Sleep Synthesizer

.gitignore

@@ -3,3 +3,4 @@ __pycache__/
 .claude/
 docs/
 sample_plot_*.png
+data/

captionizer.py

@@ -53,6 +53,8 @@ def run(
     from mhc.dataset import MHCDataset
     from mhc.transformer import MHCTransformer
     from mhc.constants import MHC_CHANNEL_CONFIG
+    from extractors.cross_channel import CrossChannelExtractor
+    from synthesizers.sleep import SleepSynthesizer
     from extractors.statistical import StatisticalExtractor
     from extractors.structural import StructuralExtractor
     from models.local import LocalConfig, LocalModel
@@ -66,6 +68,7 @@ def run(
         StatisticalExtractor(MHC_CHANNEL_CONFIG),
         StructuralExtractor(MHC_CHANNEL_CONFIG),
         SemanticExtractor(MHC_CHANNEL_CONFIG),
+        CrossChannelExtractor(MHC_CHANNEL_CONFIG, synthesizers=[SleepSynthesizer()]),
     ])
 
     captionizer = Captionizer(dataset, MHCTransformer(), annotator)

explorer.py

@@ -17,6 +17,8 @@
 
 from annotator import Annotator
 from extractors import ChannelConfig
+from extractors.cross_channel import CrossChannelExtractor
+from synthesizers.sleep import SleepSynthesizer
 from extractors.statistical import StatisticalExtractor
 from extractors.structural import StructuralExtractor
 from mhc.constants import MHC_CHANNEL_CONFIG
@@ -25,6 +27,9 @@
 from timef.schema import Recording, SignalView
 from transformer import Transformer
 
+IN_BED_AWAKE_LABEL = "in_bed_not_sleeping"
+IN_BED_AWAKE_TARGET = "InBedAwake"
+
 
 def _parse_args() -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Interactive explorer for MHC rows, signals, and detector outputs.")
@@ -87,6 +92,7 @@ def __init__(
         self.annotator = Annotator([
             StatisticalExtractor(channel_config),
             StructuralExtractor(channel_config),
+            CrossChannelExtractor(channel_config, synthesizers=[SleepSynthesizer()]),
         ])
 
         self.row_index = min(max(0, row_index), len(self.dataset) - 1)
@@ -99,9 +105,9 @@ def __init__(
         self.detail_mode = "events"
         self.details_scroll = 0
         self.details_page_lines = 12
-        self.hit_target_names = self._available_detector_names()
+        self.hit_target_names = self._available_hit_target_names()
         self.hit_target = self.hit_target_names[0] if self.hit_target_names else None
-        self.search_status = "Use hit< / hit> to jump to the selected detector."
+        self.search_status = "Use hit< / hit> to jump to the selected event."
 
         self._ignore_widget_events = False
 
@@ -131,18 +137,10 @@ def __init__(
             self.detail_tab_buttons[label] = Button(ax, label)
         self.detail_up_ax = self.fig.add_axes([0.935, 0.085, 0.022, 0.028])
         self.detail_down_ax = self.fig.add_axes([0.958, 0.085, 0.022, 0.028])
-        self.prev_hit_ax = self.fig.add_axes([0.76, 0.698, 0.035, 0.038])
-        self.next_hit_ax = self.fig.add_axes([0.945, 0.698, 0.035, 0.038])
-        self.hit_target_buttons: dict[str, Button] = {}
-        if self.hit_target_names:
-            n_targets = len(self.hit_target_names)
-            total_gap = 0.004 * max(0, n_targets - 1)
-            available_width = 0.145
-            width = (available_width - total_gap) / max(1, n_targets)
-            for i, detector_name in enumerate(self.hit_target_names):
-                x0 = 0.805 + i * (width + 0.004)
-                ax = self.fig.add_axes([x0, 0.698, width, 0.038])
-                self.hit_target_buttons[detector_name] = Button(ax, detector_name.replace("Detector", "").lower())
+        self.prev_target_ax = self.fig.add_axes([0.76, 0.698, 0.045, 0.038])
+        self.next_target_ax = self.fig.add_axes([0.81, 0.698, 0.045, 0.038])
+        self.prev_hit_ax = self.fig.add_axes([0.895, 0.698, 0.040, 0.038])
+        self.next_hit_ax = self.fig.add_axes([0.94, 0.698, 0.040, 0.038])
         overlay_labels = ["trend", "spike", "drop", "nonwear"]
         self.overlay_buttons: dict[str, Button] = {}
         start_x = 0.83
@@ -164,6 +162,8 @@ def __init__(
         self.reset_zoom_button = Button(self.reset_zoom_ax, "reset")
         self.prev_row_button = Button(self.prev_row_ax, "<")
         self.next_row_button = Button(self.next_row_ax, ">")
+        self.prev_target_button = Button(self.prev_target_ax, "target<")
+        self.next_target_button = Button(self.next_target_ax, "target>")
         self.prev_hit_button = Button(self.prev_hit_ax, "hit<")
         self.next_hit_button = Button(self.next_hit_ax, "hit>")
         self.detail_up_button = Button(self.detail_up_ax, "^")
@@ -175,12 +175,12 @@ def __init__(
         self.reset_zoom_button.on_clicked(lambda _: self.render(reset_zoom=True))
         self.prev_row_button.on_clicked(lambda _: self._set_row(self.row_index - 1))
         self.next_row_button.on_clicked(lambda _: self._set_row(self.row_index + 1))
+        self.prev_target_button.on_clicked(lambda _: self._cycle_hit_target(-1))
+        self.next_target_button.on_clicked(lambda _: self._cycle_hit_target(1))
         self.prev_hit_button.on_clicked(lambda _: self._jump_to_hit(-1))
         self.next_hit_button.on_clicked(lambda _: self._jump_to_hit(1))
         self.detail_up_button.on_clicked(lambda _: self._scroll_details(-1))
         self.detail_down_button.on_clicked(lambda _: self._scroll_details(1))
-        for detector_name, button in self.hit_target_buttons.items():
-            button.on_clicked(lambda _, name=detector_name: self._set_hit_target(name))
         for label, button in self.detail_tab_buttons.items():
             button.on_clicked(lambda _, name=label: self._set_detail_mode(name))
         for label, button in self.overlay_buttons.items():
@@ -198,13 +198,19 @@ def _load_row_bundle(self, row_index: int) -> Recording:
         recording.annotations.extend(self.annotator.annotate(recording))
         return recording
 
-    def _available_detector_names(self) -> list[str]:
+    def _available_hit_target_names(self) -> list[str]:
         names = {
             detector.__class__.__name__
             for detectors in self.channel_config.detectors.values()
             for detector in detectors
         }
-        return sorted(names)
+        return sorted(names) + [IN_BED_AWAKE_TARGET]
+
+    @staticmethod
+    def _hit_target_button_label(hit_target: str) -> str:
+        if hit_target == IN_BED_AWAKE_TARGET:
+            return "inbed+awake"
+        return hit_target.replace("Detector", "").lower()
 
     def _set_row(self, row_index: int) -> None:
         row_index = min(max(0, int(row_index)), len(self.dataset) - 1)
@@ -249,10 +255,18 @@ def _on_toggle(self, label: str) -> None:
     def _set_hit_target(self, detector_name: str) -> None:
         if detector_name != self.hit_target:
             self.hit_target = detector_name
-            self.search_status = f"Jump target set to {detector_name}."
-            self._update_hit_target_button_styles()
+            self.search_status = f"Jump target set to {self._hit_target_button_label(detector_name)}."
         self.render(reset_zoom=False)
 
+    def _cycle_hit_target(self, step: int) -> None:
+        if not self.hit_target_names:
+            return
+        if self.hit_target not in self.hit_target_names:
+            self._set_hit_target(self.hit_target_names[0])
+            return
+        current = self.hit_target_names.index(self.hit_target)
+        self._set_hit_target(self.hit_target_names[(current + step) % len(self.hit_target_names)])
+
     def _set_detail_mode(self, mode: str) -> None:
         if mode != self.detail_mode:
             self.detail_mode = mode
@@ -285,6 +299,10 @@ def _on_key_press(self, event) -> None:
             self._jump_to_hit(1)
         elif event.key == "p":
             self._jump_to_hit(-1)
+        elif event.key == "[":
+            self._cycle_hit_target(-1)
+        elif event.key == "]":
+            self._cycle_hit_target(1)
 
     def _on_scroll(self, event) -> None:
         if event.inaxes is not self.ax_details:
@@ -315,9 +333,16 @@ def _row_detector_events(self, row_index: int) -> tuple[tuple[tuple[str, object]
         recording = self._load_row_bundle(row_index)
         return tuple(tuple(self._detector_events(signal)) for signal in recording.iter_channels())
 
+    def _signal_has_hit_target(self, row_index: int, signal_index: int) -> bool:
+        if self.hit_target == IN_BED_AWAKE_TARGET:
+            recording = self._load_row_bundle(row_index)
+            return bool(self._cross_channel_windows(recording, signal_index, IN_BED_AWAKE_LABEL))
+        row_signal_events = self._row_detector_events(row_index)[signal_index]
+        return any(detector_name == self.hit_target for detector_name, _ in row_signal_events)
+
     def _jump_to_hit(self, step: int) -> None:
         if self.hit_target is None:
-            self.search_status = "No detector target is available."
+            self.search_status = "No search target is available."
             self.render(reset_zoom=False)
             return
 
@@ -328,17 +353,19 @@ def _jump_to_hit(self, step: int) -> None:
         for offset in range(1, n_rows * n_signals):
             candidate = (flat_index + step * offset) % (n_rows * n_signals)
             row_index, signal_index = divmod(candidate, n_signals)
-            row_signal_events = self._row_detector_events(row_index)[signal_index]
-            if any(detector_name == self.hit_target for detector_name, _ in row_signal_events):
+            if self._signal_has_hit_target(row_index, signal_index):
                 self.row_index = row_index
                 self.signal_index = signal_index
                 self.details_scroll = 0
-                self.search_status = f"Jumped to row {row_index}, signal {signal_index} with {self.hit_target}."
+                self.search_status = (
+                    f"Jumped to row {row_index}, signal {signal_index} "
+                    f"with {self._hit_target_button_label(self.hit_target)}."
+                )
                 self._sync_widgets()
                 self.render(reset_zoom=True)
                 return
 
-        self.search_status = f"No hits found for {self.hit_target} in the scanned dataset."
+        self.search_status = f"No hits found for {self._hit_target_button_label(self.hit_target)} in the scanned dataset."
         self.render(reset_zoom=False)
 
     @staticmethod
@@ -350,6 +377,14 @@ def _captions_for_signal(recording: Recording, signal_idx: int) -> dict[str, lis
             grouped.setdefault(annotation.caption_type, []).append(annotation.text)
         return grouped
 
+    @staticmethod
+    def _cross_channel_windows(recording: Recording, signal_idx: int, label: str) -> list[tuple[int, int]]:
+        return [
+            annotation.window
+            for annotation in recording.annotations_for_signal(signal_idx)
+            if annotation.label == label and annotation.window is not None
+        ]
+
     @staticmethod
     def _overview_matrix(recording: Recording) -> np.ma.MaskedArray:
         rows = []
@@ -381,16 +416,15 @@ def _style_widgets(self) -> None:
         ):
             button.label.set_fontsize(8.5)
 
-        for button in self.hit_target_buttons.values():
-            button.label.set_fontsize(8)
         for button in self.detail_tab_buttons.values():
             button.label.set_fontsize(7.5)
         self.detail_up_button.label.set_fontsize(8)
         self.detail_down_button.label.set_fontsize(8)
+        self.prev_target_button.label.set_fontsize(7.2)
+        self.next_target_button.label.set_fontsize(7.2)
         for button in self.overlay_buttons.values():
             button.label.set_fontsize(7)
         self._sync_widgets()
-        self._update_hit_target_button_styles()
         self._update_detail_tab_styles()
         self._update_overlay_button_styles()
 
@@ -418,22 +452,6 @@ def _update_overlay_button_styles(self) -> None:
             button.label.set_color(text)
             button.label.set_fontweight("bold" if enabled else "normal")
 
-    def _update_hit_target_button_styles(self) -> None:
-        for detector_name, button in self.hit_target_buttons.items():
-            active = detector_name == self.hit_target
-            face = "#204a87" if active else "#f4f5f7"
-            edge = "#f4d35e" if active else "#c7cdd6"
-            text = "white" if active else "#5f6b7a"
-            button.ax.set_facecolor(face)
-            button.ax.patch.set_edgecolor(edge)
-            button.ax.patch.set_linewidth(2.0 if active else 1.1)
-            for spine in button.ax.spines.values():
-                spine.set_edgecolor(edge)
-                spine.set_linewidth(2.0 if active else 1.1)
-            button.hovercolor = "#3465a4" if active else "#eaedf2"
-            button.label.set_color(text)
-            button.label.set_fontweight("bold" if active else "normal")
-
     @staticmethod
     def _build_detail_lines(title: str, lines: list[str], width: int) -> list[str]:
         rendered = [title]
@@ -469,6 +487,7 @@ def render(self, reset_zoom: bool = False) -> None:
         signal = recording.signal(self.signal_index)
         detector_events = self._detector_events(signal)
         captions = self._captions_for_signal(recording, self.signal_index)
+        cross_channel_windows = self._cross_channel_windows(recording, self.signal_index, IN_BED_AWAKE_LABEL)
         display_name = signal.display_name
         unit = signal.unit or ""
         _, _, decimals = self.channel_config.meta.get(signal.name, (signal.name, "", 2))
@@ -493,6 +512,8 @@ def render(self, reset_zoom: bool = False) -> None:
         if self.show_nonwear:
             for start, end in _nan_regions(y):
                 self.ax_main.axvspan(start, end, color="#d62728", alpha=0.08, label="nonwear")
+        for start, end in cross_channel_windows:
+            self.ax_main.axvspan(start, end, color="#f4d35e", alpha=0.22, label="in bed, awake")
 
         for detector_name, result in detector_events:
             if result.event_type == "trend" and self.show_trends:
@@ -609,14 +630,26 @@ def render(self, reset_zoom: bool = False) -> None:
         self.ax_hit_target.text(
             0.0,
             1.02,
-            f"Find {self.hit_target.replace('Detector', '').lower()} hits" if self.hit_target else "Find hits",
+            "Find Hits",
             transform=self.ax_hit_target.transAxes,
             ha="left",
             va="bottom",
             fontsize=8.5,
             color="#444444",
             weight="bold",
         )
+        self.ax_hit_target.text(
+            0.0,
+            0.55,
+            self._hit_target_button_label(self.hit_target),
+            transform=self.ax_hit_target.transAxes,
+            ha="left",
+            va="center",
+            fontsize=8.5,
+            color="#333333",
+            family="monospace",
+            weight="bold",
+        )
         self.ax_hit_target.text(
             1.0,
             1.02,
@@ -692,9 +725,10 @@ def render(self, reset_zoom: bool = False) -> None:
                     "click a signal on the right or the overview heatmap to change channel",
                     "up/down changes row",
                     "left/right changes signal",
-                    "choose a detector target above the signal list",
-                    "n / p jump to next or previous hit for that detector",
+                    "target< / target> changes the jump target",
+                    "n / p jump to next or previous hit for that target",
                     "hit< / hit> buttons do the same",
+                    "[ / ] also changes the jump target",
                     "mouse wheel over details scrolls",
                     "PageUp/PageDown also scroll details",
                     "overlay buttons toggle detector layers",

extractors/__init__.py

@@ -18,7 +18,7 @@
 
 DEFAULT_TEMPLATES_PATH = pathlib.Path(__file__).resolve().parent.parent / "templates" / "templates.json"
 
-VALID_CAPTION_TYPES = ("statistical", "structural", "semantic")
+VALID_CAPTION_TYPES = ("statistical", "structural", "semantic", "cross_channel")
 
 
 _ACTIVITY_RE = re.compile(r"HKWorkoutActivityType(.+)$")

extractors/cross_channel.py

@@ -0,0 +1,25 @@
+#
+# SPDX-FileCopyrightText: 2026 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+# SPDX-FileCopyrightText: 2026 This source file is part of the SensorTSLM open-source project.
+#
+# SPDX-License-Identifier: MIT
+#
+from __future__ import annotations
+
+from extractors import CaptionExtractor, ChannelConfig
+from synthesizers import CrossChannelSynthesizer
+from timef.schema import Annotation, Recording
+
+
+class CrossChannelExtractor(CaptionExtractor):
+    caption_type = "cross_channel"
+
+    def __init__(self, config: ChannelConfig, synthesizers: list[CrossChannelSynthesizer]):
+        super().__init__(config)
+        self.synthesizers = synthesizers
+
+    def extract(self, row: Recording) -> list[Annotation]:
+        results: list[Annotation] = []
+        for synth in self.synthesizers:
+            results.extend(synth.synthesize(row, self.config))
+        return results

synthesizers/__init__.py

@@ -0,0 +1,31 @@
+#
+# SPDX-FileCopyrightText: 2026 Stanford University, ETH Zurich, and the project authors (see CONTRIBUTORS.md)
+# SPDX-FileCopyrightText: 2026 This source file is part of the SensorTSLM open-source project.
+#
+# SPDX-License-Identifier: MIT
+#
+from __future__ import annotations
+
+import abc
+
+import numpy as np
+
+from extractors import ChannelConfig
+from timef.schema import Annotation, Recording
+
+
+class CrossChannelSynthesizer(abc.ABC):
+    @abc.abstractmethod
+    def synthesize(self, row: Recording, config: ChannelConfig) -> list[Annotation]: ...
+
+
+def contiguous_windows(mask: np.ndarray, min_duration: int) -> list[tuple[int, int]]:
+    if not mask.any():
+        return []
+
+    padded = np.concatenate(([False], mask, [False]))
+    diffs = np.diff(padded.astype(np.int8))
+    starts = np.where(diffs == 1)[0]
+    ends = np.where(diffs == -1)[0]
+    keep = (ends - starts) >= min_duration
+    return list(zip(starts[keep].tolist(), ends[keep].tolist()))