fix calibibrations near 0

pioreactor/background_jobs/od_reading.py

@@ -1260,3 +1260,4 @@ def click_od_reading(
         calibration=possible_calibration,
     )
     od.block_until_disconnected()
+

pioreactor/calibrations/utils.py

@@ -24,12 +24,14 @@ def bold(string: str) -> str:
 def calculate_poly_curve_of_best_fit(x: list[float], y: list[float], degree: int) -> list[float]:
     import numpy as np
 
-    # weigh the last point, the "blank measurement", more.
+    # weigh the smallest point, the "blank measurement", more.
     # 1. It's far away from the other points
     # 2. We have prior knowledge that OD~0 when V~0.
     n = len(x)
     weights = np.ones_like(x)
-    weights[-1] = n / 2
+    weights[0] = n / 2
+
+    x, y = zip(*sorted(zip(x, y), key=lambda t: t[0]))
 
     try:
         coefs = np.polyfit(x, y, deg=degree, w=weights)

pioreactor/structs.py

@@ -210,7 +210,7 @@ def ipredict(self, y: Y, enforce_bounds=False) -> X:
         coef_shift = zeros_like(poly)
         coef_shift[-1] = y
         solve_for_poly = poly - coef_shift
-        roots_ = roots(solve_for_poly)
+        roots_ = roots(solve_for_poly).tolist()
         plausible_sols_: list[X] = sorted([real(r) for r in roots_ if (abs(imag(r)) < 1e-10)])
 
         if len(plausible_sols_) == 0:

pioreactor/tests/test_od_calibration.py

@@ -6,6 +6,8 @@
 
 from pioreactor.calibrations.utils import calculate_poly_curve_of_best_fit
 from pioreactor.calibrations.utils import curve_to_callable
+from pioreactor.structs import ODCalibration
+from pioreactor.utils.timing import current_utc_datetime
 
 
 def test_linear_data_produces_linear_curve_in_range_even_if_high_degree() -> None:
@@ -24,3 +26,32 @@ def test_linear_data_produces_linear_curve_in_range_even_if_high_degree() -> Non
     curve_callable = curve_to_callable("poly", curve_data_)
     for od_, v_ in zip(od, curve_callable(od)):
         assert (v_ - od_ * 0.5) < 0.035
+
+
+def test_mandys_data_for_pathological_poly() -> None:
+
+    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]
+
+    curve_data_ = calculate_poly_curve_of_best_fit(od, v, degree=3)  # type: ignore
+    curve_callable = curve_to_callable("poly", curve_data_)
+    assert abs(curve_callable(0.002) - 0.002) < 0.1
+
+    mcal = ODCalibration(
+            calibration_name='mandy',
+            calibrated_on_pioreactor_unit='pio1',
+            created_at=current_utc_datetime(),
+            curve_data_=curve_data_,
+            curve_type='poly',
+            recorded_data={'x': od, 'y': v},
+            ir_led_intensity=70.0,
+            angle='90',
+            pd_channel='2')
+
+    assert abs(mcal.predict(0.002) - curve_callable(0.002)) < 1e-10
+    assert abs(mcal.ipredict(0.002) - 0.002) < 0.1
+
+
+
+
+

pioreactor/tests/test_od_reading.py

@@ -1120,3 +1120,9 @@ def test_missing_calibration_data():
     cal_transformer = CachedCalibrationTransformer()
     cal_transformer.models = {"1": lambda v: v * 2}
     assert cal_transformer({"1": 1.0, "2": 2.0}) == {"1": 2.0, "2": 2.0}
+
+
+def test_mandys_calibration():
+    from pioreactor.calibrations import load_calibration
+    mcal = structs.ODCalibration(calibration_name='mandy', calibrated_on_pioreactor_unit='pio1', created_at=current_utc_datetime(), curve_data_=[-0.03112259838616315, 0.14606367297714123, 0.05224678328234911, 0.009665339167023364], curve_type='poly', x='voltage', y='od600s', recorded_data={'x': [0.0, 0.139, 0.155, 0.378, 0.671, 0.993, 1.82, 4.061], 'y': [0.0, 0.0158, 0.0322, 0.0589, 0.1002, 0.1648, 0.4045, 0.5463]}, ir_led_intensity=70.0, angle='90', pd_channel='2')
+    assert 0.0 < mcal.ipredict(0.002, enforce_bounds=True) < 1.0