python-microscopy 25.6.5__cp39-cp39-win_amd64.whl

PYME/Acquire/Hardware/focus_locks/reflection_focus_lock.py

@@ -0,0 +1,684 @@
+
+# This file is for focus locks which involve some sort of reflection off of the coverslip.
+from simple_pid import PID
+import os
+import numpy as np
+from scipy import optimize
+from PYME.util import webframework
+import requests
+import threading
+import logging
+logger = logging.getLogger(__name__)
+import time
+try:
+    # get monotonic time to ensure that time deltas are always positive
+    _current_time = time.monotonic
+except AttributeError:
+    # time.monotonic() not available (using python < 3.3), fallback to time.time()
+    _current_time = time.time
+
+
+class GaussFitter1D(object):
+    """
+    1D gaussian fitter for use with focus locks which either have line-cameras, or whose frames are summed alone one
+    direction to create a line profile, the peak position of which indicates the current focal position.
+    """
+    def __init__(self, maxfev=200, min_amp=0, max_sigma=np.finfo(float).max):
+        """
+
+        Parameters
+        ----------
+        maxfev: int
+            see scipy.optimize.leastsq argument by the same name
+        min_amp : float
+            minimum fit result amplitude which we are willing to accept as a
+            successful fit.
+        max_sigma : float
+            maximum fit result sigma which we are willing to accept as a
+            successful fit.
+        """
+        self.maxfev = maxfev
+        self._min_amp = min_amp
+        self._max_sigma = max_sigma
+
+    def _model_function(self, parameters, position):
+        """
+        1D gaussian
+        Parameters
+        ----------
+        parameters : tuple
+            fit model parameters
+        distance : ndarray
+            1D position array [pixel]
+        Returns
+        -------
+        model : ndarray
+        """
+        amplitude, center, sigma, bx, b = parameters
+        return amplitude * np.exp(-((position - center) ** 2) / (2 * sigma ** 2)) + bx * position + b
+
+    def _error_function(self, parameters, position, data):
+        """
+        """
+        return data - self._model_function(parameters, position)
+
+    def _calc_guess(self, position, data):
+        offset = data.min()
+        amplitude = data.max() - offset
+        max_ind = np.argmax(data)
+        fwhm = np.sum(data > offset + 0.5 * amplitude)
+        # amplitude, center, sigma, bx, b = parameters
+        return amplitude, position[max_ind], fwhm / 2.355, (data[-1] - data[0]) / (position[-1] - data[0]), offset
+
+    def fit(self, position, data):
+        guess = self._calc_guess(position, data)
+
+        (res, cov_x, infodict, mesg, res_code) = optimize.leastsq(self._error_function, guess, args=(position, data),
+                                                                 full_output=True, maxfev=self.maxfev)
+
+        success = res_code > 0 and res_code < 5 and res[0] > self._min_amp and res[2] < self._max_sigma
+        return tuple(res.astype('f')), success
+        
+        # # estimate uncertainties
+        # residuals = infodict['fvec']  # note that fvec is error function evaluation, or (data - model_function)
+        # try:
+        #     # calculate residual variance, a.k.a. reduced chi-squared
+        #     residual_variance = np.sum(residuals ** 2) / (len(position) - len(guess))
+        #     # multiply cov by residual variance for estimating parameter variance
+        #     errors = np.sqrt(np.diag(residual_variance * cov_x))
+        # except (
+        #         TypeError,
+        #         ValueError) as e:  # cov_x is None for singular matrices -> ~no curvature along at least one dimension
+        #     print(str(e))
+        #     errors = -1 * np.ones_like(res)
+        #
+        # return tuple(res.astype('f')), tuple(errors.astype('f'))
+
+class ReflectedLinePIDFocusLock(PID):
+    """
+    The hardware implementation of this focus lock is an NIR laser piped into the objective straight, but slightly off-
+    center, such that some of it is reflected off of the coverslip-to-(sample immersion media) interface and collected
+    by the objective. This light then passes through a beamsplitter and is imaged as a stripe onto a camera using a
+    cylindrical lens. The stripe's (in our case, vertical) position on the camera therefore indicates the distance
+    betweem the objective and the sample.
+
+    This class takes camera frames, sums them along the direction parallel to the stripe, crops a part of the resulting
+    1D line profile and fits it using the GaussianFitter1D class above. The center position of the fitted Gaussian is
+    fed into the PID servo to determine an appropriate correction. We use an "offsetPiezo" so that we can image fields
+    of view with axial coordinates relative to the coverslip rather than absolute axial position (which is influenced by
+    coverslips sagging from media, etc.).
+    """
+    def __init__(self, scope, piezo, p=1., i=0.1, d=0.05, sample_time=0.01, 
+                 mode='frame', fit_roi_size=75, min_amp=0, 
+                 max_sigma=np.finfo(float).max, min_lateral_sigma=0,
+                 trigger_failsafe=True, multiplier=1):
+        """
+
+        Parameters
+        ----------
+        scope: PYME.Acquire.Hardware.microscope.Microscope
+        piezo: PYME.Acquire.Hardware.Piezos.offsetPiezoREST.OffsetPiezoClient
+        p: float
+        i: float
+        d: float
+        sample_time: float
+            See simple_pid.PID, but this servo does not have a tolerance on the lock position, but rather a dead-time
+            of-sorts by only updating at ~regular time intervals. The correction is only changed once per sample_time.
+        mode: str
+            flag, where 'frame' queries on each frame and 'time' queries at fixed times by polling at sample_time
+        fit_roi_size : int
+            size of profile to crop about the peak for actual fitting, allowing
+            us to fit partial profiles and save some time
+        min_amp : float
+            minimum fit result amplitude which we are willing to accept as a
+            valid peak measurement we can use to correct the focus.
+        max_sigma : float
+            maximum fit result sigma which we are willing to accept as a valid
+            peak measurement we can use to correct the focus.
+        min_lateral_sigma : float
+            minimum standard dev along the dimension we sum (squash) to get the
+            profile. If the lateral sigma is below this we reject the frame for
+            fitting because we expect a long spread profile.
+        trigger_failsafe : bool
+            if True, try to kill lasers if the profile intensity saturates a
+            majority of the pixels on the focus lock camera
+        
+        """
+        self.scope = scope
+        self.piezo = piezo
+        self._piezo_control_lock = threading.Lock()
+        self._piezo_home = 0.5 * (self.piezo.GetMax() - self.piezo.GetMin())
+
+        self._lock_ok = False
+        self._ok_tolerance = 5
+
+        self.fit_roi_size = fit_roi_size
+        self._fitter = GaussFitter1D(min_amp=min_amp, max_sigma=max_sigma)
+        self._min_lateral_sigma = min_lateral_sigma
+        
+        self.peak_position = self.scope.frameWrangler.currentFrame.shape[1] * 0.5  # default to half of the camera size
+        self.subtraction_profile = None
+
+        self.use_failsafe = trigger_failsafe and hasattr(scope, 'failsafe')
+
+        PID.__init__(self, p, i, d, setpoint=self.peak_position, auto_mode=False, sample_time=sample_time)
+
+        self._mode = mode
+        self._polling = False
+        self.multiplier = multiplier
+
+    @property
+    def mode(self):
+        return self._mode
+
+    @mode.setter
+    def mode(self, update_mode):
+        self.deregister()
+        self._mode = update_mode
+        self.register()
+
+    def _poll(self):
+        while self._polling:
+            t = time.time()
+            self.on_frame()
+            # throttle this to whatever we set cycle time to
+            time.sleep(max(self.sample_time - time.time() - t, 0))
+
+
+    def StartPolling(self):
+        self._polling = True
+        self._thread = threading.Thread(target=self._poll)
+        self._thread.start()
+
+    def StopPolling(self):
+        self._polling = False
+        self._thread.join()
+
+    @webframework.register_endpoint('/GetPeakPosition', output_is_json=False)
+    def GetPeakPosition(self):
+        return self.peak_position
+
+    @webframework.register_endpoint('/LockEnabled', output_is_json=False)
+    def LockEnabled(self):
+        return self.auto_mode
+
+    @webframework.register_endpoint('/EnableLock', output_is_json=False)
+    def EnableLock(self, enable=True):
+        """
+        Returns offset to last-known offset before enabling the lock.
+
+        The servo is generally more robust to changing its setpoint when it is running than when you toggle it off, move
+        off the setpoint, and then slam it on again. This just makes the slam small.
+        """
+
+        # enable could be a string
+        enable = enable and not (enable == 'False')
+
+        if enable:
+            # make sure piezo is ready
+            retry = 0
+            while not self.piezo.OnTarget() and retry < 3:
+                logger.debug('waiting for piezo to stop moving')
+                time.sleep(0.1)
+                retry += 1
+            logger.debug('Enabling focus lock')
+            self.set_auto_mode(True)
+        else: # disable
+            # take out the lock so we can log offset and disable 'at once'
+            with self._piezo_control_lock:
+                self.piezo.LogFocusCorrection(self.piezo.GetOffset())
+                self.set_auto_mode(False)
+                logger.debug('Disabling focus lock')
+    
+    @webframework.register_endpoint('/EnableLockAndHome', output_is_json=False)
+    def EnableLockAndHome(self):
+        self.EnableLock()
+        self.piezo.MoveTo(0, self._piezo_home)
+
+    @webframework.register_endpoint('/DisableLock', output_is_json=False)
+    def DisableLock(self):
+        self.EnableLock(False)
+
+    def register(self):
+        if self.mode == 'time':
+            self.StartPolling()
+        else:
+            self.scope.frameWrangler.onFrameGroup.connect(self.on_frame)
+
+    def deregister(self):
+        if self.mode == 'time':
+            self.StopPolling()
+        else:
+            self.scope.frameWrangler.onFrameGroup.disconnect(self.on_frame)
+
+    @webframework.register_endpoint('/ToggleLock', output_is_json=False)
+    def ToggleLock(self):
+        self.set_auto_mode(~self.auto_mode)
+
+    @webframework.register_endpoint('/ChangeSetpoint', output_is_json=False)
+    def ChangeSetpoint(self, setpoint=None):
+        if setpoint is None:
+            self.setpoint = self.peak_position
+        else:
+            self.setpoint = float(setpoint)
+    
+    @webframework.register_endpoint('/UpdateHome', output_is_json=False)
+    def UpdateHome(self, home):
+        self._piezo_home = float(home)
+
+    @webframework.register_endpoint('/SetSubtractionProfile', output_is_json=False)
+    def SetSubtractionProfile(self):
+        """
+        Set a profile to subtract before any fitting is performed on each frame
+        Returns
+        -------
+
+        """
+        self.subtraction_profile = self.scope.frameWrangler.currentFrame.squeeze().sum(axis=0).astype(float)
+
+
+    @property
+    def fit_roi_size(self):
+        return self._fit_roi_size
+
+    @fit_roi_size.setter
+    def fit_roi_size(self, roi_size):
+        self._fit_roi_size = roi_size
+        self._roi_position = np.arange(roi_size)
+    
+    @webframework.register_endpoint('/LockOK', output_is_json=False)
+    def LockOK(self):
+        """Check whether the lock is enabled, and the lock is on target
+
+        Returns
+        -------
+        bool
+            lock is enabled and on-target
+        """
+        return self.LockEnabled() and self.lockable()
+    
+    def lockable(self, tolerance=None):
+        """check whether the profile is being fit OK and within tolerance of the
+        setpoint
+
+        Parameters
+        ----------
+        tolerance : float, optional
+            maximum deviation, in pixels, to be considered 'lockable', by 
+            default None
+
+        Returns
+        -------
+        bool
+            whether the focus lock _could_ lock easily if we enabled it
+        """
+        return self._lock_ok and self.on_target(tolerance)
+    
+    def on_target(self, tolerance=None):
+        """check whether the focus lock profile is within a target tolerance of
+        the setpoint
+
+        Parameters
+        ----------
+        tolerance : float, optional
+            maximum deviation, in pixels, to be considered 'lockable', by 
+            default None
+
+        Returns
+        -------
+        bool
+            whether the last-updated focus lock profile was sufficiently close 
+            to where we want it
+        """
+        if tolerance == None:
+            tolerance = self._ok_tolerance
+        return bool(abs(self.peak_position - self.setpoint) < tolerance)
+    
+    @webframework.register_endpoint('/ReacquireLock', output_is_json=False)
+    def ReacquireLock(self, start_at=0.0, step_size=3., pause=0.75, retries=0):
+        """Routine to call if we've lost the lock. The lock is disabled,
+        objective is moved to its lowest position, and we step upwards gradually
+        until we get decent fits on the profile and the profile is sufficiently
+        close to where we think it should be, then we renabled. Objective will
+        be sent back to its lowest position if we cannot reacquire the lock.
+
+        Parameters
+        ----------
+        start_at: float, optional
+            offset to start the scan at (10 positions chosen 'spirally' out
+            before linearly stepping through the range from bottom up)
+        step_size : float, optional
+            number of microns to step the objective position by when searching, 
+            by default 3.
+        pause : float, optional
+            seconds to pause after each offset change before checking if we can
+            lock
+        """
+        from itertools import zip_longest
+        step_size = float(step_size)
+        start_at = float(start_at)
+        pause = float(pause)
+        logger.info('reacquiring lock')
+        self.DisableLock()
+
+        # get our range
+        min_offset = self.piezo.GetMinOffset()
+        max_offset = self.piezo.GetMaxOffset()
+        start_at = max(min_offset, min(max_offset, start_at))  # clip
+        
+        # set up scan positions
+        scan_up = np.arange(start_at, max_offset + step_size, step_size).tolist()
+        scan_up.append(max_offset)
+        scan_down = np.arange(start_at - step_size, min_offset, -step_size).tolist()
+        scan_down.append(min_offset)
+        scan_positions = [item for sub in zip_longest(scan_up, scan_down) for item in sub]
+        scan_positions = [pos for pos in scan_positions if pos is not None]
+        assert len(scan_positions) > 0
+        cut = min(len(scan_positions), 10)
+        # try not to be overly mean to the pifoc, step small after first 10
+        scan_positions = scan_positions[:cut] + sorted(scan_positions)
+
+        n = -1
+        while n < retries:
+            n += 1
+            for pos in scan_positions:
+                logger.debug('looking for focus, offset: %.1f' % pos)
+                self.piezo.SetOffset(pos)
+
+                time.sleep(pause)
+                if self.lockable(self._ok_tolerance):
+                    logger.info('found focus, offset %.1f' % pos)
+                    self.EnableLock()
+                    return
+        
+        logger.debug('failed to find focus, lowering objective')
+        self.piezo.SetOffset(min_offset)
+    
+    @webframework.register_endpoint('/DisableLockAfterAcquiring', 
+                                    output_is_json=False)
+    def DisableLockAfterAcquiring(self, target_tolerance=1):
+        self.EnableLock()  # make sure we have the lock on
+        if not self.on_target(float(target_tolerance)):
+            logger.info('not locked to target tolerance, waiting 0.5 s')
+            time.sleep(0.5)
+        if not self.LockOK():
+            logger.info('lock not OK, pausing for 5 s')
+            time.sleep(5)
+            if not self.LockOK():
+                logger.info('still not OK, starting pause/reacquire sequence')
+                time.sleep(5)
+                if hasattr(self.scope, '_stage_leveler'):
+                    pos = self.scope.GetPos()
+                    offset = self.scope._stage_leveler.lookup_offset(pos['x'],
+                                                                     pos['y'])
+                    self.ReacquireLock(start_at=offset)
+                else:
+                    self.ReacquireLock()
+                time.sleep(0.5)
+            else:
+                logger.debug('lock OK')
+        
+        self.DisableLock()
+    
+    @webframework.register_endpoint('/DisableLockAfterAcquiringIfEnabled', 
+                                    output_is_json=False)
+    def DisableLockAfterAcquiringIfEnabled(self, target_tolerance=1):
+        """
+        Helper function to allow protocols used in automated workflows to make 
+        sure they have the right focal plane without barring that protocols
+        use for manual imaging without the focus lock on/set up
+        """
+        if self.LockEnabled():
+            self.DisableLockAfterAcquiring(float(target_tolerance))
+    
+    @property
+    def _failsafe_threshold(self):
+        frame_shape = self.scope.frameWrangler.currentFrame.shape
+        return 0.5 * frame_shape[0] * frame_shape[1] * self.scope.cam.noise_properties['SaturationThreshold']
+
+    def find_peak(self, profile):
+        """
+
+        Parameters
+        ----------
+        profile: np.ndarray
+            1D array of the pixel intensities after summing along direction orthogonal to axis the focus-lock beam moves
+            along
+
+        Returns
+        -------
+        success : bool
+            Whether the fit converged
+        peak_position : float
+            center position of the reflection on the camera [pix]
+
+        """
+        crop_start = np.argmax(profile) - int(0.5 * self._fit_roi_size)
+        start, stop = max(crop_start, 0), min(crop_start + self.fit_roi_size, profile.shape[0])
+        self._fit_results, success = self._fitter.fit(self._roi_position[:stop - start], profile[start:stop])
+        return self._fit_results[1] + start, success
+
+    def on_frame(self, **kwargs):
+        # get focus position
+        cf = self.scope.frameWrangler.currentFrame.squeeze()
+        profile = cf.sum(axis=0).astype(float)
+        
+        if self.use_failsafe and profile.sum() > self._failsafe_threshold:
+            self.scope.failsafe.kill(message='focus lock profile suggests heat danger')
+        
+        try:
+            assert np.std(cf.sum(axis=1)) > self._min_lateral_sigma
+            
+            if self.subtraction_profile is not None:
+                peak_position, success = self.find_peak(profile - self.subtraction_profile)
+            else:
+                peak_position, success = self.find_peak(profile)
+            assert success
+        except AssertionError:
+            self._lock_ok = False
+            # restart the integration / derivatives so we don't go wild when we
+            # eventually get a good fit again
+            self.reset()
+            return
+        
+        self.peak_position = peak_position
+        self._lock_ok = True
+
+        # calculate correction
+        elapsed_time =_current_time() - self._last_time
+        correction = self(self.peak_position)
+        # note that correction only updates if elapsed_time is larger than sample time - don't apply same correction 2x.
+        with self._piezo_control_lock:
+            if self.auto_mode and elapsed_time > self.sample_time:
+                # logger.debug('Correction: %.2f' % correction)
+                # logger.debug('components %s' % (self.components,))
+                self.piezo.CorrectOffset(correction*self.multiplier)
+
+
+class RLPIDFocusLockClient(object):
+    def __init__(self, host='127.0.0.1', port=9798, name='focus_lock'):
+        self.host = host
+        self.port = port
+        self.name = name
+
+        self.base_url = 'http://%s:%d' % (host, port)
+        self._session = requests.Session()
+        self._enabled = False
+
+    @property
+    def lock_enabled(self):
+        """Returns a cached version of the lock state, which while helpful in
+        some instances (notably whether to accept a correction from the server)
+        should usually not replace `LockEnabled`
+
+        Returns
+        -------
+        bool
+        """
+        return self._enabled
+
+    def LockEnabled(self):
+        response = self._session.get(self.base_url + '/LockEnabled')
+        self._enabled = bool(response.json())
+        return self.lock_enabled
+    
+    def LockOK(self):
+        response = self._session.get(self.base_url + '/LockOK')
+        return bool(response.json())
+
+    def EnableLock(self, enable=True):
+        self._enabled = enable
+        return self._session.get(self.base_url + '/EnableLock?enable=%s' % enable)
+    
+    def EnableLockAndHome(self):
+        self._enabled = True
+        return self._session.get(self.base_url + '/EnableLockAndHome')
+
+    def DisableLock(self):
+        self._enabled = False
+        r = self._session.get(self.base_url + '/DisableLock')
+        return r
+
+    def GetPeakPosition(self):
+        response = self._session.get(self.base_url + '/GetPeakPosition')
+        return float(response.json())
+
+    def ChangeSetpoint(self, setpoint=None):
+        if setpoint is None:
+            setpoint = self.GetPeakPosition()
+        return self._session.get(self.base_url + '/ChangeSetpoint?setpoint=%3.3f' % (setpoint,))
+    
+    def UpdateHome(self, home):
+        return self._session.get(self.base_url + '/UpdateHome?home=%3.3f' % (home,))
+
+    def ToggleLock(self):
+        if self.lock_enabled:
+            self.DisableLock()
+        else:
+            self.EnableLock()
+
+    def SetSubtractionProfile(self):
+        return self._session.get(self.base_url + '/SetSubtractionProfile')
+    
+    def ReacquireLock(self, start_at=0, step_size=3):
+        return self._session.get(self.base_url + '/ReacquireLock?step_size=%3.3f&start_at=%3.3f' % (step_size, start_at))
+    
+    def DisableLockAfterAcquiring(self, target_tolerance=1):
+        self._enabled = False
+        r = self._session.get(self.base_url + '/DisableLockAfterAcquiring?target_tolerance=%3.3f' % target_tolerance)
+        return r
+    
+    def DisableLockAfterAcquiringIfEnabled(self, target_tolerance=1):
+        self._enabled = False
+        r = self._session.get(self.base_url + '/DisableLockAfterAcquiringIfEnabled?target_tolerance=%3.3f' % target_tolerance)
+        return r
+
+
+class RLPIDFocusLockServer(webframework.APIHTTPServer, ReflectedLinePIDFocusLock):
+    def __init__(self, scope, piezo, port=9798, **kwargs):
+        ReflectedLinePIDFocusLock.__init__(self, scope, piezo, **kwargs)
+
+        server_address = ('127.0.0.1', port)
+        self.port = port
+
+
+        webframework.APIHTTPServer.__init__(self, server_address)
+        self.daemon_threads = True
+
+        self._server_thread = threading.Thread(target=self._thread_target)
+        self._server_thread.daemon_threads = True
+
+        self._server_thread.start()
+
+    @property
+    def lock_enabled(self):
+        return self.auto_mode
+
+    def _thread_target(self):
+        try:
+            logger.info('Starting piezo on 127.0.0.1:%d' % (self.port,))
+            self.serve_forever()
+        finally:
+            logger.info('Shutting down ...')
+            self.shutdown()
+            self.server_close()
+
+
+class FocusLogger(object):
+    _dtype = [('time', '<f4'), ('focus', '<f4')]
+
+    def __init__(self, position_handle, log_interval=1.0):
+        """
+        Logs focus position (or really any float return by the function passed
+        to this initialization) to and hdf file at a specified interval.
+
+        Parameters
+        ----------
+        position_handle : function
+            function handle to call to get position to log.
+        log_interval : float, optional
+            approximate time between successive logs, in seconds, by default 1.0
+        """
+        self._position_handle = position_handle
+        self._log_file = None
+        self._log_interval = log_interval
+        self._poll_thread = None
+        self._logging = False
+        self._start_time = 0
+    
+    def set_interval(self, log_interval):
+        self._log_interval = log_interval
+    
+    def ensure_stopped(self):
+        """
+        Stop any current logging. Note that we let the h5rFile poll thread
+        do the hdf file closing
+        """
+        self._logging = False
+        try:
+            self._poll_thread.join()
+        except AttributeError:
+            pass
+    
+    def start_logging(self, log_file, log_interval=None):
+        """
+        Create a log file and start storing focus position values at a set time
+        interval.
+
+        Parameters
+        ----------
+        log_file : str
+            path to create hdf file storing contents in `focus_log` table.
+        log_interval : float, optional
+            approximate time between successive logs, in seconds, by default 1.
+        """
+        from PYME.IO.h5rFile import H5RFile
+
+        self.ensure_stopped()
+        if log_interval != None:
+            self.set_interval(log_interval)
+            
+        log_dir, log_stub = os.path.split(log_file)
+        os.makedirs(log_dir, exist_ok=True)
+        log_stub, ext = os.path.splitext(log_file)
+        if ext != '.hdf':
+            log_file = os.path.join(log_dir, log_stub + '.hdf')
+        
+        self._log_file = H5RFile(log_file, mode='a', 
+                                 keep_alive_timeout=max(20.0, 
+                                                        self._log_interval))
+        self._logging = True
+        self._poll_thread = threading.Thread(target=self._poll)
+        logger.debug('starting focus logger')
+        self._start_time = _current_time()
+        self._poll_thread.start()
+    
+    def _poll(self):
+        while self._logging:
+            d = np.array([(_current_time() - self._start_time, 
+                           self._position_handle())],
+                         dtype=self._dtype)
+            
+            self._log_file.appendToTable('focus_log', d)
+
+            time.sleep(self._log_interval)