlan;
+ if (!plan || !Array.isArray(plan.tactics)) return;
+ // Only act when an active scripted_protocol tactic declares temperature binding.
+ const activeTactic = plan.tactics.find(
+ t => t.state === 'active'
+ && t.kind === 'scripted_protocol'
+ && Array.isArray(t.live_bind)
+ && t.live_bind.includes('temperature')
+ );
+ if (!activeTactic) return;
+
+ const root = document.getElementById('experiment-overview-root');
+ if (!root) return;
+ // _renderOpsReadout stamps data-livebind="temperature" on the gauge div
+ // when the readout label normalises to "temperature".
+ const gauge = root.querySelector('.ops-node.active .ops-gauge[data-livebind="temperature"]');
+ if (!gauge) return;
+ const gv = gauge.querySelector('.ops-gv');
+ if (!gv) return;
+
+ const s = data.sample;
+ const water = s.water_c != null
+ ? parseFloat(s.water_c).toFixed(1) + '°C'
+ : '—';
+ const sp = s.setpoint_c != null
+ ? ' → '
+ + parseFloat(s.setpoint_c).toFixed(1)
+ + '°C'
+ : '';
+ gv.innerHTML = water + sp;
+ },
+
setView(view) {
if (view === this.activeView) return;
this.activeView = view;
@@ -193,7 +195,7 @@ const ExperimentOverview = {
});
// Re-render against the last fetched strategy (no re-fetch on tab
// switch — refresh happens on tab activation in the bootstrap).
- this.render(this.activeStrategy || STUB_STRATEGY);
+ this.render(this.activeStrategy);
},
render(s) {
@@ -204,13 +206,32 @@ const ExperimentOverview = {
}
// Tear down any prior ticker before we blow away the SVG it pointed at.
this._stopNowTicker();
+ // Reset plan-picker state on each full render so the picker doesn't persist
+ // across tactic-event-driven re-renders.
+ this._planPickerOpen = false;
+ this._pickerItems = null;
+ // Rules view requires the strategy snapshot; show an empty state when absent.
+ // Overview view uses this.activePlan — the null/empty case is handled inside
+ // _renderOperationSpine (it renders the idle state).
+ if (this.activeView === 'rules' && !s) {
+ root.innerHTML = '
+
`
+ : `
What are we doing today?'; + } + + function setScreen(name) { if (el) el.dataset.screen = name; } + function planActive() { + return !!el && el.dataset.screen === 'plan' && !el.classList.contains('dismissed') + && el.style.display !== 'none'; + } + + function dismiss() { + if (!el || el.classList.contains('dismissed')) return; + el.classList.add('dismissed'); + let done = false; + const finish = () => { + if (done) return; + done = true; + el.style.display = 'none'; + el.setAttribute('aria-hidden', 'true'); + }; + el.addEventListener('transitionend', finish, { once: true }); + setTimeout(finish, 650); + } + + // ── status / error helpers ──────────────────────────────────────── + function setThinkingLabel(text) { + const l = document.querySelector('#v2-plan-thinking .v2-plan-thinking-label'); + if (l && text) l.textContent = text; + } + // Elapsed-time counter so a long think reads as progress, not a hang. Starts + // when the thinking indicator first shows and runs until it's hidden (turn end). + let _thinkTimer = null; + let _thinkStart = 0; + function _thinkTick() { + const t = $('v2-plan-thinking'); + if (!t) return; + let el = t.querySelector('.v2-plan-elapsed'); + if (!el) { + el = document.createElement('span'); + el.className = 'v2-plan-elapsed'; + el.style.cssText = 'margin-left:6px;opacity:.55;font-variant-numeric:tabular-nums;'; + t.appendChild(el); + } + const s = Math.round((Date.now() - _thinkStart) / 1000); + el.textContent = s > 0 ? s + 's' : ''; + } + function showThinking(on, label) { + const t = $('v2-plan-thinking'); + if (t) t.classList.toggle('hidden', !on); + if (on && label) setThinkingLabel(label); + if (on) { + if (!_thinkTimer) { + _thinkStart = Date.now(); + _thinkTick(); + _thinkTimer = setInterval(_thinkTick, 1000); + } + } else if (_thinkTimer) { + clearInterval(_thinkTimer); + _thinkTimer = null; + const el = t && t.querySelector('.v2-plan-elapsed'); + if (el) el.textContent = ''; + } + } + // Human-readable "what's happening right now" from a tool activity event, + // so the status line names the live operation instead of a static string. + function prettyTool(act) { + const raw = (act && (act.label || act.name)) || 'the next step'; + const s = String(raw).replace(/_/g, ' ').trim(); + return s.charAt(0).toUpperCase() + s.slice(1) + '…'; + } + function errorVisible() { const e = $('v2-plan-error'); return !!e && !e.classList.contains('hidden'); } + function showPlanError(msg) { + const e = $('v2-plan-error'); if (!e) return; + e.textContent = msg; e.classList.remove('hidden'); + showThinking(false); + } + function hidePlanError() { const e = $('v2-plan-error'); if (e) e.classList.add('hidden'); } + + function clearAsk() { const m = $('v2-plan-ask'); if (m) m.innerHTML = ''; } + function resetSummary() { + const list = $('v2-plan-summary'); + if (list) list.innerHTML = '
'); + } + + // Plan-writing tools → refresh THE PLAN panel during the turn (debounced), + // not only at turn_end (ask_user_choice pauses the turn before it ends). + const PLAN_TOOLS = new Set([ + 'create_campaign', 'create_plan_item', 'link_plan_items', 'update_plan_item', + 'delete_plan_item', 'propose_plan', 'get_plan_status', 'validate_plan', + ]); + let planRefreshTimer = null; + function schedulePlanRefresh() { + if (planRefreshTimer) clearTimeout(planRefreshTimer); + planRefreshTimer = setTimeout(() => { planRefreshTimer = null; refreshPlanPanel(); }, 600); + } + + function safeStringify(v) { + try { + const s = (typeof v === 'string') ? v : JSON.stringify(v, null, 2); + return s.length > 4000 ? s.slice(0, 4000) + '\n…' : s; + } catch (e) { return String(v); } + } + function fillToolBody(body, act) { + body.innerHTML = ''; + // grid-template-rows reveal (landing.css) needs ONE collapsible child — + // append blocks into a single inner wrapper, not directly onto body. + const inner = document.createElement('div'); + body.appendChild(inner); + const inputStr = (act.input != null) ? safeStringify(act.input) : ''; + const full = act.full || act.summary || ''; + const block = (label, text) => { + const l = document.createElement('div'); l.className = 'v2-act-block-label'; l.textContent = label; + const b = document.createElement('pre'); b.className = 'v2-act-block'; b.textContent = text; + inner.append(l, b); + }; + if (inputStr) block('input', inputStr); + if (full) block('result', full); + if (!inputStr && !full) { + const e = document.createElement('div'); e.className = 'v2-act-block-label'; e.textContent = 'no details'; + inner.append(e); + } + } + function buildToolCard(act, done) { + const card = document.createElement('div'); + card.className = 'v2-act-tool' + (done ? (act.is_error ? ' done err' : ' done') : ''); + const head = document.createElement('button'); + head.className = 'v2-act-tool-head'; head.type = 'button'; + head.setAttribute('aria-expanded', 'false'); + const ic = document.createElement('span'); ic.className = 'v2-act-ic'; + ic.innerHTML = done ? (act.is_error ? '⚠' : '✓') : ''; + const label = document.createElement('span'); label.className = 'v2-act-label'; + label.textContent = act.label || act.name || 'tool'; + const sum = document.createElement('span'); sum.className = 'v2-act-summary'; + sum.textContent = done ? (act.summary || '') : ''; + const chev = document.createElement('span'); chev.className = 'v2-act-chev'; chev.textContent = '›'; + head.append(ic, label, sum, chev); + const body = document.createElement('div'); body.className = 'v2-act-tool-body'; + fillToolBody(body, act); + head.addEventListener('click', () => { + const open = card.classList.toggle('open'); + head.setAttribute('aria-expanded', open ? 'true' : 'false'); + }); + card.append(head, body); + return card; + } + function updateToolCard(card, act) { + card.classList.add('done'); + if (act.is_error) card.classList.add('err'); + const ic = card.querySelector('.v2-act-ic'); if (ic) ic.textContent = act.is_error ? '⚠' : '✓'; + const sum = card.querySelector('.v2-act-summary'); if (sum) sum.textContent = act.summary || ''; + const body = card.querySelector('.v2-act-tool-body'); if (body) fillToolBody(body, act); + } + function captureCampaignId(text) { + if (!text) return; + const s = String(text); + const m = s.match(/campaign_id[=:\s]+([0-9a-f]{6,})/i) || s.match(/\(id:\s*([0-9a-f]{6,})/i); + if (m) capturedCampaignId = m[1]; + } + + function applyActivity(act) { + if (!planActive() || !act) return; + const f = feedEl(); if (!f) return; + switch (act.kind) { + case 'turn_start': + feedTextEl = null; feedThinkingEl = null; pendingNewPage = true; hidePlanError(); clearFallback(); + clearPlanReady(); // new work in flight — drop any "ready" state + showThinking(true, 'reviewing your campaign and plan…'); + break; + case 'thinking': { + // Stream the model's reasoning summary live into the feed as a dim + // block, so the wait shows what the agent is actually considering. + showThinking(true); + const chunk = act.text || ''; + if (!chunk) { setThinkingLabel('thinking through the next step…'); break; } + if (!feedThinkingEl) { + feedThinkingEl = document.createElement('div'); + feedThinkingEl.className = 'v2-act-think'; + feedThinkingEl.style.cssText = + 'font-style:italic;opacity:.7;white-space:pre-wrap;margin:2px 0 8px;font-size:12.5px;line-height:1.5;'; + feedThinkingEl._raw = ''; + feedTarget().appendChild(feedThinkingEl); + } + feedThinkingEl._raw += chunk; + feedThinkingEl.textContent = feedThinkingEl._raw; + feedHadContent = true; + setThinkingLabel('reasoning…'); + scrollFeedIfNearBottom(); + break; + } + case 'text': { + const chunk = act.text || ''; + if (!chunk) break; + // The reasoning that immediately precedes the spoken answer is + // wrap-up meta ("let me wrap this up concisely and offer to + // export…") — drop the block entirely so the feed keeps the + // answer, not the narration of getting there. Reasoning that + // precedes a TOOL is left in place (tool_start only nulls the + // pointer) as the rationale for that action. + if (feedThinkingEl) { feedThinkingEl.remove(); feedThinkingEl = null; } + if (!feedTextEl) { + feedTextEl = document.createElement('div'); + feedTextEl.className = 'v2-act-text'; + feedTextEl._raw = ''; + feedTarget().appendChild(feedTextEl); + } + feedTextEl._raw += chunk; + feedTextEl.innerHTML = renderMd(feedTextEl._raw); + feedHadContent = true; showThinking(true, 'composing the response…'); scrollFeedIfNearBottom(); + break; + } + case 'tool_start': { + // ask_user_choice IS the active question (rendered separately in + // #v2-plan-ask) — don't also show it as a feed card. + if (act.name === 'ask_user_choice') break; + feedTextEl = null; feedThinkingEl = null; + const card = buildToolCard(act, false); + feedTarget().appendChild(card); + (runningTools[act.name] = runningTools[act.name] || []).push(card); + feedHadContent = true; showThinking(true, prettyTool(act)); scrollFeedIfNearBottom(); + break; + } + case 'tool_result': { + captureCampaignId(act.summary); + captureCampaignId(act.full); + if (PLAN_TOOLS.has(act.name)) schedulePlanRefresh(); + if (act.name === 'propose_plan' && !act.is_error) planProposed = true; + if (act.name === 'ask_user_choice') break; + feedTextEl = null; feedThinkingEl = null; + const arr = runningTools[act.name] || []; + const card = arr.pop(); + if (card) updateToolCard(card, act); + else feedTarget().appendChild(buildToolCard(act, true)); + feedHadContent = true; setThinkingLabel('working through the next step…'); scrollFeedIfNearBottom(); + break; + } + case 'turn_end': + showThinking(false); feedTextEl = null; feedThinkingEl = null; + refreshPlanPanel(); + if (!current && !feedHadContent) showFallback(); + // Plan proposed and the agent has settled (no pending question) → + // the design is done. Surface a clear "ready" state instead of + // leaving the user parked on the last wizard step. + if (planProposed && !current) showPlanReady(); + break; + case 'turn_error': + showPlanError(act.error || 'Something went wrong — open the conversation for detail.'); + break; + } + } + + function showFallback() { + const f = feedEl(); if (!f || f.querySelector('.v2-plan-fallback')) return; + const d = document.createElement('div'); + d.className = 'v2-plan-fallback'; + d.innerHTML = 'Gently replied in prose — open the conversation to read it.'; + d.querySelector('a').addEventListener('click', openChat); + feedTarget().appendChild(d); + } + + // ── plan-ready state ─────────────────────────────────────────────── + // Once the agent has proposed the plan and gone quiet, the wizard is done. + // Mark the screen "ready": rename the header, count phases/items from the + // panel, and promote "open workspace" to the obvious primary action — so the + // finish line is signposted instead of looking like one more wizard step. + function planCounts() { + let phases = 0, items = 0; + planPages.forEach(p => { + if (p.name !== 'Tasks') phases++; + items += (p.items || []).length; + }); + return { phases, items }; + } + function showPlanReady() { + const sec = document.querySelector('.v2-screen-plan'); + if (!sec) return; + sec.classList.add('ready'); + showThinking(false); + const who = sec.querySelector('.v2-plan-who'); + const title = sec.querySelector('.v2-plan-title'); + if (who) who.textContent = 'Gently · plan ready'; + if (title) { + const { phases, items } = planCounts(); + title.textContent = items + ? `Your plan is ready — ${items} item${items === 1 ? '' : 's'} across ${phases} phase${phases === 1 ? '' : 's'}` + : 'Your plan is ready'; + } + const cont = $('v2-plan-continue'); + if (cont) cont.textContent = 'Open the workspace ›'; + const exp = $('v2-plan-export'); + if (exp) exp.hidden = false; // the plan is final → offer the download + } + function clearPlanReady() { + const sec = document.querySelector('.v2-screen-plan'); + if (!sec || !sec.classList.contains('ready')) return; + sec.classList.remove('ready'); + const who = sec.querySelector('.v2-plan-who'); + const title = sec.querySelector('.v2-plan-title'); + if (who) who.textContent = 'Gently · planning'; + if (title) title.textContent = "Let's design your run"; + const cont = $('v2-plan-continue'); + if (cont) cont.textContent = 'Continue in workspace ›'; + const exp = $('v2-plan-export'); + if (exp) exp.hidden = true; + } + + // ── export the finished plan as a shareable markdown doc ──────────── + // Replaces the agent's end-of-plan "want me to export this?" prose with a + // real action: pull the enriched plan tree (/export) and render it to + // markdown client-side so the biologist can drop it in a doc or share it. + function specToLines(spec) { + let s = spec; + if (typeof s === 'string') { try { s = JSON.parse(s); } catch { return s ? ['- ' + s] : []; } } + if (!s || typeof s !== 'object') return []; + const out = []; + const fmt = (v) => Array.isArray(v) ? v.join(', ') : (typeof v === 'object' ? JSON.stringify(v) : String(v)); + const pick = (k, label) => { if (s[k] != null && s[k] !== '') out.push(`- **${label}:** ${fmt(s[k])}`); }; + pick('strain', 'Strain'); pick('goal', 'Goal'); + if (Array.isArray(s.channels) && s.channels.length) { + out.push('- **Channels:** ' + s.channels.map(c => `${c.name || '?'} (${c.excitation_nm || '?'} nm${c.exposure_ms ? `, ${c.exposure_ms} ms` : ''})`).join(', ')); + } + pick('num_slices', 'Slices'); pick('interval_s', 'Interval (s)'); pick('temperature_c', 'Temperature (°C)'); + pick('num_embryos', 'Embryos'); pick('start_stage', 'Start stage'); pick('stop_condition', 'Stop condition'); + pick('criteria', 'Criteria'); pick('success_criteria', 'Success criteria'); + return out; + } + function buildPlanMarkdown(tree) { + const L = []; + L.push(`# ${tree.description || tree.shorthand || 'Experimental plan'}`, ''); + if (tree.target) L.push(`**Goal:** ${tree.target}`, ''); + if (tree.shorthand) L.push(`**Plan ID:** \`${tree.shorthand}\``, ''); + L.push(`_Exported from Gently — ${new Date().toLocaleString()}_`, ''); + const renderItems = (items, prefix) => { + (items || []).slice().sort((a, b) => (a.phase_order || 0) - (b.phase_order || 0)).forEach((it, idx) => { + L.push(`### ${prefix}${idx + 1} ${it.title || '(task)'} \`${it.type || 'task'}\``, ''); + if (it.description) L.push(it.description, ''); + const sl = specToLines(it.spec); + if (sl.length) L.push(...sl, ''); + const refs = it.references || []; + if (refs.length) { + L.push('**References:**'); + refs.forEach((r, i) => L.push(`${i + 1}. ${r.citation || r.id || ''}${r.source ? ` _(${r.source})_` : ''}`)); + L.push(''); + } + }); + }; + if ((tree.items || []).length) { L.push('## Tasks', ''); renderItems(tree.items, ''); } + (tree.children || []).forEach((ph, pi) => { + if (!ph) return; + L.push(`## ${ph.display_name || ph.description || ph.shorthand || `Phase ${pi + 1}`}`, ''); + if (ph.target) L.push(ph.target, ''); + renderItems(ph.items, `${pi + 1}.`); + }); + return L.join('\n').replace(/\n{3,}/g, '\n\n').trimEnd() + '\n'; + } + async function resolveCampaignId() { + if (capturedCampaignId) return capturedCampaignId; + try { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); const t = (d.campaigns || [])[0]; return (t && t.campaign && t.campaign.id) || null; } + } catch (e) { /* offline */ } + return null; + } + async function exportPlan() { + const btn = $('v2-plan-export'); + const id = await resolveCampaignId(); + if (!id) { showPlanError('No plan to export yet.'); return; } + if (btn) { btn.disabled = true; btn.textContent = '↓ Exporting…'; } + try { + const r = await fetch(`/api/campaigns/${encodeURIComponent(id)}/export`); + if (!r.ok) throw new Error(`export ${r.status}`); + const tree = await r.json(); + const md = buildPlanMarkdown(tree); + const blob = new Blob([md], { type: 'text/markdown' }); + const url = URL.createObjectURL(blob); + const a = document.createElement('a'); + a.href = url; + a.download = `${(tree.shorthand || 'plan').replace(/[^\w.-]+/g, '_')}.md`; + document.body.appendChild(a); a.click(); a.remove(); + setTimeout(() => URL.revokeObjectURL(url), 1000); + } catch (e) { + showPlanError('Could not export the plan — open the conversation to export it manually.'); + } finally { + if (btn) { btn.disabled = false; btn.textContent = '↓ Export plan'; } + } + } + + // ── THE PLAN panel: mirror the real campaign tree ────────────────── + async function refreshPlanPanel() { + try { + let tree = null; + if (capturedCampaignId) { + const r = await fetch(`/api/campaigns/${encodeURIComponent(capturedCampaignId)}/tree`); + if (r.ok) tree = await r.json(); + } + if (!tree) { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); tree = (d.campaigns || [])[0] || null; } + } + if (tree) renderPlanTree(tree); + } catch (e) { /* keep whatever is shown */ } + } + function planName(c) { + c = c || {}; + return c.shorthand || c.display_name || c.description || 'Plan'; + } + // Phases read better by their human name ("Phase 1 — Reporter validation") + // than by their code shorthand ("nrp-p1"), which looks like a machine id. + function phaseName(c) { + c = c || {}; + return c.display_name || c.description || c.shorthand || 'Phase'; + } + // THE PLAN renders as a pager — one phase per page with ‹ Prev / Next ›, + // a position label, and dots — instead of one long scroll. planPage is held + // across re-renders (the panel refetches on every plan-writing tool) so the + // page you're reading doesn't snap back to the start mid-design. + let planPage = 0; + let planPages = []; // [{ name, items }] + let planTitleText = ''; + + function renderPlanTree(tree) { + if (!tree) return; + const phases = tree.children || []; + const rootItems = tree.items || []; + if (!phases.length && !rootItems.length) return; // nothing to show yet — keep placeholder + const pages = []; + if (rootItems.length) pages.push({ name: 'Tasks', items: rootItems }); + phases.forEach(phase => { + if (!phase) return; + pages.push({ name: phaseName(phase.campaign), items: phase.items || [] }); + }); + planPages = pages; + planTitleText = planName(tree.campaign); + if (planPage >= pages.length) planPage = pages.length - 1; + if (planPage < 0) planPage = 0; + drawPlanPage(); + } + + function drawPlanPage() { + const list = $('v2-plan-summary'); + if (!list) return; + const pages = planPages; + const n = pages.length; + if (!n) return; + const i = Math.min(Math.max(planPage, 0), n - 1); + const page = pages[i]; + + list.innerHTML = ''; + const title = document.createElement('div'); + title.className = 'v2-plan-title-row'; + title.textContent = planTitleText; + list.appendChild(title); + + if (n > 1) { + const bar = document.createElement('div'); + bar.className = 'v2-plan-pager'; + const prev = document.createElement('button'); + prev.className = 'v2-plan-pager-btn'; prev.type = 'button'; prev.textContent = '‹ Prev'; + prev.disabled = i === 0; + prev.addEventListener('click', () => { if (planPage > 0) { planPage--; drawPlanPage(); } }); + const pos = document.createElement('span'); + pos.className = 'v2-plan-pager-pos'; + pos.textContent = page.name; // position shown by the dots below + pos.title = `${page.name} · ${i + 1} of ${n}`; + const next = document.createElement('button'); + next.className = 'v2-plan-pager-btn'; next.type = 'button'; next.textContent = 'Next ›'; + next.disabled = i === n - 1; + next.addEventListener('click', () => { if (planPage < n - 1) { planPage++; drawPlanPage(); } }); + bar.append(prev, pos, next); + list.appendChild(bar); + } else { + const h = document.createElement('div'); + h.className = 'v2-plan-phase-h'; + h.textContent = page.name; + list.appendChild(h); + } + + const tasks = document.createElement('div'); + tasks.className = 'v2-plan-phase'; + const items = page.items || []; + // phase ordinal (1-based) for "P.I" numbering; the rootItems "Tasks" page + // isn't a phase, so it numbers items bare (1, 2, …). + const phaseOrd = pages.slice(0, i + 1).filter(p => p.name !== 'Tasks').length; + if (items.length) { + items.forEach((it, idx) => { + const type = String(it.type || '').toLowerCase(); + const t = document.createElement('div'); + t.className = 'v2-plan-task type-' + (type || 'other'); + const num = document.createElement('span'); + num.className = 'v2-task-num'; + num.textContent = phaseOrd ? `${phaseOrd}.${idx + 1}` : `${idx + 1}`; + const dot = document.createElement('span'); + dot.className = 'v2-task-dot'; + dot.title = type || 'task'; + const ttl = document.createElement('span'); + ttl.className = 'v2-task-ttl'; + ttl.textContent = it.title || it.shorthand || '(task)'; + t.append(num, dot, ttl); + if (it.estimated_days) { + const d = document.createElement('span'); + d.className = 'v2-task-days'; + d.textContent = `${it.estimated_days}d`; + t.append(d); + } + tasks.appendChild(t); + }); + } else { + const e = document.createElement('div'); + e.className = 'v2-plan-task v2-plan-task-empty'; + e.textContent = 'no items in this phase yet'; + tasks.appendChild(e); + } + list.appendChild(tasks); + + if (n > 1) { + const dots = document.createElement('div'); + dots.className = 'v2-plan-dots'; + for (let d = 0; d < n; d++) { + const dot = document.createElement('button'); + dot.className = 'v2-plan-dot' + (d === i ? ' active' : ''); + dot.type = 'button'; + dot.setAttribute('aria-label', `Go to ${pages[d].name} (${d + 1} of ${n})`); + dot.addEventListener('click', () => { planPage = d; drawPlanPage(); }); + dots.appendChild(dot); + } + list.appendChild(dots); + } + } + + // ── ask rendering (the active question) ──────────────────────────── + function labelFor(data, sel) { + const opts = (data && data.options) || []; + const one = (s) => { + const o = opts.find(o => o && (o.id === s || o.value === s || o.label === s)); + return o ? o.label : String(s); + }; + return Array.isArray(sel) ? sel.map(one).join(', ') : one(sel); + } + function recordPick(data, sel) { + const list = $('v2-plan-summary'); + if (!list) return; + const empty = list.querySelector('.v2-plan-side-empty'); + if (empty) empty.remove(); + const matched = (data && data.options || []).some(o => o && (o.id === sel || o.value === sel || o.label === sel)); + const row = document.createElement('div'); + row.className = 'v2-plan-row' + (matched ? '' : ' v2-plan-row-freetext'); + row.innerHTML = ''; + row.querySelector('.k').textContent = (data && data.question) || 'Choice'; + row.querySelector('.v').textContent = labelFor(data, sel); + list.appendChild(row); + } + function renderAsk() { + const mount = $('v2-plan-ask'); + if (!mount || !current || typeof AgentChat === 'undefined' || !AgentChat.buildAskCard) return; + showThinking(false); hidePlanError(); clearFallback(); + const data = current.data, reqId = current.reqId; + const hasControl = AgentChat.hasControl ? AgentChat.hasControl() : true; + const card = AgentChat.buildAskCard(data, { + reqId, isWake: current.isWake, hasControl, + onPick: (sel) => { + recordPick(data, sel); + AgentChat.answerChoice(reqId, sel); + current = null; clearAsk(); showThinking(true); + }, + }); + mount.innerHTML = ''; + mount.appendChild(card); + const first = mount.querySelector('button:not([disabled])'); + if (first) setTimeout(() => first.focus(), 30); + } + + let planKickedOff = false; // guard: design-kickoff fires once per session + async function startPlan() { + setScreen('plan'); + // Re-entering the wizard (Back → Plan again) must NOT re-fire the + // kickoff — that stacked duplicate "/plan" + design turns. Just show + // the wizard with its existing state. + if (planKickedOff) return; + planKickedOff = true; + resetSummary(); clearAsk(); clearActivity(); + current = null; + showThinking(true); + // Campaigns are persistent agent memory (not session state), so the + // agent always builds on an existing one — which leaves a user wanting a + // fresh plan stuck. So if an active campaign exists, ask up front: + // continue it (the default) or start a brand-new one. With NO campaign + // there's nothing to continue, so skip the gate and design straight away + // (that path is fresh anyway). + let campaign = null; + try { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); campaign = (d.campaigns || [])[0] || null; } + } catch (e) { /* offline / no API — just design */ } + if (campaign) renderCampaignChoice(campaign); + else kickoffDesign('continue'); + } + + // Enter plan mode, then prompt design. The prompt differs by intent: build + // on the active campaign, or set it aside and create a new one. A free-typed + // answer from the choice card becomes the design brief directly. + function kickoffDesign(mode) { + showThinking(true); + if (typeof AgentChat === 'undefined' || !AgentChat.runCommand) return; + AgentChat.runCommand('/plan'); + if (mode === 'fresh') { + AgentChat.runCommand( + "I want to start a brand-new experiment, not continue any existing " + + "campaign. Create a new campaign and let's design it from scratch — " + + "what should we capture?" + ); + } else if (mode === 'continue') { + AgentChat.runCommand("Let's design this run — what should it capture?"); + } else { + // free text from the choice card's "Something else…" escape + AgentChat.runCommand(String(mode)); + } + } + + // Continue-vs-fresh gate, shown only when an active campaign exists. Reuses + // the agent ask-card styling so it's visually identical to the agent's own + // questions; picking routes into kickoffDesign rather than the agent bridge. + function renderCampaignChoice(tree) { + const mount = $('v2-plan-ask'); + if (!mount || typeof AgentChat === 'undefined' || !AgentChat.buildAskCard) { + kickoffDesign('continue'); + return; + } + showThinking(false); hidePlanError(); clearFallback(); + const name = planName((tree && tree.campaign) || {}); + const data = { + question: `You have an active campaign — **${name}**. Design the next run inside it, or start something new?`, + options: [ + { id: 'continue', label: `Continue ${name}`, description: 'Design the next run inside your existing campaign' }, + { id: 'fresh', label: 'Start a brand-new campaign', description: 'Set the existing plan aside and plan from scratch' }, + ], + }; + const hasControl = AgentChat.hasControl ? AgentChat.hasControl() : true; + const card = AgentChat.buildAskCard(data, { + reqId: 'landing-campaign-choice', isWake: false, hasControl, + onPick: (sel) => { clearAsk(); kickoffDesign(sel); }, + }); + mount.innerHTML = ''; + mount.appendChild(card); + const first = mount.querySelector('button:not([disabled])'); + if (first) setTimeout(() => first.focus(), 30); + } + + function openScope() { + dismiss(); + if (typeof switchTab === 'function') switchTab('devices'); + } + function openChat() { + dismiss(); + if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) { + setTimeout(() => AgentChat.togglePanel(true), 300); + } + } + function sendFreeform(text) { + const v = (text || '').trim(); + dismiss(); + if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) { + AgentChat.togglePanel(true); + if (v && AgentChat.runCommand) setTimeout(() => AgentChat.runCommand(v), 300); + } + } + + function init() { + el = $('v2-landing'); + if (!el || typeof ClientEventBus === 'undefined') return; // flag off → no-op + greet(); + + el.querySelectorAll('[data-landing]').forEach(btn => btn.addEventListener('click', () => { + const kind = btn.dataset.landing; + if (kind === 'plan') startPlan(); + else if (kind === 'standalone') openScope(); + })); + + const esc = $('v2-escape'), escToggle = $('v2-escape-toggle'), + escInput = $('v2-escape-input'), escSend = $('v2-escape-send'); + if (escToggle && esc && escInput) { + escToggle.addEventListener('click', () => { + const open = esc.classList.toggle('open'); + escToggle.setAttribute('aria-expanded', open ? 'true' : 'false'); + if (open) setTimeout(() => escInput.focus(), 120); + }); + const submit = () => sendFreeform(escInput.value); + if (escSend) escSend.addEventListener('click', submit); + escInput.addEventListener('keydown', e => { + if (e.key === 'Enter') { e.preventDefault(); submit(); } + else if (e.key === 'Escape') { e.stopPropagation(); esc.classList.remove('open'); escToggle.setAttribute('aria-expanded', 'false'); } + }); + } + + const skip = $('v2-landing-skip'); + if (skip) skip.addEventListener('click', dismiss); + + // Theme toggle (header's is occluded by the overlay). Mirrors + // _header.html: flip data-theme on both roots + persist. + const themeBtn = $('v2-landing-theme'); + if (themeBtn) themeBtn.addEventListener('click', () => { + const cur = document.documentElement.getAttribute('data-theme') + || document.body.getAttribute('data-theme') || 'light'; + const next = cur === 'dark' ? 'light' : 'dark'; + document.documentElement.setAttribute('data-theme', next); + document.body.setAttribute('data-theme', next); + localStorage.setItem('gently-theme', next); + }); + + const back = $('v2-plan-back'); + if (back) back.addEventListener('click', () => setScreen('welcome')); + const planChat = $('v2-plan-chat'); + if (planChat) planChat.addEventListener('click', openChat); + const cont = $('v2-plan-continue'); + if (cont) cont.addEventListener('click', dismiss); + const exp = $('v2-plan-export'); + if (exp) exp.addEventListener('click', exportPlan); + + // The agent's questions + work render in the plan stage while it's active; + // once we've receded into the workspace, AskStage (#ask-stage) takes over. + ClientEventBus.on('AGENT_ASK', ({ request_id, choice_data, origin }) => { + if (!planActive()) return; + current = { reqId: request_id, data: choice_data || {}, isWake: origin === 'wake' }; + renderAsk(); + }); + ClientEventBus.on('ASK_CLEARED', ({ request_id }) => { + if (request_id === '*' || (current && request_id === current.reqId)) { + current = null; clearAsk(); + if (planActive() && !errorVisible()) showThinking(true); + // A question was just answered — the agent's continuation is the + // next step, so open a fresh feed page for it. (A turn stays one + // stream across an ask_user_choice pause, so turn_start alone + // would lump every step of the design into a single page.) + pendingNewPage = true; + } + }); + ClientEventBus.on('AGENT_CONTROL', () => { if (current && planActive()) renderAsk(); }); + ClientEventBus.on('AGENT_ACTIVITY', (act) => applyActivity(act)); + + document.addEventListener('keydown', e => { + if (e.key !== 'Escape' || !el || el.classList.contains('dismissed')) return; + if (el.dataset.screen === 'plan') setScreen('welcome'); // step back, don't bail + else dismiss(); + }); + } + + document.addEventListener('DOMContentLoaded', init); + + return { + dismiss, + show: () => { + if (!el) return; + el.style.display = ''; + el.removeAttribute('aria-hidden'); + el.classList.remove('dismissed'); + setScreen('welcome'); + greet(); + }, + }; +})(); diff --git a/gently/ui/web/static/js/logconsole.js b/gently/ui/web/static/js/logconsole.js new file mode 100644 index 00000000..36fac475 --- /dev/null +++ b/gently/ui/web/static/js/logconsole.js @@ -0,0 +1,217 @@ +/** + * Process console — the header drawer over the agent and device-layer output. + * + * The desktop shell spawns the backend with no console window, so when + * something misbehaves mid-session there is nowhere to look. This reads the + * same two streams the operator would have had on a terminal: + * + * Agent {storage}/logs/gently_*.log via /api/logs/agent + * Device layer supervisor-captured stdout via /api/device-layer/log, + * falling back to the layer's own log file when it runs + * externally and the supervisor captured nothing. + * + * Polling runs ONLY while the drawer is open. A console that keeps fetching + * behind a closed panel is exactly the kind of hidden work that made the camera + * streams fight each other. + */ +const LogConsole = (function () { + const POLL_MS = 2000; + const LIMIT = 600; + + let _wired = false, _open = false, _src = 'agent', _follow = true; + let _timer = null, _inFlight = false, _dirty = false, _lastKey = ''; + const D = {}; + + const $ = id => document.getElementById(id); + + function cacheDom() { + ['logc', 'logc-open', 'logc-scrim', 'logc-close', 'logc-body', 'logc-file', + 'logc-status', 'logc-level', 'logc-follow', 'logc-copy', 'logc-dot'] + .forEach(id => { D[id] = $(id); }); + } + + // ── fetching ────────────────────────────────────────────────────────── + async function fetchAgent(level) { + const q = new URLSearchParams({ limit: String(LIMIT) }); + if (level) q.set('level', level); + const r = await fetch(`/api/logs/agent?${q}`); + if (!r.ok) throw new Error(`${r.status}`); + return r.json(); + } + + async function fetchDevice(level) { + // Prefer the supervisor's live captured stdout — it exists even before + // anything has been flushed to a file. + try { + const r = await fetch(`/api/device-layer/log?limit=${LIMIT}`); + if (r.ok) { + const d = await r.json(); + if (d && Array.isArray(d.lines) && d.lines.length) { + return { file: 'device layer (captured stdout)', lines: d.lines }; + } + } + } catch (_) { /* fall through to the file */ } + const q = new URLSearchParams({ limit: String(LIMIT) }); + if (level) q.set('level', level); + const r2 = await fetch(`/api/logs/device?${q}`); + if (!r2.ok) throw new Error(`${r2.status}`); + return r2.json(); + } + + async function refresh() { + if (!_open) return; + // A refresh asked for while a poll is in flight must not be dropped — + // changing the tab or the level filter would otherwise appear to do + // nothing until the next tick. Remember it and re-run on completion. + if (_inFlight) { _dirty = true; return; } + _inFlight = true; + const level = D['logc-level'] ? D['logc-level'].value : ''; + try { + const d = _src === 'agent' ? await fetchAgent(level) : await fetchDevice(level); + render(d); + setStatus(''); + } catch (e) { + setStatus(`could not read log (${e.message})`); + } finally { + _inFlight = false; + if (_dirty) { _dirty = false; refresh(); } + } + } + + // ── rendering ───────────────────────────────────────────────────────── + function render(d) { + const lines = (d && d.lines) || []; + D['logc-file'].textContent = d && d.file ? d.file : 'no log file yet'; + // Skip the DOM write when nothing changed, so following does not fight + // a user who has scrolled up to read something. + const key = `${lines.length}|${lines[lines.length - 1] || ''}`; + if (key === _lastKey) return; + _lastKey = key; + + if (!lines.length) { + // An empty result under a filter is not an empty log — say which. + const level = D['logc-level'] ? D['logc-level'].value : ''; + if (level) { + D['logc-body'].textContent = + `No ${level.toLowerCase()} lines in the last ${LIMIT}. Set the filter to All to see everything.`; + } else { + D['logc-body'].textContent = _src === 'agent' + ? 'Nothing logged yet. The agent writes to {storage}/logs/gently_*.log.' + : 'Nothing logged yet. Start the device layer from the Devices tab.'; + } + return; + } + + const frag = document.createDocumentFragment(); + for (const ln of lines) { + const row = document.createElement('span'); + row.className = 'logc-line' + severityClass(ln); + row.textContent = ln; + frag.appendChild(row); + } + D['logc-body'].replaceChildren(frag); + + if (_follow) D['logc-body'].scrollTop = D['logc-body'].scrollHeight; + flagProblems(lines); + } + + function severityClass(ln) { + if (/\b(ERROR|CRITICAL|Traceback)\b/.test(ln)) return ' is-error'; + if (/\bWARNING\b/.test(ln)) return ' is-warn'; + return ''; + } + + // A quiet dot on the header button when the tail contains errors, so a + // failure that happens while the drawer is closed is still noticed. + function flagProblems(lines) { + if (!D['logc-dot']) return; + const bad = lines.slice(-80).some(ln => /\b(ERROR|CRITICAL|Traceback)\b/.test(ln)); + D['logc-dot'].hidden = !bad; + } + + function setStatus(msg) { + if (D['logc-status']) D['logc-status'].textContent = msg || ''; + } + + // ── open / close ────────────────────────────────────────────────────── + function open() { + if (_open) return; + _open = true; + D['logc'].hidden = false; + D['logc-open'].setAttribute('aria-expanded', 'true'); + _lastKey = ''; + refresh(); + _timer = setInterval(refresh, POLL_MS); + D['logc-body'].focus(); + } + + function close() { + if (!_open) return; + _open = false; + D['logc'].hidden = true; + D['logc-open'].setAttribute('aria-expanded', 'false'); + if (_timer) { clearInterval(_timer); _timer = null; } + } + + function toggle() { _open ? close() : open(); } + + function selectSource(src) { + if (src === _src) return; + _src = src; + _lastKey = ''; + document.querySelectorAll('.logc-tab').forEach(t => + t.classList.toggle('is-active', t.dataset.src === src)); + D['logc-body'].textContent = ''; + refresh(); + } + + function wire() { + if (_wired) return; + cacheDom(); + if (!D['logc'] || !D['logc-open']) return; // page without the header + _wired = true; + + D['logc-open'].addEventListener('click', toggle); + D['logc-close'].addEventListener('click', close); + D['logc-scrim'].addEventListener('click', close); + document.querySelectorAll('.logc-tab').forEach(t => + t.addEventListener('click', () => selectSource(t.dataset.src))); + D['logc-level'].addEventListener('change', () => { _lastKey = ''; refresh(); }); + + D['logc-follow'].addEventListener('click', () => { + _follow = !_follow; + D['logc-follow'].setAttribute('aria-pressed', String(_follow)); + D['logc-follow'].classList.toggle('is-on', _follow); + if (_follow) D['logc-body'].scrollTop = D['logc-body'].scrollHeight; + }); + D['logc-follow'].classList.add('is-on'); + + // Scrolling up is an intent to read — stop yanking the view to the end. + D['logc-body'].addEventListener('scroll', () => { + const el = D['logc-body']; + const atEnd = el.scrollHeight - el.scrollTop - el.clientHeight < 24; + if (_follow !== atEnd) { + _follow = atEnd; + D['logc-follow'].setAttribute('aria-pressed', String(_follow)); + D['logc-follow'].classList.toggle('is-on', _follow); + } + }); + + D['logc-copy'].addEventListener('click', async () => { + try { + await navigator.clipboard.writeText(D['logc-body'].textContent || ''); + setStatus('copied'); + setTimeout(() => setStatus(''), 1500); + } catch (_) { setStatus('copy blocked by the browser'); } + }); + + document.addEventListener('keydown', e => { + if (e.key === 'Escape' && _open) { e.preventDefault(); close(); return; } + // Ctrl/Cmd+` — the shell convention for "show me the console". + if ((e.ctrlKey || e.metaKey) && e.key === '`') { e.preventDefault(); toggle(); } + }); + } + + document.addEventListener('DOMContentLoaded', wire); + return { open, close, toggle }; +})(); diff --git a/gently/ui/web/static/js/notebook.js b/gently/ui/web/static/js/notebook.js new file mode 100644 index 00000000..1130a31a --- /dev/null +++ b/gently/ui/web/static/js/notebook.js @@ -0,0 +1,196 @@ +/** + * NotebookApp — the LIBRARY "Notebook" tab. + * + * The reading room for the shared lab notebook: a thread rail (the inquiry + * spine) + kind filter, rendering Notes from the read API (/api/notebook). + * Read-only for now; authoring/curation arrive in a later increment. + */ +const NotebookApp = (() => { + let inited = false; + let kindFilter = ''; // '' | observation | finding | question + let threadFilter = ''; // '' = all notes + + const $ = (id) => document.getElementById(id); + + async function fetchJSON(url) { + try { + const r = await fetch(url); + if (!r.ok) return null; + return await r.json(); + } catch (e) { + return null; + } + } + + function kindMeta(kind) { + return ({ + observation: { label: 'Observation', cls: 'nb-k-obs' }, + finding: { label: 'Finding', cls: 'nb-k-find' }, + question: { label: 'Question', cls: 'nb-k-q' }, + })[kind] || { label: kind || 'note', cls: '' }; + } + + async function loadThreads() { + const rail = $('nb-threads'); + if (!rail) return; + const data = await fetchJSON('/api/notebook/threads'); + const threads = (data && data.threads) || []; + rail.innerHTML = ''; + const mk = (id, label, count, active) => { + const b = document.createElement('button'); + b.className = 'nb-thread' + (active ? ' active' : ''); + b.textContent = label + (count != null ? ` ${count}` : ''); + b.addEventListener('click', () => { threadFilter = id; loadThreads(); loadNotes(); }); + return b; + }; + rail.appendChild(mk('', 'All notes', null, threadFilter === '')); + threads.forEach(t => rail.appendChild(mk(t.id, t.id, t.count, threadFilter === t.id))); + } + + function card(n) { + const km = kindMeta(n.kind); + const el = document.createElement('div'); + el.className = 'nb-card'; + + const head = document.createElement('div'); + head.className = 'nb-card-head'; + const badge = document.createElement('span'); + badge.className = 'nb-badge ' + km.cls; + badge.textContent = km.label; + const author = document.createElement('span'); + author.className = 'nb-author'; + author.textContent = n.author || ''; + const status = document.createElement('span'); + status.className = 'nb-status'; + status.textContent = n.status || ''; + head.append(badge, author, status); + + const body = document.createElement('div'); + body.className = 'nb-body-text'; + body.textContent = n.title || n.body || ''; + + el.append(head, body); + + const chips = [] + .concat((n.strains || []).map(s => '🧬 ' + s)) + .concat((n.embryos || []).map(e => '◌ ' + e)) + .concat((n.threads || []).map(t => '# ' + t)); + if (chips.length) { + const row = document.createElement('div'); + row.className = 'nb-chips'; + chips.forEach(text => { + const c = document.createElement('span'); + c.className = 'nb-chip'; + c.textContent = text; + row.appendChild(c); + }); + el.appendChild(row); + } + return el; + } + + async function loadNotes() { + const list = $('nb-notes'); + if (!list) return; + const params = new URLSearchParams(); + if (kindFilter) params.set('kind', kindFilter); + if (threadFilter) params.set('thread', threadFilter); + const qs = params.toString(); + const data = await fetchJSON('/api/notebook/notes' + (qs ? `?${qs}` : '')); + if (!data || data.available === false) { + list.innerHTML = '
+ ${esc(p.text)}
+ ${(p.note_ids || []).map(id => `${esc(id)}`).join('')}
+ `).join('');
+ const nexts = (data.suggested_next || []).map(s => `${esc(s)} `).join('');
+ box.innerHTML =
+ ` — ExperimentOverview reads
+ * window.OPERATIONS_SCENARIOS[name] and skips all fetches.
+ *
+ * Scenarios:
+ * temp_strain — scripted_protocol active (temp-change burst protocol)
+ * expression_onset — reactive_monitor active (reporter rising)
+ * hatching_detect — reactive_monitor active (watch=hatching, status=watching)
+ * transmission_survey — exclusive_burst active (brightfield only)
+ * decided_plan — all planned, nothing run yet
+ * async_multi — standing_timelapse per-embryo cadence + layered reactive_monitor
+ * idle — null (no operation running)
+ */
+window.OPERATIONS_SCENARIOS = {
+
+ /* ------------------------------------------------------------------ */
+ temp_strain: {
+ session_id: '20260628_1432_tempstrain_a',
+ title: 'Temperature-strain run · E01',
+ goal: 'Acquire volumes before, during, and after a +4 °C step to 32 °C; capture reporter response to heat stress.',
+ tactics: [
+ {
+ id: 'ts-1', seq: 1,
+ name: 'Monitor — low cadence',
+ kind: 'standing_timelapse', state: 'done',
+ scope: { mode: 'global' },
+ rationale: 'Baseline acquisition before thermal perturbation.',
+ structure: { cadence_s: 180 },
+ live_bind: ['cadence'],
+ live: { summary: '22 min · ended on signal' },
+ relations: {}
+ },
+ {
+ id: 'ts-2', seq: 2,
+ name: 'Transmission burst — baseline',
+ kind: 'exclusive_burst', state: 'done',
+ scope: { mode: 'global' },
+ rationale: 'Brightfield snapshot before setpoint change.',
+ structure: { frames: 3, mode: 'brightfield' },
+ live_bind: [],
+ live: { summary: '3 bursts · brightfield' },
+ relations: {}
+ },
+ {
+ id: 'ts-3', seq: 3,
+ name: 'Temp-change burst protocol',
+ kind: 'scripted_protocol', state: 'active',
+ scope: { mode: 'global' },
+ rationale: 'Systematic volume capture before, during ramp, and after thermal lock. Laser off during ramp to limit phototoxicity.',
+ structure: {
+ phases: [
+ { name: 'before', state: 'done', count: '1/1 done' },
+ { name: 'during', state: 'active', count: '2 · awaiting lock' },
+ { name: 'after', state: 'todo', count: '0/1' }
+ ]
+ },
+ live_bind: ['temperature', 'current_burst'],
+ live: {
+ target: '→ 32.0 °C',
+ summary: 'started 3m ago',
+ desc: 'bursts before · setpoint change · bursts through ramp · bursts after lock — laser off',
+ readouts: [
+ {
+ label: 'stage temp',
+ bind: 'temperature',
+ value: '29.4→32.0°C',
+ bar: 62
+ },
+ {
+ label: 'current burst',
+ value: '#3 during',
+ sub: '60f · 1Hz · brightfield'
+ }
+ ],
+ phases: [
+ { name: 'before', state: 'done', count: '1/1 done', pips: ['before'] },
+ { name: 'during', state: 'active', count: '2 · awaiting lock', pips: ['during', 'during', 'pending'] },
+ { name: 'after', state: 'todo', count: '0/1', pips: ['pending'] }
+ ]
+ },
+ relations: {}
+ },
+ {
+ id: 'ts-4', seq: 4,
+ name: 'Recovery monitor — low cadence',
+ kind: 'standing_timelapse', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Resume gentle monitoring once temperature settles.',
+ structure: { cadence_s: 180 },
+ live_bind: ['cadence'],
+ live: {
+ summary: 'queued · 30 min after lock',
+ desc: 'resume gentle monitoring once temperature settles'
+ },
+ relations: { after: ['ts-3'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ expression_onset: {
+ session_id: '20260628_0915_onset_b',
+ title: 'Reporter-onset watch · E04',
+ goal: 'Detect first appearance of the fluorescent reporter; capture onset dynamics at high temporal resolution.',
+ tactics: [
+ {
+ id: 'eo-1', seq: 1,
+ name: 'Monitor — low cadence',
+ kind: 'standing_timelapse', state: 'done',
+ scope: { mode: 'global' },
+ rationale: 'Baseline acquisition before signal appears.',
+ structure: { cadence_s: 180 },
+ live_bind: ['cadence'],
+ live: { summary: '1h 40m · baseline' },
+ relations: {}
+ },
+ {
+ id: 'eo-2', seq: 2,
+ name: 'Expression monitoring',
+ kind: 'reactive_monitor', state: 'active',
+ scope: { mode: 'global' },
+ rationale: 'Accelerate cadence on signal, ramp 488 down on saturation, burst on stable structure.',
+ structure: { watch: 'reporter onset', reaction: 'accelerate + ramp laser', status: 'watching' },
+ live_bind: ['signal', 'cadence'],
+ live: {
+ target: 'reporter onset',
+ summary: 'signal rising',
+ desc: 'accelerate cadence on signal · ramp 488 down on saturation · burst on stable structure',
+ readouts: [
+ {
+ label: 'reporter signal',
+ value: 'rising',
+ sub: '+14% over 6 min',
+ bar: 48
+ },
+ {
+ label: 'cadence',
+ value: '120s → 30s',
+ sub: 'accelerated on onset'
+ },
+ {
+ label: '488 power',
+ value: '5% → 3%',
+ sub: 'ramped to limit saturation'
+ }
+ ]
+ },
+ relations: {}
+ },
+ {
+ id: 'eo-3', seq: 3,
+ name: 'Burst on good structure',
+ kind: 'exclusive_burst', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Capture a burst once the reporter pattern holds.',
+ structure: { frames: 60, mode: 'fluorescence' },
+ live_bind: [],
+ live: {
+ summary: 'queued · when structure stable',
+ desc: 'capture a burst once the reporter pattern holds'
+ },
+ relations: { after: ['eo-2'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ hatching_detect: {
+ session_id: '20260627_2210_hatch_c',
+ title: 'Pre-hatching vigil · E11',
+ goal: 'Detect and capture the hatching event; accelerate acquisition as hatching approaches.',
+ tactics: [
+ {
+ id: 'hd-1', seq: 1,
+ name: 'Pre-terminal monitoring',
+ kind: 'reactive_monitor', state: 'active',
+ scope: { mode: 'global' },
+ rationale: 'Low cadence now; speed up as hatching approaches.',
+ structure: { watch: 'hatching', reaction: 'accelerate near event', status: 'watching' },
+ live_bind: ['cadence'],
+ live: {
+ target: 'hatching',
+ summary: 'watching',
+ desc: 'low cadence now · speed up as hatching approaches',
+ readouts: [
+ { label: 'est. time to hatch', value: '~38 min', sub: 'from motion + morphology' },
+ { label: 'cadence', value: '180s', sub: 'will speed up near event' }
+ ]
+ },
+ relations: {}
+ },
+ {
+ id: 'hd-2', seq: 2,
+ name: 'Hatching speedup',
+ kind: 'standing_timelapse', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'High cadence through hatching.',
+ structure: { cadence_s: 30 },
+ live_bind: ['cadence'],
+ live: {
+ summary: 'queued · ~T-10 min',
+ desc: 'high cadence through hatching'
+ },
+ relations: { after: ['hd-1'] }
+ },
+ {
+ id: 'hd-3', seq: 3,
+ name: 'Post-hatch monitor',
+ kind: 'standing_timelapse', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Resume normal cadence after the event.',
+ structure: { cadence_s: 120 },
+ live_bind: ['cadence'],
+ live: { summary: 'queued · after event' },
+ relations: { after: ['hd-2'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ transmission_survey: {
+ session_id: '20260628_1100_survey_a',
+ title: 'Transmission survey · plate A',
+ goal: 'Survey all embryos with brightfield only; no laser excitation.',
+ tactics: [
+ {
+ id: 'srv-1', seq: 1,
+ name: 'Transmission burst',
+ kind: 'exclusive_burst', state: 'active',
+ scope: { mode: 'global' },
+ rationale: 'LED/brightfield bursts, no laser — DIC-like contrast.',
+ structure: { frames: 30, mode: 'brightfield', phase: 'capturing' },
+ live_bind: ['current_burst'],
+ live: {
+ summary: 'capturing',
+ desc: 'LED/brightfield bursts, no laser — DIC-like contrast',
+ readouts: [
+ { label: 'bursts captured', value: '7', sub: 'across 3 embryos' },
+ { label: 'illumination', value: 'LED · laser off', sub: 'brightfield' }
+ ]
+ },
+ relations: {}
+ },
+ {
+ id: 'srv-2', seq: 2,
+ name: 'Volume at best plane',
+ kind: 'oneshot', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Full volume capture at the best focal plane after operator review.',
+ structure: { note: 'operator selects plane' },
+ live_bind: [],
+ live: { summary: 'queued · operator review' },
+ relations: { after: ['srv-1'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ decided_plan: {
+ session_id: '20260628_1500_tempstrain_b',
+ title: 'Temperature-strain run · E02',
+ goal: 'Repeat the thermal strain protocol on a second embryo cohort.',
+ tactics: [
+ {
+ id: 'dp-1', seq: 1,
+ name: 'Transmission burst — baseline',
+ kind: 'exclusive_burst', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Brightfield baseline before any change.',
+ structure: { frames: 3, mode: 'brightfield' },
+ live_bind: [],
+ live: {
+ summary: 'queued · first',
+ desc: 'brightfield baseline before any change'
+ },
+ relations: {}
+ },
+ {
+ id: 'dp-2', seq: 2,
+ name: 'Temp-change burst protocol',
+ kind: 'scripted_protocol', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Thermal step to 30.0 °C with phased acquisition.',
+ structure: {
+ phases: [
+ { name: 'before', state: 'todo', count: '0/1' },
+ { name: 'during', state: 'todo', count: '0/3' },
+ { name: 'after', state: 'todo', count: '0/1' }
+ ]
+ },
+ live_bind: ['temperature', 'current_burst'],
+ live: { target: '→ 30.0 °C', summary: 'queued · second' },
+ relations: { after: ['dp-1'] }
+ },
+ {
+ id: 'dp-3', seq: 3,
+ name: 'Recovery monitor',
+ kind: 'standing_timelapse', state: 'planned',
+ scope: { mode: 'global' },
+ rationale: 'Low-cadence monitoring after temperature settles.',
+ structure: { cadence_s: 180 },
+ live_bind: ['cadence'],
+ live: { summary: 'queued · last' },
+ relations: { after: ['dp-2'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ async_multi: {
+ session_id: '20260628_1630_async_multi',
+ title: 'Async multi-embryo run · 4 embryos',
+ goal: 'Per-embryo asynchronous acquisition with individual cadence phases; overlay a hatching watch on the two most advanced.',
+ tactics: [
+ {
+ id: 'am-1', seq: 1,
+ name: 'Async timelapse — per-embryo cadence',
+ kind: 'standing_timelapse', state: 'active',
+ scope: { mode: 'embryos', embryo_ids: ['E01', 'E02', 'E03', 'E04'] },
+ rationale: 'Each embryo runs at its own cadence based on developmental stage and reporter state.',
+ structure: {
+ cadence_s: 120,
+ per_embryo: [
+ { embryo_id: 'E01', cadence_phase: 'normal', interval_s: 180 },
+ { embryo_id: 'E02', cadence_phase: 'fast', interval_s: 30 },
+ { embryo_id: 'E03', cadence_phase: 'burst', interval_s: 0 },
+ { embryo_id: 'E04', cadence_phase: 'paused', interval_s: null }
+ ]
+ },
+ live_bind: ['cadence'],
+ live: {
+ summary: 'running · 4 embryos',
+ readouts: [
+ { label: 'active embryos', value: '3 / 4', sub: 'E04 paused' },
+ { label: 'cadence range', value: '30–180s', sub: 'per-embryo mode' }
+ ]
+ },
+ relations: {}
+ },
+ {
+ id: 'am-2', seq: 2,
+ name: 'Hatching watch — E01, E02',
+ kind: 'reactive_monitor', state: 'active',
+ scope: { mode: 'embryos', embryo_ids: ['E01', 'E02'] },
+ rationale: 'Overlay a hatching detector on the two most advanced embryos.',
+ structure: { watch: 'hatching', reaction: 'accelerate + alert', status: 'armed' },
+ live_bind: ['signal'],
+ live: {
+ target: 'hatching',
+ summary: 'armed · E01, E02',
+ desc: 'watching for hatching onset on the two most advanced embryos',
+ readouts: [
+ { label: 'watch status', value: 'armed', sub: 'no event yet' },
+ { label: 'scope', value: 'E01, E02', sub: '2 of 4 embryos' }
+ ]
+ },
+ relations: { layered_on: ['am-1'] }
+ }
+ ]
+ },
+
+ /* ------------------------------------------------------------------ */
+ idle: null
+};
diff --git a/gently/ui/web/static/js/projection-viewer.js b/gently/ui/web/static/js/projection-viewer.js
index 1f5f530e..5cf7719d 100644
--- a/gently/ui/web/static/js/projection-viewer.js
+++ b/gently/ui/web/static/js/projection-viewer.js
@@ -118,6 +118,10 @@ const ProjectionViewer = {
this.projections = [];
this.selectedMethod = null;
this.isOpen = true;
+ // Clear any volume from a previous open so a failed /api/volume-raw fetch
+ // can't leave the prior embryo/timepoint's 3D data bound (stale-render).
+ this.volumeData = null;
+ this.volumeShape = null;
const modal = document.getElementById('projection-viewer-modal');
const loading = document.getElementById('pv-loading');
@@ -280,6 +284,10 @@ const ProjectionViewer = {
},
selectMethod(method) {
+ // If the 3D view is requested but no volume loaded (e.g. /api/volume-raw
+ // failed while projections succeeded), fall back to the projections grid
+ // rather than showing an empty, never-initialized 3D panel.
+ if (method === '3d_viewer' && !this.volumeData) method = null;
this.selectedMethod = method;
this.renderProjections();
this.renderTabs();
@@ -298,6 +306,19 @@ const ProjectionViewer = {
this.updateViewerVisibility();
},
+ // Resize the WebGL canvas + camera to the container's current width.
+ // (Height is fixed at 400px; only width tracks the layout.) The animation
+ // loop handles re-rendering.
+ _resize3D() {
+ const container = document.getElementById('pv-3d-container');
+ if (!container || !this.renderer3d || !this.camera3d) return;
+ const w = container.clientWidth || 500;
+ const h = 400;
+ this.renderer3d.setSize(w, h);
+ this.camera3d.aspect = w / h;
+ this.camera3d.updateProjectionMatrix();
+ },
+
// 3D Viewer Methods
init3DViewer() {
const container = document.getElementById('pv-3d-container');
@@ -319,6 +340,22 @@ const ProjectionViewer = {
container.innerHTML = '';
container.appendChild(this.renderer3d.domElement);
+ // Keep the WebGL canvas in sync with its container width — the chat
+ // panel can dock/resize and the window can resize. The animation loop
+ // re-renders every frame, so on a size change we only need to resize the
+ // renderer + camera (coalesced to one rAF). Also listen for the explicit
+ // layout-change event the chat dock fires on collapse/expand + resize.
+ if (this._resizeObserver) this._resizeObserver.disconnect();
+ this._resizeObserver = new ResizeObserver(() => {
+ if (this._resizeRaf) cancelAnimationFrame(this._resizeRaf);
+ this._resizeRaf = requestAnimationFrame(() => this._resize3D());
+ });
+ this._resizeObserver.observe(container);
+ if (!this._onLayoutChanged) {
+ this._onLayoutChanged = () => this._resize3D();
+ window.addEventListener('gently:layout-changed', this._onLayoutChanged);
+ }
+
// Root group is the object the user rotates. Raymarched volume
// mesh is added here. The group scale flips Y so the image
// orientation matches 2D projections.
@@ -609,6 +646,18 @@ const ProjectionViewer = {
cancelAnimationFrame(this.animationId);
this.animationId = null;
}
+ if (this._resizeObserver) {
+ this._resizeObserver.disconnect();
+ this._resizeObserver = null;
+ }
+ if (this._resizeRaf) {
+ cancelAnimationFrame(this._resizeRaf);
+ this._resizeRaf = null;
+ }
+ if (this._onLayoutChanged) {
+ window.removeEventListener('gently:layout-changed', this._onLayoutChanged);
+ this._onLayoutChanged = null;
+ }
// Dispose the volume cube's geometry, material, and 3D texture.
if (this.volumeMesh) {
this.volumeMesh.geometry?.dispose();
diff --git a/gently/ui/web/static/js/replay-recorder.js b/gently/ui/web/static/js/replay-recorder.js
new file mode 100644
index 00000000..fbccd282
--- /dev/null
+++ b/gently/ui/web/static/js/replay-recorder.js
@@ -0,0 +1,461 @@
+/* Session replay recorder — rrweb capture + semantic action log.
+ *
+ * Design contract (docs/superpowers/specs/2026-07-13-session-replay-design.md):
+ * the app always wins over the recording. Everything here is wrapped so that any
+ * failure degrades or disables the recorder silently — it must never throw into
+ * the page, block the main thread, or surface errors to the UI.
+ *
+ * The client is deliberately blind: it does not know the gently session id.
+ * It POSTs batches to /replay/ingest and the server files them under the
+ * active session (or an unassigned bucket). Removal = delete this file and
+ * its template include.
+ */
+(function () {
+ "use strict";
+
+ if (window.__gentlyReplay) return; // double-include guard
+ var STATE = {
+ tab: Math.random().toString(16).slice(2, 10),
+ rrwebBuf: [],
+ actionBuf: [],
+ dropped: 0,
+ failures: 0,
+ disabled: false,
+ stopFn: null,
+ flushTimer: null,
+ };
+ window.__gentlyReplay = STATE;
+
+ var INGEST_URL = "/replay/ingest";
+ var FLUSH_MS = 4000; // short interval: bounds loss at tab close / app quit
+ // Count-based cap, NOT bytes: sizing would mean JSON.stringify on every
+ // rrweb event on the main thread (mutation-storm hot path). Serialization
+ // happens exactly once, at flush. 20k events ≫ one flush interval's worth.
+ var MAX_BUF_EVENTS = 20000; // drop-oldest beyond this (app > data)
+ var MAX_FAILURES = 5; // consecutive ingest failures before self-disable
+ var CHECKOUT_MS = 5 * 60 * 1000; // periodic full snapshots: cheap seeking later
+ // Live camera ![]()
gets base64 data-URI src swaps at frame rate — recording
+ // it would add ~100KB+ per frame on the main thread. Blocked from capture;
+ // the bus-summary action records that frames were flowing instead.
+ var BLOCK_SELECTOR = "#op-img-bottom, #op-img-spim";
+ // Machine-driven, high-churn regions: the live map re-renders at stage-poll
+ // rate, the 3D occupancy canvas animates, the temperature graph redraws on
+ // every reading. In 'balanced' fidelity these are blocked from the DOM stream
+ // (a placeholder box replays in their place) — they're the bulk of the volume.
+ var HIGH_CHURN =
+ "#devices-map-svg, #occ3d-container, #occ3d-minimap, #devices-temp-graph";
+
+ // Recording fidelity, most-specific first: a ?replay= URL override (for
+ // an ad-hoc high/low-fidelity capture), else the server default stamped on the
+ // recorder's
@@ -27,5 +28,6 @@
+
@@ -2748,7 +2852,7 @@ const EmbryosManager = {
${item.stage ? this.formatStageName(item.stage) : (item.detected ? 'DETECTED' : 'Not detected')}
- ${confDisplay} confidence
+ ${confHtml}
${transitionalHtml}
${detectorFindingsHtml}
@@ -2979,13 +3083,22 @@ const EmbryosManager = {
container.classList.remove('visible');
container.innerHTML = '';
}
+ // Filmstrip side panel — clearing innerHTML lets the :empty CSS
+ // rule collapse the panel and let the rows reclaim full width.
+ const filmstripDetail = document.getElementById('filmstrip-detail');
+ if (filmstripDetail) {
+ filmstripDetail.innerHTML = '';
+ }
this.detailPanelVisible = false;
this.currentDetailItem = null;
- // Clear eval dot highlight
+ // Clear eval dot + filmstrip cell highlight
document.querySelectorAll('.eval-dot.active').forEach(dot => {
dot.classList.remove('active');
});
+ document.querySelectorAll('.filmstrip-cell.active').forEach(cell => {
+ cell.classList.remove('active');
+ });
},
// Navigate to previous/next item in detail panel
diff --git a/gently/ui/web/static/js/events.js b/gently/ui/web/static/js/events.js
index 02365e40..998431a1 100644
--- a/gently/ui/web/static/js/events.js
+++ b/gently/ui/web/static/js/events.js
@@ -41,6 +41,40 @@ function getEventBadgeClass(eventType) {
return 'default';
}
+// Log-record helpers --------------------------------------------------
+// LOG_RECORD events come from the Python logging bridge. We collapse the
+// generic "LOG_RECORD" type into the actual level (DEBUG / INFO / WARN /
+// ERROR) so the table is readable -- otherwise every row in a busy
+// session reads the same string in the Type column.
+function isLogEvent(event) {
+ return event && event.event_type === 'LOG_RECORD';
+}
+
+function logLevelLabel(d) {
+ // levelname is fastest path; fall back to numeric mapping if missing.
+ const lvl = (d && (d.level_name || '')).toString().toUpperCase();
+ if (lvl) {
+ if (lvl === 'WARNING') return 'WARN';
+ if (lvl === 'CRITICAL') return 'CRIT';
+ return lvl;
+ }
+ const n = d && Number(d.level);
+ if (!isFinite(n)) return 'LOG';
+ if (n >= 50) return 'CRIT';
+ if (n >= 40) return 'ERROR';
+ if (n >= 30) return 'WARN';
+ if (n >= 20) return 'INFO';
+ return 'DEBUG';
+}
+
+function logBadgeClass(d) {
+ const label = logLevelLabel(d);
+ if (label === 'DEBUG') return 'log-debug';
+ if (label === 'INFO') return 'log-info';
+ if (label === 'WARN') return 'log-warn';
+ return 'log-error'; // ERROR / CRIT collapse together
+}
+
// Search helper functions
function escapeRegex(str) {
return str.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
@@ -67,12 +101,17 @@ function eventMatchesSearch(event) {
}
function highlightSearchTerms(text) {
- if (!searchQuery || !text) return text;
+ // Escape first — event keys/values/messages are arbitrary text (perception
+ // prose, file paths, agent output) and are inserted via innerHTML by the
+ // callers. Escaping here closes the XSS hole at every call site; the
+ // injected tags are the only markup we add.
+ const safe = escapeHtml(text == null ? '' : String(text));
+ if (!searchQuery) return safe;
try {
const regex = new RegExp(`(${escapeRegex(searchQuery)})`, 'gi');
- return String(text).replace(regex, '$1');
+ return safe.replace(regex, '$1');
} catch (e) {
- return text;
+ return safe;
}
}
@@ -212,45 +251,81 @@ function addEventToTable(event, prepend = true) {
if (hasImage) tr.classList.add('has-image');
tr.dataset.eventId = event.event_id || '';
- const badgeClass = getEventBadgeClass(event.event_type);
-
- // Image indicator icon
- const imageIndicator = hasImage
- ? `
-
- `
- : '';
-
- // Thumbnail preview
- const thumbnailHtml = hasImage
- ? ``
- : '';
-
- tr.innerHTML = `
- ${formatEventData(event.data)}
${JSON.stringify(event.data, null, 2)}`;
- } else {
- dataDiv.innerHTML = formatEventData(event.data);
- }
- });
+ if (isLogEvent(event)) {
+ // Log rows have a compact, distinctive shape: level badge in the
+ // Type column, logger name + message in the Data column. Click to
+ // toggle a pre with the full payload (incl. exception trace).
+ tr.classList.add('log-row');
+ const d = event.data || {};
+ const badgeCls = logBadgeClass(d);
+ const label = logLevelLabel(d);
+ const message = highlightSearchTerms(d.message || '');
+ const loggerName = highlightSearchTerms(d.logger || '-');
+ const excTag = d.exc_text ? ' ⏎ trace…' : '';
+ tr.innerHTML = `
+
+ ${loggerName}${excTag}
+
${d.logger || ''} ${d.func || ''}:${d.line || ''}\n` +
+ `${(d.message || '')}${tracePart}`;
+ } else {
+ dataDiv.innerHTML =
+ `${loggerName}` +
+ `${excTag}`;
+ }
+ });
+ } else {
+ const badgeClass = getEventBadgeClass(event.event_type);
+
+ // Image indicator icon
+ const imageIndicator = hasImage
+ ? `
+
+ `
+ : '';
+
+ // Thumbnail preview
+ const thumbnailHtml = hasImage
+ ? ``
+ : '';
+
+ tr.innerHTML = `
+ ${formatEventData(event.data)}
${JSON.stringify(event.data, null, 2)}`;
+ } else {
+ dataDiv.innerHTML = formatEventData(event.data);
+ }
+ });
+ }
if (prepend) {
tbody.insertBefore(tr, tbody.firstChild);
diff --git a/gently/ui/web/static/js/experiment-overview.js b/gently/ui/web/static/js/experiment-overview.js
index 33032a40..a5be6444 100644
--- a/gently/ui/web/static/js/experiment-overview.js
+++ b/gently/ui/web/static/js/experiment-overview.js
@@ -1,161 +1,91 @@
/**
- * Experiment Overview Tab — vector-graphics view of the planned timelapse.
+ * Experiment Overview Tab — vector-graphics view of the live imaging tactics
+ * (cadence patterns + reactive-monitoring rules) for the running experiment.
*
- * Data source priority:
- * 1. GET /api/experiments/current/strategy — live snapshot from FileStore.
- * 2. STUB_STRATEGY below — used when the live fetch
- * fails or no session exists.
- *
- * The render path is data-shape-driven and doesn't care which source the
- * snapshot came from — only ``ExperimentOverview.isLive`` differs so the
- * header badge can say "live" or "mockup · stubbed data".
+ * Data source: GET /api/experiments/current/strategy — the live snapshot from
+ * FileStore. When there is no active experiment (or the fetch isn't ready), the
+ * view shows a calm empty state; it never renders stubbed/mock data.
*/
-const STUB_STRATEGY = {
- session_id: "20260522_1430_dopaminergic_demo_a3f8e1c2",
- session_name: "dopaminergic-reporter demo",
- started_at: "2026-05-22T14:30:00",
- now_offset_s: 8100, // 2h 15min into the run
- horizon_s: 14400, // 4h total view window (past + projected)
- base_interval_s: 120,
- dose_budget_base_ms: 50000,
- per_timepoint_ms: 500, // 50 slices × 10ms
- monitoring_modes: [
- {
- name: "expression_monitoring",
- description: "Anticipating fluorescent-reporter onset on Test embryos: accelerate to 60s on signal, ramp 488 down on saturation.",
- applies_to_roles: ["test"],
- params: {
- fast_interval: 60,
- rampdown_step_pct: 1.0,
- rampdown_floor_pct: 2.0,
- rampdown_ceiling_pct: 6.0
- }
- },
- {
- name: "pre_terminal_monitoring",
- description: "Anticipating organism pre-terminal stage (pretzel): accelerate to 30s on detection.",
- applies_to_roles: ["test"],
- params: { fast_interval: 30 }
- }
- ],
- triggers: [
- { id: "t1", kind: "interval_rule", label: "signal onset",
- when_text: "dopaminergic ≥ WEAK", then_text: "120s → 60s",
- applies_to: ["test"], one_time: true },
- { id: "t2", kind: "power_rule", label: "488 ramp down",
- when_text: "intensity = SATURATING (×3)", then_text: "488 ↓ 1%/step, floor 2%",
- applies_to: ["test"] },
- { id: "t3", kind: "burst", label: "structure-triggered burst",
- when_text: "structure_quality = GOOD", then_text: "burst 200 frames @ 20 Hz",
- applies_to: ["test"] },
- { id: "t4", kind: "interval_rule", label: "pre-terminal speedup",
- when_text: "stage = pretzel", then_text: "60s → 30s",
- applies_to: ["test"], one_time: true }
- ],
- embryos: [
- {
- id: "E1", role: "test", color: "#ff66cc", icon: "★",
- dose_used_ms: 12500, dose_budget_ms: 50000,
- tp_acquired: 25,
- stop_condition: "hatching+3 OR 24h duration",
- stop_kind: "bounded",
- laser_488_pct_now: 3.0,
- phases: [
- { mode: "base", start: 0, end: 1800, cadence_s: 120 },
- { mode: "fast", start: 1800, end: 3600, cadence_s: 60 },
- { mode: "burst", start: 3600, end: 3610, frames: 200, hz: 20 },
- { mode: "cooldown", start: 3610, end: 3640, cadence_s: 60 },
- { mode: "fast", start: 3640, end: 8100, cadence_s: 60 }
- ],
- trigger_events: [
- { trigger_id: "t1", at: 1800 },
- { trigger_id: "t3", at: 3600 },
- { trigger_id: "t2", at: 5400, count: 3 }
- ],
- power_history_488: [
- { at: 0, pct: 5.0 },
- { at: 5400, pct: 4.0 },
- { at: 5460, pct: 3.0 },
- { at: 8100, pct: 3.0 }
- ],
- // Future projection at current cadence (60s, fast). Hatching not
- // deterministic so projected_end_s is null — render fades to ∞.
- projected_cadence_s: 60,
- projected_end_s: null
- },
- {
- id: "E2", role: "test", color: "#ff66cc", icon: "★",
- dose_used_ms: 6500, dose_budget_ms: 50000,
- tp_acquired: 13,
- stop_condition: "hatching+3 OR 24h duration",
- stop_kind: "bounded",
- laser_488_pct_now: 5.0,
- phases: [
- { mode: "base", start: 0, end: 8100, cadence_s: 120 }
- ],
- trigger_events: [],
- power_history_488: [
- { at: 0, pct: 5.0 },
- { at: 8100, pct: 5.0 }
- ],
- projected_cadence_s: 120,
- projected_end_s: null
- },
- {
- id: "E3", role: "test", color: "#ff66cc", icon: "★",
- dose_used_ms: 38000, dose_budget_ms: 50000,
- tp_acquired: 76,
- stop_condition: "manual",
- stop_kind: "open_ended",
- laser_488_pct_now: 5.0,
- phases: [
- { mode: "base", start: 0, end: 8100, cadence_s: 120 }
- ],
- trigger_events: [],
- power_history_488: [
- { at: 0, pct: 5.0 },
- { at: 8100, pct: 5.0 }
- ],
- // Projected dose-exhaust horizon = 4.0h from now (warning condition)
- projected_cadence_s: 120,
- projected_end_s: null,
- dose_exhaust_at_s: 12000 // budget will run out at this elapsed time
- },
- {
- id: "C1", role: "calibration", color: "#22d3ee", icon: "◆",
- dose_used_ms: 33500, dose_budget_ms: 500000, // 10× multiplier
- tp_acquired: 67,
- stop_condition: "manual",
- stop_kind: "open_ended",
- laser_488_pct_now: 5.0,
- phases: [
- { mode: "base", start: 0, end: 8100, cadence_s: 120 }
- ],
- trigger_events: [],
- power_history_488: [
- { at: 0, pct: 5.0 },
- { at: 8100, pct: 5.0 }
- ],
- projected_cadence_s: 120,
- projected_end_s: null
- }
- ]
-};
const ExperimentOverview = {
initialized: false,
expandedMode: null,
activeView: 'overview', // 'overview' | 'rules'
- activeStrategy: null, // last fetched/loaded snapshot
- isLive: false, // true when activeStrategy came from the API
+ activeStrategy: null, // last fetched strategy snapshot (rules view)
+ activePlan: null, // last fetched/loaded operation plan (overview spine)
+ isLive: false, // true when data came from the API
+ scenarioMode: false, // true when ?scenario=' +
+ 'No active experiment — rules and monitoring modes will appear here once a run is live.
';
+ return;
+ }
try {
root.innerHTML = '';
if (this.activeView === 'rules') {
this._renderRulesView(root, s);
} else {
- this._renderOverviewView(root, s);
- this._startNowTicker();
+ // Operation spine — data-driven tactic plan renderer.
+ // The swimlane view is retired; this renders this.activePlan.
+ this._renderOperationSpine(root, this.activePlan);
+ }
+ // Kick off the async Linked-plans panel (overview tab only).
+ // Fire-and-forget: appends a placeholder immediately, fills after fetch.
+ if (this.activeView === 'overview') {
+ this._initLinkedPlansPanel(root).catch(e =>
+ console.warn('[ExperimentOverview] linked-plans panel error:', e));
}
console.log('[ExperimentOverview] rendered OK, view=', this.activeView);
} catch (err) {
@@ -222,20 +243,6 @@ const ExperimentOverview = {
}
},
- // The "now" marker advances with wall-clock time and shows a countdown to
- // the next base-interval acquisition. We update only the marker group's
- // transform + the chip text, never re-rendering the whole SVG. Tick rate
- // is ~4 Hz which keeps the line motion visibly smooth without burning
- // cycles. Skipped while the tab is hidden.
- _startNowTicker() {
- this._stopNowTicker();
- const tick = () => {
- if (!this._nowTickerCtx) return;
- if (!document.hidden) this._updateNowMarker();
- this._nowTickerHandle = setTimeout(tick, 250);
- };
- this._nowTickerHandle = setTimeout(tick, 250);
- },
_stopNowTicker() {
if (this._nowTickerHandle) {
@@ -244,64 +251,256 @@ const ExperimentOverview = {
}
},
- _updateNowMarker() {
- const ctx = this._nowTickerCtx;
- if (!ctx || !ctx.marker.isConnected) return;
- const elapsedRealS = (Date.now() - ctx.renderedAtMs) / 1000;
- const effOffsetS = Math.min(
- ctx.renderedOffsetS + elapsedRealS,
- ctx.horizonS
- );
- const x = ctx.xForT(effOffsetS);
- ctx.marker.setAttribute('transform', `translate(${x},0)`);
-
- // Wall-clock from session-anchored time so the line and the clock
- // can't drift apart even if the client clock is wrong.
- const wallMs = ctx.startedAtMs + effOffsetS * 1000;
- const d = new Date(wallMs);
- const hh = String(d.getHours()).padStart(2, '0');
- const mm = String(d.getMinutes()).padStart(2, '0');
- const ss = String(d.getSeconds()).padStart(2, '0');
-
- let label = `${hh}:${mm}:${ss}`;
- if (ctx.baseIntervalS > 0) {
- const nextTickS = Math.ceil(effOffsetS / ctx.baseIntervalS) * ctx.baseIntervalS;
- const remainS = Math.max(0, Math.round(nextTickS - effOffsetS));
- const rm = Math.floor(remainS / 60);
- const rs = String(remainS % 60).padStart(2, '0');
- label += ` · next ${rm}:${rs}`;
+
+ // =================================================================
+ // Linked-plans panel — session ↔ plan items (F / Task 4)
+ // Symmetric with the Plans-tab Sessions section (campaigns.js).
+ // Endpoints: GET /api/sessions/{id}/plans
+ // POST /api/campaigns/{cid}/items/{iid}/sessions
+ // DELETE .../sessions/{session_id}
+ // =================================================================
+
+ // Initialise and append the Linked-plans panel to the ops-wrap in root.
+ // Async: appends a loading placeholder immediately, fills after fetch.
+ // No-op when no session_id is known (e.g. store not yet initialised).
+ async _initLinkedPlansPanel(root) {
+ if (!this._currentSessionId) return;
+ const wrap = root.querySelector('.ops-wrap');
+ if (!wrap) return;
+
+ // Append placeholder before the async fetch so layout is stable.
+ const panelEl = document.createElement('div');
+ panelEl.className = 'ops-lp';
+ panelEl.innerHTML = 'Loading linked plans…
';
+ wrap.appendChild(panelEl);
+
+ const sid = this._currentSessionId;
+ try {
+ const [linkedData, campaignsData] = await Promise.all([
+ fetch(`/api/sessions/${encodeURIComponent(sid)}/plans`, { cache: 'no-store' })
+ .then(r => r.ok ? r.json() : { plans: [] })
+ .catch(() => ({ plans: [] })),
+ fetch('/api/campaigns', { cache: 'no-store' })
+ .then(r => r.ok ? r.json() : { campaigns: [] })
+ .catch(() => ({ campaigns: [] })),
+ ]);
+ const plans = linkedData.plans || [];
+ const campaignNameMap = {};
+ this._flattenCampaignNames(campaignsData.campaigns || [], campaignNameMap);
+ this._fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sid);
+ } catch (e) {
+ console.warn('[ExperimentOverview] linked-plans init error:', e);
+ panelEl.innerHTML = 'Could not load linked plans.
';
}
- ctx.chipText.textContent = label;
-
- // Size the chip to fit; flip to the left of the line if we're near
- // the right edge so it stays on-screen.
- const textLen = label.length * 6.2 + 12;
- const nearEnd = x + textLen + 8 > ctx.laneRight;
- if (nearEnd) {
- ctx.chipBg.setAttribute('x', -textLen - 4);
- ctx.chipBg.setAttribute('width', textLen);
- ctx.chipText.setAttribute('x', -textLen + 2);
+ },
+
+ // Build a map of campaign_id → display name from the /api/campaigns tree.
+ _flattenCampaignNames(trees, map) {
+ const walk = (tree) => {
+ const c = tree.campaign;
+ if (c && c.id) map[c.id] = c.description || c.shorthand || c.id;
+ for (const child of (tree.children || [])) walk(child);
+ };
+ for (const tree of (trees || [])) walk(tree);
+ },
+
+ // Build a flat list of {id, title, status, campaign_id, campaign_name}
+ // from the /api/campaigns tree, for the plan-item picker.
+ _flattenCampaignItems(trees, campaignNameMap) {
+ const items = [];
+ const walk = (tree, inheritedCid, inheritedName) => {
+ const c = tree.campaign;
+ const cid = (c && c.id) || inheritedCid;
+ const name = (c && (c.description || c.shorthand)) || inheritedName || cid;
+ for (const item of (tree.items || [])) {
+ items.push({
+ id: item.id,
+ title: item.title || item.id,
+ status: typeof item.status === 'string' ? item.status
+ : (item.status && item.status.value) || 'planned',
+ campaign_id: cid,
+ campaign_name: name,
+ });
+ }
+ for (const child of (tree.children || [])) walk(child, cid, name);
+ };
+ for (const tree of (trees || [])) walk(tree, null, null);
+ return items;
+ },
+
+ // Render the linked-plans panel HTML into panelEl and wire button events.
+ _fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sessionId) {
+ const ESC = this._opsESC.bind(this);
+
+ // Header: section label + "+ link to a plan" button
+ let html = `
+ Linked plans
+
+
`;
+
+ // Linked plan-item rows (title · campaign · status · delink)
+ if (plans.length > 0) {
+ html += '';
+ for (const p of plans) {
+ const cname = campaignNameMap[p.campaign_id] || p.campaign_id || '—';
+ const sCls = p.status === 'completed' ? 'done'
+ : p.status === 'in_progress' ? 'active' : 'planned';
+ html += `
';
} else {
- ctx.chipBg.setAttribute('x', 4);
- ctx.chipBg.setAttribute('width', textLen);
- ctx.chipText.setAttribute('x', 10);
+ html += '
+ ${ESC(p.title || p.id)}
+ ${ESC(cname)}
+ ${ESC(p.status || 'planned')}
+
+
`;
+ }
+ html += 'Not linked to any plan
';
+ }
+
+ // Inline picker — shown when _planPickerOpen is set
+ if (this._planPickerOpen) {
+ if (this._pickerItems === null) {
+ // Still fetching — show loading state
+ html += 'Loading plan items…
';
+ } else {
+ const linkedIds = new Set(plans.map(p => p.id));
+ const available = this._pickerItems.filter(it => !linkedIds.has(it.id));
+ const opts = available.length === 0
+ ? ''
+ : available.map(it =>
+ ``
+ ).join('');
+ html += `
+
+
`;
+ }
+ }
+
+ panelEl.innerHTML = html;
+
+ // Wire events directly on the rendered buttons.
+ const sid = sessionId;
+ const linkBtn = panelEl.querySelector('#ops-lp-link-btn');
+ if (linkBtn) {
+ linkBtn.addEventListener('click', () =>
+ this._openPlanPickerInPanel(panelEl, plans, campaignNameMap, sid));
+ }
+ panelEl.querySelectorAll('.ops-lp-delink').forEach(btn => {
+ btn.addEventListener('click', () =>
+ this._delinkPlanItem(panelEl, btn.dataset.itemId, btn.dataset.campaignId, sid));
+ });
+ const submitBtn = panelEl.querySelector('#ops-lp-picker-link');
+ if (submitBtn) {
+ submitBtn.addEventListener('click', () => this._submitPlanLink(panelEl, sid));
+ }
+ const cancelBtn = panelEl.querySelector('#ops-lp-picker-cancel');
+ if (cancelBtn) {
+ cancelBtn.addEventListener('click', () => {
+ this._planPickerOpen = false;
+ this._pickerItems = null;
+ this._fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sid);
+ });
}
},
- _renderOverviewView(root, s) {
- root.appendChild(this._renderHeader(s));
- root.appendChild(this._renderModes(s));
- root.appendChild(this._renderModeExpanded(s));
- root.appendChild(this._renderSwimlanes(s));
+ // Open the inline plan-item picker: set loading state, fetch /api/campaigns,
+ // flatten to items, re-render with the picker populated.
+ async _openPlanPickerInPanel(panelEl, plans, campaignNameMap, sessionId) {
+ this._planPickerOpen = true;
+ this._pickerItems = null; // show loading
+ this._fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sessionId);
+ try {
+ const res = await fetch('/api/campaigns', { cache: 'no-store' });
+ if (!res.ok) throw new Error(`HTTP ${res.status}`);
+ const data = await res.json();
+ this._pickerItems = this._flattenCampaignItems(data.campaigns || [], campaignNameMap);
+ } catch (err) {
+ console.error('[ExperimentOverview] plan picker fetch error:', err);
+ this._pickerItems = [];
+ }
+ if (this._planPickerOpen) {
+ this._fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sessionId);
+ }
+ },
+
+ // POST the selected plan item → session link, then refetch and re-render.
+ async _submitPlanLink(panelEl, sessionId) {
+ const select = panelEl.querySelector('#ops-lp-picker-sel');
+ const value = select && select.value;
+ if (!value || !value.includes('::')) return;
+ const [campaignId, itemId] = value.split('::', 2);
+ if (!campaignId || !itemId) return;
+
+ this._planPickerOpen = false;
+ this._pickerItems = null;
+ panelEl.innerHTML = '
+
+
+
+ Linking…
';
+ try {
+ const res = await fetch(
+ `/api/campaigns/${encodeURIComponent(campaignId)}/items/${encodeURIComponent(itemId)}/sessions`,
+ {
+ method: 'POST',
+ headers: { 'Content-Type': 'application/json' },
+ body: JSON.stringify({ session_id: sessionId }),
+ },
+ );
+ if (!res.ok) throw new Error(`HTTP ${res.status}`);
+ } catch (err) {
+ console.error('[ExperimentOverview] plan link error:', err);
+ }
+ await this._refetchLinkedPlans(panelEl, sessionId);
+ },
+
+ // DELETE the plan-item → session edge, then refetch and re-render.
+ async _delinkPlanItem(panelEl, itemId, campaignId, sessionId) {
+ panelEl.innerHTML = 'Unlinking…
';
+ try {
+ const res = await fetch(
+ `/api/campaigns/${encodeURIComponent(campaignId)}/items/${encodeURIComponent(itemId)}/sessions/${encodeURIComponent(sessionId)}`,
+ { method: 'DELETE' },
+ );
+ if (!res.ok) throw new Error(`HTTP ${res.status}`);
+ } catch (err) {
+ console.error('[ExperimentOverview] plan delink error:', err);
+ }
+ await this._refetchLinkedPlans(panelEl, sessionId);
+ },
+
+ // Refetch linked plans + campaigns after a link/delink op, then re-render.
+ async _refetchLinkedPlans(panelEl, sessionId) {
+ try {
+ const [linkedData, campaignsData] = await Promise.all([
+ fetch(`/api/sessions/${encodeURIComponent(sessionId)}/plans`, { cache: 'no-store' })
+ .then(r => r.ok ? r.json() : { plans: [] })
+ .catch(() => ({ plans: [] })),
+ fetch('/api/campaigns', { cache: 'no-store' })
+ .then(r => r.ok ? r.json() : { campaigns: [] })
+ .catch(() => ({ campaigns: [] })),
+ ]);
+ const plans = linkedData.plans || [];
+ const campaignNameMap = {};
+ this._flattenCampaignNames(campaignsData.campaigns || [], campaignNameMap);
+ this._fillLinkedPlansPanel(panelEl, plans, campaignNameMap, sessionId);
+ } catch (e) {
+ console.warn('[ExperimentOverview] linked-plans refetch error:', e);
+ panelEl.innerHTML = 'Could not reload linked plans.
';
+ }
},
+
+
_renderRulesView(root, s) {
// Compact header echoing the session identity
const header = el('div', 'expov-header');
const metaRow = el('div', 'expov-header-row expov-header-row-meta');
metaRow.appendChild(elText('span', 'expov-session-name', s.session_name));
metaRow.appendChild(elText('span', 'expov-session-id', s.session_id));
- metaRow.appendChild(elText('span', 'expov-mockup-badge', 'mockup · stubbed data'));
header.appendChild(metaRow);
root.appendChild(header);
@@ -313,52 +512,6 @@ const ExperimentOverview = {
root.appendChild(this._renderRulesTable(s));
},
- // -----------------------------------------------------------------
- // Header — session identification + key metrics strip
- // (page-level title lives in .experiment-header-bar above)
- // -----------------------------------------------------------------
- _renderHeader(s) {
- const elapsedH = Math.floor(s.now_offset_s / 3600);
- const elapsedM = Math.floor((s.now_offset_s % 3600) / 60);
- const wrap = el('div', 'expov-header');
-
- // Session identification — the navbar already carries the id on
- // every tab, so we only render a name line when it actually adds
- // info (i.e. a human label, not a hash). The data-source badge is
- // still useful and gets its own row so it stays visible.
- const metaRow = el('div', 'expov-header-row expov-header-row-meta');
- if (s.session_name && s.session_name !== s.session_id) {
- metaRow.appendChild(elText('span', 'expov-session-name', s.session_name));
- }
- if (this.isLive) {
- metaRow.appendChild(elText('span', 'expov-live-badge', 'live'));
- } else {
- metaRow.appendChild(elText('span', 'expov-mockup-badge', 'mockup · stubbed data'));
- }
- wrap.appendChild(metaRow);
-
- // Compact key-metric strip
- const roleCounts = {};
- s.embryos.forEach(e => { roleCounts[e.role] = (roleCounts[e.role] || 0) + 1; });
- const roleStr = Object.entries(roleCounts).map(([r, n]) => `${n} ${r}`).join(' · ');
- const metricsRow = el('div', 'expov-header-row expov-header-row-metrics');
- const metric = (label, val) => {
- const m = el('span', 'expov-metric');
- m.appendChild(elText('span', 'expov-metric-val', val));
- m.appendChild(elText('span', 'expov-metric-lbl', label));
- return m;
- };
- metricsRow.appendChild(metric('elapsed', `${elapsedH}h ${elapsedM}m`));
- metricsRow.appendChild(metric('base', `${s.base_interval_s}s`));
- const budgetText = (s.dose_budget_base_ms != null && isFinite(s.dose_budget_base_ms))
- ? `${(s.dose_budget_base_ms / 1000).toFixed(0)}s × role`
- : 'no limit';
- metricsRow.appendChild(metric('budget', budgetText));
- metricsRow.appendChild(metric('embryos', `${s.embryos.length} · ${roleStr}`));
- wrap.appendChild(metricsRow);
-
- return wrap;
- },
// -----------------------------------------------------------------
// Monitoring mode chips + expanded panel
@@ -424,803 +577,653 @@ const ExperimentOverview = {
return name.split('_').map(w => w.charAt(0).toUpperCase() + w.slice(1)).join(' ');
},
- // -----------------------------------------------------------------
- // Legend
- // -----------------------------------------------------------------
- _renderLegend() {
- const wrap = el('div', 'expov-legend');
- const items = [
- ['base', 'base cadence'],
- ['fast', 'fast cadence'],
- ['burst', 'burst window'],
- ['cooldown', 'cooldown'],
- ['paused', 'paused'],
- ];
- items.forEach(([cls, label]) => {
- const item = el('span', 'expov-legend-item');
- item.appendChild(elClass('span', `expov-legend-swatch ${cls}`));
- item.appendChild(elText('span', '', label));
- wrap.appendChild(item);
- });
- const projItem = el('span', 'expov-legend-item');
- projItem.appendChild(elClass('span', 'expov-legend-swatch projected'));
- projItem.appendChild(elText('span', '', 'projected'));
- wrap.appendChild(projItem);
-
- const glyphs = [
- ['◇', 'trigger fired'],
- ['●', 'now'],
- ['■', 'stop condition'],
- ['∞', 'open-ended'],
- ['▲', 'burst start'],
- ['⚠', 'budget warning']
- ];
- glyphs.forEach(([g, label]) => {
- const item = el('span', 'expov-legend-item');
- item.appendChild(elText('span', 'expov-legend-glyph', g));
- item.appendChild(elText('span', '', label));
- wrap.appendChild(item);
- });
- return wrap;
- },
- // -----------------------------------------------------------------
- // Swimlanes SVG — the main visualization
- // -----------------------------------------------------------------
- _renderSwimlanes(s) {
- const wrap = el('div', 'expov-swimlanes-wrap');
-
- // Compact inline legend above the SVG
- const legend = el('div', 'expov-mini-legend');
- const swatches = [
- ['base', 'base'],
- ['fast', 'fast'],
- ['burst', 'burst'],
- ['cooldown', 'cooldown']
- ];
- swatches.forEach(([k, label]) => {
- const item = el('span', 'expov-mini-legend-item');
- const sw = el('span', `expov-mini-legend-swatch ${k}`);
- item.appendChild(sw);
- item.appendChild(elText('span', '', label));
- legend.appendChild(item);
- });
- const projItem = el('span', 'expov-mini-legend-item');
- projItem.appendChild(elClass('span', 'expov-mini-legend-swatch projected'));
- projItem.appendChild(elText('span', '', 'projected'));
- legend.appendChild(projItem);
- wrap.appendChild(legend);
-
- // Layout constants (logical pixels in the SVG viewBox)
- const LEFT = 180; // label gutter
- const RIGHT = 80; // right gutter for stop icon + ∞
- const LANE_W = 900; // lane drawing area
- const W = LEFT + LANE_W + RIGHT;
-
- const ROW_H = 100; // per-embryo row total height
- const LANE_H = 28; // cadence lane height
- const POWER_H = 22; // power strip height
- const DOSE_H = 12; // dose gauge height
- const ROW_PAD = 14; // top padding inside row
- const TOP_AXIS_H = 36; // top axis area (time labels + wall-clock)
- const BOTTOM_PAD = 8;
-
- const rows = s.embryos.length;
- const H = TOP_AXIS_H + rows * ROW_H + BOTTOM_PAD;
-
- const svg = svgEl('svg', {
- class: 'expov-swimlanes-svg',
- viewBox: `0 0 ${W} ${H}`,
- preserveAspectRatio: 'xMinYMin meet'
- });
+ // =================================================================
+ // Operation Spine — data-driven plan renderer (replaces swimlanes)
+ // =================================================================
- // Time scale helpers
- const xForT = (t) => LEFT + (t / s.horizon_s) * LANE_W;
- const nowX = xForT(s.now_offset_s);
-
- // ----- top axis: hour ticks with wall-clock annotation
- const startedAt = new Date(s.started_at);
- const axisG = svgEl('g');
- for (let h = 0; h <= Math.ceil(s.horizon_s / 3600); h++) {
- const x = xForT(h * 3600);
- axisG.appendChild(svgEl('line', {
- x1: x, x2: x, y1: TOP_AXIS_H - 6, y2: H - BOTTOM_PAD,
- class: 'expov-svg-axis', 'stroke-opacity': h === 0 ? 0.55 : 0.12
- }));
- axisG.appendChild(svgEl('text', {
- x: x + 4, y: 12, class: 'expov-svg-axis-label'
- }, `+${h}h`));
- // Wall-clock subtitle
- const wallClock = new Date(startedAt.getTime() + h * 3600 * 1000);
- const hh = String(wallClock.getHours()).padStart(2, '0');
- const mm = String(wallClock.getMinutes()).padStart(2, '0');
- axisG.appendChild(svgEl('text', {
- x: x + 4, y: 22,
- class: 'expov-svg-axis-wallclock'
- }, `${hh}:${mm}`));
+ // Minimal HTML escaper — values in readouts may contain trusted HTML
+ // (e.g. 32.0°C) so they are rendered with
+ // innerHTML; all other user/model strings go through _opsESC.
+ _opsESC(s) {
+ return String(s == null ? '' : s)
+ .replace(/[&<>"]/g, c => ({ '&': '&', '<': '<', '>': '>', '"': '"' }[c]));
+ },
+
+ // Entry point: render the operation spine into `root`.
+ // plan = the plan object (tactics array) or null for idle/unavailable.
+ _renderOperationSpine(root, plan) {
+ const ESC = this._opsESC.bind(this);
+
+ if (!plan || !Array.isArray(plan.tactics) || plan.tactics.length === 0) {
+ root.innerHTML = `
+
+
`;
+
+ // Wire CTA buttons — same open+send pattern as landing.js sendFreeform.
+ function _opsOpenAgent(prompt) {
+ if (typeof AgentChat === 'undefined' || !AgentChat.togglePanel) return;
+ AgentChat.togglePanel(true);
+ if (prompt && AgentChat.runCommand) setTimeout(() => AgentChat.runCommand(prompt), 300);
+ }
+ const briefBtn = root.querySelector('[data-ops-brief]');
+ if (briefBtn) briefBtn.addEventListener('click', () => _opsOpenAgent(''));
+ root.querySelectorAll('[data-ops-prompt]').forEach(chip => {
+ chip.addEventListener('click', () => _opsOpenAgent(chip.dataset.opsPrompt));
+ });
+ return;
}
- svg.appendChild(axisG);
-
- // ----- "now" marker: translatable group containing the vertical line
- // and a live clock chip. The chip advances every tick and shows the
- // countdown to the next base-interval acquisition window. The group
- // gets translated by _tickNow, so we don't rebuild SVG every second.
- const nowMarker = svgEl('g', { class: 'expov-svg-now-marker' });
- nowMarker.appendChild(svgEl('line', {
- x1: 0, x2: 0, y1: TOP_AXIS_H - 4, y2: H - BOTTOM_PAD,
- class: 'expov-svg-now-line'
- }));
- // Chip sits just below the axis labels (which live at y=12 and y=22)
- // so it doesn't sit on top of the "+0h / wallclock" annotation when
- // the now-line is near the start of the timeline.
- const chipBg = svgEl('rect', {
- x: 4, y: TOP_AXIS_H - 6, width: 120, height: 14, rx: 7,
- class: 'expov-svg-now-chip-bg'
- });
- const chipText = svgEl('text', {
- x: 10, y: TOP_AXIS_H + 4, class: 'expov-svg-now-label'
- }, '');
- nowMarker.appendChild(chipBg);
- nowMarker.appendChild(chipText);
- svg.appendChild(nowMarker);
-
- // Stash the bits the ticker needs to update without re-rendering.
- this._nowTickerCtx = {
- marker: nowMarker,
- chipBg: chipBg,
- chipText: chipText,
- xForT,
- startedAtMs: new Date(s.started_at).getTime(),
- renderedAtMs: Date.now(),
- renderedOffsetS: s.now_offset_s,
- baseIntervalS: s.base_interval_s || 0,
- horizonS: s.horizon_s,
- laneLeft: LEFT,
- laneRight: LEFT + LANE_W,
- };
- this._updateNowMarker();
-
- // ----- one group per embryo
- s.embryos.forEach((emb, i) => {
- const rowTop = TOP_AXIS_H + i * ROW_H;
- const rowG = svgEl('g');
- rowG.appendChild(this._renderLaneRow(s, emb, {
- LEFT, LANE_W, RIGHT, W, ROW_H, LANE_H, POWER_H, DOSE_H, ROW_PAD,
- TOP_AXIS_H, rowTop, xForT, nowX
- }));
- svg.appendChild(rowG);
- });
- wrap.appendChild(svg);
- return wrap;
+ const tactics = plan.tactics;
+ const hasActive = tactics.some(t => t.state === 'active');
+ // Index of the first queued (planned) tactic — gets the "next" badge.
+ const firstPlannedIdx = tactics.findIndex(t => t.state === 'planned');
+
+ // Roster lens: visible when embryos + role metadata are both available.
+ // Gracefully absent if either fetch failed or returned nothing (backward compat
+ // with plans that pre-date D2 — spine renders exactly as before).
+ const rosterEmbryos = this._rosterEmbryos || [];
+ const rolesMap = this._rolesMap;
+ const rosterCtx = (rosterEmbryos.length > 0 && rolesMap && rolesMap.size > 0)
+ ? { embryos: rosterEmbryos, rolesMap }
+ : null;
+ const rosterHtml = rosterCtx
+ ? `Operations
+ No operation running
+ +
+
+
+ — or start from a template
+
+
+
+
+
+ Population roster — by class & role
+ ${this._renderRosterLens(rosterEmbryos, rolesMap, plan, ESC)}`
+ : '';
+ const spineLabel = rosterCtx
+ ? 'Tactic spine — role-scoped
'
+ : '';
+
+ const spineNodes = tactics
+ .map((t, idx) => this._renderOpsTactic(t, idx, firstPlannedIdx, ESC, rosterCtx, tactics))
+ .join('');
+
+ root.innerHTML = `
+
+
`;
+ this._wireSpineExpand(root);
},
- _renderLaneRow(s, emb, dim) {
- const { LEFT, LANE_W, W, ROW_H, LANE_H, POWER_H, DOSE_H, ROW_PAD,
- rowTop, xForT, nowX } = dim;
- const g = svgEl('g');
-
- // Hairline divider above each row (except first)
- if (rowTop > dim.TOP_AXIS_H) {
- g.appendChild(svgEl('line', {
- x1: 8, x2: W - 8, y1: rowTop, y2: rowTop,
- class: 'expov-svg-row-divider'
- }));
+ // Render a single tactic node.
+ // rosterCtx = { embryos, rolesMap } | null — when present, adds role-scope badge (D2).
+ // tactics = full tactics array — used to resolve relation ids to names.
+ _renderOpsTactic(t, idx, firstPlannedIdx, ESC, rosterCtx = null, tactics = []) {
+ const STATE_LABEL = { done: 'done', active: 'in use', planned: 'queued', paused: 'paused' };
+ const seq = String(t.seq || idx + 1).padStart(2, '0');
+ const stateLabel = STATE_LABEL[t.state] || t.state;
+ // First queued tactic gets a "next" badge — COCKED instrument marker.
+ const isFirstQueued = t.state === 'planned' && idx === firstPlannedIdx;
+ const nextBadge = isFirstQueued
+ ? ''
+ : '';
+
+ const live = t.live || {};
+ const target = live.target || '';
+ const summary = live.summary || '';
+ const desc = live.desc || '';
+
+ // Scope chip/badge — compact chip for planned/done/paused (always visible, no embryo
+ // list needed); full badge with embryo resolution for active state (D2 roster lens).
+ const isExpandable = (t.state === 'planned' || t.state === 'done' || t.state === 'paused');
+ const expandKey = this._tacticExpandKey(t);
+ const scopeBadge = isExpandable
+ ? this._renderOpsScopeChip(t.scope, ESC)
+ : (rosterCtx ? this._renderOpsScopeBadge(t.scope, rosterCtx.embryos, rosterCtx.rolesMap, ESC) : '');
+
+ // Chevron toggle — only for expandable (planned / done / paused) tactics.
+ const chevron = isExpandable
+ ? ``
+ : '';
+
+ // Header row: name · target · scope badge · summary · chevron
+ let inner = `
+ Operations · ${hasActive ? 'live' : 'idle'}
+ ${ESC(plan.title || '')}
+ +
+ done
+ in use
+ queued
+
+ ${rosterHtml}
+ ${spineLabel}
+ ${spineNodes}
+
+ ${ESC(t.name)}
+ ${target ? `${ESC(target)}` : ''}
+ ${scopeBadge}
+ ${summary ? `${ESC(summary)}` : ''}
+ ${chevron}
+
+ ${desc ? `${ESC(desc)}
` : ''}`;
+
+ // AUDIT: FLATTEN the active card — readouts on the panel face, separated by
+ // a hairline rule. No nested card-in-card boxes.
+ if (t.state === 'active' && live.readouts && live.readouts.length) {
+ inner += `+
+ ${live.readouts.map(r => this._renderOpsReadout(r, ESC)).join('')}
+
`;
}
- // ---- Left label gutter ---------------------------------------
- // Single header line + phase pill. Power/dose labels are at the
- // y-position of their respective sub-rows, right-aligned in the gutter.
- const labelY = rowTop + ROW_PAD + 12;
-
- // Header line: icon · ID · role (· 10× hint for calibration)
- g.appendChild(svgEl('text', {
- x: 14, y: labelY + 1, class: 'expov-svg-role-icon',
- fill: emb.color
- }, emb.icon));
- g.appendChild(svgEl('text', {
- x: 32, y: labelY, class: 'expov-svg-label'
- }, emb.id));
- // role tag — eyebrow above the id (avoids colliding with long ids)
- g.appendChild(svgEl('text', {
- x: 14, y: rowTop + ROW_PAD - 1,
- class: 'expov-svg-role-tag'
- }, emb.role));
-
- // Phase pill: current mode at glance
- const currentPhase = emb.phases[emb.phases.length - 1];
- const pillY = labelY + 7;
- const pillH = 14;
- const phaseLabel = currentPhase.mode === 'burst'
- ? `BURST · ${currentPhase.hz}Hz`
- : `${currentPhase.mode.toUpperCase()} · ${currentPhase.cadence_s}s`;
- const pillW = Math.max(70, phaseLabel.length * 6 + 12);
- const pillX = 32;
- const phaseColors = {
- base: '#6b7280',
- fast: '#fb923c',
- burst: '#ef4444',
- cooldown: '#a78bfa',
- paused: '#3b82f6'
- };
- const pillFill = phaseColors[currentPhase.mode] || '#6b7280';
- g.appendChild(svgEl('rect', {
- x: pillX, y: pillY, width: pillW, height: pillH, rx: 7,
- fill: pillFill, 'fill-opacity': 0.22,
- stroke: pillFill, 'stroke-opacity': 0.65, 'stroke-width': 1
- }));
- g.appendChild(svgEl('text', {
- x: pillX + pillW / 2, y: pillY + 10,
- 'text-anchor': 'middle',
- fill: pillFill, 'font-size': 9.5, 'font-weight': 700,
- 'font-family': "'JetBrains Mono', monospace"
- }, phaseLabel));
-
- // Tiny tp annotation under the pill (no stop — that's at lane right edge)
- g.appendChild(svgEl('text', {
- x: 32, y: pillY + pillH + 12,
- class: 'expov-svg-sublabel'
- }, `${emb.tp_acquired} tp acquired`));
-
- // ---- Cadence lane --------------------------------------------
- const laneY = rowTop + ROW_PAD;
- const laneMid = laneY + LANE_H / 2;
- const laneBottom = laneY + LANE_H;
-
- // Phases — solid colored rects, no ticks. Cadence is read from the
- // phase pill in the gutter and the optional inline cadence label.
- // Min 4px visual width so micro-phases (burst, cooldown) stay visible.
- emb.phases.forEach(ph => {
- const x0 = xForT(ph.start);
- const x1Raw = xForT(ph.end);
- const x1 = Math.max(x1Raw, x0 + 4);
- const width = x1 - x0;
- const cls = `expov-svg-phase-${ph.mode}`;
- g.appendChild(svgEl('rect', {
- x: x0, y: laneY, width, height: LANE_H, rx: 2,
- class: cls
- }));
- // Cadence text inside the rect is intentionally omitted — the
- // gutter pill (currentPhase) and the colored rect (mode) already
- // convey it. Keep an inline label only for cooldown, which is a
- // transient state the pill won't be showing.
- if (ph.mode === 'cooldown' && ph.cadence_s && width >= 42) {
- g.appendChild(svgEl('text', {
- x: x0 + width / 2, y: laneMid + 3.5,
- 'text-anchor': 'middle',
- class: 'expov-svg-phase-label'
- }, `${ph.cadence_s}s · cool`));
- }
- // Burst: keep the bright block + balloon since it's the most
- // attention-worthy event in the lane
- if (ph.mode === 'burst') {
- const bx = (xForT(ph.start) + xForT(ph.end)) / 2;
- const balloonY = laneY - 12;
- const halfW = 30;
- g.appendChild(svgEl('rect', {
- x: bx - halfW, y: balloonY - 10, width: halfW * 2, height: 12, rx: 3,
- class: 'expov-svg-burst-balloon-bg'
- }));
- g.appendChild(svgEl('text', {
- x: bx, y: balloonY - 1,
- 'text-anchor': 'middle',
- class: 'expov-svg-burst-label'
- }, `${ph.frames}f · ${ph.hz}Hz`));
- g.appendChild(svgEl('line', {
- x1: bx, x2: bx, y1: balloonY + 2, y2: laneY,
- stroke: '#ef4444', 'stroke-width': 1, 'stroke-opacity': 0.7
- }));
- }
- });
+ // Kind-specific structure for the active state.
+ if (t.state === 'active') {
+ inner += this._renderOpsKindActive(t, live, ESC);
+ } else if (t.state === 'planned') {
+ inner += this._renderOpsKindPlanned(t, ESC);
+ inner += this._renderOpsExpandBody(t, ESC, tactics);
+ }
- // ---- Acquisition density heatmap ----------------------------
- // Instead of one hairline per acquisition (reads as a barcode),
- // we encode acquisition density as a luminance gradient over
- // the past portion of the lane: sparse = lane stays muted,
- // dense = a brighter band. The eye reads acquisition rate as
- // brightness — no discrete marks, no clutter.
- //
- // Counts are derived from phase cadence then rescaled to match
- // the authoritative `tp_acquired`, so the gradient never lies
- // about how many timepoints fired even when the backend phase
- // history is stale or incorrect.
- const tickEnd = s.now_offset_s;
- const ackPhases = emb.phases
- .map((ph, i) => ({ ph, i }))
- .filter(({ ph }) => ph.mode !== 'burst' && ph.cadence_s);
- const predicted = ackPhases.map(({ ph }) => {
- const phEnd = Math.min(ph.end ?? tickEnd, tickEnd);
- const dur = phEnd - ph.start;
- return dur > 0 ? Math.max(1, Math.floor(dur / ph.cadence_s) + 1) : 0;
- });
- const predictedTotal = predicted.reduce((a, b) => a + b, 0);
- const actualTotal = Number.isFinite(emb.tp_acquired)
- ? emb.tp_acquired : predictedTotal;
- const scale = predictedTotal > 0 ? actualTotal / predictedTotal : 0;
- const acquisitions = [];
- ackPhases.forEach(({ ph }, idx) => {
- const phEnd = Math.min(ph.end ?? tickEnd, tickEnd);
- const dur = phEnd - ph.start;
- if (dur <= 0) return;
- const n = Math.max(1, Math.round(predicted[idx] * scale));
- for (let j = 0; j < n; j++) {
- acquisitions.push(ph.start + (dur * (j + 0.5)) / n);
+ // Fix #1: surface flat live.* telemetry keys not covered by structured
+ // readouts/phases. Render for active (in-progress telemetry) and done
+ // (completion data such as sustained_hz, mp4_path, last_fired).
+ // Skip planned — no live data is bound yet.
+ if (t.state === 'active' || t.state === 'done') {
+ const SKIP = new Set(['readouts', 'phases', 'target', 'summary', 'desc']);
+ const flatEntries = Object.entries(live).filter(([k]) => !SKIP.has(k));
+ if (flatEntries.length) {
+ const humanKey = k => k.replace(/_/g, ' ');
+ const pairs = flatEntries.map(([k, v]) => {
+ const vStr = v == null ? '—' : String(v);
+ return `${ESC(humanKey(k))}${ESC(vStr)}`;
+ }).join('');
+ inner += `${pairs}
`;
}
- });
+ }
- if (acquisitions.length > 0 && tickEnd > 0) {
- // Layer 1 (background): smoothed luminance gradient
- // encoding overall acquisition density along the lane.
- // The triangular kernel kills aliasing stripes caused by
- // evenly-spaced acquisitions falling into bins.
- const BINS = 64;
- const binSec = tickEnd / BINS;
- const raw = new Array(BINS).fill(0);
- for (const t of acquisitions) {
- const bin = Math.min(BINS - 1, Math.max(0, Math.floor(t / binSec)));
- raw[bin] += 1;
- }
- const kernel = [1, 2, 3, 4, 5, 4, 3, 2, 1];
- const kSum = kernel.reduce((a, b) => a + b, 0);
- const kOff = Math.floor(kernel.length / 2);
- const density = new Array(BINS).fill(0);
- for (let i = 0; i < BINS; i++) {
- let acc = 0, w = 0;
- for (let k = 0; k < kernel.length; k++) {
- const j = i + k - kOff;
- if (j < 0 || j >= BINS) continue;
- acc += raw[j] * kernel[k];
- w += kernel[k];
- }
- density[i] = w > 0 ? acc / w * (kSum / w) : 0;
- }
- const maxD = Math.max(...density, 1e-6);
- const gradId = `expov-density-${(emb.id || 'e').replace(/\W+/g, '_')}-r${rowTop}`;
- const grad = svgEl('linearGradient', {
- id: gradId, x1: '0%', x2: '100%', y1: '0%', y2: '0%'
- });
- for (let i = 0; i < BINS; i++) {
- const intensity = density[i] / maxD;
- // Lower ceiling than the heatmap-only version (0.22 vs
- // 0.38) because the dots above will carry the per-event
- // signal; the band just hints at rate.
- const alpha = 0.03 + 0.22 * intensity;
- grad.appendChild(svgEl('stop', {
- offset: `${(i / (BINS - 1)) * 100}%`,
- 'stop-color': '#ffffff',
- 'stop-opacity': alpha.toFixed(3),
- }));
- }
- g.appendChild(grad);
- const pastW = xForT(tickEnd) - LEFT;
- if (pastW > 0) {
- g.appendChild(svgEl('rect', {
- x: LEFT, y: laneY,
- width: pastW, height: LANE_H,
- fill: `url(#${gradId})`,
- rx: 2,
- 'pointer-events': 'none'
- }));
- }
- // Layer 2 (foreground): one soft round dot per acquisition
- // along the top edge of the lane — keeps the per-event
- // temporal discreteness the heatmap alone hides.
- const dotY = laneY + 2;
- for (const t of acquisitions) {
- const tx = xForT(t);
- g.appendChild(svgEl('circle', {
- cx: tx, cy: dotY, r: 1.3,
- class: 'expov-svg-acq-dot'
- }));
- }
+ // Expand body for done + paused tactics (appended after live-facts).
+ if (t.state === 'done' || t.state === 'paused') {
+ inner += this._renderOpsExpandBody(t, ESC, tactics);
}
- // ---- Cadence-change markers ---------------------------------
- // Where consecutive phases differ in cadence (or mode), drop a
- // vertical divider across the lane and a "300→60s · T34" chip
- // above so the change is named and time-stamped in the lane.
- // Apply the same scale factor used for tick rendering so the
- // T# stamps shown on diamonds and cadence chips agree with the
- // visible tick density and the authoritative tp_acquired count.
- // Otherwise the chip might say "T118" on an embryo where we
- // only drew 54 ticks — visually contradictory.
- const tpIndexAt = (atS) => {
- let count = 0;
- for (const ph of emb.phases) {
- if (!ph.cadence_s) continue;
- if (atS < ph.start) break;
- const phEnd = Math.min(atS, ph.end ?? atS);
- count += Math.floor((phEnd - ph.start) / ph.cadence_s) + 1;
- }
- return Math.max(1, Math.round(count * scale));
- };
- // Track placed chip x-positions to avoid stacking chips on top
- // of one another (e.g. the burst-balloon already sits there).
- const placedChipX = [];
- const burstXs = emb.phases
- .filter(p => p.mode === 'burst')
- .map(p => xForT(p.start));
- const isCollision = (x) => {
- const min = 70; // px buffer
- if (burstXs.some(bx => Math.abs(bx - x) < min)) return true;
- return placedChipX.some(px => Math.abs(px - x) < min);
- };
- // Walk phases and detect transitions, but COLLAPSE consecutive
- // identical (mode + cadence) phases so a row of redundant phase
- // records doesn't generate redundant dividers/chips.
- let prevEffective = emb.phases[0];
- for (let i = 1; i < emb.phases.length; i++) {
- const curr = emb.phases[i];
- const prev = prevEffective;
- const sameCadence = prev.cadence_s === curr.cadence_s;
- const sameMode = prev.mode === curr.mode;
- if (sameCadence && sameMode) {
- continue; // collapse: prevEffective stays the same
+ const cardExpandAttr = isExpandable
+ ? ` data-tactic-expand-id="${ESC(expandKey)}"`
+ : '';
+
+ return `
+
+
`;
+ },
+
+ // -----------------------------------------------------------------
+ // Expandable tactic detail — click-to-expand for queued/done/paused
+ // -----------------------------------------------------------------
+
+ // Stable key used to persist expand state across re-renders.
+ _tacticExpandKey(t) {
+ return String(t.id || t.seq || t.name || '');
+ },
+
+ // Compact inline scope chip — always shown in the collapsed header.
+ // Works without embryo list; uses this._rolesMap for role color if available.
+ _renderOpsScopeChip(scope, ESC) {
+ const rolesMap = this._rolesMap;
+ if (!scope || scope.mode === 'global') {
+ return 'global';
+ }
+ if (scope.mode === 'role') {
+ const role = scope.role || '';
+ const roleInfo = rolesMap ? rolesMap.get(role) : null;
+ const color = (roleInfo && roleInfo.ui_color) || '#8b949e';
+ const bg = this._hexToRgba(color, 0.12);
+ const border = this._hexToRgba(color, 0.35);
+ return `role: ${ESC(role)}`;
+ }
+ if (scope.mode === 'embryos') {
+ const ids = (scope.embryo_ids || []).join(', ');
+ return `${ESC(ids) || '—'}`;
+ }
+ return '';
+ },
+
+ // Expanded detail body — rationale, scope, structure, relations, live.readouts.
+ // Rendered hidden by default; _wireSpineExpand toggles the `hidden` class.
+ _renderOpsExpandBody(t, ESC, tactics) {
+ const rows = [];
+
+ // Rationale
+ if (t.rationale) {
+ rows.push(``);
+ }
+
+ // Scope — resolved readable form
+ const scope = t.scope;
+ if (scope) {
+ let scopeText = 'all embryos';
+ if (scope.mode === 'role') {
+ scopeText = `role: ${scope.role || ''}`;
+ } else if (scope.mode === 'embryos') {
+ scopeText = (scope.embryo_ids || []).join(', ') || '—';
}
- prevEffective = curr;
- if (prev.mode === 'burst' || curr.mode === 'burst') continue;
- const cx = xForT(curr.start);
- if (cx > xForT(s.now_offset_s)) continue;
- // Divider is cheap to keep even on collision; the chip is what
- // crowds the space, so we skip just the chip when crowded.
- g.appendChild(svgEl('line', {
- x1: cx, x2: cx, y1: laneY, y2: laneBottom,
- class: 'expov-svg-cadence-divider'
- }));
- if (isCollision(cx)) continue;
- const tp = tpIndexAt(curr.start);
- const prevS = prev.cadence_s ?? '?';
- const currS = curr.cadence_s ?? '?';
- const chipText = `${prevS}→${currS}s · T${tp}`;
- const chipW = chipText.length * 5.6 + 10;
- const chipY = laneY - 13;
- g.appendChild(svgEl('rect', {
- x: cx - chipW / 2, y: chipY,
- width: chipW, height: 12, rx: 3,
- class: 'expov-svg-cadence-chip-bg'
- }));
- g.appendChild(svgEl('text', {
- x: cx, y: chipY + 9,
- 'text-anchor': 'middle',
- class: 'expov-svg-cadence-chip'
- }, chipText));
- placedChipX.push(cx);
+ rows.push(``);
}
- // ---- Power-change chips -------------------------------------
- // Same visual language as cadence chips, but parked in a row
- // above so the two encodings stack neatly when they happen at
- // the same trigger. Each chip names the rule outcome
- // ("488 ↓ 5%→3%") and the timepoint it landed at.
- const placedPowerChipX = [];
- const hist488 = emb.power_history_488 || [];
- // Walk the history, collect actual transitions (pairs where pct
- // changes), then cluster consecutive close ones so a multi-step
- // ramp gets a single annotation.
- const transitions = [];
- for (let k = 0; k < hist488.length - 1; k++) {
- const a = hist488[k];
- const b = hist488[k + 1];
- if (a.pct === b.pct) continue;
- transitions.push({ from: a, to: b });
+ // Structure — kind-specific
+ const struct = t.structure || {};
+ if (t.kind === 'standing_timelapse' && struct.cadence_s != null) {
+ rows.push(``);
}
- const CLUSTER_S = 60;
- const clusters = [];
- for (const tr of transitions) {
- const last = clusters[clusters.length - 1];
- if (last && tr.to.at - last[last.length - 1].to.at <= CLUSTER_S) {
- last.push(tr);
- } else {
- clusters.push([tr]);
+ if (t.kind === 'scripted_protocol') {
+ const phases = (struct.phases || []);
+ if (phases.length) {
+ const pHtml = phases.map(p =>
+ ``
+ ).join('');
+ rows.push(``);
}
}
- for (const cluster of clusters) {
- const first = cluster[0];
- const tail = cluster[cluster.length - 1];
- // Anchor the chip at the actual change time, not at any
- // trailing anchor record (those can land past `now` and
- // get hidden by the past-only guard).
- const atS = Math.min(tail.to.at, s.now_offset_s);
- const cx = xForT(atS);
- const arrow = tail.to.pct < first.from.pct ? '↓' : '↑';
- const chipText = `488 ${arrow} ${first.from.pct}%→${tail.to.pct}% · T${tpIndexAt(atS)}`;
- const chipW = chipText.length * 5.6 + 10;
- // Sit just above the burst-balloon band (which lives at
- // laneY-22..-10) so we stay within this row's vertical
- // budget — laneY-40 would have crossed into the row above.
- // Burst balloons live at separate x positions on every
- // case I've seen, so dropping the burst-collision check
- // lets the chip render even when a burst is on the same
- // lane elsewhere.
- const chipY = laneY - 25;
- const crowded =
- placedPowerChipX.some(px => Math.abs(px - cx) < 70);
- g.appendChild(svgEl('line', {
- x1: cx, x2: cx, y1: chipY + 12, y2: laneY,
- class: 'expov-svg-power-chip-stem'
- }));
- if (crowded) continue;
- g.appendChild(svgEl('rect', {
- x: cx - chipW / 2, y: chipY,
- width: chipW, height: 12, rx: 3,
- class: 'expov-svg-power-chip-bg'
- }));
- g.appendChild(svgEl('text', {
- x: cx, y: chipY + 9,
- 'text-anchor': 'middle',
- class: 'expov-svg-power-chip'
- }, chipText));
- placedPowerChipX.push(cx);
+ if (t.kind === 'exclusive_burst' || t.kind === 'burst') {
+ if (struct.frames != null) {
+ rows.push(``);
+ }
+ if (struct.mode) {
+ rows.push(``);
+ }
+ }
+ if (t.kind === 'reactive_monitor' && struct.watch) {
+ rows.push(``);
}
- // Projected future segment (dashed) past 'now' to a horizon —
- // skipped entirely when the embryo has been terminated, since
- // there's no future to project. projEndT is hoisted because
- // downstream code (stop-icon, dose-exhaust line) anchors to it.
- const isTerminated = emb.terminated_at_s != null
- && emb.terminated_at_s <= s.now_offset_s;
- const projStartT = s.now_offset_s;
- let projEndT = isTerminated ? emb.terminated_at_s : s.horizon_s;
- let projEndsAtBudget = false;
- if (!isTerminated) {
- if (emb.projected_end_s) projEndT = Math.min(projEndT, emb.projected_end_s);
- if (emb.dose_exhaust_at_s && emb.dose_exhaust_at_s < projEndT) {
- projEndT = emb.dose_exhaust_at_s;
- projEndsAtBudget = true;
- }
- const xProjStart = xForT(projStartT);
- const xProjEnd = xForT(projEndT);
- if (xProjEnd > xProjStart) {
- g.appendChild(svgEl('line', {
- x1: xProjStart, y1: laneMid, x2: xProjEnd, y2: laneMid,
- class: projEndsAtBudget
- ? 'expov-svg-projected-bar warn'
- : 'expov-svg-projected-bar'
- }));
+ // Relations — resolve tactic IDs to names
+ const relations = t.relations || {};
+ const afterIds = Array.isArray(relations.after) ? relations.after : [];
+ if (afterIds.length) {
+ const tacticIdMap = {};
+ for (const tac of (tactics || [])) {
+ if (tac.id) tacticIdMap[tac.id] = tac.name || tac.id;
}
+ const names = afterIds.map(id => tacticIdMap[id] || id);
+ rows.push(``);
}
- // Terminated cap: small vertical stop bar at the termination
- // point + a "■ DONE · T##" label below the lane so a finished
- // embryo doesn't look like it's still acquiring.
- if (isTerminated) {
- const termX = xForT(emb.terminated_at_s);
- g.appendChild(svgEl('line', {
- x1: termX, x2: termX,
- y1: laneY - 2, y2: laneBottom + 2,
- class: 'expov-svg-terminated-bar'
- }));
- g.appendChild(svgEl('rect', {
- x: termX - 2, y: laneY + LANE_H / 2 - 3,
- width: 6, height: 6,
- class: 'expov-svg-terminated-stop'
- }));
- const tp = tpIndexAt(emb.terminated_at_s);
- const capText = `DONE · T${tp}`;
- g.appendChild(svgEl('text', {
- x: termX + 6, y: laneBottom + 9,
- class: 'expov-svg-terminated-label'
- }, capText));
+
+ // Live readouts (queued/done tactics may carry pre-set readout definitions)
+ const live = t.live || {};
+ if (live.readouts && live.readouts.length) {
+ rows.push(``);
}
- // Trigger diamonds — placed in the upper half of the lane to avoid
- // colliding with the burst balloon above. Each diamond gets a tiny
- // T# label below it so the user can see at which timepoint the
- // rule fired without hovering.
- (emb.trigger_events || []).forEach(te => {
- const x = xForT(te.at);
- const dy = laneY + 6;
- const size = 4;
- const trig = s.triggers.find(t => t.id === te.trigger_id);
- const label = trig ? trig.label : te.trigger_id;
- const dia = svgEl('polygon', {
- points: `${x},${dy-size} ${x+size},${dy} ${x},${dy+size} ${x-size},${dy}`,
- class: 'expov-svg-trigger-diamond expov-svg-tooltip-target'
+ if (!rows.length) return '';
+
+ const isOpen = this._expandedTacticIds.has(this._tacticExpandKey(t));
+ return ``;
+ },
+
+ // Wire click-to-expand on all expandable tactic cards in root after innerHTML is set.
+ // Persist expand state in _expandedTacticIds so it survives debounced re-renders.
+ _wireSpineExpand(root) {
+ root.querySelectorAll('.ops-card[data-tactic-expand-id]').forEach(card => {
+ const expandId = card.dataset.tacticExpandId;
+ const body = card.querySelector('.ops-expand-body');
+ const chevron = card.querySelector('.ops-expand-chevron');
+ if (!body) return;
+
+ card.addEventListener('click', (e) => {
+ // Let clicks on interactive elements inside the body bubble freely.
+ if (e.target.closest('a, button:not(.ops-expand-chevron)')) return;
+ const isExpanded = !body.classList.contains('hidden');
+ if (isExpanded) {
+ body.classList.add('hidden');
+ if (chevron) chevron.classList.remove('open');
+ this._expandedTacticIds.delete(expandId);
+ } else {
+ body.classList.remove('hidden');
+ if (chevron) chevron.classList.add('open');
+ this._expandedTacticIds.add(expandId);
+ }
});
- const tooltip = svgEl('title');
- tooltip.textContent = `${label}\n${trig?.when_text || ''} → ${trig?.then_text || ''}` +
- (te.count ? ` (×${te.count})` : '');
- dia.appendChild(tooltip);
- g.appendChild(dia);
- g.appendChild(svgEl('text', {
- x: x, y: laneBottom + 9,
- 'text-anchor': 'middle',
- class: 'expov-svg-trigger-tp'
- }, `T${tpIndexAt(te.at)}`));
});
+ },
+
+ // Render a readout gauge. `r.value` may contain trusted HTML (span markup).
+ // Stamps data-livebind on the outer div so _handleTempUpdate (and future
+ // live-binding) can find the gauge in-place without a full re-render.
+ // Priority: r.bind (explicit semantic key) > normalised r.label.
+ _renderOpsReadout(r, ESC) {
+ const bindKey = r.bind
+ ? r.bind
+ : (r.label
+ ? r.label.toLowerCase().replace(/[^a-z0-9]+/g, '_').replace(/^_|_$/g, '')
+ : '');
+ const bindAttr = bindKey ? ` data-livebind="${ESC(bindKey)}"` : '';
+ return `${seq} · ${stateLabel}${nextBadge ? ' ' + nextBadge : ''}
+ ${inner}
+
+
`;
+ },
- // Dose-exhaust warning: ⚠ + time-to-exhaust positioned ABOVE the lane
- // so it doesn't overlap with the dashed projected bar
- if (emb.dose_exhaust_at_s && emb.dose_exhaust_at_s < s.horizon_s) {
- const exhX = xForT(emb.dose_exhaust_at_s);
- const remain = emb.dose_exhaust_at_s - s.now_offset_s;
- const rh = Math.floor(remain / 3600);
- const rm = Math.floor((remain % 3600) / 60);
- const exhText = `⚠ budget exhausts in ${rh > 0 ? rh + 'h ' : ''}${rm}m`;
- g.appendChild(svgEl('text', {
- x: exhX - 4, y: laneY - 5,
- 'text-anchor': 'end',
- fill: 'var(--accent-orange)',
- 'font-size': 10,
- 'font-weight': 600,
- 'font-family': "'JetBrains Mono', monospace"
- }, exhText));
- // Small dotted vertical marker so the user can see WHERE on the lane
- g.appendChild(svgEl('line', {
- x1: exhX, x2: exhX, y1: laneY, y2: laneY + LANE_H,
- stroke: 'var(--accent-orange)',
- 'stroke-width': 1.5,
- 'stroke-dasharray': '2 2',
- opacity: 0.7
- }));
+ // Render one phase in the scripted_protocol stepper.
+ // AUDIT: the active phase is the HEADLINE — CSS makes it larger.
+ _renderOpsPhase(p, ESC) {
+ const pips = (p.pips || [])
+ .map(k => ``)
+ .join('');
+ const ic = p.state === 'done' ? '✓'
+ : p.state === 'active' ? '▶'
+ : (p.icon || '·');
+ return `${ESC(r.label)}
+ ${r.value}
+ ${r.bar != null
+ ? ``
+ : ''}
+ ${r.sub ? `${ESC(r.sub)}
` : ''}
+
+
`;
+ },
+
+ // Kind-specific structure for ACTIVE tactics.
+ _renderOpsKindActive(t, live, ESC) {
+ if (!t.kind) return '';
+
+ // scripted_protocol → before/during/after phase stepper.
+ // Prefer live.phases (may carry pip/count state); fall back to structure.phases.
+ if (t.kind === 'scripted_protocol') {
+ const phases = live.phases || (t.structure && t.structure.phases) || [];
+ if (!phases.length) return '';
+ return `${ic}${ESC(p.name)}
+ ${ESC(p.count || '')}
+ ${pips ? `${pips}
` : ''}
+
+ ${phases.map(p => this._renderOpsPhase(p, ESC)).join('')}
+
`;
}
- // Open-ended ∞ glyph at right edge
- if (emb.stop_kind === 'open_ended') {
- g.appendChild(svgEl('text', {
- x: LEFT + LANE_W + 8, y: laneMid + 5,
- class: 'expov-svg-infinity'
- }, '∞'));
- } else {
- g.appendChild(svgEl('text', {
- x: xForT(projEndT) + 6, y: laneMid + 4,
- class: 'expov-svg-stop-icon expov-svg-stop-hatch'
- }, '■'));
+
+ // standing_timelapse → compact per-embryo cadence strip.
+ if (t.kind === 'standing_timelapse') {
+ const perEmbryo = t.structure && t.structure.per_embryo;
+ if (!perEmbryo || !perEmbryo.length) return '';
+ const rows = perEmbryo.map(e => {
+ const intervalStr = e.interval_s != null ? `${ESC(e.interval_s)}s` : '—';
+ return `
+ ${ESC(e.embryo_id)}
+ ${ESC(e.cadence_phase)}
+ ${intervalStr}
+
`;
+ }).join('');
+ return `${rows}
`;
+ }
+
+ // reactive_monitor → armed/watching/fired status badge.
+ if (t.kind === 'reactive_monitor') {
+ const st = (t.structure && t.structure.status) || 'armed';
+ return `${ESC(st)}
`;
+ }
+
+ // exclusive_burst / oneshot / custom — readouts only (already rendered above).
+ return '';
+ },
+
+ // Kind-specific structure for PLANNED (queued) tactics — compact hints.
+ _renderOpsKindPlanned(t, ESC) {
+ if (!t.kind) return '';
+
+ if (t.kind === 'scripted_protocol') {
+ const phases = (t.structure && t.structure.phases) || [];
+ if (!phases.length) return '';
+ return `
+ ${phases.map(p => this._renderOpsPhase(p, ESC)).join('')}
+
`;
+ }
+
+ if (t.kind === 'standing_timelapse' && t.structure && t.structure.cadence_s) {
+ return `cadence · ${ESC(t.structure.cadence_s)}s
`;
+ }
+
+ if (t.kind === 'reactive_monitor' && t.structure && t.structure.watch) {
+ return `watch · ${ESC(t.structure.watch)}
`;
+ }
+
+ if ((t.kind === 'oneshot' || t.kind === 'custom') && t.structure && t.structure.note) {
+ return `${ESC(t.structure.note)}
`;
+ }
+
+ return '';
+ },
+
+ // =================================================================
+ // D2 — Roster Lens: embryo population by role class + role
+ // =================================================================
+
+ // Fetch the current embryo roster from /api/embryos/positions.
+ // Returns [] on failure or when no embryos have positions yet.
+ async _loadRoster() {
+ try {
+ const resp = await fetch('/api/embryos/positions', { cache: 'no-store' });
+ if (!resp.ok) return [];
+ const data = await resp.json();
+ return Array.isArray(data.embryos) ? data.embryos : [];
+ } catch (e) {
+ console.warn('[ExperimentOverview] roster fetch error:', e);
+ return [];
}
+ },
- // ---- Power strip ---------------------------------------------
- // Visual encoding makes "steady" vs "ramping" obvious:
- // • Steady segments = thin grey horizontal line
- // • Ramping segments = bright cyan line + filled area + dot at each step
- // • Step transitions get a small arrow (↓ or ↑) and a delta tag
- const powerY = laneY + LANE_H + 6;
- const powerH = POWER_H;
- const powerYBase = powerY + powerH;
- g.appendChild(svgEl('line', {
- x1: LEFT, x2: LEFT + LANE_W, y1: powerYBase, y2: powerYBase,
- class: 'expov-svg-power-baseline'
- }));
- const yForPct = (pct) => powerYBase - (pct / 10) * powerH;
-
- const hist = emb.power_history_488 || [];
- if (hist.length > 1) {
- // Detect ramp clusters: consecutive change-steps with x-spacing <
- // CLUSTER_PX get grouped, annotated once at the cluster end.
- const CLUSTER_PX = 20;
- const stepEvents = []; // each: {fromIdx, toIdx, isRamp}
- for (let k = 0; k < hist.length - 1; k++) {
- if (hist[k].pct !== hist[k+1].pct) {
- stepEvents.push({ fromIdx: k, toIdx: k+1 });
+ // Fetch the roles registry from /api/roles.
+ // Returns a Map(name → {ui_color, ui_icon, role_class, default_cadence_seconds}).
+ // Returns empty Map on failure.
+ async _loadRolesMap() {
+ try {
+ const resp = await fetch('/api/roles', { cache: 'no-store' });
+ if (!resp.ok) return new Map();
+ const data = await resp.json();
+ const map = new Map();
+ if (Array.isArray(data.roles)) {
+ for (const r of data.roles) {
+ map.set(r.name, r);
}
}
- // Group consecutive close steps into clusters
- const clusters = [];
- stepEvents.forEach(step => {
- const last = clusters[clusters.length - 1];
- const stepX = xForT(hist[step.toIdx].at);
- if (last) {
- const lastX = xForT(hist[last[last.length-1].toIdx].at);
- if (Math.abs(stepX - lastX) < CLUSTER_PX) {
- last.push(step);
- return;
- }
- }
- clusters.push([step]);
- });
+ return map;
+ } catch (e) {
+ console.warn('[ExperimentOverview] roles fetch error:', e);
+ return new Map();
+ }
+ },
- // Draw horizontal "steady" segments + vertical "step" lines for all
- // adjacent (hist[k], hist[k+1]) pairs.
- for (let k = 0; k < hist.length - 1; k++) {
- const x0 = xForT(hist[k].at);
- const x1 = xForT(hist[k+1].at);
- const y = yForPct(hist[k].pct);
- const yNext = yForPct(hist[k+1].pct);
- g.appendChild(svgEl('line', {
- x1: x0, x2: x1, y1: y, y2: y,
- class: 'expov-svg-power-steady'
- }));
- if (hist[k].pct !== hist[k+1].pct) {
- g.appendChild(svgEl('line', {
- x1: x1, x2: x1, y1: y, y2: yNext,
- class: 'expov-svg-power-step'
- }));
- g.appendChild(svgEl('circle', {
- cx: x1, cy: yNext, r: 2.2,
- class: 'expov-svg-power-stepdot'
- }));
- }
+ // Convert a hex color (#rrggbb) to rgba(r,g,b,alpha) for inline styles.
+ _hexToRgba(hex, alpha) {
+ const h = (hex || '#888888').replace('#', '');
+ const r = parseInt(h.slice(0, 2), 16) || 0;
+ const g = parseInt(h.slice(2, 4), 16) || 0;
+ const b = parseInt(h.slice(4, 6), 16) || 0;
+ return `rgba(${r},${g},${b},${alpha})`;
+ },
+
+ // Cross-reference: find the name of the active (or most recently done) tactic
+ // that covers a given embryo (by embryo_id + role).
+ // Scope resolution: global → covers all; role → covers matching role;
+ // embryos → covers listed ids. Returns '' when no tactic found.
+ // NOTE: mirrors resolve_scope_embryos() in gently/app/orchestration/role_scope.py — keep in sync if a new scope mode is added.
+ _resolveCurrentTactic(embryoId, role, plan) {
+ if (!plan || !Array.isArray(plan.tactics)) return '';
+ const covers = (t) => {
+ const scope = t.scope || { mode: 'global' };
+ if (scope.mode === 'global') return true;
+ if (scope.mode === 'role') return scope.role === role;
+ if (scope.mode === 'embryos') {
+ return Array.isArray(scope.embryo_ids) && scope.embryo_ids.includes(embryoId);
}
- // Final tail to lane right edge
- const last = hist[hist.length - 1];
- const lastX = xForT(last.at);
- const lastY = yForPct(last.pct);
- g.appendChild(svgEl('line', {
- x1: lastX, x2: LEFT + LANE_W, y1: lastY, y2: lastY,
- class: 'expov-svg-power-steady'
- }));
-
- // One annotation per cluster — bracket + "5% → 3%" label
- clusters.forEach(cluster => {
- const first = cluster[0];
- const tail = cluster[cluster.length - 1];
- const xStart = xForT(hist[first.fromIdx].at);
- const xEnd = xForT(hist[tail.toIdx].at);
- const pctStart = hist[first.fromIdx].pct;
- const pctEnd = hist[tail.toIdx].pct;
- const arrow = pctEnd < pctStart ? '↓' : '↑';
- const yMid = (yForPct(pctStart) + yForPct(pctEnd)) / 2;
- // Bracket: small horizontal line above the cluster steps
- const bracketY = Math.min(yForPct(pctStart), yForPct(pctEnd)) - 6;
- g.appendChild(svgEl('path', {
- d: `M ${xStart} ${bracketY+3} L ${xStart} ${bracketY} L ${xEnd+2} ${bracketY} L ${xEnd+2} ${bracketY+3}`,
- class: 'expov-svg-power-ramp-bracket'
- }));
- // Label "488 ↓ 5%→3%" anchored just right of the bracket end
- g.appendChild(svgEl('text', {
- x: xEnd + 6, y: bracketY + 4,
- class: 'expov-svg-power-ramp-label'
- }, `${arrow} ${pctStart}%→${pctEnd}%`));
- });
+ return false;
+ };
+ // Prefer the active tactic covering this embryo.
+ const active = plan.tactics.find(t => t.state === 'active' && covers(t));
+ if (active) return active.name;
+ // Fall back to the most recently done tactic (last in array order).
+ for (let i = plan.tactics.length - 1; i >= 0; i--) {
+ if (plan.tactics[i].state === 'done' && covers(plan.tactics[i])) {
+ return plan.tactics[i].name;
+ }
+ }
+ return '';
+ },
- // Subtle filled area under the curve — helps read overall level
- const areaPts = [`${xForT(hist[0].at)},${powerYBase}`];
- for (let k = 0; k < hist.length; k++) {
- const x = xForT(hist[k].at);
- const y = yForPct(hist[k].pct);
- areaPts.push(`${x},${y}`);
- if (k < hist.length - 1) {
- const xNext = xForT(hist[k+1].at);
- areaPts.push(`${xNext},${y}`);
- }
+ // Render a scope badge for a tactic node in the spine.
+ // Colors for role-scoped badges come from the roles registry (API), not CSS.
+ // Global and explicit-embryos scopes use the static `.ops-scope-global` class.
+ _renderOpsScopeBadge(scope, embryos, rolesMap, ESC) {
+ if (!scope || scope.mode === 'global') {
+ return '→ all embryos';
+ }
+ if (scope.mode === 'role') {
+ const role = scope.role || '';
+ const roleInfo = rolesMap ? rolesMap.get(role) : null;
+ const color = (roleInfo && roleInfo.ui_color) || '#8b949e';
+ const matchIds = embryos
+ .filter(e => e.role === role)
+ .map(e => e.embryo_id)
+ .join(', ');
+ const label = matchIds
+ ? `→ ${ESC(role)} · ${ESC(matchIds)}`
+ : `→ ${ESC(role)}`;
+ const bg = this._hexToRgba(color, 0.12);
+ const border = this._hexToRgba(color, 0.35);
+ return `${label}`;
+ }
+ if (scope.mode === 'embryos') {
+ const ids = ESC((scope.embryo_ids || []).join(', '));
+ return `→ ${ids}`;
+ }
+ return '';
+ },
+
+ // Render the D2 roster lens: embryos grouped by role class then by role.
+ // SUBJECTS section is foregrounded; REFERENCES section is compact/muted.
+ // Role colors/icons come from the rolesMap (API data), not from CSS constants.
+ // Returns empty string when embryos array is empty (backward compat).
+ _renderRosterLens(embryos, rolesMap, plan, ESC) {
+ if (!embryos || embryos.length === 0) return '';
+
+ // Group embryos by role_class then by role, preserving first-seen order.
+ const CLASS_ORDER_PREF = ['subject', 'reference'];
+ const classOrder = [];
+ const byClass = {};
+
+ for (const emb of embryos) {
+ const roleInfo = rolesMap.get(emb.role);
+ const cls = (roleInfo && roleInfo.role_class) || 'subject';
+ if (!byClass[cls]) {
+ byClass[cls] = { roleOrder: [], byRole: {} };
+ classOrder.push(cls);
+ }
+ const section = byClass[cls];
+ if (!section.byRole[emb.role]) {
+ section.byRole[emb.role] = [];
+ section.roleOrder.push(emb.role);
}
- areaPts.push(`${LEFT + LANE_W},${yForPct(last.pct)}`);
- areaPts.push(`${LEFT + LANE_W},${powerYBase}`);
- g.appendChild(svgEl('polygon', {
- points: areaPts.join(' '),
- class: 'expov-svg-power-area'
- }));
+ section.byRole[emb.role].push(emb);
}
- // Power label with current value — "@" reads as "at this power"
- // and avoids confusion with the bullet-separator used elsewhere
- g.appendChild(svgEl('text', {
- x: LEFT - 8, y: powerY + powerH / 2 + 3,
- 'text-anchor': 'end',
- class: 'expov-svg-sublabel'
- }, `488 @ ${emb.laser_488_pct_now}%`));
-
- // ---- Dose gauge ----------------------------------------------
- const doseY = powerYBase + 6;
- const doseW = LANE_W;
- g.appendChild(svgEl('rect', {
- x: LEFT, y: doseY, width: doseW, height: DOSE_H, rx: 2,
- class: 'expov-svg-dose-track'
- }));
- const dosePct = emb.dose_used_ms / emb.dose_budget_ms;
- const fillCls = dosePct > 0.85 ? 'expov-svg-dose-fill-crit'
- : dosePct > 0.60 ? 'expov-svg-dose-fill-warn'
- : 'expov-svg-dose-fill-ok';
- g.appendChild(svgEl('rect', {
- x: LEFT, y: doseY, width: Math.max(1, doseW * dosePct), height: DOSE_H, rx: 2,
- class: fillCls
- }));
- // Dose label (shows 10× hint for calibration role)
- const doseLabel = emb.role === 'calibration' ? 'dose (10×)' : 'dose';
- g.appendChild(svgEl('text', {
- x: LEFT - 8, y: doseY + DOSE_H - 2,
- 'text-anchor': 'end',
- class: 'expov-svg-sublabel'
- }, doseLabel));
- // Inside the bar: usage figure — "used of budget" is more scannable
- // than "x / y s" which reads like a fraction
- const usedS = (emb.dose_used_ms / 1000).toFixed(1);
- const budgetS = (emb.dose_budget_ms / 1000).toFixed(1);
- const doseText = emb.dose_budget_ms > 0
- ? `${usedS}s of ${budgetS}s (${Math.round(dosePct * 100)}%)`
- : `${usedS}s used`;
- g.appendChild(svgEl('text', {
- x: LEFT + 6, y: doseY + DOSE_H - 2,
- class: 'expov-svg-dose-text'
- }, doseText));
-
- return g;
+
+ // Canonical class order: subjects first.
+ classOrder.sort((a, b) => {
+ const ai = CLASS_ORDER_PREF.indexOf(a);
+ const bi = CLASS_ORDER_PREF.indexOf(b);
+ return (ai < 0 ? 99 : ai) - (bi < 0 ? 99 : bi);
+ });
+
+ const totalCount = embryos.length;
+ const totalRoles = classOrder.reduce((n, cls) => n + byClass[cls].roleOrder.length, 0);
+
+ const classSections = classOrder.map(cls => {
+ const { roleOrder, byRole } = byClass[cls];
+ const isSubject = cls === 'subject';
+
+ const classHeaderInner = isSubject
+ ? `Subjects— adaptive tactics / scenarios`
+ : `References— steady acquisition`;
+
+ const roleGroups = roleOrder.map(role => {
+ const roleEmbyros = byRole[role];
+ const roleInfo = rolesMap.get(role);
+ const uiColor = (roleInfo && roleInfo.ui_color) || '#8b949e';
+ const uiIcon = (roleInfo && roleInfo.ui_icon) || '';
+ const bgRgba = this._hexToRgba(uiColor, 0.08);
+ const ids = roleEmbyros.map(e => e.embryo_id).join(', ');
+
+ const embryoRows = roleEmbyros.map(emb => {
+ const cadencePhase = emb.cadence_phase || 'normal';
+ const strain = emb.strain || '—';
+ const label = emb.user_label || emb.embryo_id;
+ const tacticName = this._resolveCurrentTactic(emb.embryo_id, emb.role, plan);
+ const stateStr = emb.is_complete ? 'done'
+ : cadencePhase === 'paused' ? 'paused'
+ : 'active';
+ const compact = isSubject ? '' : ' compact';
+ const chipBg = this._hexToRgba(uiColor, 0.15);
+ const chipBorder = this._hexToRgba(uiColor, 0.4);
+ return `
+ ${ESC(label)}
+ ${uiIcon ? ESC(uiIcon) + ' ' : ''}${ESC(role)}
+ ${ESC(strain)}
+ ${ESC(cadencePhase)}
+ ${ESC(tacticName || '—')}
+ ${ESC(stateStr)}
+
`;
+ }).join('');
+
+ return `
+
`;
+ }).join('');
+
+ return `
+ ${ESC(role.toUpperCase())}
+ ·
+ ${roleEmbyros.length} embryo${roleEmbyros.length !== 1 ? 's' : ''}
+ ${ESC(ids)}
+
+ ${embryoRows}
+
+
`;
+ }).join('');
+
+ return `${classHeaderInner}
+ ${roleGroups}
+
+
`;
},
// -----------------------------------------------------------------
diff --git a/gently/ui/web/static/js/gallery.js b/gently/ui/web/static/js/gallery.js
index 51ee4207..259e6636 100644
--- a/gently/ui/web/static/js/gallery.js
+++ b/gently/ui/web/static/js/gallery.js
@@ -422,13 +422,19 @@ const CalibrationProfileView = {
/** Compact SPIM live indicator used inside the metrics strip.
* Carries the same IDs as the old big preview so SpimLivePreview's
- * apply-on-render logic continues to work unchanged. */
+ * apply-on-render logic continues to work unchanged. The thumb is a
+ * button — click to open the floating popout for a larger view. */
_renderSpimIndicator() {
return `
+ Population roster
+ ${totalCount} embryo${totalCount !== 1 ? 's' : ''} · ${totalRoles} role${totalRoles !== 1 ? 's' : ''}
+
+ ${classSections}
+
SPIM
- ![]()
+
@@ -1329,21 +1335,33 @@ const SpimLivePreview = {
const placeholder = document.getElementById('cal-spim-placeholder');
const metaEl = document.getElementById('cal-spim-meta');
const led = document.getElementById('cal-spim-led');
- if (!img) return; // not in profile view
const latest = embryoId ? this._latestByEmbryo[embryoId] : null;
- if (latest) {
- img.src = `data:image/png;base64,${latest.base64_png}`;
- img.classList.add('has-frame');
- if (placeholder) placeholder.hidden = true;
- if (metaEl) metaEl.textContent = this._formatMeta(latest);
- if (led) led.classList.remove('idle');
- } else {
- img.removeAttribute('src');
- img.classList.remove('has-frame');
- if (placeholder) placeholder.hidden = false;
- if (metaEl) metaEl.textContent = '—';
- if (led) led.classList.add('idle');
+
+ if (img) {
+ if (latest) {
+ img.src = `data:image/png;base64,${latest.base64_png}`;
+ img.classList.add('has-frame');
+ if (placeholder) placeholder.hidden = true;
+ if (metaEl) metaEl.textContent = this._formatMeta(latest);
+ if (led) led.classList.remove('idle');
+ } else {
+ img.removeAttribute('src');
+ img.classList.remove('has-frame');
+ if (placeholder) placeholder.hidden = false;
+ if (metaEl) metaEl.textContent = '—';
+ if (led) led.classList.add('idle');
+ }
+ }
+
+ // Mirror into popout if it's open — the popout lives outside the
+ // calibration panel's innerHTML reset, so we paint it independently.
+ if (typeof SpimPopout !== 'undefined') {
+ SpimPopout.paint(latest ? {
+ base64_png: latest.base64_png,
+ meta: this._formatMeta(latest),
+ embryoId,
+ } : null);
}
},
@@ -1375,6 +1393,227 @@ const SpimLivePreview = {
document.addEventListener('DOMContentLoaded', () => SpimLivePreview.init());
+// ==========================================
+// SPIM live popout (floating draggable window)
+// ==========================================
+// Lazy-built floating window that mirrors SpimLivePreview at a larger
+// size. Draggable via the header bar, resizable from the bottom-right
+// corner. Position and size persist in localStorage so the window
+// re-opens where the operator last left it. Closes on Escape.
+const SpimPopout = {
+ _STORAGE_KEY: 'gently.spimPopout.v1',
+ _root: null,
+ _isOpen: false,
+
+ _ensureBuilt() {
+ if (this._root) return this._root;
+
+ const el = document.createElement('div');
+ el.className = 'cal-spim-popout';
+ el.id = 'cal-spim-popout';
+ el.hidden = true;
+ el.innerHTML = `
+
+
+ SPIM Live
+
+
+
+
+
+ ![]()
+
+
+ `;
+ document.body.appendChild(el);
+ this._root = el;
+
+ // Restore persisted geometry
+ const saved = this._loadGeometry();
+ if (saved) {
+ el.style.left = `${saved.left}px`;
+ el.style.top = `${saved.top}px`;
+ el.style.width = `${saved.width}px`;
+ el.style.height = `${saved.height}px`;
+ }
+
+ el.querySelector('#cal-spim-popout-close').addEventListener('click', () => this.close());
+ this._wireDrag(el);
+ this._wireResizeObserver(el);
+
+ return el;
+ },
+
+ open() {
+ const el = this._ensureBuilt();
+ if (this._isOpen) return;
+ el.hidden = false;
+ this._isOpen = true;
+
+ // Clamp into viewport in case window was resized while popout was hidden
+ this._clampIntoViewport(el);
+
+ // Paint current frame for the selected embryo
+ const selected = (typeof CalibrationManager !== 'undefined')
+ ? CalibrationManager.selectedEmbryoId : null;
+ if (selected && typeof SpimLivePreview !== 'undefined') {
+ const latest = SpimLivePreview._latestByEmbryo[selected];
+ this.paint(latest ? {
+ base64_png: latest.base64_png,
+ meta: SpimLivePreview._formatMeta(latest),
+ embryoId: selected,
+ } : null);
+ } else {
+ this.paint(null);
+ }
+
+ document.addEventListener('keydown', this._onKey);
+ },
+
+ close() {
+ if (!this._root || !this._isOpen) return;
+ this._root.hidden = true;
+ this._isOpen = false;
+ document.removeEventListener('keydown', this._onKey);
+ },
+
+ toggle() {
+ this._isOpen ? this.close() : this.open();
+ },
+
+ /** Called by SpimLivePreview whenever the current embryo's latest
+ * frame changes. Frame is {base64_png, meta, embryoId} or null. */
+ paint(frame) {
+ if (!this._root || !this._isOpen) return;
+ const img = this._root.querySelector('#cal-spim-popout-img');
+ const placeholder = this._root.querySelector('#cal-spim-popout-placeholder');
+ const meta = this._root.querySelector('#cal-spim-popout-meta');
+ const embryoEl = this._root.querySelector('#cal-spim-popout-embryo');
+ const led = this._root.querySelector('#cal-spim-popout-led');
+
+ if (frame) {
+ img.src = `data:image/png;base64,${frame.base64_png}`;
+ img.classList.add('has-frame');
+ placeholder.hidden = true;
+ meta.textContent = frame.meta || '—';
+ embryoEl.textContent = frame.embryoId || '';
+ led.classList.remove('idle');
+ } else {
+ img.removeAttribute('src');
+ img.classList.remove('has-frame');
+ placeholder.hidden = false;
+ meta.textContent = '—';
+ embryoEl.textContent = '';
+ led.classList.add('idle');
+ }
+ },
+
+ _onKey: (e) => {
+ if (e.key === 'Escape') SpimPopout.close();
+ },
+
+ _wireDrag(el) {
+ const header = el.querySelector('#cal-spim-popout-header');
+ let dragging = false;
+ let startX = 0, startY = 0, startLeft = 0, startTop = 0;
+
+ header.addEventListener('pointerdown', (e) => {
+ // Don't start drag on the close button
+ if (e.target.closest('.cal-spim-popout-close')) return;
+ dragging = true;
+ const rect = el.getBoundingClientRect();
+ startX = e.clientX;
+ startY = e.clientY;
+ startLeft = rect.left;
+ startTop = rect.top;
+ // Switch to absolute positioning if currently default
+ el.style.left = `${startLeft}px`;
+ el.style.top = `${startTop}px`;
+ el.style.right = 'auto';
+ el.style.bottom = 'auto';
+ header.setPointerCapture(e.pointerId);
+ el.classList.add('dragging');
+ });
+
+ header.addEventListener('pointermove', (e) => {
+ if (!dragging) return;
+ const dx = e.clientX - startX;
+ const dy = e.clientY - startY;
+ let nextLeft = startLeft + dx;
+ let nextTop = startTop + dy;
+ // Keep at least 40px of header on-screen
+ const w = el.offsetWidth;
+ const h = el.offsetHeight;
+ nextLeft = Math.max(-(w - 80), Math.min(window.innerWidth - 80, nextLeft));
+ nextTop = Math.max(0, Math.min(window.innerHeight - 40, nextTop));
+ el.style.left = `${nextLeft}px`;
+ el.style.top = `${nextTop}px`;
+ });
+
+ const endDrag = (e) => {
+ if (!dragging) return;
+ dragging = false;
+ el.classList.remove('dragging');
+ try { header.releasePointerCapture(e.pointerId); } catch (_) {}
+ this._saveGeometry(el);
+ };
+ header.addEventListener('pointerup', endDrag);
+ header.addEventListener('pointercancel', endDrag);
+ },
+
+ _wireResizeObserver(el) {
+ if (typeof ResizeObserver === 'undefined') return;
+ let saveTimer = null;
+ const ro = new ResizeObserver(() => {
+ if (!this._isOpen) return;
+ clearTimeout(saveTimer);
+ saveTimer = setTimeout(() => this._saveGeometry(el), 250);
+ });
+ ro.observe(el);
+ },
+
+ _clampIntoViewport(el) {
+ const rect = el.getBoundingClientRect();
+ if (rect.left + 80 > window.innerWidth || rect.top + 40 > window.innerHeight
+ || rect.left < -(rect.width - 80) || rect.top < 0) {
+ // Recenter
+ const w = Math.min(rect.width || 520, window.innerWidth - 40);
+ const h = Math.min(rect.height || 440, window.innerHeight - 40);
+ el.style.width = `${w}px`;
+ el.style.height = `${h}px`;
+ el.style.left = `${Math.max(20, (window.innerWidth - w) / 2)}px`;
+ el.style.top = `${Math.max(20, (window.innerHeight - h) / 2)}px`;
+ }
+ },
+
+ _saveGeometry(el) {
+ const rect = el.getBoundingClientRect();
+ const data = {
+ left: Math.round(rect.left),
+ top: Math.round(rect.top),
+ width: Math.round(rect.width),
+ height: Math.round(rect.height),
+ };
+ try { localStorage.setItem(this._STORAGE_KEY, JSON.stringify(data)); } catch (_) {}
+ },
+
+ _loadGeometry() {
+ try {
+ const raw = localStorage.getItem(this._STORAGE_KEY);
+ if (!raw) return null;
+ const data = JSON.parse(raw);
+ if (typeof data.left !== 'number') return null;
+ return data;
+ } catch (_) { return null; }
+ },
+};
+
// Legacy wrappers kept for backward compatibility
function renderCalibrationGallery() { CalibrationManager.render(); }
@@ -1392,3 +1631,173 @@ function filterByEmbryo(list) {
if (!state.embryoFilter) return list;
return list.filter(img => img.metadata?.embryo_id === state.embryoFilter);
}
+
+// ==========================================
+// GalleryTab — top-level Gallery tab controller
+// ==========================================
+
+const GalleryTab = {
+ _allItems: [],
+ _embryoFilter: '',
+ _typeFilter: '',
+
+ async init() {
+ const panel = document.getElementById('gallery-tab-body');
+ if (!panel) return;
+
+ // Wire filter controls (idempotent)
+ const embryoSel = document.getElementById('gallery-embryo-filter');
+ const typeSel = document.getElementById('gallery-type-filter');
+ const refreshBtn = document.getElementById('gallery-refresh-btn');
+ if (embryoSel && !embryoSel._gtWired) {
+ embryoSel._gtWired = true;
+ embryoSel.addEventListener('change', () => {
+ this._embryoFilter = embryoSel.value;
+ this._renderGrid();
+ });
+ }
+ if (typeSel && !typeSel._gtWired) {
+ typeSel._gtWired = true;
+ typeSel.addEventListener('change', () => {
+ this._typeFilter = typeSel.value;
+ this._renderGrid();
+ });
+ }
+ if (refreshBtn && !refreshBtn._gtWired) {
+ refreshBtn._gtWired = true;
+ refreshBtn.addEventListener('click', () => this._load());
+ }
+
+ await this._load();
+ },
+
+ async _load() {
+ const panel = document.getElementById('gallery-tab-body');
+ if (!panel) return;
+ panel.innerHTML = '
+ Awaiting SPIM frame…
+
+ Loading…
';
+ try {
+ const data = await fetch('/api/snapshots').then(r => r.json());
+ const items = data.snapshots || [];
+ // Sort newest first
+ items.sort((a, b) => (b.timestamp || '').localeCompare(a.timestamp || ''));
+ this._allItems = items;
+ this._populateEmbroyFilter(items);
+ this._renderGrid();
+ } catch (err) {
+ panel.innerHTML = 'Failed to load gallery — check connection.
';
+ }
+ },
+
+ _populateEmbroyFilter(items) {
+ const sel = document.getElementById('gallery-embryo-filter');
+ if (!sel) return;
+ const embryos = [...new Set(items.map(i => i.metadata?.embryo_id).filter(Boolean))].sort();
+ const cur = sel.value;
+ // Rebuild options beyond the "All embryos" placeholder
+ while (sel.options.length > 1) sel.remove(1);
+ embryos.forEach(eid => {
+ const opt = document.createElement('option');
+ opt.value = eid;
+ opt.textContent = eid;
+ sel.appendChild(opt);
+ });
+ if (cur && embryos.includes(cur)) sel.value = cur;
+ },
+
+ _renderGrid() {
+ const panel = document.getElementById('gallery-tab-body');
+ if (!panel) return;
+
+ let items = this._allItems;
+ if (this._embryoFilter) {
+ items = items.filter(i => (i.metadata?.embryo_id || '') === this._embryoFilter);
+ }
+ if (this._typeFilter) {
+ items = items.filter(i => i.data_type === this._typeFilter);
+ }
+
+ if (items.length === 0) {
+ panel.innerHTML = 'No images match the current filter.
';
+ return;
+ }
+
+ const html = `${items.map((img, idx) => this._itemHtml(img, idx)).join('')}
`;
+ panel.innerHTML = html;
+
+ // Wire click handlers
+ panel.querySelectorAll('.gallery-tab-item').forEach(el => {
+ el.addEventListener('click', () => {
+ const idx = parseInt(el.dataset.idx, 10);
+ Lightbox.open(items, idx, 'gallery');
+ });
+ });
+ },
+
+ _itemHtml(img, idx) {
+ const embryo = img.metadata?.embryo_id || '';
+ const ts = img.timestamp ? img.timestamp.slice(0, 19).replace('T', ' ') : '';
+ const typeLabel = img.data_type || 'image';
+ const thumb = img.base64_png
+ ? ``
+ : `${typeLabel}
`;
+ return `
+
+ ${thumb}
+
+ `;
+ },
+};
+
+// ==========================================
+// showGentlyToast — lightweight global toast (volume acquired, etc.)
+// ==========================================
+
+/**
+ * Show a brief toast notification with an optional action link.
+ * @param {string} message - Primary message text
+ * @param {string|null} actionLabel - Label for the action button (null = no button)
+ * @param {Function|null} actionFn - Callback invoked when the action is clicked
+ * @param {number} [duration=6000] - Auto-dismiss delay in ms
+ */
+function showGentlyToast(message, actionLabel, actionFn, duration = 6000) {
+ // Remove any existing gently-toast
+ document.querySelectorAll('.gently-toast').forEach(t => t.remove());
+
+ const toast = document.createElement('div');
+ toast.className = 'gently-toast';
+
+ const msgSpan = document.createElement('span');
+ msgSpan.className = 'gently-toast-msg';
+ msgSpan.textContent = message;
+ toast.appendChild(msgSpan);
+
+ if (actionLabel && actionFn) {
+ const actionBtn = document.createElement('button');
+ actionBtn.className = 'gently-toast-action';
+ actionBtn.textContent = actionLabel;
+ actionBtn.addEventListener('click', () => {
+ actionFn();
+ toast.remove();
+ });
+ toast.appendChild(actionBtn);
+ }
+
+ const dismiss = document.createElement('button');
+ dismiss.className = 'gently-toast-dismiss';
+ dismiss.setAttribute('aria-label', 'Dismiss');
+ dismiss.textContent = '×';
+ dismiss.addEventListener('click', () => toast.remove());
+ toast.appendChild(dismiss);
+
+ document.body.appendChild(toast);
+ // Trigger transition
+ requestAnimationFrame(() => toast.classList.add('visible'));
+
+ const timer = setTimeout(() => toast.remove(), duration);
+ dismiss.addEventListener('click', () => clearTimeout(timer));
+}
diff --git a/gently/ui/web/static/js/home.js b/gently/ui/web/static/js/home.js
new file mode 100644
index 00000000..bf5cad17
--- /dev/null
+++ b/gently/ui/web/static/js/home.js
@@ -0,0 +1,189 @@
+/**
+ * HomeApp — the landing tab.
+ *
+ * A light at-a-glance landing surface: recent sessions, recent plans, recent
+ * images, a thin status line, and a "Start / continue an experiment" button
+ * that launches the setup flow (the wizard, which no longer auto-pops in chat).
+ *
+ * Read-only fetches against existing endpoints (/api/sessions, /api/campaigns,
+ * /api/home/recent-images); mirrors the ReviewApp/CampaignsApp module pattern.
+ */
+const HomeApp = (() => {
+ let _inited = false;
+ const SESSIONS_N = 5;
+ const CAMPAIGNS_N = 5;
+ const IMAGES_N = 8;
+ // Recent images are stable (latest projection per embryo). refresh() runs on
+ // every Home-tab entry, so guard against redundant disk-walking fetches:
+ // skip if one is in flight or the strip was loaded within IMAGES_TTL_MS.
+ const IMAGES_TTL_MS = 15000;
+ let _imgState = { at: 0, inflight: false };
+
+ function relTime(iso) {
+ if (!iso) return '';
+ const t = Date.parse(iso);
+ if (isNaN(t)) return '';
+ const s = Math.max(0, (Date.now() - t) / 1000);
+ if (s < 60) return 'just now';
+ if (s < 3600) return `${Math.floor(s / 60)}m ago`;
+ if (s < 86400) return `${Math.floor(s / 3600)}h ago`;
+ const d = Math.floor(s / 86400);
+ return d < 30 ? `${d}d ago` : new Date(t).toLocaleDateString();
+ }
+
+ function empty(el, msg) {
+ el.innerHTML = `
+
+ ${typeLabel}
+ ${embryo ? `${embryo}
` : ''}
+ ${ts ? `${ts}
` : ''}
+ ${escapeHtml(msg)}
`;
+ }
+
+ function wireGoTab(scope) {
+ (scope || document).querySelectorAll('[data-go-tab]').forEach(el => {
+ if (el._goWired) return;
+ el._goWired = true;
+ el.addEventListener('click', (e) => {
+ e.preventDefault();
+ if (typeof switchTab === 'function') switchTab(el.dataset.goTab);
+ });
+ });
+ }
+
+ async function loadSessions() {
+ const el = document.getElementById('home-recent-sessions');
+ if (!el) return;
+ try {
+ const data = await (await fetch('/api/sessions')).json();
+ const sessions = (data.sessions || []).slice(0, SESSIONS_N);
+ if (!sessions.length) { empty(el, 'No sessions yet.'); return; }
+ el.innerHTML = sessions.map(s => {
+ const live = s.active ? 'live' : '';
+ const resume = s.active ? '' :
+ ``;
+ return `
+
`;
+ }).join('');
+ el.querySelectorAll('[data-resume]').forEach(b => b.addEventListener('click', async () => {
+ b.disabled = true;
+ b.textContent = 'Resuming…';
+ try {
+ await fetch(`/api/sessions/${encodeURIComponent(b.dataset.resume)}/resume`, { method: 'POST' });
+ } catch (_) { b.disabled = false; b.textContent = 'Resume'; }
+ }));
+ } catch (e) { empty(el, 'Could not load sessions.'); }
+ }
+
+ async function loadCampaigns() {
+ const el = document.getElementById('home-recent-campaigns');
+ if (!el) return;
+ try {
+ const data = await (await fetch('/api/campaigns')).json();
+ const items = (data.campaigns || []).slice(0, CAMPAIGNS_N);
+ if (!items.length) { empty(el, 'No plans yet.'); return; }
+ el.innerHTML = items.map(t => {
+ const c = t.campaign || {};
+ const st = t.status || {};
+ const name = c.shorthand || c.description || 'Untitled plan';
+ const total = st.total || 0;
+ const chip = total ? `${st.completed || 0}/${total} done` : '';
+ return `
+
${resume}
+ ${escapeHtml(s.name || s.session_id)}${live}
+
+
+ ${escapeHtml(name)}${chip}
+
`;
+ }).join('');
+ wireGoTab(el);
+ } catch (e) { empty(el, 'Could not load plans.'); }
+ }
+
+ async function loadImages(force) {
+ const el = document.getElementById('home-recent-images');
+ if (!el) return;
+ if (_imgState.inflight) return;
+ // _imgState.at is set only after a completed fetch (images or empty),
+ // never after an error — so failures still retry on the next entry.
+ if (!force && _imgState.at && (Date.now() - _imgState.at) < IMAGES_TTL_MS) return;
+ _imgState.inflight = true;
+ try {
+ const data = await (await fetch(`/api/home/recent-images?limit=${IMAGES_N}`)).json();
+ // Latest projection per embryo across recent sessions (server orders
+ // most-recent session first).
+ const recent = (data.images || []).slice(0, IMAGES_N);
+ if (!recent.length) {
+ empty(el, 'No images yet — they appear once a session has captured volumes.');
+ _imgState.at = Date.now();
+ return;
+ }
+ el.innerHTML = '' + recent.map(s => {
+ const tp = (s.timepoint != null) ? ` · t${s.timepoint}` : '';
+ const label = `${s.embryo_id || ''}${tp}`;
+ const sub = s.session_name && s.session_name !== s.session_id
+ ? ` (${s.session_name})` : '';
+ const src = `/api/sessions/${encodeURIComponent(s.session_id)}`
+ + `/projection?embryo=${encodeURIComponent(s.embryo_id)}`
+ + `&t=${encodeURIComponent(s.timepoint)}`;
+ return `
';
+ _imgState.at = Date.now();
+ } catch (e) {
+ empty(el, 'Could not load images.');
+ } finally {
+ _imgState.inflight = false;
+ }
+ }
+
+ function updateStatus() {
+ const el = document.getElementById('home-status');
+ if (!el) return;
+ // Read the shared ConnectionStatus store, not a one-shot snapshot of
+ // state.connected — the latter was read once at tab init (before the
+ // /ws handshake) and never corrected, showing "Offline" while the
+ // header pill said "Online".
+ const connected = (typeof ConnectionStatus !== 'undefined')
+ ? ConnectionStatus.get().gentlyConnected
+ : (typeof state !== 'undefined' && state.connected);
+ const n = (typeof state !== 'undefined' && Array.isArray(state.embryos)) ? state.embryos.length : 0;
+ el.textContent = connected
+ ? `Connected · ${n} embryo${n === 1 ? '' : 's'} in view`
+ : 'Offline — start the agent to connect.';
+ }
+
+ function refresh() {
+ updateStatus();
+ loadSessions();
+ loadCampaigns();
+ loadImages();
+ }
+
+ function init() {
+ if (!_inited) {
+ _inited = true;
+ wireGoTab(document.getElementById('home-content'));
+ const start = document.getElementById('home-start-btn');
+ if (start) start.addEventListener('click', () => {
+ if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) {
+ AgentChat.togglePanel(true);
+ // Let the panel's WS connect before sending the command.
+ if (AgentChat.runCommand) setTimeout(() => AgentChat.runCommand('/wizard'), 250);
+ }
+ });
+ // Re-render the status line on every connection change. subscribe()
+ // replays the current snapshot immediately, so a late init still
+ // renders correct state. Registered once (inside the _inited guard).
+ if (typeof ConnectionStatus !== 'undefined') {
+ ConnectionStatus.subscribe(() => updateStatus());
+ }
+ }
+ refresh(); // re-fetch on every entry to the tab
+ }
+
+ // Self-initialise on load when Home is the default-active tab (switchTab's
+ // lazy-init hook only fires on a tab click / hash route, not initial paint).
+ document.addEventListener('DOMContentLoaded', () => {
+ const home = document.getElementById('home-content');
+ if (home && home.classList.contains('active')) init();
+ });
+
+ return { init, refresh };
+})();
diff --git a/gently/ui/web/static/js/landing.js b/gently/ui/web/static/js/landing.js
new file mode 100644
index 00000000..7d82c553
--- /dev/null
+++ b/gently/ui/web/static/js/landing.js
@@ -0,0 +1,888 @@
+/**
+ * V2Landing (ux_v2): the agent-first welcome AND the in-place plan wizard.
+ *
+ * Clicking "Plan an experiment" switches the landing to a plan screen, enters
+ * plan mode, and renders the agent's work IN THE WIZARD — not the chat REPL:
+ * - the agent's reasoning + tool calls render as a tidy, claude.ai-style
+ * collapsible activity feed (#v2-plan-activity), fed by the AGENT_ACTIVITY
+ * event that agent-chat.js mirrors off the /ws/agent stream;
+ * - the agent's ask_user_choice questions render as button cards
+ * (#v2-plan-ask) via AgentChat.buildAskCard;
+ * - "THE PLAN" panel (#v2-plan-summary) mirrors the REAL plan (phases→tasks)
+ * fetched from /api/campaigns once a turn settles.
+ * Chat is the last resort (the escape pill / "Open conversation").
+ *
+ * No-ops unless #v2-landing is present (flag off → v1 untouched, overlay absent).
+ */
+const V2Landing = (() => {
+ let el = null;
+ let current = null; // the ask currently in #v2-plan-ask
+ let feedTextEl = null; // current accumulating prose paragraph in the feed
+ let feedThinkingEl = null; // current accumulating reasoning (thinking) block
+ let runningTools = {}; // tool name -> stack of running card elements
+ let feedHadContent = false; // did this turn surface anything in the feed?
+ let capturedCampaignId = null; // best-effort id scraped from tool results
+ let planProposed = false; // propose_plan ran → plan is ready to commit
+
+ const $ = (id) => document.getElementById(id);
+
+ function greet() {
+ const g = $('v2-landing-greeting');
+ if (!g) return;
+ const h = new Date().getHours();
+ const t = h < 5 ? 'Still here.' : h < 12 ? 'Good morning.'
+ : h < 18 ? 'Good afternoon.' : 'Good evening.';
+ g.innerHTML = t + '
+ 
+
`;
+ }).join('') + 'What are we doing today?'; + } + + function setScreen(name) { if (el) el.dataset.screen = name; } + function planActive() { + return !!el && el.dataset.screen === 'plan' && !el.classList.contains('dismissed') + && el.style.display !== 'none'; + } + + function dismiss() { + if (!el || el.classList.contains('dismissed')) return; + el.classList.add('dismissed'); + let done = false; + const finish = () => { + if (done) return; + done = true; + el.style.display = 'none'; + el.setAttribute('aria-hidden', 'true'); + }; + el.addEventListener('transitionend', finish, { once: true }); + setTimeout(finish, 650); + } + + // ── status / error helpers ──────────────────────────────────────── + function setThinkingLabel(text) { + const l = document.querySelector('#v2-plan-thinking .v2-plan-thinking-label'); + if (l && text) l.textContent = text; + } + // Elapsed-time counter so a long think reads as progress, not a hang. Starts + // when the thinking indicator first shows and runs until it's hidden (turn end). + let _thinkTimer = null; + let _thinkStart = 0; + function _thinkTick() { + const t = $('v2-plan-thinking'); + if (!t) return; + let el = t.querySelector('.v2-plan-elapsed'); + if (!el) { + el = document.createElement('span'); + el.className = 'v2-plan-elapsed'; + el.style.cssText = 'margin-left:6px;opacity:.55;font-variant-numeric:tabular-nums;'; + t.appendChild(el); + } + const s = Math.round((Date.now() - _thinkStart) / 1000); + el.textContent = s > 0 ? s + 's' : ''; + } + function showThinking(on, label) { + const t = $('v2-plan-thinking'); + if (t) t.classList.toggle('hidden', !on); + if (on && label) setThinkingLabel(label); + if (on) { + if (!_thinkTimer) { + _thinkStart = Date.now(); + _thinkTick(); + _thinkTimer = setInterval(_thinkTick, 1000); + } + } else if (_thinkTimer) { + clearInterval(_thinkTimer); + _thinkTimer = null; + const el = t && t.querySelector('.v2-plan-elapsed'); + if (el) el.textContent = ''; + } + } + // Human-readable "what's happening right now" from a tool activity event, + // so the status line names the live operation instead of a static string. + function prettyTool(act) { + const raw = (act && (act.label || act.name)) || 'the next step'; + const s = String(raw).replace(/_/g, ' ').trim(); + return s.charAt(0).toUpperCase() + s.slice(1) + '…'; + } + function errorVisible() { const e = $('v2-plan-error'); return !!e && !e.classList.contains('hidden'); } + function showPlanError(msg) { + const e = $('v2-plan-error'); if (!e) return; + e.textContent = msg; e.classList.remove('hidden'); + showThinking(false); + } + function hidePlanError() { const e = $('v2-plan-error'); if (e) e.classList.add('hidden'); } + + function clearAsk() { const m = $('v2-plan-ask'); if (m) m.innerHTML = ''; } + function resetSummary() { + const list = $('v2-plan-summary'); + if (list) list.innerHTML = '
The plan will take shape here as Gently designs it.
';
+ planPage = 0; planPages = []; planTitleText = '';
+ }
+
+ // ── activity feed: paginated, ONE agent step (turn) per page ───────
+ // Instead of one ever-growing scroll, each agent turn — its reasoning +
+ // the tool calls it made — is a page you flip through with ‹ Prev / Next ›.
+ // The current question stays pinned below the feed (#v2-plan-ask). A new
+ // turn auto-advances to its page; you can flip back to review earlier steps.
+ let feedPages = []; // .v2-act-page elements, one per turn
+ let feedPage = 0; // index currently shown
+ let curPageEl = null; // page receiving this turn's content
+ let pendingNewPage = false; // a turn started; open a fresh page on first content
+
+ function feedEl() { return $('v2-plan-activity'); }
+ function feedPagesWrap() { return feedEl()?.querySelector('.v2-feed-pages'); }
+ function clearActivity() {
+ const f = feedEl();
+ if (f) {
+ f.innerHTML =
+ '' +
+ '' +
+ '';
+ }
+ feedPages = []; feedPage = 0; curPageEl = null; pendingNewPage = false;
+ feedTextEl = null; feedThinkingEl = null; runningTools = {}; feedHadContent = false;
+ capturedCampaignId = null; planProposed = false;
+ clearPlanReady();
+ hidePlanError();
+ }
+ function newFeedPage() {
+ const wrap = feedPagesWrap(); if (!wrap) return null;
+ const page = document.createElement('div');
+ page.className = 'v2-act-page';
+ wrap.appendChild(page);
+ feedPages.push(page);
+ curPageEl = page;
+ feedPage = feedPages.length - 1; // auto-advance to the live step
+ feedTextEl = null;
+ drawFeedPager();
+ return page;
+ }
+ // Where this turn's prose/tool cards land. Opens a fresh page the first time
+ // content arrives after a turn_start (so content-less command turns don't
+ // leave empty pages), and lazily on the very first content.
+ function feedTarget() {
+ if (pendingNewPage || !curPageEl) { newFeedPage(); pendingNewPage = false; }
+ return curPageEl;
+ }
+ function viewingLatest() { return feedPage >= feedPages.length - 1; }
+ function drawFeedPager() {
+ const f = feedEl(); if (!f) return;
+ const n = feedPages.length;
+ const i = Math.min(Math.max(feedPage, 0), Math.max(n - 1, 0));
+ feedPages.forEach((p, idx) => p.classList.toggle('active', idx === i));
+ const bar = f.querySelector('.v2-feed-pager-bar');
+ const dots = f.querySelector('.v2-feed-dots');
+ if (!bar || !dots) return;
+ if (n <= 1) { bar.hidden = true; dots.hidden = true; return; }
+ bar.hidden = false; dots.hidden = false;
+ bar.innerHTML = '';
+ const mkBtn = (txt, disabled, fn) => {
+ const b = document.createElement('button');
+ b.className = 'v2-plan-pager-btn'; b.type = 'button'; b.textContent = txt;
+ b.disabled = disabled; b.addEventListener('click', fn);
+ return b;
+ };
+ const pos = document.createElement('span');
+ pos.className = 'v2-plan-pager-pos'; pos.textContent = `Step ${i + 1} of ${n}`;
+ bar.append(
+ mkBtn('‹ Prev', i === 0, () => { if (feedPage > 0) { feedPage--; drawFeedPager(); } }),
+ pos,
+ mkBtn('Next ›', i === n - 1, () => { if (feedPage < n - 1) { feedPage++; drawFeedPager(); } }),
+ );
+ dots.innerHTML = '';
+ for (let d = 0; d < n; d++) {
+ const dot = document.createElement('button');
+ dot.className = 'v2-plan-dot' + (d === i ? ' active' : '');
+ dot.type = 'button';
+ dot.setAttribute('aria-label', `Step ${d + 1} of ${n}`);
+ dot.addEventListener('click', () => { feedPage = d; drawFeedPager(); });
+ dots.appendChild(dot);
+ }
+ }
+ function scrollFeedIfNearBottom() {
+ if (!viewingLatest()) return; // don't yank the user off an earlier step
+ const m = document.querySelector('.v2-screen-plan .v2-plan-main');
+ if (m && (m.scrollHeight - m.scrollTop - m.clientHeight) < 140) m.scrollTop = m.scrollHeight;
+ }
+ function clearFallback() { feedEl()?.querySelectorAll('.v2-plan-fallback').forEach(n => n.remove()); }
+
+ // Render the agent's prose like the chat does (reuses AgentChat.mdToHtml —
+ // escapes then renders bold/italic/code/line-breaks), so the feed isn't raw
+ // markdown. Falls back to escaped text if the helper isn't available.
+ function renderMd(s) {
+ if (typeof AgentChat !== 'undefined' && AgentChat.mdToHtml) return AgentChat.mdToHtml(s);
+ const esc = (typeof escapeHtml === 'function') ? escapeHtml(String(s)) : String(s);
+ return esc.replace(/\n/g, ''); + } + + // Plan-writing tools → refresh THE PLAN panel during the turn (debounced), + // not only at turn_end (ask_user_choice pauses the turn before it ends). + const PLAN_TOOLS = new Set([ + 'create_campaign', 'create_plan_item', 'link_plan_items', 'update_plan_item', + 'delete_plan_item', 'propose_plan', 'get_plan_status', 'validate_plan', + ]); + let planRefreshTimer = null; + function schedulePlanRefresh() { + if (planRefreshTimer) clearTimeout(planRefreshTimer); + planRefreshTimer = setTimeout(() => { planRefreshTimer = null; refreshPlanPanel(); }, 600); + } + + function safeStringify(v) { + try { + const s = (typeof v === 'string') ? v : JSON.stringify(v, null, 2); + return s.length > 4000 ? s.slice(0, 4000) + '\n…' : s; + } catch (e) { return String(v); } + } + function fillToolBody(body, act) { + body.innerHTML = ''; + // grid-template-rows reveal (landing.css) needs ONE collapsible child — + // append blocks into a single inner wrapper, not directly onto body. + const inner = document.createElement('div'); + body.appendChild(inner); + const inputStr = (act.input != null) ? safeStringify(act.input) : ''; + const full = act.full || act.summary || ''; + const block = (label, text) => { + const l = document.createElement('div'); l.className = 'v2-act-block-label'; l.textContent = label; + const b = document.createElement('pre'); b.className = 'v2-act-block'; b.textContent = text; + inner.append(l, b); + }; + if (inputStr) block('input', inputStr); + if (full) block('result', full); + if (!inputStr && !full) { + const e = document.createElement('div'); e.className = 'v2-act-block-label'; e.textContent = 'no details'; + inner.append(e); + } + } + function buildToolCard(act, done) { + const card = document.createElement('div'); + card.className = 'v2-act-tool' + (done ? (act.is_error ? ' done err' : ' done') : ''); + const head = document.createElement('button'); + head.className = 'v2-act-tool-head'; head.type = 'button'; + head.setAttribute('aria-expanded', 'false'); + const ic = document.createElement('span'); ic.className = 'v2-act-ic'; + ic.innerHTML = done ? (act.is_error ? '⚠' : '✓') : ''; + const label = document.createElement('span'); label.className = 'v2-act-label'; + label.textContent = act.label || act.name || 'tool'; + const sum = document.createElement('span'); sum.className = 'v2-act-summary'; + sum.textContent = done ? (act.summary || '') : ''; + const chev = document.createElement('span'); chev.className = 'v2-act-chev'; chev.textContent = '›'; + head.append(ic, label, sum, chev); + const body = document.createElement('div'); body.className = 'v2-act-tool-body'; + fillToolBody(body, act); + head.addEventListener('click', () => { + const open = card.classList.toggle('open'); + head.setAttribute('aria-expanded', open ? 'true' : 'false'); + }); + card.append(head, body); + return card; + } + function updateToolCard(card, act) { + card.classList.add('done'); + if (act.is_error) card.classList.add('err'); + const ic = card.querySelector('.v2-act-ic'); if (ic) ic.textContent = act.is_error ? '⚠' : '✓'; + const sum = card.querySelector('.v2-act-summary'); if (sum) sum.textContent = act.summary || ''; + const body = card.querySelector('.v2-act-tool-body'); if (body) fillToolBody(body, act); + } + function captureCampaignId(text) { + if (!text) return; + const s = String(text); + const m = s.match(/campaign_id[=:\s]+([0-9a-f]{6,})/i) || s.match(/\(id:\s*([0-9a-f]{6,})/i); + if (m) capturedCampaignId = m[1]; + } + + function applyActivity(act) { + if (!planActive() || !act) return; + const f = feedEl(); if (!f) return; + switch (act.kind) { + case 'turn_start': + feedTextEl = null; feedThinkingEl = null; pendingNewPage = true; hidePlanError(); clearFallback(); + clearPlanReady(); // new work in flight — drop any "ready" state + showThinking(true, 'reviewing your campaign and plan…'); + break; + case 'thinking': { + // Stream the model's reasoning summary live into the feed as a dim + // block, so the wait shows what the agent is actually considering. + showThinking(true); + const chunk = act.text || ''; + if (!chunk) { setThinkingLabel('thinking through the next step…'); break; } + if (!feedThinkingEl) { + feedThinkingEl = document.createElement('div'); + feedThinkingEl.className = 'v2-act-think'; + feedThinkingEl.style.cssText = + 'font-style:italic;opacity:.7;white-space:pre-wrap;margin:2px 0 8px;font-size:12.5px;line-height:1.5;'; + feedThinkingEl._raw = ''; + feedTarget().appendChild(feedThinkingEl); + } + feedThinkingEl._raw += chunk; + feedThinkingEl.textContent = feedThinkingEl._raw; + feedHadContent = true; + setThinkingLabel('reasoning…'); + scrollFeedIfNearBottom(); + break; + } + case 'text': { + const chunk = act.text || ''; + if (!chunk) break; + // The reasoning that immediately precedes the spoken answer is + // wrap-up meta ("let me wrap this up concisely and offer to + // export…") — drop the block entirely so the feed keeps the + // answer, not the narration of getting there. Reasoning that + // precedes a TOOL is left in place (tool_start only nulls the + // pointer) as the rationale for that action. + if (feedThinkingEl) { feedThinkingEl.remove(); feedThinkingEl = null; } + if (!feedTextEl) { + feedTextEl = document.createElement('div'); + feedTextEl.className = 'v2-act-text'; + feedTextEl._raw = ''; + feedTarget().appendChild(feedTextEl); + } + feedTextEl._raw += chunk; + feedTextEl.innerHTML = renderMd(feedTextEl._raw); + feedHadContent = true; showThinking(true, 'composing the response…'); scrollFeedIfNearBottom(); + break; + } + case 'tool_start': { + // ask_user_choice IS the active question (rendered separately in + // #v2-plan-ask) — don't also show it as a feed card. + if (act.name === 'ask_user_choice') break; + feedTextEl = null; feedThinkingEl = null; + const card = buildToolCard(act, false); + feedTarget().appendChild(card); + (runningTools[act.name] = runningTools[act.name] || []).push(card); + feedHadContent = true; showThinking(true, prettyTool(act)); scrollFeedIfNearBottom(); + break; + } + case 'tool_result': { + captureCampaignId(act.summary); + captureCampaignId(act.full); + if (PLAN_TOOLS.has(act.name)) schedulePlanRefresh(); + if (act.name === 'propose_plan' && !act.is_error) planProposed = true; + if (act.name === 'ask_user_choice') break; + feedTextEl = null; feedThinkingEl = null; + const arr = runningTools[act.name] || []; + const card = arr.pop(); + if (card) updateToolCard(card, act); + else feedTarget().appendChild(buildToolCard(act, true)); + feedHadContent = true; setThinkingLabel('working through the next step…'); scrollFeedIfNearBottom(); + break; + } + case 'turn_end': + showThinking(false); feedTextEl = null; feedThinkingEl = null; + refreshPlanPanel(); + if (!current && !feedHadContent) showFallback(); + // Plan proposed and the agent has settled (no pending question) → + // the design is done. Surface a clear "ready" state instead of + // leaving the user parked on the last wizard step. + if (planProposed && !current) showPlanReady(); + break; + case 'turn_error': + showPlanError(act.error || 'Something went wrong — open the conversation for detail.'); + break; + } + } + + function showFallback() { + const f = feedEl(); if (!f || f.querySelector('.v2-plan-fallback')) return; + const d = document.createElement('div'); + d.className = 'v2-plan-fallback'; + d.innerHTML = 'Gently replied in prose — open the conversation to read it.'; + d.querySelector('a').addEventListener('click', openChat); + feedTarget().appendChild(d); + } + + // ── plan-ready state ─────────────────────────────────────────────── + // Once the agent has proposed the plan and gone quiet, the wizard is done. + // Mark the screen "ready": rename the header, count phases/items from the + // panel, and promote "open workspace" to the obvious primary action — so the + // finish line is signposted instead of looking like one more wizard step. + function planCounts() { + let phases = 0, items = 0; + planPages.forEach(p => { + if (p.name !== 'Tasks') phases++; + items += (p.items || []).length; + }); + return { phases, items }; + } + function showPlanReady() { + const sec = document.querySelector('.v2-screen-plan'); + if (!sec) return; + sec.classList.add('ready'); + showThinking(false); + const who = sec.querySelector('.v2-plan-who'); + const title = sec.querySelector('.v2-plan-title'); + if (who) who.textContent = 'Gently · plan ready'; + if (title) { + const { phases, items } = planCounts(); + title.textContent = items + ? `Your plan is ready — ${items} item${items === 1 ? '' : 's'} across ${phases} phase${phases === 1 ? '' : 's'}` + : 'Your plan is ready'; + } + const cont = $('v2-plan-continue'); + if (cont) cont.textContent = 'Open the workspace ›'; + const exp = $('v2-plan-export'); + if (exp) exp.hidden = false; // the plan is final → offer the download + } + function clearPlanReady() { + const sec = document.querySelector('.v2-screen-plan'); + if (!sec || !sec.classList.contains('ready')) return; + sec.classList.remove('ready'); + const who = sec.querySelector('.v2-plan-who'); + const title = sec.querySelector('.v2-plan-title'); + if (who) who.textContent = 'Gently · planning'; + if (title) title.textContent = "Let's design your run"; + const cont = $('v2-plan-continue'); + if (cont) cont.textContent = 'Continue in workspace ›'; + const exp = $('v2-plan-export'); + if (exp) exp.hidden = true; + } + + // ── export the finished plan as a shareable markdown doc ──────────── + // Replaces the agent's end-of-plan "want me to export this?" prose with a + // real action: pull the enriched plan tree (/export) and render it to + // markdown client-side so the biologist can drop it in a doc or share it. + function specToLines(spec) { + let s = spec; + if (typeof s === 'string') { try { s = JSON.parse(s); } catch { return s ? ['- ' + s] : []; } } + if (!s || typeof s !== 'object') return []; + const out = []; + const fmt = (v) => Array.isArray(v) ? v.join(', ') : (typeof v === 'object' ? JSON.stringify(v) : String(v)); + const pick = (k, label) => { if (s[k] != null && s[k] !== '') out.push(`- **${label}:** ${fmt(s[k])}`); }; + pick('strain', 'Strain'); pick('goal', 'Goal'); + if (Array.isArray(s.channels) && s.channels.length) { + out.push('- **Channels:** ' + s.channels.map(c => `${c.name || '?'} (${c.excitation_nm || '?'} nm${c.exposure_ms ? `, ${c.exposure_ms} ms` : ''})`).join(', ')); + } + pick('num_slices', 'Slices'); pick('interval_s', 'Interval (s)'); pick('temperature_c', 'Temperature (°C)'); + pick('num_embryos', 'Embryos'); pick('start_stage', 'Start stage'); pick('stop_condition', 'Stop condition'); + pick('criteria', 'Criteria'); pick('success_criteria', 'Success criteria'); + return out; + } + function buildPlanMarkdown(tree) { + const L = []; + L.push(`# ${tree.description || tree.shorthand || 'Experimental plan'}`, ''); + if (tree.target) L.push(`**Goal:** ${tree.target}`, ''); + if (tree.shorthand) L.push(`**Plan ID:** \`${tree.shorthand}\``, ''); + L.push(`_Exported from Gently — ${new Date().toLocaleString()}_`, ''); + const renderItems = (items, prefix) => { + (items || []).slice().sort((a, b) => (a.phase_order || 0) - (b.phase_order || 0)).forEach((it, idx) => { + L.push(`### ${prefix}${idx + 1} ${it.title || '(task)'} \`${it.type || 'task'}\``, ''); + if (it.description) L.push(it.description, ''); + const sl = specToLines(it.spec); + if (sl.length) L.push(...sl, ''); + const refs = it.references || []; + if (refs.length) { + L.push('**References:**'); + refs.forEach((r, i) => L.push(`${i + 1}. ${r.citation || r.id || ''}${r.source ? ` _(${r.source})_` : ''}`)); + L.push(''); + } + }); + }; + if ((tree.items || []).length) { L.push('## Tasks', ''); renderItems(tree.items, ''); } + (tree.children || []).forEach((ph, pi) => { + if (!ph) return; + L.push(`## ${ph.display_name || ph.description || ph.shorthand || `Phase ${pi + 1}`}`, ''); + if (ph.target) L.push(ph.target, ''); + renderItems(ph.items, `${pi + 1}.`); + }); + return L.join('\n').replace(/\n{3,}/g, '\n\n').trimEnd() + '\n'; + } + async function resolveCampaignId() { + if (capturedCampaignId) return capturedCampaignId; + try { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); const t = (d.campaigns || [])[0]; return (t && t.campaign && t.campaign.id) || null; } + } catch (e) { /* offline */ } + return null; + } + async function exportPlan() { + const btn = $('v2-plan-export'); + const id = await resolveCampaignId(); + if (!id) { showPlanError('No plan to export yet.'); return; } + if (btn) { btn.disabled = true; btn.textContent = '↓ Exporting…'; } + try { + const r = await fetch(`/api/campaigns/${encodeURIComponent(id)}/export`); + if (!r.ok) throw new Error(`export ${r.status}`); + const tree = await r.json(); + const md = buildPlanMarkdown(tree); + const blob = new Blob([md], { type: 'text/markdown' }); + const url = URL.createObjectURL(blob); + const a = document.createElement('a'); + a.href = url; + a.download = `${(tree.shorthand || 'plan').replace(/[^\w.-]+/g, '_')}.md`; + document.body.appendChild(a); a.click(); a.remove(); + setTimeout(() => URL.revokeObjectURL(url), 1000); + } catch (e) { + showPlanError('Could not export the plan — open the conversation to export it manually.'); + } finally { + if (btn) { btn.disabled = false; btn.textContent = '↓ Export plan'; } + } + } + + // ── THE PLAN panel: mirror the real campaign tree ────────────────── + async function refreshPlanPanel() { + try { + let tree = null; + if (capturedCampaignId) { + const r = await fetch(`/api/campaigns/${encodeURIComponent(capturedCampaignId)}/tree`); + if (r.ok) tree = await r.json(); + } + if (!tree) { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); tree = (d.campaigns || [])[0] || null; } + } + if (tree) renderPlanTree(tree); + } catch (e) { /* keep whatever is shown */ } + } + function planName(c) { + c = c || {}; + return c.shorthand || c.display_name || c.description || 'Plan'; + } + // Phases read better by their human name ("Phase 1 — Reporter validation") + // than by their code shorthand ("nrp-p1"), which looks like a machine id. + function phaseName(c) { + c = c || {}; + return c.display_name || c.description || c.shorthand || 'Phase'; + } + // THE PLAN renders as a pager — one phase per page with ‹ Prev / Next ›, + // a position label, and dots — instead of one long scroll. planPage is held + // across re-renders (the panel refetches on every plan-writing tool) so the + // page you're reading doesn't snap back to the start mid-design. + let planPage = 0; + let planPages = []; // [{ name, items }] + let planTitleText = ''; + + function renderPlanTree(tree) { + if (!tree) return; + const phases = tree.children || []; + const rootItems = tree.items || []; + if (!phases.length && !rootItems.length) return; // nothing to show yet — keep placeholder + const pages = []; + if (rootItems.length) pages.push({ name: 'Tasks', items: rootItems }); + phases.forEach(phase => { + if (!phase) return; + pages.push({ name: phaseName(phase.campaign), items: phase.items || [] }); + }); + planPages = pages; + planTitleText = planName(tree.campaign); + if (planPage >= pages.length) planPage = pages.length - 1; + if (planPage < 0) planPage = 0; + drawPlanPage(); + } + + function drawPlanPage() { + const list = $('v2-plan-summary'); + if (!list) return; + const pages = planPages; + const n = pages.length; + if (!n) return; + const i = Math.min(Math.max(planPage, 0), n - 1); + const page = pages[i]; + + list.innerHTML = ''; + const title = document.createElement('div'); + title.className = 'v2-plan-title-row'; + title.textContent = planTitleText; + list.appendChild(title); + + if (n > 1) { + const bar = document.createElement('div'); + bar.className = 'v2-plan-pager'; + const prev = document.createElement('button'); + prev.className = 'v2-plan-pager-btn'; prev.type = 'button'; prev.textContent = '‹ Prev'; + prev.disabled = i === 0; + prev.addEventListener('click', () => { if (planPage > 0) { planPage--; drawPlanPage(); } }); + const pos = document.createElement('span'); + pos.className = 'v2-plan-pager-pos'; + pos.textContent = page.name; // position shown by the dots below + pos.title = `${page.name} · ${i + 1} of ${n}`; + const next = document.createElement('button'); + next.className = 'v2-plan-pager-btn'; next.type = 'button'; next.textContent = 'Next ›'; + next.disabled = i === n - 1; + next.addEventListener('click', () => { if (planPage < n - 1) { planPage++; drawPlanPage(); } }); + bar.append(prev, pos, next); + list.appendChild(bar); + } else { + const h = document.createElement('div'); + h.className = 'v2-plan-phase-h'; + h.textContent = page.name; + list.appendChild(h); + } + + const tasks = document.createElement('div'); + tasks.className = 'v2-plan-phase'; + const items = page.items || []; + // phase ordinal (1-based) for "P.I" numbering; the rootItems "Tasks" page + // isn't a phase, so it numbers items bare (1, 2, …). + const phaseOrd = pages.slice(0, i + 1).filter(p => p.name !== 'Tasks').length; + if (items.length) { + items.forEach((it, idx) => { + const type = String(it.type || '').toLowerCase(); + const t = document.createElement('div'); + t.className = 'v2-plan-task type-' + (type || 'other'); + const num = document.createElement('span'); + num.className = 'v2-task-num'; + num.textContent = phaseOrd ? `${phaseOrd}.${idx + 1}` : `${idx + 1}`; + const dot = document.createElement('span'); + dot.className = 'v2-task-dot'; + dot.title = type || 'task'; + const ttl = document.createElement('span'); + ttl.className = 'v2-task-ttl'; + ttl.textContent = it.title || it.shorthand || '(task)'; + t.append(num, dot, ttl); + if (it.estimated_days) { + const d = document.createElement('span'); + d.className = 'v2-task-days'; + d.textContent = `${it.estimated_days}d`; + t.append(d); + } + tasks.appendChild(t); + }); + } else { + const e = document.createElement('div'); + e.className = 'v2-plan-task v2-plan-task-empty'; + e.textContent = 'no items in this phase yet'; + tasks.appendChild(e); + } + list.appendChild(tasks); + + if (n > 1) { + const dots = document.createElement('div'); + dots.className = 'v2-plan-dots'; + for (let d = 0; d < n; d++) { + const dot = document.createElement('button'); + dot.className = 'v2-plan-dot' + (d === i ? ' active' : ''); + dot.type = 'button'; + dot.setAttribute('aria-label', `Go to ${pages[d].name} (${d + 1} of ${n})`); + dot.addEventListener('click', () => { planPage = d; drawPlanPage(); }); + dots.appendChild(dot); + } + list.appendChild(dots); + } + } + + // ── ask rendering (the active question) ──────────────────────────── + function labelFor(data, sel) { + const opts = (data && data.options) || []; + const one = (s) => { + const o = opts.find(o => o && (o.id === s || o.value === s || o.label === s)); + return o ? o.label : String(s); + }; + return Array.isArray(sel) ? sel.map(one).join(', ') : one(sel); + } + function recordPick(data, sel) { + const list = $('v2-plan-summary'); + if (!list) return; + const empty = list.querySelector('.v2-plan-side-empty'); + if (empty) empty.remove(); + const matched = (data && data.options || []).some(o => o && (o.id === sel || o.value === sel || o.label === sel)); + const row = document.createElement('div'); + row.className = 'v2-plan-row' + (matched ? '' : ' v2-plan-row-freetext'); + row.innerHTML = ''; + row.querySelector('.k').textContent = (data && data.question) || 'Choice'; + row.querySelector('.v').textContent = labelFor(data, sel); + list.appendChild(row); + } + function renderAsk() { + const mount = $('v2-plan-ask'); + if (!mount || !current || typeof AgentChat === 'undefined' || !AgentChat.buildAskCard) return; + showThinking(false); hidePlanError(); clearFallback(); + const data = current.data, reqId = current.reqId; + const hasControl = AgentChat.hasControl ? AgentChat.hasControl() : true; + const card = AgentChat.buildAskCard(data, { + reqId, isWake: current.isWake, hasControl, + onPick: (sel) => { + recordPick(data, sel); + AgentChat.answerChoice(reqId, sel); + current = null; clearAsk(); showThinking(true); + }, + }); + mount.innerHTML = ''; + mount.appendChild(card); + const first = mount.querySelector('button:not([disabled])'); + if (first) setTimeout(() => first.focus(), 30); + } + + let planKickedOff = false; // guard: design-kickoff fires once per session + async function startPlan() { + setScreen('plan'); + // Re-entering the wizard (Back → Plan again) must NOT re-fire the + // kickoff — that stacked duplicate "/plan" + design turns. Just show + // the wizard with its existing state. + if (planKickedOff) return; + planKickedOff = true; + resetSummary(); clearAsk(); clearActivity(); + current = null; + showThinking(true); + // Campaigns are persistent agent memory (not session state), so the + // agent always builds on an existing one — which leaves a user wanting a + // fresh plan stuck. So if an active campaign exists, ask up front: + // continue it (the default) or start a brand-new one. With NO campaign + // there's nothing to continue, so skip the gate and design straight away + // (that path is fresh anyway). + let campaign = null; + try { + const r = await fetch('/api/campaigns'); + if (r.ok) { const d = await r.json(); campaign = (d.campaigns || [])[0] || null; } + } catch (e) { /* offline / no API — just design */ } + if (campaign) renderCampaignChoice(campaign); + else kickoffDesign('continue'); + } + + // Enter plan mode, then prompt design. The prompt differs by intent: build + // on the active campaign, or set it aside and create a new one. A free-typed + // answer from the choice card becomes the design brief directly. + function kickoffDesign(mode) { + showThinking(true); + if (typeof AgentChat === 'undefined' || !AgentChat.runCommand) return; + AgentChat.runCommand('/plan'); + if (mode === 'fresh') { + AgentChat.runCommand( + "I want to start a brand-new experiment, not continue any existing " + + "campaign. Create a new campaign and let's design it from scratch — " + + "what should we capture?" + ); + } else if (mode === 'continue') { + AgentChat.runCommand("Let's design this run — what should it capture?"); + } else { + // free text from the choice card's "Something else…" escape + AgentChat.runCommand(String(mode)); + } + } + + // Continue-vs-fresh gate, shown only when an active campaign exists. Reuses + // the agent ask-card styling so it's visually identical to the agent's own + // questions; picking routes into kickoffDesign rather than the agent bridge. + function renderCampaignChoice(tree) { + const mount = $('v2-plan-ask'); + if (!mount || typeof AgentChat === 'undefined' || !AgentChat.buildAskCard) { + kickoffDesign('continue'); + return; + } + showThinking(false); hidePlanError(); clearFallback(); + const name = planName((tree && tree.campaign) || {}); + const data = { + question: `You have an active campaign — **${name}**. Design the next run inside it, or start something new?`, + options: [ + { id: 'continue', label: `Continue ${name}`, description: 'Design the next run inside your existing campaign' }, + { id: 'fresh', label: 'Start a brand-new campaign', description: 'Set the existing plan aside and plan from scratch' }, + ], + }; + const hasControl = AgentChat.hasControl ? AgentChat.hasControl() : true; + const card = AgentChat.buildAskCard(data, { + reqId: 'landing-campaign-choice', isWake: false, hasControl, + onPick: (sel) => { clearAsk(); kickoffDesign(sel); }, + }); + mount.innerHTML = ''; + mount.appendChild(card); + const first = mount.querySelector('button:not([disabled])'); + if (first) setTimeout(() => first.focus(), 30); + } + + function openScope() { + dismiss(); + if (typeof switchTab === 'function') switchTab('devices'); + } + function openChat() { + dismiss(); + if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) { + setTimeout(() => AgentChat.togglePanel(true), 300); + } + } + function sendFreeform(text) { + const v = (text || '').trim(); + dismiss(); + if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) { + AgentChat.togglePanel(true); + if (v && AgentChat.runCommand) setTimeout(() => AgentChat.runCommand(v), 300); + } + } + + function init() { + el = $('v2-landing'); + if (!el || typeof ClientEventBus === 'undefined') return; // flag off → no-op + greet(); + + el.querySelectorAll('[data-landing]').forEach(btn => btn.addEventListener('click', () => { + const kind = btn.dataset.landing; + if (kind === 'plan') startPlan(); + else if (kind === 'standalone') openScope(); + })); + + const esc = $('v2-escape'), escToggle = $('v2-escape-toggle'), + escInput = $('v2-escape-input'), escSend = $('v2-escape-send'); + if (escToggle && esc && escInput) { + escToggle.addEventListener('click', () => { + const open = esc.classList.toggle('open'); + escToggle.setAttribute('aria-expanded', open ? 'true' : 'false'); + if (open) setTimeout(() => escInput.focus(), 120); + }); + const submit = () => sendFreeform(escInput.value); + if (escSend) escSend.addEventListener('click', submit); + escInput.addEventListener('keydown', e => { + if (e.key === 'Enter') { e.preventDefault(); submit(); } + else if (e.key === 'Escape') { e.stopPropagation(); esc.classList.remove('open'); escToggle.setAttribute('aria-expanded', 'false'); } + }); + } + + const skip = $('v2-landing-skip'); + if (skip) skip.addEventListener('click', dismiss); + + // Theme toggle (header's is occluded by the overlay). Mirrors + // _header.html: flip data-theme on both roots + persist. + const themeBtn = $('v2-landing-theme'); + if (themeBtn) themeBtn.addEventListener('click', () => { + const cur = document.documentElement.getAttribute('data-theme') + || document.body.getAttribute('data-theme') || 'light'; + const next = cur === 'dark' ? 'light' : 'dark'; + document.documentElement.setAttribute('data-theme', next); + document.body.setAttribute('data-theme', next); + localStorage.setItem('gently-theme', next); + }); + + const back = $('v2-plan-back'); + if (back) back.addEventListener('click', () => setScreen('welcome')); + const planChat = $('v2-plan-chat'); + if (planChat) planChat.addEventListener('click', openChat); + const cont = $('v2-plan-continue'); + if (cont) cont.addEventListener('click', dismiss); + const exp = $('v2-plan-export'); + if (exp) exp.addEventListener('click', exportPlan); + + // The agent's questions + work render in the plan stage while it's active; + // once we've receded into the workspace, AskStage (#ask-stage) takes over. + ClientEventBus.on('AGENT_ASK', ({ request_id, choice_data, origin }) => { + if (!planActive()) return; + current = { reqId: request_id, data: choice_data || {}, isWake: origin === 'wake' }; + renderAsk(); + }); + ClientEventBus.on('ASK_CLEARED', ({ request_id }) => { + if (request_id === '*' || (current && request_id === current.reqId)) { + current = null; clearAsk(); + if (planActive() && !errorVisible()) showThinking(true); + // A question was just answered — the agent's continuation is the + // next step, so open a fresh feed page for it. (A turn stays one + // stream across an ask_user_choice pause, so turn_start alone + // would lump every step of the design into a single page.) + pendingNewPage = true; + } + }); + ClientEventBus.on('AGENT_CONTROL', () => { if (current && planActive()) renderAsk(); }); + ClientEventBus.on('AGENT_ACTIVITY', (act) => applyActivity(act)); + + document.addEventListener('keydown', e => { + if (e.key !== 'Escape' || !el || el.classList.contains('dismissed')) return; + if (el.dataset.screen === 'plan') setScreen('welcome'); // step back, don't bail + else dismiss(); + }); + } + + document.addEventListener('DOMContentLoaded', init); + + return { + dismiss, + show: () => { + if (!el) return; + el.style.display = ''; + el.removeAttribute('aria-hidden'); + el.classList.remove('dismissed'); + setScreen('welcome'); + greet(); + }, + }; +})(); diff --git a/gently/ui/web/static/js/logconsole.js b/gently/ui/web/static/js/logconsole.js new file mode 100644 index 00000000..36fac475 --- /dev/null +++ b/gently/ui/web/static/js/logconsole.js @@ -0,0 +1,217 @@ +/** + * Process console — the header drawer over the agent and device-layer output. + * + * The desktop shell spawns the backend with no console window, so when + * something misbehaves mid-session there is nowhere to look. This reads the + * same two streams the operator would have had on a terminal: + * + * Agent {storage}/logs/gently_*.log via /api/logs/agent + * Device layer supervisor-captured stdout via /api/device-layer/log, + * falling back to the layer's own log file when it runs + * externally and the supervisor captured nothing. + * + * Polling runs ONLY while the drawer is open. A console that keeps fetching + * behind a closed panel is exactly the kind of hidden work that made the camera + * streams fight each other. + */ +const LogConsole = (function () { + const POLL_MS = 2000; + const LIMIT = 600; + + let _wired = false, _open = false, _src = 'agent', _follow = true; + let _timer = null, _inFlight = false, _dirty = false, _lastKey = ''; + const D = {}; + + const $ = id => document.getElementById(id); + + function cacheDom() { + ['logc', 'logc-open', 'logc-scrim', 'logc-close', 'logc-body', 'logc-file', + 'logc-status', 'logc-level', 'logc-follow', 'logc-copy', 'logc-dot'] + .forEach(id => { D[id] = $(id); }); + } + + // ── fetching ────────────────────────────────────────────────────────── + async function fetchAgent(level) { + const q = new URLSearchParams({ limit: String(LIMIT) }); + if (level) q.set('level', level); + const r = await fetch(`/api/logs/agent?${q}`); + if (!r.ok) throw new Error(`${r.status}`); + return r.json(); + } + + async function fetchDevice(level) { + // Prefer the supervisor's live captured stdout — it exists even before + // anything has been flushed to a file. + try { + const r = await fetch(`/api/device-layer/log?limit=${LIMIT}`); + if (r.ok) { + const d = await r.json(); + if (d && Array.isArray(d.lines) && d.lines.length) { + return { file: 'device layer (captured stdout)', lines: d.lines }; + } + } + } catch (_) { /* fall through to the file */ } + const q = new URLSearchParams({ limit: String(LIMIT) }); + if (level) q.set('level', level); + const r2 = await fetch(`/api/logs/device?${q}`); + if (!r2.ok) throw new Error(`${r2.status}`); + return r2.json(); + } + + async function refresh() { + if (!_open) return; + // A refresh asked for while a poll is in flight must not be dropped — + // changing the tab or the level filter would otherwise appear to do + // nothing until the next tick. Remember it and re-run on completion. + if (_inFlight) { _dirty = true; return; } + _inFlight = true; + const level = D['logc-level'] ? D['logc-level'].value : ''; + try { + const d = _src === 'agent' ? await fetchAgent(level) : await fetchDevice(level); + render(d); + setStatus(''); + } catch (e) { + setStatus(`could not read log (${e.message})`); + } finally { + _inFlight = false; + if (_dirty) { _dirty = false; refresh(); } + } + } + + // ── rendering ───────────────────────────────────────────────────────── + function render(d) { + const lines = (d && d.lines) || []; + D['logc-file'].textContent = d && d.file ? d.file : 'no log file yet'; + // Skip the DOM write when nothing changed, so following does not fight + // a user who has scrolled up to read something. + const key = `${lines.length}|${lines[lines.length - 1] || ''}`; + if (key === _lastKey) return; + _lastKey = key; + + if (!lines.length) { + // An empty result under a filter is not an empty log — say which. + const level = D['logc-level'] ? D['logc-level'].value : ''; + if (level) { + D['logc-body'].textContent = + `No ${level.toLowerCase()} lines in the last ${LIMIT}. Set the filter to All to see everything.`; + } else { + D['logc-body'].textContent = _src === 'agent' + ? 'Nothing logged yet. The agent writes to {storage}/logs/gently_*.log.' + : 'Nothing logged yet. Start the device layer from the Devices tab.'; + } + return; + } + + const frag = document.createDocumentFragment(); + for (const ln of lines) { + const row = document.createElement('span'); + row.className = 'logc-line' + severityClass(ln); + row.textContent = ln; + frag.appendChild(row); + } + D['logc-body'].replaceChildren(frag); + + if (_follow) D['logc-body'].scrollTop = D['logc-body'].scrollHeight; + flagProblems(lines); + } + + function severityClass(ln) { + if (/\b(ERROR|CRITICAL|Traceback)\b/.test(ln)) return ' is-error'; + if (/\bWARNING\b/.test(ln)) return ' is-warn'; + return ''; + } + + // A quiet dot on the header button when the tail contains errors, so a + // failure that happens while the drawer is closed is still noticed. + function flagProblems(lines) { + if (!D['logc-dot']) return; + const bad = lines.slice(-80).some(ln => /\b(ERROR|CRITICAL|Traceback)\b/.test(ln)); + D['logc-dot'].hidden = !bad; + } + + function setStatus(msg) { + if (D['logc-status']) D['logc-status'].textContent = msg || ''; + } + + // ── open / close ────────────────────────────────────────────────────── + function open() { + if (_open) return; + _open = true; + D['logc'].hidden = false; + D['logc-open'].setAttribute('aria-expanded', 'true'); + _lastKey = ''; + refresh(); + _timer = setInterval(refresh, POLL_MS); + D['logc-body'].focus(); + } + + function close() { + if (!_open) return; + _open = false; + D['logc'].hidden = true; + D['logc-open'].setAttribute('aria-expanded', 'false'); + if (_timer) { clearInterval(_timer); _timer = null; } + } + + function toggle() { _open ? close() : open(); } + + function selectSource(src) { + if (src === _src) return; + _src = src; + _lastKey = ''; + document.querySelectorAll('.logc-tab').forEach(t => + t.classList.toggle('is-active', t.dataset.src === src)); + D['logc-body'].textContent = ''; + refresh(); + } + + function wire() { + if (_wired) return; + cacheDom(); + if (!D['logc'] || !D['logc-open']) return; // page without the header + _wired = true; + + D['logc-open'].addEventListener('click', toggle); + D['logc-close'].addEventListener('click', close); + D['logc-scrim'].addEventListener('click', close); + document.querySelectorAll('.logc-tab').forEach(t => + t.addEventListener('click', () => selectSource(t.dataset.src))); + D['logc-level'].addEventListener('change', () => { _lastKey = ''; refresh(); }); + + D['logc-follow'].addEventListener('click', () => { + _follow = !_follow; + D['logc-follow'].setAttribute('aria-pressed', String(_follow)); + D['logc-follow'].classList.toggle('is-on', _follow); + if (_follow) D['logc-body'].scrollTop = D['logc-body'].scrollHeight; + }); + D['logc-follow'].classList.add('is-on'); + + // Scrolling up is an intent to read — stop yanking the view to the end. + D['logc-body'].addEventListener('scroll', () => { + const el = D['logc-body']; + const atEnd = el.scrollHeight - el.scrollTop - el.clientHeight < 24; + if (_follow !== atEnd) { + _follow = atEnd; + D['logc-follow'].setAttribute('aria-pressed', String(_follow)); + D['logc-follow'].classList.toggle('is-on', _follow); + } + }); + + D['logc-copy'].addEventListener('click', async () => { + try { + await navigator.clipboard.writeText(D['logc-body'].textContent || ''); + setStatus('copied'); + setTimeout(() => setStatus(''), 1500); + } catch (_) { setStatus('copy blocked by the browser'); } + }); + + document.addEventListener('keydown', e => { + if (e.key === 'Escape' && _open) { e.preventDefault(); close(); return; } + // Ctrl/Cmd+` — the shell convention for "show me the console". + if ((e.ctrlKey || e.metaKey) && e.key === '`') { e.preventDefault(); toggle(); } + }); + } + + document.addEventListener('DOMContentLoaded', wire); + return { open, close, toggle }; +})(); diff --git a/gently/ui/web/static/js/notebook.js b/gently/ui/web/static/js/notebook.js new file mode 100644 index 00000000..1130a31a --- /dev/null +++ b/gently/ui/web/static/js/notebook.js @@ -0,0 +1,196 @@ +/** + * NotebookApp — the LIBRARY "Notebook" tab. + * + * The reading room for the shared lab notebook: a thread rail (the inquiry + * spine) + kind filter, rendering Notes from the read API (/api/notebook). + * Read-only for now; authoring/curation arrive in a later increment. + */ +const NotebookApp = (() => { + let inited = false; + let kindFilter = ''; // '' | observation | finding | question + let threadFilter = ''; // '' = all notes + + const $ = (id) => document.getElementById(id); + + async function fetchJSON(url) { + try { + const r = await fetch(url); + if (!r.ok) return null; + return await r.json(); + } catch (e) { + return null; + } + } + + function kindMeta(kind) { + return ({ + observation: { label: 'Observation', cls: 'nb-k-obs' }, + finding: { label: 'Finding', cls: 'nb-k-find' }, + question: { label: 'Question', cls: 'nb-k-q' }, + })[kind] || { label: kind || 'note', cls: '' }; + } + + async function loadThreads() { + const rail = $('nb-threads'); + if (!rail) return; + const data = await fetchJSON('/api/notebook/threads'); + const threads = (data && data.threads) || []; + rail.innerHTML = ''; + const mk = (id, label, count, active) => { + const b = document.createElement('button'); + b.className = 'nb-thread' + (active ? ' active' : ''); + b.textContent = label + (count != null ? ` ${count}` : ''); + b.addEventListener('click', () => { threadFilter = id; loadThreads(); loadNotes(); }); + return b; + }; + rail.appendChild(mk('', 'All notes', null, threadFilter === '')); + threads.forEach(t => rail.appendChild(mk(t.id, t.id, t.count, threadFilter === t.id))); + } + + function card(n) { + const km = kindMeta(n.kind); + const el = document.createElement('div'); + el.className = 'nb-card'; + + const head = document.createElement('div'); + head.className = 'nb-card-head'; + const badge = document.createElement('span'); + badge.className = 'nb-badge ' + km.cls; + badge.textContent = km.label; + const author = document.createElement('span'); + author.className = 'nb-author'; + author.textContent = n.author || ''; + const status = document.createElement('span'); + status.className = 'nb-status'; + status.textContent = n.status || ''; + head.append(badge, author, status); + + const body = document.createElement('div'); + body.className = 'nb-body-text'; + body.textContent = n.title || n.body || ''; + + el.append(head, body); + + const chips = [] + .concat((n.strains || []).map(s => '🧬 ' + s)) + .concat((n.embryos || []).map(e => '◌ ' + e)) + .concat((n.threads || []).map(t => '# ' + t)); + if (chips.length) { + const row = document.createElement('div'); + row.className = 'nb-chips'; + chips.forEach(text => { + const c = document.createElement('span'); + c.className = 'nb-chip'; + c.textContent = text; + row.appendChild(c); + }); + el.appendChild(row); + } + return el; + } + + async function loadNotes() { + const list = $('nb-notes'); + if (!list) return; + const params = new URLSearchParams(); + if (kindFilter) params.set('kind', kindFilter); + if (threadFilter) params.set('thread', threadFilter); + const qs = params.toString(); + const data = await fetchJSON('/api/notebook/notes' + (qs ? `?${qs}` : '')); + if (!data || data.available === false) { + list.innerHTML = '
Notebook unavailable.
';
+ return;
+ }
+ const notes = data.notes || [];
+ if (!notes.length) {
+ list.innerHTML =
+ 'No notes yet — the notebook fills as the agent ' +
+ 'records observations, findings, and open questions.
';
+ return;
+ }
+ list.innerHTML = '';
+ notes.forEach(n => list.appendChild(card(n)));
+ }
+
+ function setupFilters() {
+ document.querySelectorAll('#notebook-content [data-nb-kind]').forEach(btn => {
+ btn.addEventListener('click', () => {
+ kindFilter = btn.dataset.nbKind;
+ document.querySelectorAll('#notebook-content [data-nb-kind]')
+ .forEach(b => b.classList.toggle('active', b === btn));
+ loadNotes();
+ });
+ });
+ }
+
+ // ── Ask the notebook ───────────────────────────────────────────────
+ function renderAskResult(data) {
+ const box = $('nb-ask-result');
+ if (!box) return;
+ box.hidden = false;
+ if (!data || data.available === false) {
+ box.innerHTML = 'The notebook is unavailable right now.
';
+ return;
+ }
+ const cov = data.coverage || 'covered';
+ const covLabel = { covered: 'Grounded in the notebook', partial: 'Partially covered', not_in_notebook: 'Not in the notebook yet' }[cov] || cov;
+ const points = (data.points || []).map(p => `
+ ${esc(covLabel)}
` +
+ `${esc(data.answer || '')}
` +
+ (points ? `Why
- ${points}
Try next
- ${nexts}
Thinking over the notebook…
'; }
+ const body = { question: q };
+ if (threadFilter) body.thread = threadFilter; // ask within the selected thread
+ try {
+ const r = await fetch('/api/notebook/ask', {
+ method: 'POST', headers: { 'Content-Type': 'application/json' }, body: JSON.stringify(body),
+ });
+ renderAskResult(await r.json());
+ } catch (e) {
+ if (box) box.innerHTML = 'Something went wrong asking the notebook.
';
+ }
+ }
+
+ function setupAsk() {
+ const go = $('nb-ask-go'), input = $('nb-ask-input');
+ if (go) go.addEventListener('click', ask);
+ if (input) input.addEventListener('keydown', e => { if (e.key === 'Enter') { e.preventDefault(); ask(); } });
+ }
+
+ function esc(s) {
+ return (typeof escapeHtml === 'function') ? escapeHtml(String(s == null ? '' : s))
+ : String(s == null ? '' : s).replace(/[&<>"]/g, c => ({ '&': '&', '<': '<', '>': '>', '"': '"' }[c]));
+ }
+
+ function refresh() { loadThreads(); loadNotes(); }
+
+ function init() {
+ if (inited) { refresh(); return; }
+ inited = true;
+ setupFilters();
+ setupAsk();
+ refresh();
+ // Notebook writes ride the CONTEXT_UPDATED event — live-refresh if visible.
+ if (typeof ClientEventBus !== 'undefined') {
+ ClientEventBus.on('CONTEXT_UPDATED', () => {
+ if (typeof state !== 'undefined' && state.tab === 'notebook') refresh();
+ });
+ }
+ }
+
+ return { init };
+})();
diff --git a/gently/ui/web/static/js/occupancy3d.js b/gently/ui/web/static/js/occupancy3d.js
new file mode 100644
index 00000000..b9cfb7ee
--- /dev/null
+++ b/gently/ui/web/static/js/occupancy3d.js
@@ -0,0 +1,489 @@
+// ══════════════════════════════════════════════════════════════════════
+// 3D Optical Space — live digital-twin of the addressable imaging volume
+//
+// Renders the acquisition cuboid (the box of voxels being scanned) with the
+// live light-sheet plane inside it, plus a Z-neighbourhood reference frame.
+// An HTML overlay (mode badge + readouts + a top-down minimap) carries the
+// GLOBAL context: where in the addressable XY stage range this cuboid sits,
+// and the embryos around it.
+//
+// Why two representations: the addressable stage XY (~tens of mm), the cuboid
+// footprint (~hundreds of µm) and the piezo Z range (~µm) differ by ~100x, so
+// a single literal-scale 3D box would draw the cuboid invisibly small. The 3D
+// scene therefore stays in one µm scale around the cuboid; the minimap (2D)
+// handles the much larger stage extent. Some scales are local by design — see
+// FOV_UM / the outer-frame sizing below.
+//
+// Data:
+// DEVICE_STATE_UPDATE → live Piezo.Position (sheet Z), Galvo.A/B, XYStage,
+// and the firmware box (minimap extent).
+// SCAN_GEOMETRY_UPDATE → cuboid extents, num_slices, pencil/sheet mode.
+// EMBRYOS_UPDATE → minimap markers.
+// Bootstrap via /api/devices/scan_geometry + /api/embryos/current.
+//
+// Mirrors the DevicesManager IIFE pattern (devices.js) and reuses the
+// Three.js scaffold + drag-orbit from projection-viewer.js.
+// ══════════════════════════════════════════════════════════════════════
+
+const Occupancy3DManager = (function () {
+ 'use strict';
+
+ // --- Tunables / approximations (v1) --------------------------------
+ // Camera FOV footprint of the SPIM cuboid in µm. SPIM is 0.1625 µm/px;
+ // a ~2048px sCMOS ROI ≈ 333 µm. Not currently streamed, so we use a
+ // constant until SCAN_GEOMETRY_UPDATE carries fov_um. (Documented approx.)
+ const FOV_UM = 333.0;
+ const MAX_SLICE_LINES = 30; // cap drawn slice outlines for perf
+ const COLORS = {
+ outer: 0x33414d,
+ cuboid: 0x14b8c4,
+ cuboidFace: 0x14b8c4,
+ sheet: 0x39d0ff,
+ slice: 0x2a6f78,
+ beam: 0xffd166,
+ };
+
+ // --- Module state --------------------------------------------------
+ let _initialized = false;
+ let _scene = null, _camera = null, _renderer = null, _root = null;
+ let _animationId = null, _resizeObserver = null, _resizeRaf = null, _onLayoutChanged = null;
+ let _isDragging = false, _prevMouse = { x: 0, y: 0 };
+ const _rot = { x: -0.6, y: 0.6 };
+ let _zoom = 1.7;
+
+ // Live data caches
+ let _geom = null; // last SCAN_GEOMETRY_UPDATE.data
+ let _firmwareBox = null; // {x:[min,max], y:[min,max]} µm
+ let _stage = { x: null, y: null };
+ let _piezoZ = null; // live axial position (µm)
+ let _galvo = { a: null, b: null };
+ let _embryos = []; // [{x,y,role,id}]
+ let _scaler = null;
+
+ // Scene object handles (rebuilt as geometry changes)
+ let _outerBox = null, _cuboid = null, _cuboidEdges = null;
+ let _sheet = null, _beam = null, _sliceGroup = null;
+
+ // DOM
+ let _container = null, _modeEl = null, _readoutsEl = null, _minimapEl = null, _demoBtn = null;
+ let _demoTimer = null;
+
+ // ===================================================================
+ // Init / scene scaffold
+ // ===================================================================
+ function init() {
+ if (_initialized) { _resize(); return; }
+ if (typeof THREE === 'undefined') {
+ console.warn('[occupancy3d] THREE not loaded');
+ return;
+ }
+ _container = document.getElementById('occ3d-container');
+ _modeEl = document.getElementById('occ3d-mode');
+ _readoutsEl = document.getElementById('occ3d-readouts');
+ _minimapEl = document.getElementById('occ3d-minimap');
+ _demoBtn = document.getElementById('occ3d-demo-btn');
+ if (!_container) return;
+
+ _buildScene();
+ _wireInteraction();
+ if (_demoBtn) _demoBtn.addEventListener('click', toggleDemo);
+
+ // Subscribe to live data (mirror devices.js:1553-1559)
+ if (typeof ClientEventBus !== 'undefined') {
+ ClientEventBus.on('DEVICE_STATE_UPDATE', handleDeviceState);
+ ClientEventBus.on('SCAN_GEOMETRY_UPDATE', handleScanGeometry);
+ ClientEventBus.on('EMBRYOS_UPDATE', handleEmbryos);
+ }
+ _bootstrap();
+
+ _initialized = true;
+ _rebuildSceneObjects();
+ _renderReadouts();
+ _renderMinimap();
+ _animate();
+ // Container is 0×0 while the tab is hidden; size once it's visible.
+ requestAnimationFrame(_resize);
+ }
+
+ function _buildScene() {
+ const w = _container.clientWidth || 600;
+ const h = _container.clientHeight || 460;
+
+ _scene = new THREE.Scene();
+ _camera = new THREE.PerspectiveCamera(45, w / h, 0.01, 100);
+ _camera.position.set(0, 0, _zoom);
+
+ _renderer = new THREE.WebGLRenderer({ antialias: true });
+ _renderer.setSize(w, h);
+ _renderer.setClearColor(0x0a0e12);
+ _container.innerHTML = '';
+ _container.appendChild(_renderer.domElement);
+
+ _root = new THREE.Group();
+ _root.rotation.x = _rot.x;
+ _root.rotation.y = _rot.y;
+ _scene.add(_root);
+
+ // Keep the canvas in sync with its container (chat dock / window resize).
+ if (_resizeObserver) _resizeObserver.disconnect();
+ _resizeObserver = new ResizeObserver(() => {
+ if (_resizeRaf) cancelAnimationFrame(_resizeRaf);
+ _resizeRaf = requestAnimationFrame(_resize);
+ });
+ _resizeObserver.observe(_container);
+ if (!_onLayoutChanged) {
+ _onLayoutChanged = () => _resize();
+ window.addEventListener('gently:layout-changed', _onLayoutChanged);
+ }
+ }
+
+ function _resize() {
+ if (!_renderer || !_container) return;
+ const w = _container.clientWidth || 600;
+ const h = _container.clientHeight || 460;
+ if (w === 0 || h === 0) return;
+ _camera.aspect = w / h;
+ _camera.updateProjectionMatrix();
+ _renderer.setSize(w, h);
+ }
+
+ function _wireInteraction() {
+ const el = _renderer.domElement;
+ el.addEventListener('mousedown', (e) => {
+ _isDragging = true; _prevMouse = { x: e.clientX, y: e.clientY };
+ });
+ el.addEventListener('mousemove', (e) => {
+ if (!_isDragging) return;
+ _root.rotation.y += (e.clientX - _prevMouse.x) * 0.01;
+ _root.rotation.x += (e.clientY - _prevMouse.y) * 0.01;
+ _rot.x = _root.rotation.x; _rot.y = _root.rotation.y;
+ _prevMouse = { x: e.clientX, y: e.clientY };
+ });
+ window.addEventListener('mouseup', () => { _isDragging = false; });
+ el.addEventListener('wheel', (e) => {
+ e.preventDefault();
+ _zoom = Math.max(0.4, Math.min(6, _zoom + e.deltaY * 0.002));
+ _camera.position.z = _zoom;
+ }, { passive: false });
+ el.addEventListener('dblclick', () => {
+ _rot.x = -0.6; _rot.y = 0.6; _zoom = 1.7;
+ _root.rotation.x = _rot.x; _root.rotation.y = _rot.y;
+ _camera.position.z = _zoom;
+ });
+ }
+
+ function _animate() {
+ _animationId = requestAnimationFrame(_animate);
+ if (_renderer && _scene && _camera) _renderer.render(_scene, _camera);
+ }
+
+ // ===================================================================
+ // Scene geometry (rebuilt when scan geometry changes)
+ // ===================================================================
+ function _disposeObj(obj) {
+ if (!obj) return;
+ _root.remove(obj);
+ obj.traverse?.((c) => {
+ c.geometry?.dispose?.();
+ if (c.material) (Array.isArray(c.material) ? c.material : [c.material]).forEach(m => m.dispose());
+ });
+ obj.geometry?.dispose?.();
+ if (obj.material) (Array.isArray(obj.material) ? obj.material : [obj.material]).forEach(m => m.dispose());
+ }
+
+ function _currentGeom() {
+ // Fall back to nominal defaults so the scene is never empty.
+ const g = _geom || {};
+ const scan = g.scan || {};
+ const derived = g.derived || {};
+ const piezoCenter = scan.piezo_center_um != null ? scan.piezo_center_um : 50.0;
+ const zExtent = derived.z_extent_um != null ? derived.z_extent_um : 50.0;
+ return {
+ numSlices: scan.num_slices != null ? scan.num_slices : 50,
+ piezoCenter,
+ zExtent,
+ mode: g.mode || 'sheet',
+ };
+ }
+
+ function _rebuildSceneObjects() {
+ if (!_root) return;
+ [_outerBox, _cuboid, _cuboidEdges, _sheet, _beam, _sliceGroup].forEach(_disposeObj);
+ _outerBox = _cuboid = _cuboidEdges = _sheet = _beam = _sliceGroup = null;
+
+ const g = _currentGeom();
+ const fov = FOV_UM;
+ // Outer Z neighbourhood centred on the cuboid so it's always framed.
+ const halfZ = Math.max(g.zExtent * 2.5, 75);
+ const zMin = g.piezoCenter - halfZ;
+ const zMax = g.piezoCenter + halfZ;
+ const halfXY = fov * 1.5;
+
+ _scaler = makeSceneScaler({
+ xRange: [-halfXY, halfXY],
+ yRange: [-halfXY, halfXY],
+ zRange: [zMin, zMax],
+ });
+ const L = (um) => _scaler.scaleLen(um);
+ const Z = (um) => _scaler.toScene(um, 'z');
+
+ // --- Outer reference frame (addressable Z × local XY) ----------
+ _outerBox = new THREE.LineSegments(
+ new THREE.EdgesGeometry(new THREE.BoxGeometry(L(2 * halfXY), L(zMax - zMin), L(2 * halfXY))),
+ new THREE.LineBasicMaterial({ color: COLORS.outer })
+ );
+ _outerBox.position.y = Z(g.piezoCenter); // box centred on its own midpoint == piezoCenter
+ _root.add(_outerBox);
+
+ // --- Acquisition cuboid (footprint × z-extent) -----------------
+ // Three.js Y is our axial (Z µm) axis; X/Z are the lateral footprint.
+ const cw = L(fov), cd = L(fov), ch = L(g.zExtent);
+ _cuboid = new THREE.Mesh(
+ new THREE.BoxGeometry(cw, ch, cd),
+ new THREE.MeshBasicMaterial({
+ color: COLORS.cuboidFace, transparent: true, opacity: 0.06,
+ depthWrite: false, side: THREE.DoubleSide,
+ })
+ );
+ _cuboid.position.y = Z(g.piezoCenter);
+ _root.add(_cuboid);
+ _cuboidEdges = new THREE.LineSegments(
+ new THREE.EdgesGeometry(new THREE.BoxGeometry(cw, ch, cd)),
+ new THREE.LineBasicMaterial({ color: COLORS.cuboid })
+ );
+ _cuboidEdges.position.y = Z(g.piezoCenter);
+ _root.add(_cuboidEdges);
+
+ // --- Slice planes (faint outlines through the cuboid) ----------
+ _sliceGroup = new THREE.Group();
+ const n = Math.max(1, Math.min(g.numSlices, MAX_SLICE_LINES));
+ const sliceMat = new THREE.LineBasicMaterial({ color: COLORS.slice, transparent: true, opacity: 0.5 });
+ for (let i = 0; i < n; i++) {
+ const frac = n === 1 ? 0.5 : i / (n - 1);
+ const zUm = (g.piezoCenter - g.zExtent / 2) + frac * g.zExtent;
+ const ring = new THREE.LineLoop(_rectXZ(cw, cd), sliceMat);
+ ring.position.y = Z(zUm);
+ _sliceGroup.add(ring);
+ }
+ _root.add(_sliceGroup);
+
+ // --- Light sheet / pencil beam ---------------------------------
+ if (g.mode === 'pencil') {
+ // Pencil: a thin beam along the lateral axis through cuboid centre.
+ _beam = new THREE.LineSegments(
+ new THREE.BufferGeometry().setFromPoints([
+ new THREE.Vector3(-cw / 2, 0, 0), new THREE.Vector3(cw / 2, 0, 0),
+ ]),
+ new THREE.LineBasicMaterial({ color: COLORS.beam })
+ );
+ _root.add(_beam);
+ } else {
+ _sheet = new THREE.Mesh(
+ new THREE.PlaneGeometry(cw, cd),
+ new THREE.MeshBasicMaterial({
+ color: COLORS.sheet, transparent: true, opacity: 0.35,
+ side: THREE.DoubleSide, depthWrite: false,
+ })
+ );
+ _sheet.rotation.x = -Math.PI / 2; // lie in the lateral (X-Z) plane
+ _root.add(_sheet);
+ }
+ _updateSheetPosition();
+ }
+
+ // A rectangle outline in the lateral (X-Z) plane, centred at origin.
+ function _rectXZ(w, d) {
+ const hw = w / 2, hd = d / 2;
+ return new THREE.BufferGeometry().setFromPoints([
+ new THREE.Vector3(-hw, 0, -hd), new THREE.Vector3(hw, 0, -hd),
+ new THREE.Vector3(hw, 0, hd), new THREE.Vector3(-hw, 0, hd),
+ ]);
+ }
+
+ // Move the sheet/beam to the live axial position (piezo µm), clamped to
+ // the cuboid extent. Falls back to the cuboid centre when no live value.
+ function _updateSheetPosition() {
+ if (!_scaler) return;
+ const g = _currentGeom();
+ const zMin = g.piezoCenter - g.zExtent / 2;
+ const zMax = g.piezoCenter + g.zExtent / 2;
+ let zUm = _piezoZ != null ? _piezoZ : g.piezoCenter;
+ zUm = Math.max(zMin, Math.min(zMax, zUm));
+ const y = _scaler.toScene(zUm, 'z');
+ if (_sheet) _sheet.position.y = y;
+ if (_beam) _beam.position.y = y;
+ }
+
+ // ===================================================================
+ // Event handlers
+ // ===================================================================
+ function handleDeviceState(payload) {
+ if (!payload) return;
+ const pos = payload.positions || {};
+ for (const name of Object.keys(pos)) {
+ const e = pos[name] || {};
+ if (e.kind === 'xy_stage') {
+ if (e.X != null) _stage.x = e.X;
+ if (e.Y != null) _stage.y = e.Y;
+ } else if (e.kind === 'piezo') {
+ if (e.Position != null) _piezoZ = e.Position;
+ } else if (e.kind === 'galvo') {
+ if (e.A != null) _galvo.a = e.A;
+ if (e.B != null) _galvo.b = e.B;
+ }
+ }
+ const box = extractFirmwareBox(payload.properties);
+ if (box) _firmwareBox = box;
+ _updateSheetPosition();
+ _renderReadouts();
+ _renderMinimap();
+ }
+
+ function handleScanGeometry(payload) {
+ if (!payload) return;
+ _geom = payload;
+ if (payload.stage_position_um) {
+ if (payload.stage_position_um.x != null) _stage.x = payload.stage_position_um.x;
+ if (payload.stage_position_um.y != null) _stage.y = payload.stage_position_um.y;
+ }
+ _rebuildSceneObjects();
+ _renderReadouts();
+ _renderMinimap();
+ }
+
+ function handleEmbryos(payload) {
+ if (!payload || !Array.isArray(payload.embryos)) return;
+ _embryos = payload.embryos.map((e) => {
+ const fine = e.position_fine || {};
+ const coarse = e.position_coarse || {};
+ const x = fine.x != null ? fine.x : coarse.x;
+ const y = fine.y != null ? fine.y : coarse.y;
+ return { x, y, role: e.role, id: e.id };
+ }).filter((e) => e.x != null && e.y != null);
+ _renderMinimap();
+ }
+
+ async function _bootstrap() {
+ try {
+ const r = await fetch('/api/devices/scan_geometry');
+ if (r.ok) handleScanGeometry(await r.json());
+ } catch (_) { /* offline — demo button covers it */ }
+ try {
+ const r = await fetch('/api/embryos/current');
+ if (r.ok) handleEmbryos(await r.json());
+ } catch (_) { /* ignore */ }
+ }
+
+ // ===================================================================
+ // HTML overlay: mode badge, readouts, minimap
+ // ===================================================================
+ function _fmt(v, digits = 1, unit = '') {
+ return v == null ? '—' : (Number(v).toFixed(digits) + unit);
+ }
+
+ function _renderReadouts() {
+ const g = _currentGeom();
+ if (_modeEl) {
+ _modeEl.textContent = g.mode === 'pencil' ? 'PENCIL' : 'SHEET';
+ _modeEl.classList.toggle('is-pencil', g.mode === 'pencil');
+ }
+ if (!_readoutsEl) return;
+ const scan = (_geom && _geom.scan) || {};
+ const derived = (_geom && _geom.derived) || {};
+ const rows = [
+ ['stage X', _fmt(_stage.x, 0, ' µm')],
+ ['stage Y', _fmt(_stage.y, 0, ' µm')],
+ ['piezo Z', _fmt(_piezoZ, 1, ' µm')],
+ ['galvo A/B', `${_fmt(_galvo.a, 3)} / ${_fmt(_galvo.b, 3)}°`],
+ ['slices', scan.num_slices != null ? String(scan.num_slices) : '—'],
+ ['Z extent', _fmt(derived.z_extent_um, 1, ' µm')],
+ ['slice step', _fmt(derived.slice_spacing_um, 3, ' µm')],
+ ];
+ _readoutsEl.innerHTML = rows
+ .map(([k, v]) => `${k}${escapeHtml(v)}
`)
+ .join('');
+ }
+
+ function _renderMinimap() {
+ if (!_minimapEl) return;
+ const VB = { w: 200, h: 120, pad: 8 };
+ const box = _firmwareBox || { x: [-25000, 25000], y: [-12000, 12000] };
+ const bw = box.x[1] - box.x[0], bh = box.y[1] - box.y[0];
+ if (!(bw > 0 && bh > 0)) return;
+ const sx = (VB.w - 2 * VB.pad) / bw;
+ const sy = (VB.h - 2 * VB.pad) / bh;
+ const s = Math.min(sx, sy);
+ const ox = VB.pad + (VB.w - 2 * VB.pad - bw * s) / 2;
+ const oy = VB.pad + (VB.h - 2 * VB.pad - bh * s) / 2;
+ const px = (x) => ox + (x - box.x[0]) * s;
+ const py = (y) => oy + (box.y[1] - y) * s; // flip Y for screen
+
+ const parts = [];
+ parts.push(`No saved tactics
'; return; }
+ host.innerHTML = items.map(t =>
+ ``).join('');
+ } catch (_) { host.innerHTML = 'Library unavailable
'; }
+ }
+
+ function subjectIds() {
+ const subs = _embryos.filter(e => e.role !== 'calibration').map(e => e.id);
+ return subs.length ? subs : _embryos.map(e => e.id);
+ }
+
+ async function startRun() {
+ const b = $('op-run-start');
+ const done = () => { if (b) { b.disabled = false; b.textContent = 'Start'; } };
+ if (b) { b.disabled = true; b.textContent = 'Starting…'; }
+ try {
+ if (_mode === 'single') {
+ if (!_selected) { toast('Select an embryo first'); return; }
+ _acquiring = true; renderSubnavMeta();
+ try {
+ await postJSON('/api/devices/acquire/volume', {
+ num_slices: Math.max(1, Number(($('op-vol-slices') || {}).value) || 50),
+ exposure_ms: Math.max(1, Number(($('op-vol-exp') || {}).value) || 10),
+ });
+ toast('Volume acquired');
+ } finally { _acquiring = false; await forceLedOff(); renderSubnavMeta(); }
+ return;
+ }
+ if (_mode === 'adaptive') {
+ const interval = Math.max(1, Number(($('op-tl-interval') || {}).value) || 120);
+ const sel = ($('op-tl-stop') || {}).value || 'manual';
+ const val = Math.max(1, Number(($('op-tl-condval') || {}).value) || 1);
+ // The orchestrator parses the COMBINED form ('timepoints:N' /
+ // 'duration:Xh'). A bare 'timepoints' silently degrades to manual,
+ // i.e. a timelapse that never stops.
+ let stop_condition = sel;
+ if (sel === 'timepoints') stop_condition = `timepoints:${val}`;
+ else if (sel === 'duration') stop_condition = `duration:${val}h`;
+ await postJSON('/api/devices/timelapse/start', {
+ embryo_ids: subjectIds(),
+ interval_seconds: interval,
+ stop_condition,
+ monitoring_mode: ($('op-tl-monitor') || {}).value || 'idle',
+ });
+ toast('Adaptive timelapse started');
+ renderRun();
+ return;
+ }
+ if (_mode === 'library') {
+ if (!_selectedLib) { toast('Pick a saved tactic'); return; }
+ const d = await postJSON('/api/operate/run-tactic',
+ { library_id: _selectedLib, embryo_ids: subjectIds() });
+ if (d.success) { toast('Tactic started'); renderRun(); }
+ else toast(`Run failed: ${(d.result && d.result.message) || '?'}`);
+ return;
+ }
+ if (_mode === 'agent') {
+ const roster = _embryos.map(e => {
+ const xy = resolveXY(e);
+ const r = e.role === 'calibration' ? 'reference' : 'subject';
+ return `${labelFor(e)}${xy ? ` (${xy.x.toFixed(0)},${xy.y.toFixed(0)})` : ''} [${r}]`;
+ }).join(', ');
+ const prompt = `I marked ${_embryos.length} embryos: ${roster}. ` +
+ 'Propose and start an Operation Plan to image them.';
+ if (typeof AgentChat !== 'undefined' && AgentChat.togglePanel) {
+ AgentChat.togglePanel(true);
+ if (AgentChat.runCommand) setTimeout(() => AgentChat.runCommand(prompt), 300);
+ } else toast('Agent chat unavailable');
+ }
+ } catch (e) {
+ toast(`Start failed (${e.status || e.message})`);
+ } finally { done(); }
+ }
+
+ // Run presence is DERIVED from the server, not from a client flag. The old
+ // design kept it in memory, so F5 during a running timelapse lost the whole
+ // panel — and left a client state machine that could re-grow into steps.
+ async function renderRun() {
+ const host = $('op-runspine'), actions = $('op-run-actions');
+ if (!host) return;
+ let tactics = [];
+ try {
+ const d = await getJSON('/api/operation_plan');
+ tactics = (d && d.plan && d.plan.tactics) || [];
+ } catch (_) { /* leave empty */ }
+ const live = tactics.filter(t => t.state === 'active' || t.state === 'paused');
+ if (actions) actions.hidden = live.length === 0;
+ if (!tactics.length) {
+ host.innerHTML = 'Nothing running.
';
+ return;
+ }
+ host.innerHTML = tactics.map(tacticCard).join('');
+ _runPaused = live.some(t => t.state === 'paused');
+ const p = $('op-run-pause');
+ if (p) p.textContent = _runPaused ? 'Resume' : 'Pause';
+ }
+ function tacticCard(t) {
+ const state = t.state || 'planned';
+ const struct = t.structure || {};
+ const meta = [];
+ if (struct.cadence_s != null) meta.push(`${struct.cadence_s}s`);
+ if (struct.interval != null) meta.push(`${struct.interval}s`);
+ if (struct.status) meta.push(struct.status);
+ if (t.live && t.live.signal != null) meta.push(`signal ${t.live.signal}`);
+ return `` +
+ `
';
+ }
+ async function pauseRun() {
+ try {
+ await postJSON(_runPaused ? '/api/devices/timelapse/resume' : '/api/devices/timelapse/pause', {});
+ toast(_runPaused ? 'Resumed' : 'Paused');
+ } catch (e) { toast(`Pause/resume failed (${e.status || e.message})`); }
+ renderRun();
+ }
+ async function stopRun() {
+ if (!window.confirm('Stop the run?')) return;
+ try { await postJSON('/api/devices/timelapse/stop', { reason: 'operator' }); toast('Run stopped'); }
+ catch (e) { toast(`Stop failed (${e.status || e.message})`); }
+ renderRun();
+ }
+
+ // ══ PANES ═══════════════════════════════════════════════════════════════
+ // Camera ownership is keyed on VISIBILITY, not on a step. Both cameras
+ // contend for MMCore, and the client swaps .src per frame with no throttle,
+ // so two live decoders is the condition that risks a Video-TDR freeze. "The
+ // camera is live while you are looking at it" guarantees at most one.
+ const PANES = {
+ bottom: {
+ onEnter() { if (_bottomWasOn && !_bottomOn) toggleBottomCam(); drawMarkers(); },
+ onLeave() { _bottomWasOn = _bottomOn; if (_bottomOn) stopBottom(); },
+ render() { renderMarkCount(); drawMarkers(); bz.render(); },
+ },
+ spim: {
+ onEnter() { if (_spimWasOn && !_spimOn) toggleSpim(); },
+ onLeave() { _spimWasOn = _spimOn; if (_spimOn) stopSpim(); forceLedOff(); },
+ render() { renderSpimTarget(); fd.render(); },
+ },
+ acquire: {
+ onEnter() { renderRun(); },
+ onLeave() {},
+ render() { renderRoster(); renderSingle(); },
+ },
+ };
+ function stopBottom() {
+ fetch('/api/devices/bottom_camera/stream/stop', { method: 'POST' }).catch(() => {});
+ applyBottomCam(false);
+ }
+ function stopSpim() {
+ fetch('/api/devices/lightsheet/live/stop', { method: 'POST' }).catch(() => {});
+ applySpim(false);
+ }
+
+ function showPane(name) {
+ if (!PANES[name] || name === _pane) return;
+ const prev = _pane;
+ _pane = name;
+ if (PANES[prev]) PANES[prev].onLeave();
+ ['bottom', 'spim', 'acquire'].forEach(p => {
+ const el = $(`op-pane-${p}`);
+ if (el) el.hidden = p !== name;
+ });
+ // Drives the CSS that hides the shared rail on Acquisition (its own
+ // roster is richer) while keeping it on Bottom / SPIM.
+ const body = $('op-body'); if (body) body.dataset.pane = name;
+ if (typeof updateViewButtons === 'function') updateViewButtons('operate-subtab-switcher', name);
+ PANES[name].onEnter();
+ PANES[name].render();
+ renderEmbryoRail();
+ renderLock();
+ }
+
+ function renderSubnavMeta() {
+ const el = $('op-subnav-meta');
+ if (!el) return;
+ const bits = [];
+ if (_bottomOn) bits.push('BOTTOM ● LIVE');
+ if (_spimOn) bits.push('SPIM ● LIVE');
+ if (_ledOn) bits.push('LED EMITTING');
+ if (_acquiring) bits.push('LASER EMITTING');
+ el.textContent = bits.join(' · ');
+ }
+
+ // ══ EVENTS ══════════════════════════════════════════════════════════════
+ function onBottomFrame(p) {
+ // Bail when hidden, or a hidden Operate keeps base64-decoding every
+ // frame behind whatever is on screen and races for stream ownership.
+ if (!_active || _pane !== 'bottom' || !p || !p.jpeg_b64) return;
+ _lastBottom = p;
+ if (p.focus_score != null) {
+ const el = $('op-bz-score');
+ if (el) el.textContent = Number(p.focus_score).toFixed(3);
+ }
+ setImg('op-img-bottom', 'op-ph-bottom', p);
+ drawMarkers();
+ }
+ function onSpimFrame(p) {
+ if (!_active || _pane !== 'spim' || !p || !p.jpeg_b64) return;
+ if (p.focus_score != null) {
+ const el = $('op-spim-score');
+ if (el) el.textContent = Number(p.focus_score).toFixed(3);
+ }
+ setImg('op-img-spim', 'op-ph-spim', p);
+ }
+ function onEmbryosUpdate(p) {
+ _embryos = (p && Array.isArray(p.embryos)) ? p.embryos : [];
+ if (_selected && !_embryos.some(e => e.id === _selected)) _selected = null;
+ // The embryo list is shared across all three panes; keep a live
+ // selection whenever it is non-empty so SPIM/Acquire aren't a dead-end
+ // ("No embryo selected") right after registering. The operator can still
+ // switch by clicking a registered embryo (bottom) or a roster row.
+ if (!_selected && _embryos.length) _selected = _embryos[0].id;
+ // Render the shared rail even when the Operate view isn't the active tab,
+ // so switching to it (or refreshing) shows the list immediately rather
+ // than waiting for the next mutation event.
+ renderEmbryoRail();
+ if (!_active) return;
+ renderRoster(); renderSpimTarget(); renderSingle();
+ }
+
+ function wire() {
+ if (_wired) return;
+ _wired = true;
+
+ if (typeof initViewSwitcher === 'function') {
+ // Click delegation only — deliberately NO `views` option.
+ //
+ // initViewSwitcher's `views` binds BARE number keys on document, and
+ // 1-6 are already global main-tab navigation (KeyboardShortcuts in
+ // app.js), with system/calibration/plan switchers claiming 1-3 too.
+ // Binding them here either steals a main-tab key or, with a guard
+ // tight enough to be safe, never fires at all — verified in-browser:
+ // app.js handles the keypress first and moves state.tab, so the
+ // guard then correctly refuses. Three peer surfaces are fine to
+ // click between; a shortcut would need a modifier to be honest.
+ initViewSwitcher('operate-subtab-switcher', showPane);
+ }
+
+ bz.wire(); fd.wire();
+
+ const cam = $('op-cam-toggle'); if (cam) cam.addEventListener('click', toggleBottomCam);
+ const det = $('op-detect'); if (det) det.addEventListener('click', runDetect);
+ const ok = $('op-confirm'); if (ok) ok.addEventListener('click', confirmMarks);
+ const cl = $('op-clear');
+ if (cl) cl.addEventListener('click', () => { _markers = []; drawMarkers(); renderMarkCount(); setDetectNote(''); });
+ const canvas = $('op-mark-canvas'); if (canvas) canvas.addEventListener('click', onCanvasClick);
+
+ // Shared embryo rail: click a row to select (delete button is guarded
+ // first so removing a false positive doesn't also select it).
+ const erail = $('op-erail-list');
+ if (erail) {
+ erail.addEventListener('click', (e) => {
+ const del = e.target.closest('[data-del]');
+ if (del) { e.stopPropagation(); deleteEmbryo(del.dataset.del); return; }
+ const row = e.target.closest('[data-embryo]');
+ if (row) selectEmbryo(row.dataset.embryo);
+ });
+ erail.addEventListener('keydown', (e) => {
+ if (e.key !== 'Enter' && e.key !== ' ') return;
+ const row = e.target.closest('[data-embryo]');
+ if (row) { e.preventDefault(); selectEmbryo(row.dataset.embryo); }
+ });
+ }
+
+ const sp = $('op-spim-toggle'); if (sp) sp.addEventListener('click', toggleSpim);
+ const led = $('op-led'); if (led) led.addEventListener('click', toggleLed);
+ const cal = $('op-calibrate'); if (cal) cal.addEventListener('click', calibrateSelected);
+ document.querySelectorAll('[data-gv]').forEach(b =>
+ b.addEventListener('click', () => nudgeGalvo(Number(b.dataset.gv))));
+ document.querySelectorAll('[data-pz]').forEach(b =>
+ b.addEventListener('click', () => nudgePiezo(Number(b.dataset.pz))));
+ document.querySelectorAll('[data-backoff]').forEach(b =>
+ b.addEventListener('click', backOff));
+
+ const modes = $('op-modes');
+ if (modes) {
+ modes.addEventListener('click', e => {
+ const b = e.target.closest('[data-mode]');
+ if (b) setMode(b.dataset.mode);
+ });
+ }
+ const stop = $('op-tl-stop');
+ if (stop) {
+ stop.addEventListener('change', () => {
+ const w = $('op-tl-condwrap');
+ if (w) w.hidden = stop.value === 'manual';
+ });
+ }
+ const lib = $('op-lib-list');
+ if (lib) {
+ lib.addEventListener('click', e => {
+ const b = e.target.closest('[data-lib]');
+ if (b) { _selectedLib = b.dataset.lib; loadLibrary(); }
+ });
+ }
+ const roster = $('op-roster');
+ if (roster) {
+ roster.addEventListener('click', e => {
+ const r = e.target.closest('[data-role-for]');
+ if (r) { e.stopPropagation(); toggleRole(r.dataset.roleFor); return; }
+ const c = e.target.closest('[data-center]');
+ if (c) {
+ e.stopPropagation();
+ const emb = _embryos.find(x => x.id === c.dataset.center);
+ if (emb) centerOnEmbryo(emb);
+ return;
+ }
+ const g = e.target.closest('[data-goto]');
+ if (g) { showPane(g.dataset.goto); return; }
+ const row = e.target.closest('[data-embryo]');
+ if (row) selectEmbryo(row.dataset.embryo);
+ });
+ roster.addEventListener('keydown', e => {
+ if (e.key !== 'Enter' && e.key !== ' ') return;
+ const row = e.target.closest('[data-embryo]');
+ if (row) { e.preventDefault(); selectEmbryo(row.dataset.embryo); }
+ });
+ }
+ const start = $('op-run-start'); if (start) start.addEventListener('click', startRun);
+ const pause = $('op-run-pause'); if (pause) pause.addEventListener('click', pauseRun);
+ const stopb = $('op-run-stop'); if (stopb) stopb.addEventListener('click', stopRun);
+
+ window.addEventListener('resize', () => { if (_active && _pane === 'bottom') drawMarkers(); });
+ // The viewport also changes size without a window resize — revealing the
+ // pane, the agent panel opening, the first frame arriving. Without this
+ // the overlay keeps whatever size it was first drawn at and every marker
+ // sits in the wrong place until the next frame happens to redraw it.
+ const camBox = $('op-cam-bottom');
+ if (camBox && typeof ResizeObserver !== 'undefined') {
+ new ResizeObserver(() => { if (_active && _pane === 'bottom') drawMarkers(); }).observe(camBox);
+ }
+
+ if (typeof ClientEventBus !== 'undefined') {
+ ClientEventBus.on('BOTTOM_CAMERA_FRAME', onBottomFrame);
+ ClientEventBus.on('LIGHTSHEET_FRAME', onSpimFrame);
+ ClientEventBus.on('EMBRYOS_UPDATE', onEmbryosUpdate);
+ ClientEventBus.on('DEVICE_STATE_UPDATE', p => {
+ const pos = p && p.positions;
+ if (!pos) return;
+ if (Array.isArray(pos.xy_stage)) _xy = { x: pos.xy_stage[0], y: pos.xy_stage[1] };
+ if (!_active) return;
+ for (const v of Object.values(pos)) {
+ if (!v || typeof v !== 'object' || v.Position == null) continue;
+ const val = Number(v.Position);
+ if (!Number.isFinite(val)) continue;
+ if (v.kind === 'fdrive') fd.absorbTelemetry(val);
+ else if (v.kind === 'bottom_z') bz.absorbTelemetry(val);
+ }
+ if (_pane === 'acquire') renderSingle();
+ });
+ }
+ }
+
+ async function activate() {
+ wire();
+ if (_active) return;
+ _active = true;
+ showPaneInitial();
+ try { onEmbryosUpdate(await getJSON('/api/embryos/current')); } catch (_) {}
+ await Promise.all([bz.refresh(), fd.refresh()]);
+ renderLock();
+ renderSubnavMeta();
+ }
+ function showPaneInitial() {
+ ['bottom', 'spim', 'acquire'].forEach(p => {
+ const el = $(`op-pane-${p}`);
+ if (el) el.hidden = p !== _pane;
+ });
+ if (typeof updateViewButtons === 'function') updateViewButtons('operate-subtab-switcher', _pane);
+ if (PANES[_pane]) { PANES[_pane].onEnter(); PANES[_pane].render(); }
+ }
+ function deactivate() {
+ if (!_active) return;
+ _active = false;
+ // Remember what was running so returning restores it, but leave nothing
+ // decoding behind a hidden view.
+ _bottomWasOn = _bottomOn; _spimWasOn = _spimOn;
+ if (_bottomOn) stopBottom();
+ if (_spimOn) stopSpim();
+ forceLedOff();
+ }
+
+ return { activate, deactivate };
+})();
diff --git a/gently/ui/web/static/js/operations-scenarios.js b/gently/ui/web/static/js/operations-scenarios.js
new file mode 100644
index 00000000..0cd72fbf
--- /dev/null
+++ b/gently/ui/web/static/js/operations-scenarios.js
@@ -0,0 +1,372 @@
+/**
+ * Operation Plan scenario fixtures — development and Chrome-MCP audit targets.
+ *
+ * Each entry is a plan object matching the real API schema returned by
+ * GET /api/operation_plan/{session_id} → { available, plan }
+ * The `.plan` is what gets passed to the renderer. Active tactics carry a
+ * `live` field (readouts + phases) that the API route merges from live
+ * telemetry; here they are baked into the fixture.
+ *
+ * Scenario dev mode: load via ?scenario=${escapeHtml(t.name || t.id)}` +
+ `${escapeHtml(state)}
` +
+ `${escapeHtml(t.kind || '')}
` +
+ (meta.length ? `` : '') +
+ (t.rationale ? `` : '') +
+ '