move to curve data structs, and remove curve_type

Author: CamDavidsonPilon

CHANGELOG.md

@@ -23,6 +23,7 @@
  - You can now restart the web server (lighttpd), and the background task queue, Huey, from the UI. Go to Leader -> "Long-running jobs", and see the "web server and queue" line.
  - Added spline curve support for calibrations, including OD standards sessions and calibration charts.
  - `pio calibrations analyze` now supports `--fit poly|spline` (default poly). You can use this to re-fit a dataset to a spline curve.
+ - Added an update helper to migrate calibration curve data into the new tagged format (`poly`/`spline`).
 
 #### Breaking changes
  - Moved Self-test to the Inventory page. Pioreactors no longer need to be assigned to an experiment to run self-test.
@@ -34,6 +35,8 @@
  - Self-test no longer creates a stirring calibration.
  - OD Reading charts in the UI previously had a sensor label next to the unit, ex: `worker01-2`. Now it is the corresponding angle from config.ini. Note: only the global config.ini is used, not specific unit_config.inis.
  - New OD and stirring calibrations are now fit with a spline, and not a polynomial.
+ - Calibration curve data is now serialized as tagged structs (`poly`/`spline`) instead of raw lists. `curve_type` is removed in fao existing calibration files are migrated during the update.
+
 
 #### Bug fixes
 

core/pioreactor/actions/pump.py

@@ -39,8 +39,9 @@ def get_default_calibration() -> structs.SimplePeristalticPumpCalibration:
         hz=250.0,
         dc=100.00,
         voltage=-1,
-        curve_type="poly",
-        curve_data_=[0.0911, 0.0] if not is_testing_env() else [5.0, 0],  # go fast if in testing
+        curve_data_=structs.PolyFitCoefficients(
+            coefficients=[0.0911, 0.0] if not is_testing_env() else [5.0, 0]
+        ),  # go fast if in testing
         recorded_data={"x": [], "y": []},
     )
 

core/pioreactor/background_jobs/od_reading.py

@@ -793,7 +793,7 @@ def hydate_models(self, calibration_data: structs.ODCalibration | None) -> None:
         self.models[channel], self.verifiers[channel] = self._hydrate_model(calibration_data)
         self.models[channel].calibration_name = calibration_name  # type: ignore
         self.logger.debug(
-            f"Using OD calibration `{calibration_name}` of type `{cal_type}` for PD channel {channel}, {calibration_data.curve_type=}, {calibration_data.curve_data_=}"
+            f"Using OD calibration `{calibration_name}` of type `{cal_type}` for PD channel {channel}, {calibration_data.curve_data_=}"
         )
 
     def _hydrate_model(
@@ -805,11 +805,13 @@ def _hydrate_model(
             self.logger.error(f"Calibration {calibration_data.calibration_name} has wrong type.")
             raise exc.CalibrationError(f"Calibration {calibration_data.calibration_name} has wrong type.")
 
-        higher_order_terms = calibration_data.curve_data_[:-1]
-        if len(higher_order_terms) == 0 or all(c == 0.0 for c in higher_order_terms):
-            self.logger.warning(
-                "Calibration curve is y(x)=constant. This is probably wrong. Check the calibration YAML file's curve_data_."
-            )
+        if calibration_data.curve_data_.type == "poly":
+            coefficients = calibration_data.curve_data_.coefficients
+            higher_order_terms = coefficients[:-1]
+            if len(higher_order_terms) == 0 or all(c == 0.0 for c in higher_order_terms):
+                self.logger.warning(
+                    "Calibration curve is y(x)=constant. This is probably wrong. Check the calibration YAML file's curve_data_."
+                )
 
         def _verify(od_reading: structs.ODReading) -> bool:
             """

core/pioreactor/calibrations/__init__.py

@@ -87,7 +87,6 @@ def list_devices() -> list[str]:
 from pioreactor.calibrations.protocols.od_reference_standard import (
     ODReferenceStandardProtocol,
 )  # noqa: F401,E402
-from pioreactor.calibrations.protocols.od_single_vial import SingleVialODProtocol  # noqa: F401,E402
 from pioreactor.calibrations.protocols.od_standards import StandardsODProtocol  # noqa: F401,E402
 from pioreactor.calibrations.protocols.pump_duration_based import DurationBasedPumpProtocol  # noqa: F401,E402
 from pioreactor.calibrations.protocols.stirring_dc_based import DCBasedStirringProtocol  # noqa: F401,E402

core/pioreactor/calibrations/protocols/od_reference_standard.py

@@ -195,7 +195,6 @@ def advance(self, ctx: SessionContext) -> SessionStep | None:
                     calibration_name=f"od{angle}-optics-calibration-jig-{timestamp}",
                     angle=angle,
                     curve_data_=curve_data_,
-                    curve_type="poly",
                     recorded_data={"x": recorded_ods, "y": recorded_voltages},
                     ir_led_intensity=ir_led_intensity,
                     pd_channel=pd_channel,
@@ -219,7 +218,6 @@ def advance(self, ctx: SessionContext) -> SessionStep | None:
                     calibration_name=f"od{angle}-optical-reference-standard-{timestamp}",
                     angle=angle,
                     curve_data_=curve_data_,
-                    curve_type="poly",
                     recorded_data={"x": recorded_ods, "y": recorded_voltages},
                     ir_led_intensity=ir_led_intensity,
                     pd_channel=pd_channel,