turbidostat now dynamically chooses the biomass signal; some UI updates

Author: CamDavidsonPilon

core/pioreactor/automations/dosing/turbidostat.py

@@ -6,10 +6,11 @@
 from pioreactor.automations import events
 from pioreactor.automations.dosing.base import DosingAutomationJob
 from pioreactor.background_jobs.od_reading import REF_keyword
+from pioreactor.calibrations import load_active_calibration
 from pioreactor.config import config
+from pioreactor.estimators import load_active_estimator
 from pioreactor.exc import CalibrationError
 from pioreactor.utils import local_persistent_storage
-from pioreactor.utils.streaming_calculations import ExponentialMovingAverage
 
 
 class Turbidostat(DosingAutomationJob):
@@ -23,6 +24,7 @@ class Turbidostat(DosingAutomationJob):
         "exchange_volume_ml": {"datatype": "float", "settable": True, "unit": "mL"},
         "target_biomass": {"datatype": "float", "settable": True},
         "biomass_signal": {"datatype": "string", "settable": True},
+        "resolved_biomass_signal": {"datatype": "string", "settable": False},
         "duration": {"datatype": "float", "settable": False, "unit": "min"},
     }
     target_biomass = None
@@ -32,7 +34,7 @@ def __init__(
         self,
         exchange_volume_ml: float | str,
         target_biomass: Optional[float | str] = None,
-        biomass_signal: str = "normalized_od",
+        biomass_signal: str = "auto",
         **kwargs,
     ) -> None:
         super().__init__(**kwargs)
@@ -50,9 +52,6 @@ def __init__(
         self.target_biomass = float(target_biomass)
 
         self.exchange_volume_ml = float(exchange_volume_ml)
-        self.ema_od = ExponentialMovingAverage(
-            config.getfloat("turbidostat.config", "od_smoothing_ema", fallback=0.5)
-        )
 
     def set_duration(self, value: float | None):
         # force duration to always be 0.25 - we want to check often.
@@ -85,14 +84,41 @@ def _resolve_od_channel(self) -> pt.PdChannel:
 
         raise ValueError("No OD signal channels found in [od_config.photodiode_channel].")
 
+    @property
+    def _od_angle(self) -> pt.PdAngle:
+        angle = config["od_config.photodiode_channel"][self._od_channel]
+        if angle in (None, "", REF_keyword):
+            raise ValueError(f"No OD signal angle configured for channel {self._od_channel}.")
+        return cast(pt.PdAngle, str(angle))
+
+    def _has_active_od_fused_estimator(self) -> bool:
+        try:
+            return load_active_estimator(pt.OD_FUSED_DEVICE) is not None
+        except Exception as e:
+            self.logger.warning(
+                "Unable to load active od_fused estimator for auto biomass signal selection: %s",
+                e,
+            )
+            return False
+
+    def _has_active_od_calibration_for_resolved_angle(self) -> bool:
+        od_device = cast(pt.ODCalibrationDevices, f"od{self._od_angle}")
+        try:
+            return load_active_calibration(od_device) is not None
+        except Exception as e:
+            self.logger.warning(
+                "Unable to load active OD calibration for device %s for auto biomass signal selection: %s",
+                od_device,
+                e,
+            )
+            return False
+
     def execute(self) -> Optional[events.DilutionEvent]:
         assert self.target_biomass is not None
-        latest_biomass = self.latest_biomass_value(self.biomass_signal, od_channel=self._od_channel)
-        if self.biomass_signal in {"od", "od_fused"}:
-            latest_biomass = self.ema_od.update(latest_biomass)
+        resolved_biomass_signal = self.resolved_biomass_signal
+        latest_biomass = self.latest_biomass_value(resolved_biomass_signal, od_channel=self._od_channel)
 
         if latest_biomass >= self.target_biomass:
-            self.ema_od.clear()  # clear the ema so that we don't cause a second dosing to occur right after.
             latest_biomass_before_dosing = latest_biomass
             target_biomass_before_dosing = self.target_biomass
 
@@ -103,13 +129,13 @@ def execute(self) -> Optional[events.DilutionEvent]:
             data = {
                 "latest_biomass": latest_biomass_before_dosing,
                 "target_biomass": target_biomass_before_dosing,
-                "biomass_signal": self.biomass_signal,
+                "resolved_biomass_signal": resolved_biomass_signal,
                 "exchange_volume_ml": self.exchange_volume_ml,
                 "volume_actually_moved_ml": results["media_ml"],
             }
 
             return events.DilutionEvent(
-                f"Latest biomass ({self.biomass_signal}) = {latest_biomass_before_dosing:.2f} ≥ Target biomass = {target_biomass_before_dosing:.2f}; cycled {results['media_ml']:.2f} mL",
+                f"Latest biomass ({resolved_biomass_signal}) = {latest_biomass_before_dosing:.2f} ≥ Target biomass = {target_biomass_before_dosing:.2f}; cycled {results['media_ml']:.2f} mL",
                 data,
             )
         else:
@@ -118,11 +144,24 @@ def execute(self) -> Optional[events.DilutionEvent]:
     def set_target_biomass(self, new_target: float) -> None:
         self.target_biomass = float(new_target)
 
+    @property
+    def resolved_biomass_signal(self) -> str:
+        if self.biomass_signal != "auto":
+            return str(self.biomass_signal)
+
+        if self._has_active_od_fused_estimator():
+            return "od_fused"
+
+        if self._has_active_od_calibration_for_resolved_angle():
+            return "od"
+
+        return "normalized_od"
+
     def set_biomass_signal(self, new_signal: str) -> None:
         self._set_biomass_signal(new_signal)
 
     def _set_biomass_signal(self, biomass_signal: str) -> None:
-        allowed = ("normalized_od", "od_fused", "od")
+        allowed = ("auto", "normalized_od", "od_fused", "od")
         if biomass_signal not in allowed:
             raise ValueError(
                 f"Unsupported biomass_signal={biomass_signal}. Use one of: {', '.join(allowed)}."

core/pioreactor/web/app.py

@@ -47,7 +47,8 @@
 
 try:
     load_plugins()
-except Exception as e:
+except BaseException as e:
+    # BaseExpection since some plugins might use SystemExit, which isn't an Exception.
     logger.debug(f"Web-server encountered error {e} when loading plugins.")
 
 

core/pioreactor/web/static/asset-manifest.json

@@ -1,7 +1,7 @@
 {
   "files": {
     "main.css": "/static/static/css/main.9c7a48b7.css",
-    "main.js": "/static/static/js/main.e4e759f0.js",
+    "main.js": "/static/static/js/main.b47da0a4.js",
     "static/media/roboto-all-500-normal.woff": "/static/static/media/roboto-all-500-normal.0ab669b7a0d19b178f57.woff",
     "static/media/roboto-all-700-normal.woff": "/static/static/media/roboto-all-700-normal.a457fde362a540fcadff.woff",
     "static/media/roboto-all-400-normal.woff": "/static/static/media/roboto-all-400-normal.c5d001fa922fa66a147f.woff",
@@ -28,10 +28,10 @@
     "static/media/roboto-greek-ext-700-normal.woff2": "/static/static/media/roboto-greek-ext-700-normal.bd9854c751441ccc1a70.woff2",
     "index.html": "/static/index.html",
     "main.9c7a48b7.css.map": "/static/static/css/main.9c7a48b7.css.map",
-    "main.e4e759f0.js.map": "/static/static/js/main.e4e759f0.js.map"
+    "main.b47da0a4.js.map": "/static/static/js/main.b47da0a4.js.map"
   },
   "entrypoints": [
     "static/css/main.9c7a48b7.css",
-    "static/js/main.e4e759f0.js"
+    "static/js/main.b47da0a4.js"
   ]
 }

core/pioreactor/web/static/index.html

@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.e4e759f0.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Pioreactor"/><link rel="apple-touch-icon" href="/static/logo192.png"/><link rel="manifest" href="/static/manifest.json"/><script defer="defer" src="/static/static/js/main.b47da0a4.js"></script><link href="/static/static/css/main.9c7a48b7.css" rel="stylesheet"></head><body><div id="root"></div></body></html>

…or/web/static/static/js/main.e4e759f0.js …or/web/static/static/js/main.b47da0a4.jscore/pioreactor/web/static/static/js/main.e4e759f0.js renamed to core/pioreactor/web/static/static/js/main.b47da0a4.js core/pioreactor/web/static/static/js/main.e4e759f0.js renamed to core/pioreactor/web/static/static/js/main.b47da0a4.js

@@ -177,9 +177,10 @@ def test_silent_automation() -> None:
 @pytest.mark.slow
 def test_turbidostat_automation() -> None:
     experiment = "test_turbidostat_automation"
-    target_od = 1.0
+    target_biomass = 1.0
     with Turbidostat(
-        target_normalized_od=target_od,
+        target_biomass=target_biomass,
+        biomass_signal="normalized_od",
         duration=60,
         exchange_volume_ml=0.25,
         unit=unit,
@@ -298,13 +299,13 @@ def test_turbidostat_automation() -> None:
         assert algo.run() is None
 
 
-def test_cant_target_both_in_turbidostat() -> None:
-    experiment = "test_cant_target_both_in_turbidostat"
+def test_rejects_invalid_biomass_signal_in_turbidostat() -> None:
+    experiment = "test_rejects_invalid_biomass_signal_in_turbidostat"
 
     with pytest.raises(ValueError):
         with Turbidostat(
-            target_od=0.5,
-            target_normalized_od=2.0,
+            target_biomass=0.5,
+            biomass_signal="garbage",
             duration=60,
             exchange_volume_ml=0.25,
             unit=unit,
@@ -314,42 +315,108 @@ def test_cant_target_both_in_turbidostat() -> None:
             pass
 
 
+def test_turbidostat_auto_prefers_active_od_fused_estimator(monkeypatch) -> None:
+    experiment = "test_turbidostat_auto_prefers_active_od_fused_estimator"
+
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_estimator",
+        lambda device: object(),
+    )
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_calibration",
+        lambda device: object(),
+    )
+
+    with Turbidostat(
+        target_biomass=0.5,
+        duration=60,
+        exchange_volume_ml=0.25,
+        unit=unit,
+        experiment=experiment,
+        skip_first_run=True,
+    ) as algo:
+        assert algo.resolved_biomass_signal == "od_fused"
+
+
+def test_turbidostat_auto_uses_active_od_calibration_without_estimator(monkeypatch) -> None:
+    experiment = "test_turbidostat_auto_uses_active_od_calibration_without_estimator"
+
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_estimator",
+        lambda device: None,
+    )
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_calibration",
+        lambda device: object(),
+    )
+
+    with Turbidostat(
+        target_biomass=0.5,
+        duration=60,
+        exchange_volume_ml=0.25,
+        unit=unit,
+        experiment=experiment,
+        skip_first_run=True,
+    ) as algo:
+        assert algo.resolved_biomass_signal == "od"
+
+
+def test_turbidostat_auto_falls_back_to_normalized_od_without_active_models(monkeypatch) -> None:
+    experiment = "test_turbidostat_auto_falls_back_to_normalized_od_without_active_models"
+
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_estimator",
+        lambda device: None,
+    )
+    monkeypatch.setattr(
+        "pioreactor.automations.dosing.turbidostat.load_active_calibration",
+        lambda device: None,
+    )
+
+    with Turbidostat(
+        target_biomass=0.5,
+        duration=60,
+        exchange_volume_ml=0.25,
+        unit=unit,
+        experiment=experiment,
+        skip_first_run=True,
+    ) as algo:
+        assert algo.resolved_biomass_signal == "normalized_od"
+
+
 def test_cant_change_target_in_turbidostat() -> None:
     experiment = "test_cant_change_target_in_turbidostat"
 
     with Turbidostat(
-        target_od=0.5,
+        target_biomass=0.5,
         duration=60,
         exchange_volume_ml=0.25,
         unit=unit,
         experiment=experiment,
         skip_first_run=True,
     ) as algo:
-        assert not algo.is_targeting_nOD
-        assert algo.target_od == 0.5
-        assert algo.target_normalized_od is None
+        assert algo.target_biomass == 0.5
 
-        algo.set_target_normalized_od(2.0)
+        algo.set_target_biomass(2.0)
 
-        assert not algo.is_targeting_nOD
-        assert algo.target_od == 0.5
-        assert algo.target_normalized_od is None
+        assert algo.target_biomass == 2.0
 
 
 @pytest.mark.slow
 def test_turbidostat_targeting_od() -> None:
     experiment = "test_turbidostat_targeting_od"
 
-    target_od = 0.2
+    target_biomass = 0.2
     with Turbidostat(
-        target_od=target_od,
+        target_biomass=target_biomass,
+        biomass_signal="od",
         duration=60,
         exchange_volume_ml=0.25,
         unit=unit,
         experiment=experiment,
         skip_first_run=True,
     ) as algo:
-        assert algo.target_od == target_od
+        assert algo.target_biomass == target_biomass
         pubsub.publish(
             f"pioreactor/{unit}/{experiment}/od_reading/ods",
             encode(
@@ -512,10 +579,11 @@ def test_changing_morbidostat_parameters_over_mqtt() -> None:
 def test_changing_turbidostat_params_over_mqtt() -> None:
     experiment = "test_changing_turbidostat_params_over_mqtt"
     og_volume = 0.5
-    og_target_od = 1.0
+    og_target_biomass = 1.0
     algo = Turbidostat(
         exchange_volume_ml=og_volume,
-        target_normalized_od=og_target_od,
+        target_biomass=og_target_biomass,
+        biomass_signal="normalized_od",
         duration=60,
         unit=unit,
         experiment=experiment,
@@ -549,10 +617,13 @@ def test_changing_turbidostat_params_over_mqtt() -> None:
 
     assert algo.exchange_volume_ml == 1.0
 
-    new_od = 1.5
-    pubsub.publish(f"pioreactor/{unit}/{experiment}/dosing_automation/target_normalized_od/set", new_od)
+    new_target_biomass = 1.5
+    pubsub.publish(
+        f"pioreactor/{unit}/{experiment}/dosing_automation/target_biomass/set",
+        new_target_biomass,
+    )
     pause()
-    assert algo.target_normalized_od == new_od
+    assert algo.target_biomass == new_target_biomass
     algo.clean_up()
 
 
@@ -672,7 +743,7 @@ def test_throughput_calculator_restart() -> None:
     with Turbidostat(
         unit=unit,
         experiment=experiment,
-        target_normalized_od=1.0,
+        target_biomass=1.0,
         duration=5 / 60,
         exchange_volume_ml=1.0,
     ) as automation_job:
@@ -693,7 +764,7 @@ def test_throughput_calculator_manual_set() -> None:
     with Turbidostat(
         unit=unit,
         experiment=experiment,
-        target_normalized_od=1.0,
+        target_biomass=1.0,
         duration=5 / 60,
         exchange_volume_ml=1.0,
     ) as automation_job:
@@ -960,7 +1031,7 @@ def test_disconnect_cleanly(fast_dosing_timers) -> None:
     algo = Turbidostat(
         unit=unit,
         experiment=experiment,
-        target_normalized_od=1.0,
+        target_biomass=1.0,
         duration=50,
         exchange_volume_ml=1.0,
     )
@@ -1027,7 +1098,7 @@ def test_what_happens_when_no_od_data_is_coming_in() -> None:
     )
 
     with Turbidostat(
-        target_normalized_od=0.1, duration=40 / 60, exchange_volume_ml=0.25, unit=unit, experiment=experiment
+        target_biomass=0.1, duration=40 / 60, exchange_volume_ml=0.25, unit=unit, experiment=experiment
     ) as algo:
         pause()
         event = algo.run()

…c/static/js/main.e4e759f0.js.LICENSE.txt …c/static/js/main.b47da0a4.js.LICENSE.txtcore/pioreactor/web/static/static/js/main.e4e759f0.js.LICENSE.txt renamed to core/pioreactor/web/static/static/js/main.b47da0a4.js.LICENSE.txt core/pioreactor/web/static/static/js/main.e4e759f0.js.LICENSE.txt renamed to core/pioreactor/web/static/static/js/main.b47da0a4.js.LICENSE.txt

@@ -251,7 +251,7 @@ def test_complex2() -> None:
             options:
               automation_name: turbidostat
               volume: 1.0
-              target_normalized_od: 5.0
+              target_biomass: 5.0
           - type: stop
             hours_elapsed: 3.0
 """