waveorder 2.2.1__py3-none-any.whl → 3.0.0__py3-none-any.whl

waveorder/calib/Calibration.py

@@ -0,0 +1,1512 @@
+import json
+import logging
+import os
+import time
+import warnings
+from datetime import datetime
+
+import matplotlib.pyplot as plt
+import numpy as np
+from importlib_metadata import version
+from iohub import open_ome_zarr
+from iohub.ngff.models import TransformationMeta
+from mpl_toolkits.axes_grid1.axes_divider import make_axes_locatable
+from napari.utils.notifications import show_warning
+from scipy.interpolate import interp1d
+from scipy.optimize import least_squares
+from scipy.stats import linregress
+
+from waveorder.calib.Optimization import BrentOptimizer, MinScalarOptimizer
+from waveorder.io.core_functions import *
+from waveorder.io.utils import MockEmitter
+
+LC_DEVICE_NAME = "MeadowlarkLC"
+
+
+class QLIPP_Calibration:
+    def __init__(
+        self,
+        mmc,
+        mm,
+        group="Channel",
+        lc_control_mode="MM-Retardance",
+        interp_method="schnoor_fit",
+        wavelength=532,
+        optimization="min_scalar",
+        print_details=True,
+    ):
+        """
+
+        Parameters
+        ----------
+        mmc : object
+            Micro-Manager core instance
+        mm : object
+            Micro-Manager Studio instance
+        group : str
+            Name of the Micro-Manager channel group used defining LC states [State0, State1, State2, ...]
+        lc_control_mode : str
+            Defined the control mode of the liquid crystals. One of the following:
+            * MM-Retardance: The retardance of the LC is set directly through the Micro-Manager LC device adapter. The
+            Micro-Manager device adapter determines the corresponding voltage which is sent to the LC.
+            * MM-Voltage: The CalibrationData class in waveorder uses the LC calibration data to determine the correct
+            LC voltage for a given retardance. The LC voltage is set through the Micro-Manager LC device adapter.
+            * DAC: The CalibrationData class in waveorder uses the LC calibration data to determine the correct
+            LC voltage for a given retardance. The voltage is applied to the IO port of the LC controller through the
+            TriggerScope DAC outputs.
+        interp_method : str
+            Method of interpolating the LC retardance-to-voltage calibration curve. One of the following:
+            * linear: linear interpolation of retardance as a function of voltage and wavelength
+            * schnoor_fit: Schnoor fit interpolation as described in https://doi.org/10.1364/AO.408383
+        wavelength : float
+            Measurement wavelength
+        optimization : str
+            LC retardance optimization method, 'min_scalar' (default) or 'brent'
+        print_details : bool
+            Set verbose option
+        """
+
+        # Micro-Manager API
+        self.mm = mm
+        self.mmc = mmc
+        self.snap_manager = mm.getSnapLiveManager()
+
+        # Meadowlark LC Device Adapter Property Names
+        self.PROPERTIES = {
+            "LCA": (LC_DEVICE_NAME, "Retardance LC-A [in waves]"),
+            "LCB": (LC_DEVICE_NAME, "Retardance LC-B [in waves]"),
+            "LCA-Voltage": (LC_DEVICE_NAME, "Voltage (V) LC-A"),
+            "LCB-Voltage": (LC_DEVICE_NAME, "Voltage (V) LC-B"),
+            "LCA-DAC": ("TS_DAC01", "Volts"),
+            "LCB-DAC": ("TS_DAC02", "Volts"),
+            "State0": (
+                LC_DEVICE_NAME,
+                "Pal. elem. 00; enter 0 to define; 1 to activate",
+            ),
+            "State1": (
+                LC_DEVICE_NAME,
+                "Pal. elem. 01; enter 0 to define; 1 to activate",
+            ),
+            "State2": (
+                LC_DEVICE_NAME,
+                "Pal. elem. 02; enter 0 to define; 1 to activate",
+            ),
+            "State3": (
+                LC_DEVICE_NAME,
+                "Pal. elem. 03; enter 0 to define; 1 to activate",
+            ),
+            "State4": (
+                LC_DEVICE_NAME,
+                "Pal. elem. 04; enter 0 to define; 1 to activate",
+            ),
+        }
+        self.group = group
+
+        # GUI Emitter
+        self.intensity_emitter = MockEmitter()
+        self.plot_sequence_emitter = MockEmitter()
+
+        # Set Mode
+        # TODO: make sure LC or TriggerScope are loaded in the respective modes
+        allowed_modes = ["MM-Retardance", "MM-Voltage", "DAC"]
+        if lc_control_mode not in allowed_modes:
+            raise ValueError(f"LC control mode must be one of {allowed_modes}")
+        self.mode = lc_control_mode
+        self.LC_DAC_conversion = 4  # convert between the input range of LCs (0-20V) and the output range of the DAC (0-5V)
+
+        # Initialize calibration class
+        allowed_interp_methods = ["schnoor_fit", "linear"]
+        if interp_method not in allowed_interp_methods:
+            raise ValueError(
+                "LC calibration data interpolation method must be one of "
+                f"{allowed_interp_methods}"
+            )
+        dir_path = mmc.getDeviceAdapterSearchPaths().get(
+            0
+        )  # MM device adapter directory
+        self.calib = CalibrationData(
+            os.path.join(dir_path, "mmgr_dal_MeadowlarkLC.csv"),
+            interp_method=interp_method,
+            wavelength=wavelength,
+        )
+
+        # Optimizer
+        if optimization == "min_scalar":
+            self.optimizer = MinScalarOptimizer(self)
+        elif optimization == "brent":
+            self.optimizer = BrentOptimizer(self)
+        else:
+            raise ModuleNotFoundError(f"No optimizer named {optimization}")
+
+        # User / Calculated Parameters
+        self.swing = None
+        self.wavelength = None
+        self.lc_bound = None
+        self.I_Black = None
+        self.ratio = 1.793
+        self.print_details = print_details
+        self.calib_scheme = "4-State"
+
+        # LC States
+        self.lca_ext = None
+        self.lcb_ext = None
+        self.lca_0 = None
+        self.lcb_0 = None
+        self.lca_45 = None
+        self.lcb_45 = None
+        self.lca_60 = None
+        self.lcb_60 = None
+        self.lca_90 = None
+        self.lcb_90 = None
+        self.lca_120 = None
+        self.lcb_120 = None
+        self.lca_135 = None
+        self.lcb_135 = None
+
+        # Calibration Outputs
+        self.I_Ext = None
+        self.I_Ref = None
+        self.I_Elliptical = None
+        self.inten = []
+        self.swing0 = None
+        self.swing45 = None
+        self.swing60 = None
+        self.swing90 = None
+        self.swing120 = None
+        self.swing135 = None
+        self.height = None
+        self.width = None
+        self.directory = None
+        self.inst_mat = None
+
+        # Shutter
+        self.shutter_device = self.mmc.getShutterDevice()
+        self._auto_shutter_state = None
+        self._shutter_state = None
+
+    def set_dacs(self, lca_dac, lcb_dac):
+        self.PROPERTIES["LCA-DAC"] = (f"TS_{lca_dac}", "Volts")
+        self.PROPERTIES["LCB-DAC"] = (f"TS_{lcb_dac}", "Volts")
+
+    def set_wavelength(self, wavelength):
+        self.calib.set_wavelength(wavelength)
+        self.wavelength = self.calib.wavelength
+
+    def set_lc(self, retardance, LC: str):
+        """
+        Set LC state to given retardance in waves
+
+        Parameters
+        ----------
+        retardance : float
+            Retardance in waves
+        LC : str
+            LCA or LCB
+
+        Returns
+        -------
+
+        """
+
+        if self.mode == "MM-Retardance":
+            set_lc_waves(self.mmc, self.PROPERTIES[f"{LC}"], retardance)
+        elif self.mode == "MM-Voltage":
+            volts = self.calib.get_voltage(retardance)
+            set_lc_voltage(self.mmc, self.PROPERTIES[f"{LC}-Voltage"], volts)
+        elif self.mode == "DAC":
+            volts = self.calib.get_voltage(retardance)
+            dac_volts = volts / self.LC_DAC_conversion
+            set_lc_daq(self.mmc, self.PROPERTIES[f"{LC}-DAC"], dac_volts)
+
+    def get_lc(self, LC: str):
+        """
+        Get LC retardance in waves
+
+        Parameters
+        ----------
+        LC : str
+            LCA or LCB
+
+        Returns
+        -------
+            LC retardance in waves
+        """
+
+        if self.mode == "MM-Retardance":
+            retardance = get_lc(self.mmc, self.PROPERTIES[f"{LC}"])
+        elif self.mode == "MM-Voltage":
+            volts = get_lc(
+                self.mmc, self.PROPERTIES[f"{LC}-Voltage"]
+            )  # returned value is in volts
+            retardance = self.calib.get_retardance(volts)
+        elif self.mode == "DAC":
+            dac_volts = get_lc(self.mmc, self.PROPERTIES[f"{LC}-DAC"])
+            volts = dac_volts * self.LC_DAC_conversion
+            retardance = self.calib.get_retardance(volts)
+
+        return retardance
+
+    def define_lc_state(self, state, lca_retardance, lcb_retardance):
+        """
+        Define of the two LCs after calibration
+
+        Parameters
+        ----------
+        state: str
+            Polarization stage (e.g. State0)
+        lca_retardance: float
+            LCA retardance in waves
+        lcb_retardance: float
+            LCB retardance in waves
+
+        Returns
+        -------
+
+        """
+
+        if self.mode == "MM-Retardance":
+            self.set_lc(lca_retardance, "LCA")
+            self.set_lc(lcb_retardance, "LCB")
+            define_meadowlark_state(self.mmc, self.PROPERTIES[state])
+        elif self.mode == "DAC":
+            lca_volts = (
+                self.calib.get_voltage(lca_retardance) / self.LC_DAC_conversion
+            )
+            lcb_volts = (
+                self.calib.get_voltage(lcb_retardance) / self.LC_DAC_conversion
+            )
+            define_config_state(
+                self.mmc,
+                self.group,
+                state,
+                [self.PROPERTIES["LCA-DAC"], self.PROPERTIES["LCB-DAC"]],
+                [lca_volts, lcb_volts],
+            )
+        elif self.mode == "MM-Voltage":
+            lca_volts = self.calib.get_voltage(lca_retardance)
+            lcb_volts = self.calib.get_voltage(lcb_retardance)
+            define_config_state(
+                self.mmc,
+                self.group,
+                state,
+                [
+                    self.PROPERTIES["LCA-Voltage"],
+                    self.PROPERTIES["LCB-Voltage"],
+                ],
+                [lca_volts, lcb_volts],
+            )
+
+    def opt_lc(self, x, device_property, reference, normalize=False):
+        if isinstance(x, list) or isinstance(x, tuple):
+            x = x[0]
+
+        self.set_lc(x, device_property)
+
+        mean = snap_and_average(self.snap_manager)
+
+        if normalize:
+            max_ = 65335
+            min_ = self.I_Black
+
+            val = (mean - min_) / (max_ - min_)
+            ref = (reference - min_) / (max_ - min_)
+
+            logging.debug(f"LC-Value: {x}")
+            logging.debug(f"F-Value:{val - ref}\n")
+            return val - ref
+
+        else:
+            logging.debug(str(mean))
+            self.intensity_emitter.emit(mean)
+            self.inten.append(mean - reference)
+
+            return np.abs(mean - reference)
+
+    def opt_lc_cons(self, x, device_property, reference, mode):
+        self.set_lc(x, device_property)
+        swing = (self.lca_ext - x) * self.ratio
+
+        if mode == "60":
+            self.set_lc(self.lcb_ext + swing, "LCB")
+
+        if mode == "120":
+            self.set_lc(self.lcb_ext - swing, "LCB")
+
+        mean = snap_and_average(self.snap_manager)
+        logging.debug(str(mean))
+
+        # append to intensity array for plotting later
+        self.intensity_emitter.emit(mean)
+        self.inten.append(mean - reference)
+
+        return np.abs(mean - reference)
+
+    def opt_lc_grid(self, a_min, a_max, b_min, b_max, step):
+        """
+        Exhaustive Search method
+
+        Finds the minimum intensity value for a given
+        grid of LCA,LCB values
+
+        :param a_min: float
+            Minimum value of LCA
+        :param a_max: float
+            Maximum value of LCA
+        :param b_min: float
+            Minimum value of LCB
+        :param b_max: float
+            Maximum value of LCB
+        :param step: float
+            step size of the grid between max/min values
+
+
+        :return best_lca: float
+            LCA value corresponding to lowest mean Intensity
+        :return best_lcb: float
+            LCB value corresponding to lowest mean Intensity
+        :return min_int: float
+            Lowest value of mean Intensity
+        """
+
+        min_int = 65536
+        better_lca = -1
+        better_lcb = -1
+
+        # coarse search
+        for lca in np.arange(a_min, a_max, step):
+            for lcb in np.arange(b_min, b_max, step):
+                self.set_lc(lca, "LCA")
+                self.set_lc(lcb, "LCB")
+
+                # current_int = np.mean(snap_image(calib.mmc))
+                current_int = snap_and_average(self.snap_manager)
+                self.intensity_emitter.emit(current_int)
+
+                if current_int < min_int:
+                    better_lca = lca
+                    better_lcb = lcb
+                    min_int = current_int
+                    logging.debug(
+                        "update (%f, %f, %f)"
+                        % (min_int, better_lca, better_lcb)
+                    )
+
+        logging.debug("coarse search done")
+        logging.debug("better lca = " + str(better_lca))
+        logging.debug("better lcb = " + str(better_lcb))
+        logging.debug("better int = " + str(min_int))
+
+        best_lca = better_lca
+        best_lcb = better_lcb
+
+        return best_lca, best_lcb, min_int
+
+    # ========== Optimization wrappers =============
+    # ==============================================
+    def opt_Iext(self):
+        self.plot_sequence_emitter.emit("Coarse")
+        logging.info("Calibrating State0 (Extinction)...")
+        logging.debug("Calibrating State0 (Extinction)...")
+
+        set_lc_state(self.mmc, self.group, "State0")
+        time.sleep(2)
+
+        # Perform exhaustive search with step 0.1 over range:
+        # 0.01 < LCA < 0.5
+        # 0.25 < LCB < 0.75
+        step = 0.1
+        logging.debug(f"================================")
+        logging.debug(f"Starting first grid search, step = {step}")
+        logging.debug(f"================================")
+
+        best_lca, best_lcb, i_ext_ = self.opt_lc_grid(
+            0.01, 0.5, 0.25, 0.75, step
+        )
+
+        logging.debug("grid search done")
+        logging.debug("lca = " + str(best_lca))
+        logging.debug("lcb = " + str(best_lcb))
+        logging.debug("intensity = " + str(i_ext_))
+
+        self.set_lc(best_lca, "LCA")
+        self.set_lc(best_lcb, "LCB")
+
+        logging.debug(f"================================")
+        logging.debug(f"Starting fine search")
+        logging.debug(f"================================")
+
+        # Perform brent optimization around results of 2nd grid search
+        # threshold not very necessary here as intensity value will
+        # vary between exposure/lamp intensities
+        self.plot_sequence_emitter.emit("Fine")
+        lca, lcb, I_ext = self.optimizer.optimize(
+            state="ext",
+            lca_bound=0.1,
+            lcb_bound=0.1,
+            reference=self.I_Black,
+            thresh=1,
+            n_iter=5,
+        )
+
+        # Set the Extinction state to values output from optimization
+        self.define_lc_state("State0", lca, lcb)
+
+        self.lca_ext = lca
+        self.lcb_ext = lcb
+        self.I_Ext = I_ext
+
+        logging.debug("fine search done")
+        logging.info(f"LCA State0 (Extinction) = {lca:.3f}")
+        logging.debug(f"LCA State0 (Extinction) = {lca:.5f}")
+        logging.info(f"LCB State0 (Extinction) = {lcb:.3f}")
+        logging.debug(f"LCB State0 (Extinction) = {lcb:.5f}")
+        logging.info(f"Intensity (Extinction) = {I_ext:.0f}")
+        logging.debug(f"Intensity (Extinction) = {I_ext:.3f}")
+
+        logging.debug("--------done--------")
+        logging.info("--------done--------")
+
+    def opt_I0(self):
+        """
+        no optimization performed for this.  Simply apply swing and read intensity
+        This is the same as "Ielliptical".  Used for both schemes.
+        :return: float
+            mean of image
+        """
+
+        logging.info("Calibrating State1 (I0)...")
+        logging.debug("Calibrating State1 (I0)...")
+
+        self.lca_0 = self.lca_ext - self.swing
+        self.lcb_0 = self.lcb_ext
+        self.set_lc(self.lca_0, "LCA")
+        self.set_lc(self.lcb_0, "LCB")
+
+        self.define_lc_state("State1", self.lca_0, self.lcb_0)
+        intensity = snap_and_average(self.snap_manager)
+        self.I_Elliptical = intensity
+        self.swing0 = np.sqrt(
+            (self.lcb_0 - self.lcb_ext) ** 2 + (self.lca_0 - self.lca_ext) ** 2
+        )
+
+        logging.info(f"LCA State1 (I0) = {self.lca_0:.3f}")
+        logging.debug(f"LCA State1 (I0) = {self.lca_0:.5f}")
+        logging.info(f"LCB State1 (I0) = {self.lcb_0:.3f}")
+        logging.debug(f"LCB State1 (I0) = {self.lcb_0:.5f}")
+        logging.info(f"Intensity (I0) = {intensity:.0f}")
+        logging.debug(f"Intensity (I0) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def opt_I45(self, lca_bound, lcb_bound):
+        """
+        optimized relative to Ielliptical (opt_I90)
+        Parameters
+        ----------
+        lca_bound
+        lcb_bound
+        Returns
+        -------
+        lca, lcb value at optimized state
+        intensity value at optimized state
+        """
+        self.inten = []
+        logging.info("Calibrating State2 (I45)...")
+        logging.debug("Calibrating State2 (I45)...")
+
+        self.set_lc(self.lca_ext, "LCA")
+        self.set_lc(self.lcb_ext - self.swing, "LCB")
+
+        self.lca_45, self.lcb_45, intensity = self.optimizer.optimize(
+            "45",
+            lca_bound,
+            lcb_bound,
+            reference=self.I_Elliptical,
+            n_iter=5,
+            thresh=0.01,
+        )
+
+        self.define_lc_state("State2", self.lca_45, self.lcb_45)
+
+        self.swing45 = np.sqrt(
+            (self.lcb_45 - self.lcb_ext) ** 2
+            + (self.lca_45 - self.lca_ext) ** 2
+        )
+
+        logging.info(f"LCA State2 (I45) = {self.lca_45:.3f}")
+        logging.debug(f"LCA State2 (I45) = {self.lca_45:.5f}")
+        logging.info(f"LCB State2 (I45) = {self.lcb_45:.3f}")
+        logging.debug(f"LCB State2 (I45) = {self.lcb_45:.5f}")
+        logging.info(f"Intensity (I45) = {intensity:.0f}")
+        logging.debug(f"Intensity (I45) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def opt_I60(self, lca_bound, lcb_bound):
+        """
+        optimized relative to Ielliptical (opt_I0_4State)
+        Parameters
+        ----------
+        lca_bound
+        lcb_bound
+        Returns
+        -------
+        lca, lcb value at optimized state
+        intensity value at optimized state
+        """
+        self.inten = []
+
+        logging.info("Calibrating State2 (I60)...")
+        logging.debug("Calibrating State2 (I60)...")
+
+        # Calculate Initial Swing for initial guess to optimize around
+        # Based on ratio calculated from ellpiticity/orientation of LC simulation
+        swing_ell = np.sqrt(
+            (self.lca_ext - self.lca_0) ** 2 + (self.lcb_ext - self.lcb_0) ** 2
+        )
+        lca_swing = np.sqrt(swing_ell**2 / (1 + self.ratio**2))
+        lcb_swing = self.ratio * lca_swing
+
+        # Optimization
+        self.set_lc(self.lca_ext + lca_swing, "LCA")
+        self.set_lc(self.lcb_ext + lcb_swing, "LCB")
+
+        self.lca_60, self.lcb_60, intensity = self.optimizer.optimize(
+            "60",
+            lca_bound,
+            lcb_bound,
+            reference=self.I_Elliptical,
+            n_iter=5,
+            thresh=0.01,
+        )
+
+        self.define_lc_state("State2", self.lca_60, self.lcb_60)
+
+        self.swing60 = np.sqrt(
+            (self.lcb_60 - self.lcb_ext) ** 2
+            + (self.lca_60 - self.lca_ext) ** 2
+        )
+
+        # Print comparison of target swing, target ratio
+        # Ratio determines the orientation of the elliptical state
+        # should be close to target.  Swing will vary to optimize ellipticity
+        logging.debug(
+            f"ratio: swing_LCB / swing_LCA = {(self.lcb_ext - self.lcb_60) / (self.lca_ext - self.lca_60):.4f} \
+              | target ratio: {-self.ratio}"
+        )
+        logging.debug(
+            f"total swing = {self.swing60:.4f} | target = {swing_ell}"
+        )
+
+        logging.info(f"LCA State2 (I60) = {self.lca_60:.3f}")
+        logging.debug(f"LCA State2 (I60) = {self.lca_60:.5f}")
+        logging.info(f"LCB State2 (I60) = {self.lcb_60:.3f}")
+        logging.debug(f"LCB State2 (I60) = {self.lcb_60:.5f}")
+        logging.info(f"Intensity (I60) = {intensity:.0f}")
+        logging.debug(f"Intensity (I60) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def opt_I90(self, lca_bound, lcb_bound):
+        """
+        optimized relative to Ielliptical (opt_I90)
+        Parameters
+        ----------
+        lca_bound
+        lcb_bound
+        Returns
+        -------
+        lca, lcb value at optimized state
+        intensity value at optimized state
+        """
+        logging.info("Calibrating State3 (I90)...")
+        logging.debug("Calibrating State3 (I90)...")
+
+        self.inten = []
+
+        self.set_lc(self.lca_ext + self.swing, "LCA")
+        self.set_lc(self.lcb_ext, "LCB")
+
+        self.lca_90, self.lcb_90, intensity = self.optimizer.optimize(
+            "90",
+            lca_bound,
+            lcb_bound,
+            reference=self.I_Elliptical,
+            n_iter=5,
+            thresh=0.01,
+        )
+
+        self.define_lc_state("State3", self.lca_90, self.lcb_90)
+
+        self.swing90 = np.sqrt(
+            (self.lcb_90 - self.lcb_ext) ** 2
+            + (self.lca_90 - self.lca_ext) ** 2
+        )
+
+        logging.info(f"LCA State3 (I90) = {self.lca_90:.3f}")
+        logging.debug(f"LCA State3 (I90) = {self.lca_90:.5f}")
+        logging.info(f"LCB State3 (I90) = {self.lcb_90:.3f}")
+        logging.debug(f"LCB State3 (I90) = {self.lcb_90:.5f}")
+        logging.info(f"Intensity (I90) = {intensity:.0f}")
+        logging.debug(f"Intensity (I90) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def opt_I120(self, lca_bound, lcb_bound):
+        """
+        optimized relative to Ielliptical (opt_I0_4State)
+        Parameters
+        ----------
+        lca_bound
+        lcb_bound
+        Returns
+        -------
+        lca, lcb value at optimized state
+        intensity value at optimized state
+        """
+        logging.info("Calibrating State3 (I120)...")
+        logging.debug("Calibrating State3 (I120)...")
+
+        # Calculate Initial Swing for initial guess to optimize around
+        # Based on ratio calculated from ellpiticity/orientation of LC simulation
+        swing_ell = np.sqrt(
+            (self.lca_ext - self.lca_0) ** 2 + (self.lcb_ext - self.lcb_0) ** 2
+        )
+        lca_swing = np.sqrt(swing_ell**2 / (1 + self.ratio**2))
+        lcb_swing = self.ratio * lca_swing
+
+        # Brent Optimization
+        self.set_lc(self.lca_ext + lca_swing, "LCA")
+        self.set_lc(self.lcb_ext - lcb_swing, "LCB")
+
+        self.lca_120, self.lcb_120, intensity = self.optimizer.optimize(
+            "120",
+            lca_bound,
+            lcb_bound,
+            reference=self.I_Elliptical,
+            n_iter=5,
+            thresh=0.01,
+        )
+
+        self.define_lc_state("State3", self.lca_120, self.lcb_120)
+
+        self.swing120 = np.sqrt(
+            (self.lcb_120 - self.lcb_ext) ** 2
+            + (self.lca_120 - self.lca_ext) ** 2
+        )
+
+        # Print comparison of target swing, target ratio
+        # Ratio determines the orientation of the elliptical state
+        # should be close to target.  Swing will vary to optimize ellipticity
+        logging.debug(
+            f"ratio: swing_LCB / swing_LCA = {(self.lcb_ext - self.lcb_120) / (self.lca_ext - self.lca_120):.4f}\
+             | target ratio: {self.ratio}"
+        )
+        logging.debug(
+            f"total swing = {self.swing120:.4f} | target = {swing_ell}"
+        )
+        logging.info(f"LCA State3 (I120) = {self.lca_120:.3f}")
+        logging.debug(f"LCA State3 (I120) = {self.lca_120:.5f}")
+        logging.info(f"LCB State3 (I120) = {self.lcb_120:.3f}")
+        logging.debug(f"LCB State3 (I120) = {self.lcb_120:.5f}")
+        logging.info(f"Intensity (I120) = {intensity:.0f}")
+        logging.debug(f"Intensity (I120) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def opt_I135(self, lca_bound, lcb_bound):
+        """
+        optimized relative to Ielliptical (opt_I0)
+        Parameters
+        ----------
+        lca_bound
+        lcb_bound
+        Returns
+        -------
+        lca, lcb value at optimized state
+        intensity value at optimized state
+        """
+
+        logging.info("Calibrating State4 (I135)...")
+        logging.debug("Calibrating State4 (I135)...")
+        self.inten = []
+
+        self.set_lc(self.lca_ext, "LCA")
+        self.set_lc(self.lcb_ext + self.swing, "LCB")
+
+        self.lca_135, self.lcb_135, intensity = self.optimizer.optimize(
+            "135",
+            lca_bound,
+            lcb_bound,
+            reference=self.I_Elliptical,
+            n_iter=5,
+            thresh=0.01,
+        )
+
+        self.define_lc_state("State4", self.lca_135, self.lcb_135)
+
+        self.swing135 = np.sqrt(
+            (self.lcb_135 - self.lcb_ext) ** 2
+            + (self.lca_135 - self.lca_ext) ** 2
+        )
+
+        logging.info(f"LCA State4 (I135) = {self.lca_135:.3f}")
+        logging.debug(f"LCA State4 (I135) = {self.lca_135:.5f}")
+        logging.info(f"LCB State4 (I135) = {self.lcb_135:.3f}")
+        logging.debug(f"LCB State4 (I135) = {self.lcb_135:.5f}")
+        logging.info(f"Intensity (I135) = {intensity:.0f}")
+        logging.debug(f"Intensity (I135) = {intensity:.3f}")
+        logging.info("--------done--------")
+        logging.debug("--------done--------")
+
+    def open_shutter(self):
+        if self.shutter_device == "":  # no shutter
+            input("Please manually open the shutter and press <Enter>")
+        else:
+            self.mmc.setShutterOpen(True)
+
+    def reset_shutter(self):
+        """
+        Return autoshutter to its original state before closing
+
+        Returns
+        -------
+
+        """
+        if self.shutter_device == "":  # no shutter
+            input(
+                "Please reset the shutter to its original state and press <Enter>"
+            )
+            logging.info(
+                "This is the end of the command-line instructions. You can return to the napari window."
+            )
+        else:
+            self.mmc.setAutoShutter(self._auto_shutter_state)
+            self.mmc.setShutterOpen(self._shutter_state)
+
+    def close_shutter_and_calc_blacklevel(self):
+        self._auto_shutter_state = self.mmc.getAutoShutter()
+        self._shutter_state = self.mmc.getShutterOpen()
+
+        if self.shutter_device == "":  # no shutter
+            show_warning(
+                "No shutter found. Please follow the command-line instructions..."
+            )
+            shutter_warning_msg = """
+            waveorder could not find an automatic shutter configured through Micro-Manager.
+            >>> If you would like manually enter the black level, enter an integer or float and press <Enter>
+            >>> If you would like to estimate the black level, please close the shutter and press <Enter>
+            """
+
+            in_string = input(shutter_warning_msg)
+            if in_string.isdigit():  # True if positive integer
+                self.I_Black = float(in_string)
+                return
+        else:
+            self.mmc.setAutoShutter(False)
+            self.mmc.setShutterOpen(False)
+
+        n_avg = 20
+        avgs = []
+        for i in range(n_avg):
+            mean = snap_and_average(self.snap_manager)
+            self.intensity_emitter.emit(mean)
+            avgs.append(mean)
+
+        blacklevel = np.mean(avgs)
+        self.I_Black = blacklevel
+
+    def calculate_extinction(
+        self, swing, black_level, intensity_extinction, intensity_elliptical
+    ):
+        """
+        Returns the extinction ratio, the ratio of the largest and smallest intensities that the imaging system can transmit above background.
+        See `/docs/calibration-guide.md` for a derivation of this expressions.
+        """
+        return np.round(
+            (1 / np.sin(np.pi * swing) ** 2)
+            * (intensity_elliptical - intensity_extinction)
+            / (intensity_extinction - black_level)
+            + 1,
+            2,
+        )
+
+    def calc_inst_matrix(self):
+        if self.calib_scheme == "4-State":
+            chi = self.swing
+            inst_mat = np.array(
+                [
+                    [1, 0, 0, -1],
+                    [1, np.sin(2 * np.pi * chi), 0, -np.cos(2 * np.pi * chi)],
+                    [
+                        1,
+                        -0.5 * np.sin(2 * np.pi * chi),
+                        np.sqrt(3) * np.cos(np.pi * chi) * np.sin(np.pi * chi),
+                        -np.cos(2 * np.pi * chi),
+                    ],
+                    [
+                        1,
+                        -0.5 * np.sin(2 * np.pi * chi),
+                        -np.sqrt(3) / 2 * np.sin(2 * np.pi * chi),
+                        -np.cos(2 * np.pi * chi),
+                    ],
+                ]
+            )
+
+            return inst_mat
+
+        if self.calib_scheme == "5-State":
+            chi = self.swing * 2 * np.pi
+
+            inst_mat = np.array(
+                [
+                    [1, 0, 0, -1],
+                    [1, np.sin(chi), 0, -np.cos(chi)],
+                    [1, 0, np.sin(chi), -np.cos(chi)],
+                    [1, -np.sin(chi), 0, -np.cos(chi)],
+                    [1, 0, -np.sin(chi), -np.cos(chi)],
+                ]
+            )
+
+            return inst_mat
+
+    def write_metadata(self, notes=None):
+        inst_mat = self.calc_inst_matrix()
+        inst_mat = np.around(inst_mat, decimals=5).tolist()
+
+        metadata = {
+            "Summary": {
+                "Timestamp": str(datetime.now()),
+                "waveorder version": version("waveorder"),
+            },
+            "Calibration": {
+                "Calibration scheme": self.calib_scheme,
+                "Swing (waves)": self.swing,
+                "Wavelength (nm)": self.wavelength,
+                "Retardance to voltage interpolation method": self.calib.interp_method,
+                "LC control mode": self.mode,
+                "Black level": np.round(self.I_Black, 2),
+                "Extinction ratio": self.extinction_ratio,
+            },
+            "Notes": notes,
+        }
+
+        if self.calib_scheme == "4-State":
+            metadata["Calibration"].update(
+                {
+                    "Channel names": [f"State{i}" for i in range(4)],
+                    "LC retardance": {
+                        f"LC{i}_{j}": np.around(
+                            getattr(self, f"lc{i.lower()}_{j}"), decimals=6
+                        )
+                        for j in ["ext", "0", "60", "120"]
+                        for i in ["A", "B"]
+                    },
+                    "LC voltage": {
+                        f"LC{i}_{j}": np.around(
+                            self.calib.get_voltage(
+                                getattr(self, f"lc{i.lower()}_{j}")
+                            ),
+                            decimals=4,
+                        )
+                        for j in ["ext", "0", "60", "120"]
+                        for i in ["A", "B"]
+                    },
+                    "Swing_0": np.around(self.swing0, decimals=3),
+                    "Swing_60": np.around(self.swing60, decimals=3),
+                    "Swing_120": np.around(self.swing120, decimals=3),
+                    "Instrument matrix": inst_mat,
+                }
+            )
+
+        elif self.calib_scheme == "5-State":
+            metadata["Calibration"].update(
+                {
+                    "Channel names": [f"State{i}" for i in range(5)],
+                    "LC retardance": {
+                        f"LC{i}_{j}": np.around(
+                            getattr(self, f"lc{i.lower()}_{j}"), decimals=6
+                        )
+                        for j in ["ext", "0", "45", "90", "135"]
+                        for i in ["A", "B"]
+                    },
+                    "LC voltage": {
+                        f"LC{i}_{j}": np.around(
+                            self.calib.get_voltage(
+                                getattr(self, f"lc{i.lower()}_{j}")
+                            ),
+                            decimals=4,
+                        )
+                        for j in ["ext", "0", "45", "90", "135"]
+                        for i in ["A", "B"]
+                    },
+                    "Swing_0": np.around(self.swing0, decimals=3),
+                    "Swing_45": np.around(self.swing45, decimals=3),
+                    "Swing_90": np.around(self.swing90, decimals=3),
+                    "Swing_135": np.around(self.swing135, decimals=3),
+                    "Instrument matrix": inst_mat,
+                }
+            )
+
+        with open(self.meta_file, "w") as metafile:
+            json.dump(metadata, metafile, indent=1)
+
+    def _add_colorbar(self, mappable):
+        last_axes = plt.gca()
+        ax = mappable.axes
+        fig = ax.figure
+        divider = make_axes_locatable(ax)
+        cax = divider.append_axes("right", size="5%", pad=0.05)
+        cbar = fig.colorbar(mappable, cax=cax)
+        plt.sca(last_axes)
+        return cbar
+
+    def _capture_state(self, state: str, n_avg: int):
+        """Set the LCs to a certain state, then snap and average over a number of images.
+
+        Parameters
+        ----------
+        state : str
+            Name of the LC config, e.g. `"State0"`
+        n_avg : int
+            Number of images to capture and average
+
+        Returns
+        -------
+        ndarray
+            Average of N images
+        """
+        with suspend_live_sm(self.snap_manager) as sm:
+            set_lc_state(self.mmc, self.group, state)
+            imgs = []
+            for i in range(n_avg):
+                imgs.append(snap_and_get_image(sm))
+        return np.mean(imgs, axis=0)
+
+    def _plot_bg_images(self, imgs):
+        img_names = (
+            ["Extinction", "0", "60", "120"]
+            if len(imgs) == 4
+            else ["Extinction", "0", "45", "90", 135]
+        )
+        fig, ax = (
+            plt.subplots(2, 2, figsize=(20, 20))
+            if len(imgs) == 4
+            else plt.subplots(3, 2, figsize=(20, 20))
+        )
+
+        img_idx = 0
+        for ax1 in range(len(ax[:, 0])):
+            for ax2 in range(len(ax[0, :])):
+                if img_idx < len(imgs):
+                    im = ax[ax1, ax2].imshow(imgs[img_idx], "gray")
+                    ax[ax1, ax2].set_title(img_names[img_idx])
+                    self._add_colorbar(im)
+                else:
+                    try:
+                        fig.delaxes(ax[2, 1])
+                    except:
+                        break
+        plt.show()
+
+    @property
+    def pol_states(self):
+        """The polarization states of this calibration.
+
+        Returns
+        -------
+        tuple
+            Names of all the polarization states.
+
+        Raises
+        ------
+        ValueError
+            Found illegal calibration state.
+        """
+        if self.calib_scheme == "4-State":
+            pols = ("ext", "0", "60", "120")
+        elif self.calib_scheme == "5-State":
+            pols = ("ext", "0", "45", "90", "135")
+        else:
+            raise ValueError(
+                f"Invalid calibration state: {self.calib_scheme}."
+            )
+        return pols
+
+    @property
+    def lc_states(self):
+        """The optimized LC retardance values of this calibration.
+
+        Returns
+        -------
+        dict
+            `Dict{"LCA": List[ext, ...], "LCB": List[ext, ...]}`
+        """
+        lc_sides = ["A", "B"]
+        return {
+            f"LC{lc_side}": [
+                self.__getattribute__("lc" + lc_side.lower() + "_" + pol)
+                for pol in self.pol_states
+            ]
+            for lc_side in lc_sides
+        }
+
+    def capture_bg(self, n_avg, directory):
+        """ "
+        This function will capture an image at every state
+        and save to specified directory
+        This may throw errors depending on the Micro-Manager config file--
+        modify 'State_' to match to the corresponding channel preset in config
+        :param: n_states (int)
+            Number of states used for calibration
+        :param: directory (string)
+            Directory to save images
+        """
+
+        if not os.path.exists(directory):
+            os.makedirs(directory)
+
+        logging.info("Capturing Background")
+        self._auto_shutter_state = self.mmc.getAutoShutter()
+        self._shutter_state = self.mmc.getShutterOpen()
+        self.mmc.setAutoShutter(False)
+        self.open_shutter()
+
+        num_states = int(self.calib_scheme[0])
+
+        # Acquire background data
+        yx_list = []
+        for channel in range(num_states):
+            logging.debug(f"Capturing Background State{channel}")
+            yx_list.append(self._capture_state(f"State{channel}", n_avg))
+            logging.debug(f"Saving Background State{channel}")
+        cyx_data = np.array(yx_list)
+        yx_scale = self.mmc.getPixelSizeUm()
+
+        # Save to zarr
+        with open_ome_zarr(
+            os.path.join(directory, "background.zarr"),
+            layout="hcs",
+            mode="w",
+            channel_names=[f"State{i}" for i in range(num_states)],
+        ) as dataset:
+            position = dataset.create_position("0", "0", "0")
+            position.create_zeros(
+                name="0",
+                shape=(1, num_states, 1, cyx_data.shape[1], cyx_data.shape[2]),
+                dtype=np.float32,
+                chunks=(1, 1, 1, cyx_data.shape[1], cyx_data.shape[2]),
+                transform=[
+                    TransformationMeta(
+                        type="scale", scale=[1, 1, 1, yx_scale, yx_scale]
+                    )
+                ],
+            )
+            position["0"][0, :, 0] = cyx_data  # save to 1C1YX array
+
+        # self._plot_bg_images(np.asarray(imgs))
+        self.reset_shutter()
+
+        return cyx_data
+
+
+class CalibrationData:
+    """
+    Interpolates LC calibration data between retardance (in waves), voltage (in mV), and wavelength (in nm)
+    """
+
+    def __init__(self, path, wavelength=532, interp_method="linear"):
+        """
+
+        Parameters
+        ----------
+        path : str
+            path to .csv calibration data file
+        wavelength : int
+            usage wavelength, in nanometers
+        interp_method : str
+            interpolation method, either "linear" or "schnoor_fit" (https://doi.org/10.1364/AO.408383)
+        """
+
+        header, raw_data = self.read_data(path)
+        self.calib_wavelengths = np.array(
+            [i[:3] for i in header[1::3]]
+        ).astype("double")
+
+        self.wavelength = None
+        self.V_min = 0.0
+        self.V_max = 20.0
+
+        if interp_method in ["linear", "schnoor_fit"]:
+            self.interp_method = interp_method
+        else:
+            raise ValueError("Unknown interpolation method.")
+
+        self.set_wavelength(wavelength)
+        if interp_method == "linear":
+            self.interpolate_data(
+                raw_data, self.calib_wavelengths
+            )  # calib_wavelengths is not used, values hardcoded
+        elif interp_method == "schnoor_fit":
+            self.fit_params = self.fit_data(raw_data, self.calib_wavelengths)
+
+        self.ret_min = self.get_retardance(self.V_max)
+        self.ret_max = self.get_retardance(self.V_min)
+
+    @staticmethod
+    def read_data(path):
+        """
+        Read raw calibration data
+
+        Example calibration data format:
+
+            Voltage(mv),490-A,490-B,Voltage(mv),546-A,546-B,Voltage(mv),630-A,630-B
+            -,-,-,-,-,-,-,-,-
+            0,490,490,0,546,546,0,630,630
+            0,970.6205,924.4288,0,932.2446,891.2008,0,899.6626,857.2885
+            200,970.7488,924.4422,200,932.2028,891.1546,200,899.5908,857.3078
+            ...
+            20000,40.5954,40.4874,20000,38.6905,39.5402,20000,35.5043,38.1445
+            -,-,-,-,-,-,-,-,-
+
+        The first row of the CSV file is a header row, structured as [Voltage (mV), XXX-A, XXX-B,
+        Voltage (nm), XXX-A, XXX-B, ...] where XXX is the calibration wavelength in nanometers. For example 532-A would
+        contain measurements of the retardance of LCA as a function of applied voltage at 532 nm. The second row
+        contains dashes in every column. The third row contains "0" in the Voltage column and the calibration wavelength
+        in the retardance columns, e.g [0, 532, 532]. The following rows contain the LC calibration data. Retardance is
+        recorded in nanometers and voltage is recorded in millivolts. The last row contains dashes in every column.
+
+        Parameters
+        ----------
+        path : str
+            path to .csv calibration data file
+
+        Returns
+        -------
+        header : list
+            Calibration data file header line. Contains information on calibration wavelength
+        raw_data : ndarray
+            Calibration data. Voltage is in millivolts and retardance is in nanometers
+
+        """
+        with open(path, "r") as f:
+            header = f.readline().strip().split(",")
+
+        raw_data = np.loadtxt(path, delimiter=",", comments="-", skiprows=3)
+        return header, raw_data
+
+    @staticmethod
+    def schnoor_fit(V, a, b1, b2, c, d, e, wavelength):
+        """
+
+        Parameters
+        ----------
+        V : float
+            Voltage in volts
+        a, b1, b2, c, d, e : float
+            Fit parameters
+        wavelength : float
+            Wavelength in nanometers
+
+        Returns
+        -------
+        retardance : float
+            Retardance in nanometers
+
+        """
+        retardance = a + (b1 + b2 / wavelength**2) / (1 + (V / c) ** d) ** e
+
+        return retardance
+
+    @staticmethod
+    def schnoor_fit_inv(retardance, a, b1, b2, c, d, e, wavelength):
+        """
+
+        Parameters
+        ----------
+        retardance : float
+            Retardance in nanometers
+        a, b1, b2, c, d, e : float
+            Fit parameters
+        wavelength : float
+            Wavelength in nanometers
+
+        Returns
+        -------
+        voltage : float
+            Voltage in volts
+
+        """
+
+        voltage = c * (
+            ((b1 + b2 / wavelength**2) / (retardance - a)) ** (1 / e) - 1
+        ) ** (1 / d)
+
+        return voltage
+
+    @staticmethod
+    def _fun(x, wavelengths, xdata, ydata):
+        fval = CalibrationData.schnoor_fit(xdata, *x, wavelengths)
+        res = ydata - fval
+        return res.flatten()
+
+    def set_wavelength(self, wavelength):
+        if (
+            len(self.calib_wavelengths) == 1
+            and wavelength != self.calib_wavelengths
+        ):
+            raise ValueError(
+                "Calibration is not provided at this wavelength. "
+                "Wavelength dependence of LC retardance vs voltage cannot be extrapolated."
+            )
+
+        if (
+            wavelength < self.calib_wavelengths.min()
+            or wavelength > self.calib_wavelengths.max()
+        ):
+            warnings.warn(
+                "Specified wavelength is outside of the calibration range. "
+                "LC retardance vs voltage data will be extrapolated at this wavelength."
+            )
+
+        self.wavelength = wavelength
+        if self.interp_method == "linear":
+            # Interpolation of calib beyond this range produce strange results.
+            if self.wavelength < 450:
+                self.wavelength = 450
+                warnings.warn(
+                    "Wavelength is limited to 450-720 nm for this interpolation method."
+                )
+            if self.wavelength > 720:
+                self.wavelength = 720
+                warnings.warn(
+                    "Wavelength is limited to 450-720 nm for this interpolation method."
+                )
+
+    def fit_data(self, raw_data, calib_wavelengths):
+        """
+        Perform Schnoor fit on interpolation data
+
+        Parameters
+        ----------
+        raw_data : np.array
+            LC calibration data in (Voltage, LCA retardance, LCB retardance) format. Only the LCA retardance vs voltage
+            curve is used.
+        calib_wavelengths : 1D np.array
+            Calibration wavelength for each (Voltage, LCA retardance, LCB retardance) set in the calibration data
+
+        Returns
+        -------
+
+        """
+        xdata = raw_data[:, 0::3] / 1000  # convert to volts
+        ydata = raw_data[:, 1::3]  # in nanometers
+
+        x0 = [10, 1000, 1e7, 1, 10, 0.1]
+        p = least_squares(
+            self._fun,
+            x0,
+            method="trf",
+            args=(calib_wavelengths, xdata, ydata),
+            bounds=((-np.inf, 0, 0, 0, 0, 0), (np.inf,) * 6),
+            x_scale=[10, 1000, 1e7, 1, 10, 0.1],
+        )
+
+        if not p.success:
+            raise RuntimeError("Schnoor fit to calibration data did not work.")
+
+        y = ydata.flatten()
+        y_hat = y - p.fun
+        slope, intercept, r_value, *_ = linregress(y, y_hat)
+        r_squared = r_value**2
+        if r_squared < 0.999:
+            warnings.warn(
+                f"Schnoor fit has R2 value of {r_squared:.5f}, fit may not have worked well."
+            )
+
+        return p.x
+
+    def interpolate_data(self, raw_data, calib_wavelengths):
+        """
+        Perform linear interpolation of LC calibration data
+
+        Parameters
+        ----------
+        raw_data : np.array
+            LC calibration data in (Voltage, LCA retardance, LCB retardance) format. Only the LCA retardance vs voltage
+            curve is used.
+        calib_wavelengths : 1D np.array
+            Calibration wavelength for each (Voltage, LCA retardance, LCB retardance) set in the calibration data
+            These values are not used in this method. Instead, the [490, 546, 630] wavelengths are hardcoded.
+
+        Returns
+        -------
+
+        """
+        # 0V to 20V step size 1 mV
+        x_range = np.arange(0, np.max(raw_data[:, ::3]), 1)
+
+        # interpolate calib - only LCA data is used
+        spline490 = interp1d(raw_data[:, 0], raw_data[:, 1])
+        spline546 = interp1d(raw_data[:, 3], raw_data[:, 4])
+        spline630 = interp1d(raw_data[:, 6], raw_data[:, 7])
+
+        if self.wavelength < 490:
+            new_a1_y = np.interp(x_range, x_range, spline490(x_range))
+            new_a2_y = np.interp(x_range, x_range, spline546(x_range))
+
+            wavelength_new = 490 + (490 - self.wavelength)
+            fact1 = np.abs(490 - wavelength_new) / (546 - 490)
+            fact2 = np.abs(546 - wavelength_new) / (546 - 490)
+
+            temp_curve = np.asarray(
+                [
+                    [
+                        i,
+                        2 * new_a1_y[i]
+                        - (fact1 * new_a1_y[i] + fact2 * new_a2_y[i]),
+                    ]
+                    for i in range(len(new_a1_y))
+                ]
+            )
+            self.spline = interp1d(temp_curve[:, 0], temp_curve[:, 1])
+            self.curve = self.spline(x_range)
+
+        elif self.wavelength > 630:
+            new_a1_y = np.interp(x_range, x_range, spline546(x_range))
+            new_a2_y = np.interp(x_range, x_range, spline630(x_range))
+
+            wavelength_new = 630 + (630 - self.wavelength)
+            fact1 = np.abs(630 - wavelength_new) / (630 - 546)
+            fact2 = np.abs(546 - wavelength_new) / (630 - 546)
+
+            temp_curve = np.asarray(
+                [
+                    [
+                        i,
+                        2 * new_a1_y[i]
+                        - (fact1 * new_a1_y[i] + fact2 * new_a2_y[i]),
+                    ]
+                    for i in range(len(new_a1_y))
+                ]
+            )
+            self.spline = interp1d(temp_curve[:, 0], temp_curve[:, 1])
+            self.curve = self.spline(x_range)
+
+        elif 490 < self.wavelength < 546:
+            new_a1_y = np.interp(x_range, x_range, spline490(x_range))
+            new_a2_y = np.interp(x_range, x_range, spline546(x_range))
+
+            fact1 = np.abs(490 - self.wavelength) / (546 - 490)
+            fact2 = np.abs(546 - self.wavelength) / (546 - 490)
+
+            temp_curve = np.asarray(
+                [
+                    [i, fact1 * new_a1_y[i] + fact2 * new_a2_y[i]]
+                    for i in range(len(new_a1_y))
+                ]
+            )
+            self.spline = interp1d(temp_curve[:, 0], temp_curve[:, 1])
+            self.curve = self.spline(x_range)
+
+        elif 546 < self.wavelength < 630:
+            new_a1_y = np.interp(x_range, x_range, spline546(x_range))
+            new_a2_y = np.interp(x_range, x_range, spline630(x_range))
+
+            fact1 = np.abs(546 - self.wavelength) / (630 - 546)
+            fact2 = np.abs(630 - self.wavelength) / (630 - 546)
+
+            temp_curve = np.asarray(
+                [
+                    [i, fact1 * new_a1_y[i] + fact2 * new_a2_y[i]]
+                    for i in range(len(new_a1_y))
+                ]
+            )
+            self.spline = interp1d(temp_curve[:, 0], temp_curve[:, 1])
+            self.curve = self.spline(x_range)
+
+        elif self.wavelength == 490:
+            self.curve = spline490(x_range)
+            self.spline = spline490
+
+        elif self.wavelength == 546:
+            self.curve = spline546(x_range)
+            self.spline = spline546
+
+        elif self.wavelength == 630:
+            self.curve = spline630(x_range)
+            self.spline = spline630
+
+        else:
+            raise ValueError(f"Wavelength {self.wavelength} not understood")
+
+    def get_voltage(self, retardance):
+        """
+
+        Parameters
+        ----------
+        retardance : float
+            retardance in waves
+
+        Returns
+        -------
+        voltage
+            voltage in volts
+
+        """
+
+        retardance = np.asarray(retardance, dtype="double")
+        voltage = None
+        ret_nanometers = retardance * self.wavelength
+
+        if retardance < self.ret_min:
+            voltage = self.V_max
+        elif retardance > self.ret_max:
+            voltage = self.V_min
+        else:
+            if self.interp_method == "linear":
+                voltage = np.abs(self.curve - ret_nanometers).argmin() / 1000
+            elif self.interp_method == "schnoor_fit":
+                voltage = self.schnoor_fit_inv(
+                    ret_nanometers, *self.fit_params, self.wavelength
+                )
+
+        return voltage
+
+    def get_retardance(self, volts):
+        """
+
+        Parameters
+        ----------
+        volts : float
+            voltage in volts
+
+        Returns
+        -------
+        retardance : float
+            retardance in waves
+
+        """
+
+        volts = np.asarray(volts, dtype="double")
+        ret_nanometers = None
+
+        if volts < self.V_min:
+            volts = self.V_min
+        elif volts >= self.V_max:
+            if self.interp_method == "linear":
+                volts = (
+                    self.V_max - 1e-3
+                )  # interpolation breaks down at upper boundary
+            else:
+                volts = self.V_max
+
+        if self.interp_method == "linear":
+            ret_nanometers = self.spline(volts * 1000)
+        elif self.interp_method == "schnoor_fit":
+            ret_nanometers = self.schnoor_fit(
+                volts, *self.fit_params, self.wavelength
+            )
+        retardance = ret_nanometers / self.wavelength
+
+        return retardance