Close ni tasks

src/navigate/controller/thread_pool.py

@@ -97,11 +97,7 @@ def run(self):
             try:
                 self._target(*self._args, **self._kwargs)
             except Exception as e:
-                print(
-                    f"{self.name} thread ended because of exception!: {e}",
-                    traceback.format_exc(),
-                )
-                logger.debug(
+                logger.exception(
                     f"{self.name} thread ended because of exception!: {e}",
                     traceback.format_exc(),
                 )
@@ -251,13 +247,7 @@ def func(*args, **kwargs):
                 try:
                     target(*args, **kwargs)
                 except Exception as e:
-                    print(
-                        threading.current_thread().name,
-                        "thread exception happened!",
-                        e,
-                        traceback.format_exc(),
-                    )
-                    logger.debug(
+                    logger.exception(
                         threading.current_thread().name,
                         "thread exception happened!",
                         e,
@@ -422,10 +412,11 @@ def localtrace(self, frame, event, arg):
         """
 
         if event == "exception":
-            print("****in local trace: exception stops the thread")
-            logger.debug("****in local trace: exception stops the thread")
             if os.getenv("GITHUB_ACTIONS") == "true":
                 return
+
+            # Silence traceback to avoid printing to console.
+            sys.tracebacklimit = 0
             raise SystemExit()
         return self.localtrace
 

src/navigate/model/devices/camera/hamamatsu.py

@@ -143,7 +143,7 @@ def __str__(self):
 
     def __del__(self):
         """Delete HamamatsuOrca class."""
-        pass
+        self.close_camera()
 
     @property
     def serial_number(self):

src/navigate/model/devices/daq/ni.py

@@ -110,8 +110,23 @@ def __str__(self) -> str:
 
     def __del__(self) -> None:
         """Destructor."""
-        if self.camera_trigger_task is not None:
-            self.stop_acquisition()
+        for task in [self.camera_trigger_task, self.master_trigger_task, self.laser_switching_task]:
+            if task:
+                try:
+                    task.stop()
+                    task.close()
+                except Exception:
+                    logger.exception(f"Error stopping task: {traceback.format_exc()}")
+
+        if self.analog_output_tasks:
+            for k, task in self.analog_output_tasks.items():
+                if task:
+                    try:
+                        task.stop()
+                        task.close()
+                    except Exception:
+                        logger.exception(f"Error stopping task: {traceback.format_exc()}")
+
 
     def set_external_trigger(self, external_trigger=None) -> None:
         """Set trigger mode.
@@ -220,7 +235,7 @@ def wait_for_external_trigger(
             return False
         # Create a digital input task and wait until either a trigger is detected,
         # or the timeout is exceeded. If timeout < 0, wait forever...
-        external_trigger_task = nidaqmx.Task("WaitDigitalEdge")
+        external_trigger_task = nidaqmx.Task()
         external_trigger_task.di_channels.add_di_chan(trigger_channel)
 
         total_wait_time = 0.0

src/navigate/model/devices/filter_wheel/asi.py

@@ -87,15 +87,15 @@ def __init__(self, device_connection, device_config):
 
         Parameters
         ----------
-        device_connection : dict
-            Dictionary of device connections.
+        device_connection : TigerController
+            Communication object for the ASI Filter Wheel.
         device_config : dict
             Dictionary of device configuration parameters.
         """
 
         super().__init__(device_connection, device_config)
 
-        #: obj: ASI Tiger Controller object.
+        #: TigerController: ASI Tiger Controller object.
         self.filter_wheel = device_connection
 
         #: dict: Configuration dictionary.
@@ -170,6 +170,10 @@ def close(self):
             logger.debug("ASI Filter Wheel - Closing Device.")
             self.filter_wheel.disconnect_from_serial()
 
+    def __del__(self):
+        """Destructor for the ASIFilterWheel class."""
+        self.close()
+
 
 @log_initialization
 class ASICubeSlider(FilterWheelBase):

src/navigate/model/devices/filter_wheel/base.py

@@ -32,6 +32,7 @@
 
 #  Standard Library Imports
 import logging
+from typing import Any, Dict
 
 # Third Party Imports
 
@@ -47,20 +48,20 @@
 class FilterWheelBase:
     """FilterWheelBase - Parent class for controlling filter wheels."""
 
-    def __init__(self, device_connection, device_config):
+    def __init__(self, device_connection: Any, device_config: Dict[str, Any]) -> None:
         """Initialize the FilterWheelBase class.
 
         Parameters
         ----------
-        device_connection : dict
-            Dictionary of device connections.
-        device_config : dict
+        device_connection : Any
+            The communication instance with the device.
+        device_config : Dict[str, Any]
             Dictionary of device configuration parameters.
         """
-        #: object: Device connection object.
+        #: Any: Device connection object.
         self.device_connection = device_connection
 
-        #: dict: Dictionary of device configuration parameters.
+        #: Dict[str, Any]: Dictionary of device configuration parameters.
         self.device_config = device_config
 
         #: dict: Dictionary of filters available on the filter wheel.
@@ -72,10 +73,14 @@ def __init__(self, device_connection, device_config):
         #: int: index of filter wheel
         self.filter_wheel_number = device_config["hardware"]["wheel_number"]
 
-    def __str__(self):
+    def __str__(self) -> str:
         """Return the string representation of the FilterWheelBase class."""
         return "FilterWheelBase"
 
+    def __del__(self) -> None:
+        """Destructor for the FilterWheelBase class."""
+        pass
+
     def check_if_filter_in_filter_dictionary(self, filter_name: str) -> bool:
         """Checks if the filter designation (string) given exists in the
         filter dictionary

src/navigate/model/devices/filter_wheel/ludl.py

@@ -161,3 +161,8 @@ def close(self):
         logger.debug("LUDLFilterWheel - Closing the Filter Wheel Serial Port")
         self.set_filter(list(self.filter_dictionary.keys())[0])
         self.serial.close()
+
+    def __del__(self):
+        """Destructor for the LUDLFilterWheel class."""
+        if self.serial.is_open:
+            self.close()

src/navigate/model/devices/filter_wheel/ni.py

@@ -33,6 +33,7 @@
 #  Standard Library Imports
 import logging
 import time
+import traceback
 
 # Third Party Imports
 import nidaqmx
@@ -144,9 +145,18 @@ def set_filter(self, filter_name, wait_until_done=True):
             except DaqError as e:
                 logger.debug(e)
 
-    def close(self):
+    def close(self) -> None:
         """Close the DAQ Filter Wheel
 
         Sets the filter wheel to the home position and then closes the port.
         """
         pass
+
+    def __del__(self) -> None:
+        """Delete the DAQFilterWheel object."""
+        if self.filter_wheel_task:
+            try:
+                self.filter_wheel_task.stop()
+                self.filter_wheel_task.close()
+            except Exception:
+                logger.exception(f"Error stopping task: {traceback.format_exc()}")

src/navigate/model/devices/filter_wheel/sutter.py

@@ -62,7 +62,7 @@ def build_filter_wheel_connection(comport, baudrate, timeout=0.25):
     Returns
     -------
     serial.Serial
-        Serial port connection to the filter wheel.
+        The serial port connection to the filter wheel.
 
     Raises
     ------
@@ -94,17 +94,18 @@ def __init__(self, device_connection, device_config):
 
         Parameters
         ----------
-        device_connection : dict
-            Dictionary of device connections.
-        device_config : dict
+        device_connection : serial.Serial
+            The communication instance with the filter wheel.
+        device_config : Dict[str, Any]
             Dictionary of device configuration parameters.
         """
         super().__init__(device_connection, device_config)
 
-        #: obj: Serial port connection to the filter wheel.
+        #: serial.Serial: Serial port connection to the filter wheel.
         self.serial = device_connection
 
-        #: dict: Dictionary of filter names and corresponding filter wheel positions.
+        #: Dict[str, Any]: Dictionary of filter names and corresponding filter wheel
+        # positions.
         self.device_config = device_config
 
         #: bool: Wait until filter wheel has completed movement.
@@ -146,20 +147,11 @@ def __init__(self, device_connection, device_config):
         # Set filter to the 0th position by default upon initialization.
         self.set_filter(list(self.filter_dictionary.keys())[0])
 
-    def __str__(self):
+    def __str__(self) -> str:
         """String representation of the class."""
         return "SutterFilterWheel"
 
-    def __enter__(self):
-        """Enter the SutterFilterWheel context manager."""
-        return self
-
-    def __exit__(self, *args, **kwargs):
-        """Exit the SutterFilterWheel context manager."""
-        logger.debug("SutterFilterWheel - Closing Device.")
-        self.close()
-
-    def filter_change_delay(self, filter_name):
+    def filter_change_delay(self, filter_name: str) -> None:
         """Calculate duration of time necessary to change filter wheel positions.
 
         Calculate duration of time necessary to change filter wheel positions.
@@ -195,7 +187,7 @@ def filter_change_delay(self, filter_name):
         except IndexError:
             self.wait_until_done_delay = 0.01
 
-    def set_filter(self, filter_name, wait_until_done=True):
+    def set_filter(self, filter_name: str, wait_until_done: bool = True):
         """Change the filter wheel to the filter designated by the filter
         position argument.
 
@@ -249,7 +241,7 @@ def set_filter(self, filter_name, wait_until_done=True):
                 # read 0D back.
                 self.read(1)
 
-    def read(self, num_bytes):
+    def read(self, num_bytes: int) -> bytes:
         """Reads the specified number of bytes from the serial port.
 
         Parameters
@@ -259,8 +251,8 @@ def read(self, num_bytes):
 
         Returns
         -------
-        bytes
-            Bytes read from the serial port.
+        response : bytes
+            The bytes read from the serial port.
 
         Raises
         ------
@@ -285,11 +277,16 @@ def read(self, num_bytes):
             )
         return self.serial.read(num_bytes)
 
-    def close(self):
+    def close(self) -> None:
         """Close the SutterFilterWheel serial port.
 
         Sets the filter wheel to the Empty-Alignment position and then closes the port.
         """
         logger.debug("SutterFilterWheel - Closing the Filter Wheel Serial Port")
         self.set_filter(list(self.filter_dictionary.keys())[0])
         self.serial.close()
+
+    def __del__(self) -> None:
+        """Delete the SutterFilterWheel class."""
+        if self.serial.is_open:
+            self.close()

src/navigate/model/devices/filter_wheel/synthetic.py

@@ -108,3 +108,7 @@ def close(self):
         Sets the filter wheel to the Empty-Alignment position and then closes the port.
         """
         pass
+
+    def __del__(self):
+        """Delete the SyntheticFilterWheel."""
+        pass

src/navigate/model/devices/galvo/ni.py

@@ -32,6 +32,7 @@
 
 #  Standard Library Imports
 import logging
+import traceback
 from typing import Any, Dict
 
 # Third Party Imports
@@ -129,5 +130,9 @@ def turn_off(self) -> None:
             task.write([0], auto_start=True)
             task.stop()
             task.close()
-        except Exception as e:
-            print(f"Galvo turn_off error: {e}")
+        except Exception:
+            logger.exception(f"Error stopping task: {traceback.format_exc()}")
+
+    def __del__(self):
+        """Close the GalvoNI at exit."""
+        self.turn_off()

src/navigate/model/devices/lasers/ni.py

@@ -32,6 +32,7 @@
 
 # Standard Library Imports
 import logging
+import traceback
 from typing import Any, Dict
 
 # Third Party Imports
@@ -234,3 +235,17 @@ def close(self) -> None:
                 self.laser_do_task.close()
         except DaqError as e:
             logger.exception(e)
+
+    def __del__(self):
+        """Delete the NI Task before exit."""
+        if self.laser_ao_task:
+            try:
+                self.laser_ao_task.close()
+            except Exception as e:
+                logger.exception(f"Error stopping task: {traceback.format_exc()}")
+
+        if self.laser_do_task:
+            try:
+                self.laser_do_task.close()
+            except Exception as e:
+                logger.exception(f"Error stopping task: {traceback.format_exc()}")

src/navigate/model/devices/mirrors/base.py

@@ -57,7 +57,7 @@ def __init__(self, microscope_name, device_connection, configuration):
             Name of microscope in configuration
         device_connection : object
             Hardware device to connect to
-        configuration : multiprocesing.managers.DictProxy
+        configuration : multiprocessing.managers.DictProxy
             Global configuration of the microscope
         """
         if microscope_name not in configuration["configuration"]["microscopes"].keys():
@@ -81,3 +81,7 @@ def __init__(self, microscope_name, device_connection, configuration):
     def __str__(self):
         """Return the string representation of the mirror."""
         return "MirrorBase"
+
+    def __del__(self) -> None:
+        """Delete the MirrorBase class."""
+        pass

src/navigate/model/devices/mirrors/imop.py

@@ -73,6 +73,10 @@ def __init__(self, microscope_name, device_connection, configuration):
         # flatten the mirror
         self.flat()
 
+    def __del__(self) -> None:
+        """Delete the ImagineOpticsMirror class."""
+        pass
+
     def flat(self):
         """Move the mirror to the flat position."""
         self.mirror_controller.flat()