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

waveorder/calib/calibration_workers.py

@@ -0,0 +1,464 @@
+from __future__ import annotations
+
+import json
+import logging
+from pathlib import Path
+
+# type hint/check
+from typing import TYPE_CHECKING
+
+import numpy as np
+from iohub import open_ome_zarr
+from napari.qt.threading import WorkerBase, WorkerBaseSignals, thread_worker
+from qtpy.QtCore import Signal
+
+from waveorder.calib.Calibration import LC_DEVICE_NAME
+from waveorder.cli import settings
+from waveorder.cli.apply_inverse_transfer_function import (
+    apply_inverse_transfer_function_cli,
+)
+from waveorder.cli.compute_transfer_function import (
+    compute_transfer_function_cli,
+)
+from waveorder.io.core_functions import set_lc_state, snap_and_average
+from waveorder.io.metadata_reader import MetadataReader
+from waveorder.io.utils import MockEmitter, add_index_to_path, model_to_yaml
+
+# avoid runtime import error
+if TYPE_CHECKING:
+    pass
+
+    from waveorder.calib.Calibration import QLIPP_Calibration
+    from waveorder.plugin.main_widget import MainWidget
+
+
+class CalibrationSignals(WorkerBaseSignals):
+    """
+    Custom Signals class that includes napari native signals
+    """
+
+    progress_update = Signal(tuple)
+    extinction_update = Signal(str)
+    intensity_update = Signal(object)
+    calib_assessment = Signal(str)
+    calib_assessment_msg = Signal(str)
+    calib_file_emit = Signal(Path)
+    plot_sequence_emit = Signal(str)
+    lc_states = Signal(tuple)
+    aborted = Signal()
+
+
+class BackgroundSignals(WorkerBaseSignals):
+    """
+    Custom Signals class that includes napari native signals
+    """
+
+    bg_image_emitter = Signal(tuple)
+    bire_image_emitter = Signal(tuple)
+    bg_path_update_emitter = Signal(Path)
+    aborted = Signal()
+
+
+class CalibrationWorkerBase(WorkerBase):
+    """
+    Base class for creating calibration workers.
+    """
+
+    def __init_subclass__(cls, signals: WorkerBaseSignals):
+        """Called when creating calibration worker classes.
+
+        Parameters
+        ----------
+        signals : WorkerBaseSignals
+            Qt Signals class for the created worker class to send data across threads.
+        """
+        super().__init_subclass__()
+        cls.signals = signals
+
+    def __init__(self, calib_window: MainWidget, calib: QLIPP_Calibration):
+        """Initialize the worker object.
+
+        Parameters
+        ----------
+        calib_window : MainWidget
+            The waveorder plugin's main GUI widget object containing metadata input.
+        calib : QLIPP_Calibration
+            waveorder calibration backend object.
+        """
+        super().__init__(SignalsClass=self.signals)
+        self.calib_window = calib_window
+        self.calib = calib
+
+    def _check_abort(self):
+        """
+        Called if the user presses the STOP button.
+        Needs to be checked after every major step to stop the process
+        """
+        if self.abort_requested:
+            self.aborted.emit()
+            raise TimeoutError("Stop Requested.")
+
+    def _write_meta_file(self, meta_file: str):
+        self.calib.meta_file = meta_file
+        self.calib.write_metadata(
+            notes=self.calib_window.ui.le_notes_field.text()
+        )
+
+
+class CalibrationWorker(CalibrationWorkerBase, signals=CalibrationSignals):
+    """
+    Class to execute calibration
+    """
+
+    def __init__(self, calib_window, calib):
+        super().__init__(calib_window, calib)
+
+    def work(self):
+        """
+        Runs the full calibration algorithm and emits necessary signals.
+        """
+
+        self.plot_sequence_emit.emit("Coarse")
+        self.calib.intensity_emitter = self.intensity_update
+        self.calib.plot_sequence_emitter = self.plot_sequence_emit
+        self.progress_update.emit((1, "Calculating Blacklevel..."))
+        self._check_abort()
+
+        logging.info("Calculating Black Level ...")
+        logging.debug("Calculating Black Level ...")
+        self.calib.close_shutter_and_calc_blacklevel()
+
+        # Calculate Blacklevel
+        logging.info(f"Black Level: {self.calib.I_Black:.0f}\n")
+        logging.debug(f"Black Level: {self.calib.I_Black:.0f}\n")
+
+        self._check_abort()
+        self.progress_update.emit((10, "Calibrating Extinction State..."))
+
+        # Open shutter
+        self.calib.open_shutter()
+
+        # Set LC Wavelength:
+        self.calib.set_wavelength(int(self.calib_window.wavelength))
+        if self.calib_window.calib_mode == "MM-Retardance":
+            self.calib_window.mmc.setProperty(
+                LC_DEVICE_NAME, "Wavelength", self.calib_window.wavelength
+            )
+
+        self._check_abort()
+
+        # Optimize States
+        (
+            self._calibrate_4state()
+            if self.calib_window.calib_scheme == "4-State"
+            else self._calibrate_5state()
+        )
+
+        # Reset shutter autoshutter
+        self.calib.reset_shutter()
+
+        # Calculate Extinction
+        extinction_ratio = self.calib.calculate_extinction(
+            self.calib.swing,
+            self.calib.I_Black,
+            self.calib.I_Ext,
+            self.calib.I_Elliptical,
+        )
+        self._check_abort()
+
+        # Update main GUI with extinction ratio
+        self.calib.extinction_ratio = extinction_ratio
+        self.extinction_update.emit(str(extinction_ratio))
+
+        # determine metadata filename
+        meta_file = (
+            Path(self.calib_window.directory) / "calibration_metadata.txt"
+        )
+        meta_file = add_index_to_path(meta_file)
+
+        # Write Metadata
+        self._write_meta_file(meta_file)
+        self.calib_file_emit.emit(self.calib.meta_file)
+        self.progress_update.emit((100, "Finished"))
+
+        self._check_abort()
+
+        # Perform calibration assessment based on retardance values
+        self._assess_calibration()
+
+        self._check_abort()
+
+        # Emit calibrated LC states for plotting
+        self.lc_states.emit((self.calib.pol_states, self.calib.lc_states))
+
+        logging.info("\n=======Finished Calibration=======\n")
+        logging.info(f"EXTINCTION = {extinction_ratio:.2f}")
+        logging.debug("\n=======Finished Calibration=======\n")
+        logging.debug(f"EXTINCTION = {extinction_ratio:.2f}")
+
+    def _calibrate_4state(self):
+        """
+        Run through the 4-state calibration algorithm
+        """
+
+        search_radius = np.min((self.calib.swing / self.calib.ratio, 0.05))
+
+        self.calib.calib_scheme = "4-State"
+
+        self._check_abort()
+
+        # Optimize Extinction State
+        self.calib.opt_Iext()
+
+        self._check_abort()
+        self.progress_update.emit((60, "Calibrating State 1..."))
+
+        # Optimize first elliptical (reference) state
+        self.calib.opt_I0()
+        self.progress_update.emit((65, "Calibrating State 2..."))
+
+        self._check_abort()
+
+        # Optimize 60 deg state
+        self.calib.opt_I60(search_radius, search_radius)
+        self.progress_update.emit((75, "Calibrating State 3..."))
+
+        self._check_abort()
+
+        # Optimize 120 deg state
+        self.calib.opt_I120(search_radius, search_radius)
+        self.progress_update.emit((85, "Writing Metadata..."))
+
+        self._check_abort()
+
+    def _calibrate_5state(self):
+        search_radius = np.min((self.calib.swing, 0.05))
+
+        self.calib.calib_scheme = "5-State"
+
+        # Optimize Extinction State
+        self.calib.opt_Iext()
+        self.progress_update.emit((50, "Calibrating State 1..."))
+
+        self._check_abort()
+
+        # Optimize First elliptical state
+        self.calib.opt_I0()
+        self.progress_update.emit((55, "Calibrating State 2..."))
+
+        self._check_abort()
+
+        # Optimize 45 deg state
+        self.calib.opt_I45(search_radius, search_radius)
+        self.progress_update.emit((65, "Calibrating State 3..."))
+
+        self._check_abort()
+
+        # Optimize 90 deg state
+        self.calib.opt_I90(search_radius, search_radius)
+        self.progress_update.emit((75, "Calibrating State 4..."))
+
+        self._check_abort()
+
+        # Optimize 135 deg state
+        self.calib.opt_I135(search_radius, search_radius)
+        self.progress_update.emit((85, "Writing Metadata..."))
+
+        self._check_abort()
+
+    def _assess_calibration(self):
+        """
+        Assesses the quality of calibration based off retardance values.
+        Attempts to determine whether certain optical components are out of place.
+        """
+
+        if self.calib.extinction_ratio >= 100:
+            self.calib_assessment.emit("good")
+            self.calib_assessment_msg.emit("Successful Calibration")
+        elif 80 <= self.calib.extinction_ratio < 100:
+            self.calib_assessment.emit("okay")
+            self.calib_assessment_msg.emit(
+                "Successful Calibration, Okay Extinction Ratio"
+            )
+        else:
+            self.calib_assessment.emit("bad")
+            message = (
+                "Possibilities are: a) linear polarizer and LC are not oriented properly, "
+                "b) circular analyzer has wrong handedness, "
+                "c) the condenser is not setup for Kohler illumination, "
+                "d) a component, such as autofocus dichroic or sample chamber, distorts the polarization state"
+            )
+
+            self.calib_assessment_msg.emit("Poor Extinction. " + message)
+
+
+class BackgroundCaptureWorker(
+    CalibrationWorkerBase, signals=BackgroundSignals
+):
+    """
+    Class to execute background capture.
+    """
+
+    def __init__(self, calib_window, calib):
+        super().__init__(calib_window, calib)
+
+    def work(self):
+        # Make the background folder
+        bg_path = (
+            Path(self.calib_window.directory)
+            / self.calib_window.ui.le_bg_folder.text()
+        )
+        bg_path = add_index_to_path(bg_path)
+        bg_path.mkdir()
+
+        self._check_abort()
+
+        # capture and return background images
+        imgs = self.calib.capture_bg(self.calib_window.n_avg, bg_path)
+
+        # build background-specific reconstruction settings
+        reconstruction_settings = settings.ReconstructionSettings(
+            input_channel_names=[
+                f"State{i}"
+                for i in range(int(self.calib_window.calib_scheme[0]))
+            ],
+            reconstruction_dimension=2,
+            birefringence=settings.BirefringenceSettings(
+                transfer_function=settings.BirefringenceTransferFunctionSettings(
+                    swing=self.calib_window.swing
+                ),
+                apply_inverse=settings.BirefringenceApplyInverseSettings(
+                    wavelength_illumination=self.calib_window.recon_wavelength
+                    / 1000,
+                    background_path="",
+                    remove_estimated_background=False,
+                    flip_orientation=False,
+                    rotate_orientation=False,
+                ),
+            ),
+        )
+
+        reconstruction_config_path = bg_path / "reconstruction_settings.yml"
+        model_to_yaml(reconstruction_settings, reconstruction_config_path)
+
+        input_data_path = bg_path / "background.zarr" / "0" / "0" / "0"
+        transfer_function_path = bg_path / "transfer_function.zarr"
+        reconstruction_path = bg_path / "reconstruction.zarr"
+
+        compute_transfer_function_cli(
+            input_position_dirpath=input_data_path,
+            config_filepath=reconstruction_config_path,
+            output_dirpath=transfer_function_path,
+        )
+
+        apply_inverse_transfer_function_cli(
+            input_position_dirpaths=[input_data_path],
+            transfer_function_dirpath=transfer_function_path,
+            config_filepath=reconstruction_config_path,
+            output_dirpath=reconstruction_path,
+            num_processes=1,
+        )
+
+        # Load reconstructions from file for layers
+        with open_ome_zarr(reconstruction_path, mode="r") as dataset:
+            self.retardance = dataset["0/0/0/0"][0, 0, 0]
+            self.birefringence = dataset["0/0/0/0"][0, :, 0]
+            scale = dataset["0/0/0"].scale
+
+        # Save metadata file and emit imgs
+        meta_file = bg_path / "polarization_calibration.txt"
+        self._write_meta_file(meta_file)
+
+        # Update last calibration file
+        note = self.calib_window.ui.le_notes_field.text()
+
+        with open(self.calib_window.last_calib_meta_file, "r") as file:
+            current_json = json.load(file)
+
+        old_note = current_json["Notes"]
+        if old_note is None or old_note == "" or old_note == note:
+            current_json["Notes"] = note
+        else:
+            current_json["Notes"] = old_note + ", " + note
+
+        with open(self.calib_window.last_calib_meta_file, "w") as file:
+            json.dump(current_json, file, indent=1)
+
+        self._check_abort()
+
+        # Emit background images + background birefringence
+        self.bg_image_emitter.emit((imgs, scale))
+        self.bire_image_emitter.emit(
+            ((self.retardance, self.birefringence[1]), scale)
+        )
+
+        # Emit bg path
+        self.bg_path_update_emitter.emit(bg_path)
+
+
+@thread_worker
+def load_calibration(calib, metadata: MetadataReader):
+    """
+    Sets MM properties based upon calibration metadata file
+
+
+    Parameters
+    ----------
+    calib:          (object) waveorder Calibration Class
+    metadata:       (object) MetadataReader instance
+
+    Returns
+    -------
+    calib           (object) updated waveorder Calibration Class
+    """
+    calib.calib_scheme = metadata.Calibration_scheme
+
+    def _set_calib_attrs(calib, metadata):
+        """Set the retardance attributes in the waveorder Calibration object"""
+        if calib.calib_scheme == "4-State":
+            lc_states = ["ext", "0", "60", "120"]
+        elif calib.calib_scheme == "5-State":
+            lc_states = ["ext", "0", "45", "90", "135"]
+        else:
+            raise ValueError(
+                "Invalid calibration scheme in metadata: {calib.calib_scheme}"
+            )
+        for side in ("A", "B"):
+            retardance_values = metadata.__getattribute__(
+                "LC" + side + "_retardance"
+            )
+            for i, state in enumerate(lc_states):
+                # set the retardance value attribute (e.g. 'lca_0')
+                retardance_name = "lc" + side.lower() + "_" + state
+                setattr(calib, retardance_name, retardance_values[i])
+                # set the swing value attribute (e.g. 'swing0')
+                if state != "ext":
+                    swing_name = "swing" + state
+                    setattr(calib, swing_name, metadata.Swing_measured[i - 1])
+
+    _set_calib_attrs(calib, metadata)
+
+    for state, lca, lcb in zip(
+        [f"State{i}" for i in range(5)],
+        metadata.LCA_retardance,
+        metadata.LCB_retardance,
+    ):
+        calib.define_lc_state(state, lca, lcb)
+
+    # Calculate black level after loading these properties
+    calib.intensity_emitter = MockEmitter()
+    calib.close_shutter_and_calc_blacklevel()
+    calib.open_shutter()
+    set_lc_state(calib.mmc, calib.group, "State0")
+    calib.I_Ext = snap_and_average(calib.snap_manager)
+    set_lc_state(calib.mmc, calib.group, "State1")
+    calib.I_Elliptical = snap_and_average(calib.snap_manager)
+    calib.reset_shutter()
+
+    yield str(
+        calib.calculate_extinction(
+            calib.swing, calib.I_Black, calib.I_Ext, calib.I_Elliptical
+        )
+    )
+
+    return calib