this runs on demo mode without updating the events for the stage. Ass…

…umes that there are shifts computed and returned.

mantis/acquisition/AcquisitionSettings.py

@@ -141,6 +141,7 @@ class MicroscopeSettings:
     use_o3_refocus: bool = False
     o3_refocus_config: Optional[ConfigSettings] = None
     o3_refocus_interval_min: Optional[int] = None
+    autotracker_config: Optional[ConfigSettings] = None
 
 
 @dataclass
@@ -198,17 +199,17 @@ def __post_init__(self):
 @dataclass
 class AutotrackerSettings:
     tracking_method: Literal['phase_cross_correlation', 'template_matching', 'multi_otsu']
+    tracking_interval: Optional[int] = 1
+    scale_yx: Optional[float] = 1.0
+    shift_limit: Optional[Union[Tuple[float, float, float], 'None']] = None
     device: Optional[str] = 'cpu'
-    tracking_arm: Literal['lf', 'ls'] = 'lf'
-    channel_to_track: Optional[str] = None
-    zyx_dampening_factor: Optional[float, float, float] = None
-    re_run_every_n_timepoints: Optional[int] = None
+    zyx_dampening_factor: Optional[Union[Tuple[float, float, float], None]] = None
     # TODO: maybe do the ROI like in the ls_microscope_settings
     template_roi_zyx: Optional[Tuple[int, int, int]] = None
     template_channel: Optional[str] = None
 
-    @validator("autotracker_method")
-    def check_autotracker_methods_options(cls, v):
+    @validator("tracking_method")
+    def check_tracking_method_options(cls, v):
         # Check if template matching options are provided and are not None
         if v == 'template_matching':
             if not all([cls.template_roi_zyx, cls.template_channel]):

mantis/acquisition/acq_engine.py

@@ -50,7 +50,7 @@
     check_ls_acq_finished,
 )
 
-# isort: on
+from mantis.acquisition.autotracker import autotracker_hook_fn
 
 
 # Define constants
@@ -212,9 +212,12 @@ def autoexposure_settings(self, settings: AutoexposureSettings):
 
     @autotracker_settings.setter
     def autotracker_settings(self, settings: AutotrackerSettings):
-        logger.debug(
-            f"{self.type.capitalize()} acquisition will have the following settings:{asdict(settings)}"
-        )
+        if settings is None:
+            logger.debug('Autotracker settings are not provided')
+        else:
+            logger.debug(
+                f"{self.type.capitalize()} acquisition will have the following settings:{asdict(settings)}"
+            )
         self._autotracker_settings = settings
 
     def setup(self):
@@ -350,6 +353,8 @@ def __init__(
         self._lf_acq_obj = None
         self._ls_acq_obj = None
 
+        globals.demo_run = demo_run
+
         if not enable_lf_acq or not enable_ls_acq:
             raise Exception('Disabling LF or LS acquisition is not currently supported')
 
@@ -686,20 +691,8 @@ def setup_autoexposure(self):
                     )
 
     def setup_autotracker(self):
-        if self._demo_run:
-            # TODO: implement autotracker in demo mode
-            logger.debug('Autotracker is not supported in demo mode')
-            return
-
-        if self.lf_acq.microscope_settings.use_autotracker:
-            logger.debug('Setting up autotracker')
-            microscope_operations.setup_autotracker(
-                self.lf_acq.mmc,
-                self.lf_acq.microscope_settings.autotracker_channel,
-                self.lf_acq.microscope_settings.autotracker_threshold,
-            )
-        else:
-            logger.debug('Autotracker is not enabled in the microscope settings')
+        logger.info('Setting up autotracker')
+        # TODO: probably setup the GPU/CPU settings here
 
     def go_to_position(self, position_index: int):
         # Move slowly for short distances such that autofocus can stay engaged.
@@ -1007,7 +1000,7 @@ def setup(self):
         logger.debug('Setting up autoexposure')
         self.setup_autoexposure()
 
-        logger.debug('Setting up auotracker')
+        logger.debug('Setting up autotracker')
         self.setup_autotracker()
 
     def acquire(self):
@@ -1029,7 +1022,20 @@ def acquire(self):
                 start_daq_counters, [self._lf_z_ctr_task, self._lf_channel_ctr_task]
             )
         lf_post_hardware_hook_fn = log_acquisition_start
-        lf_image_saved_fn = check_lf_acq_finished
+
+        # TODO: implement logic for the autotracker_img_saved_hook_fn
+        if self.lf_acq.microscope_settings.autotracker_config is not None:
+            lf_image_saved_fn = partial(
+                autotracker_hook_fn,
+                'lf',
+                self.lf_acq.autotracker_settings,
+                self.lf_acq.microscope_settings.autotracker_config,
+                self.lf_acq.slice_settings,
+                self._acq_dir,
+            )
+        else:
+            logger.info('No autotracker config found. Using default image saved hook')
+            lf_image_saved_fn = check_lf_acq_finished
 
         # define LF acquisition
         self._lf_acq_obj = Acquisition(
@@ -1059,7 +1065,19 @@ def acquire(self):
                 self.ls_acq.channel_settings.channels,
             )
             ls_post_camera_hook_fn = partial(start_daq_counters, [self._ls_z_ctr_task])
-        ls_image_saved_fn = check_ls_acq_finished
+
+        # TODO: implement logic for the autotracker_img_saved_hook_fn
+        if self.ls_acq.microscope_settings.autotracker_config is not None:
+            ls_image_saved_fn = partial(
+                autotracker_hook_fn,
+                'ls',
+                self.ls_acq.autotracker_settings,
+                self.ls_acq.slice_settings,
+                self._acq_dir,
+            )
+        else:
+            logger.info('No autotracker config found. Using default image saved hook')
+            ls_image_saved_fn = check_ls_acq_finished
 
         # define LS acquisition
         self._ls_acq_obj = Acquisition(
@@ -1134,9 +1152,6 @@ def acquire(self):
                             well_id=well_id,
                             method=self.ls_acq.autoexposure_settings.autoexposure_method,
                         )
-                    # TODO: add logic to handle skipping timepoints
-                    if t_idx < 2:
-                        self.run_autotracker(acq=self.lf_acq, well_id=well_id)
                     # Acq rate needs to be updated even if autoexposure was not rerun in this well
                     # Only do that if we are using autoexposure?
                     self.update_ls_acquisition_rates(