move this downstream

Author: CamDavidsonPilon

CHANGELOG.md

@@ -5,9 +5,9 @@
    - An `Event Logs` page for seeing the logs generated by your Pioreactors
    - A detailed overview of your cluster's leader-specific duties on the new `Leader`'s page.
      - See the Leader's filesystem, logs, update cluster clocks, and view important running jobs.
-  - View different Pioreactors' plugins on the `Plugins` page, and install to specific Pioreactor vs entire cluster.
-  - Manage your calibrations from the UI's new `Calibrations` page.
-    - View existing calibrations, set active calibrations, and download calibration files.
+   - View different Pioreactors' plugins on the `Plugins` page, and install to specific Pioreactor vs entire cluster.
+   - Manage your calibrations from the UI's new `Calibrations` page.
+     - View existing calibrations, set active calibrations, and download calibration files.
  - New calibrations API. A calibration now creates a YAML file as an artifact, stored in `~/.pioreactor/calibrations`. This makes editing, creating, sharing, and transferring calibrations much easier.
   - There's also a new CLI for calibrations:
     ```
@@ -24,6 +24,7 @@
       list        List existing calibrations for the given device.
       run         Run an interactive calibration assistant for a specific device.
       set-active  Mark a specific calibration as 'active' for that device
+      analyze     Analyze the data from a calibration.
     ```
 
     For example, to run a pump calibration, use `pio calibrations run --device media_pump`. View all your media pump calibrations with:  `pio calibrations list --device media_pump`. And to duplicate a
@@ -70,6 +71,7 @@
 ### Enhancements
  - new SQL table for `historical_experiment_assignments` that stores historical assignments to experiments.
  - UI performance improvements
+ - Better terminal plots
 
 ### Breaking changes
  - `use_calibration` under `od_reading.config` is deprecated. Use the calibrations "active" state instead.
@@ -97,9 +99,9 @@
   - removed `pioreactor.utils.gpio_helpers`
 
 ### Bug fixes
- - fix PWM3 not cleaning up correctly
- - fixed Stirring not updating to best DC % when using a calibration after changing target RPM
-
+ - Fix PWM3 not cleaning up correctly
+ - Fixed Stirring not updating to best DC % when using a calibration after changing target RPM
+ - Fixed a bug that could cause OD calibrations to map a small voltage value to a max OD.
 
 ### 24.12.10
  - Hotfix for UI settings bug

pioreactor/background_jobs/od_reading.py

@@ -660,7 +660,7 @@ def hydate_models(self, calibration_data: structs.ODCalibration | None) -> None:
             f"Using OD calibration `{name}` for channel {channel}, {calibration_data.curve_type=}, {calibration_data.curve_data_=}"
         )
 
-    def _hydrate_model(self, calibration_data: structs.ODCalibration) -> Callable[[float], float]:
+    def _hydrate_model(self, calibration_data: structs.ODCalibration) -> Callable[[pt.Voltage], pt.OD]:
         if calibration_data.curve_type == "poly":
             """
             Finds the smallest root in the range [minOD, maxOD] calibrated against.

pioreactor/calibrations/utils.py

@@ -31,7 +31,7 @@ def calculate_poly_curve_of_best_fit(x: list[float], y: list[float], degree: int
     weights = np.ones_like(x)
     weights[0] = n / 2
 
-    x, y = zip(*sorted(zip(x, y), key=lambda t: t[0]))
+    x, y = zip(*sorted(zip(x, y), key=lambda t: t[0]))  # type: ignore
 
     try:
         coefs = np.polyfit(x, y, deg=degree, w=weights)
@@ -65,6 +65,17 @@ def curve_callable(x):
         raise NotImplementedError()
 
 
+def linspace(start: float, stop: float, num: int = 50):
+    num = int(num)
+    start = start * 1.0
+    stop = stop * 1.0
+
+    step = (stop - start) / (num - 1)
+
+    for i in range(num):
+        yield start + step * i
+
+
 def plot_data(
     x: list[float],
     y: list[float],
@@ -81,7 +92,10 @@ def plot_data(
     plt.clf()
 
     if interpolation_curve:
-        plt.plot(sorted(x), [interpolation_curve(x_) for x_ in sorted(x)], color=204)
+        x_min, x_max = min(x) - 0.1, max(x) + 0.1
+        xs = list(linspace(x_min, x_max, num=100))
+        ys = [interpolation_curve(x_) for x_ in xs]
+        plt.plot(xs, ys, color=204)
         plt.plot_size(145, 26)
 
     plt.scatter(x, y, marker="hd")

pioreactor/structs.py

@@ -205,7 +205,6 @@ def ipredict(self, y: Y, enforce_bounds=False) -> X:
         from pioreactor.utils.math_helpers import closest_point_to_domain
 
         poly = self.curve_data_
-        min_X, max_X = min(self.recorded_data["x"]), max(self.recorded_data["x"])
 
         coef_shift = zeros_like(poly)
         coef_shift[-1] = y
@@ -221,6 +220,7 @@ def ipredict(self, y: Y, enforce_bounds=False) -> X:
             if not enforce_bounds:
                 return sol
 
+            min_X, max_X = min(self.recorded_data["x"]), max(self.recorded_data["x"])
             # if we are here, we let the downstream user decide how to proceed
             if min_X <= sol <= max_X:
                 return sol

pioreactor/tests/test_od_calibration.py

@@ -29,6 +29,7 @@ def test_linear_data_produces_linear_curve_in_range_even_if_high_degree() -> Non
 
 
 def test_mandys_data_for_pathological_poly() -> None:
+    # https://forum.pioreactor.com/t/very-low-od-readings-map-to-max/630/5
     od = [0.0, 0.139, 0.155, 0.378, 0.671, 0.993, 1.82, 4.061]
     v = [0.0, 0.0158, 0.0322, 0.0589, 0.1002, 0.1648, 0.4045, 0.5463]