Modified for running in Linux and New stage driver

src/navigate/controller/sub_controllers/tiling.py

@@ -266,26 +266,19 @@ def set_table(self):
         y_stop = float(self.variables["y_end"].get())
         y_tiles = int(self.variables["y_tiles"].get())
 
+        # NOTE: Removed shifting by the origin becuase, it was not clear how to set the origin.
         # shift z by coordinate origin of local z-stack
-        z_start = float(self.variables["z_start"].get()) - float(
-            self.stack_acq_widgets["start_position"].get()
-        )
-        z_stop = float(self.variables["z_end"].get()) - float(
-            self.stack_acq_widgets["end_position"].get()
-        )
+        z_start = float(self.variables["z_start"].get()) # - float(self.stack_acq_widgets["start_position"].get())
+        z_stop = float(self.variables["z_end"].get()) # - float(self.stack_acq_widgets["end_position"].get())
         z_tiles = int(self.variables["z_tiles"].get())
-
+        
         # Default to fixed theta
         r_start = float(self.stage_position_vars["theta"].get())
         r_stop = float(self.stage_position_vars["theta"].get())
         r_tiles = 1
 
-        f_start = float(self.variables["f_start"].get()) - float(
-            self.stack_acq_widgets["start_focus"].get()
-        )
-        f_stop = float(self.variables["f_end"].get()) - float(
-            self.stack_acq_widgets["end_focus"].get()
-        )
+        f_start = float(self.variables["f_start"].get()) #- float(self.stack_acq_widgets["start_focus"].get())
+        f_stop = float(self.variables["f_end"].get()) #- float(self.stack_acq_widgets["end_focus"].get())
         f_tiles = int(self.variables["f_tiles"].get())
 
         # for consistency, always go from low to high
@@ -308,11 +301,12 @@ def sort_vars(a, b):
                 return b, a
             return a, b
 
+        #NOTE: Sorting variables breaks down if the F and Z stage are not both moving in the same direction. On our microscope, the F stage moves in a negative direction for positive z-stack acquisitions. I also have a hard coded (-) in commmon_features.py to allow the focus stage to move in a negative direction.
         x_start, x_stop = sort_vars(x_start, x_stop)
         y_start, y_stop = sort_vars(y_start, y_stop)
         z_start, z_stop = sort_vars(z_start, z_stop)
         r_start, r_stop = sort_vars(r_start, r_stop)
-        f_start, f_stop = sort_vars(f_start, f_stop)
+        # f_start, f_stop = sort_vars(f_start, f_stop)
 
         overlap = float(self._percent_overlap) / 100
         table_values = compute_tiles_from_bounding_box(

src/navigate/model/device_startup_functions.py

@@ -511,8 +511,18 @@ def load_stages(
                     exception=TLFTDICommunicationError,
                 )
             )
-
-        elif stage_type == "KST101":
+        elif stage_type == "KINESIS" and platform.system() == "Linux":
+            from navigate.model.devices.stages.tl_kinesis_steppermotor import (
+                build_KINESIS_Stage_connection
+                )
+            stage_devices.append(
+                auto_redial(
+                    build_KINESIS_Stage_connection,
+                    (stage_config["serial_number"],),
+                     exception=Exception
+                     )
+                )
+        elif stage_type == "KST101" and platform.system=="Windows":
             from navigate.model.devices.stages.tl_kcube_steppermotor import (
                 build_TLKSTStage_connection,
             )
@@ -562,12 +572,8 @@ def load_stages(
                 )
             )
 
-        elif stage_type == "MS2000" and platform.system() == "Windows":
-            """Filter wheel can be controlled from the same Controller. If
-            so, then we will load this as a shared device. If not, we will create the
-            connection to the Controller.
-
-            TODO: Evaluate whether MS2000 should be able to operate as a shared device.
+        elif stage_type == "MS2000":
+            """Stage and filter wheel are independent and should not be a shared device
             """
 
             from navigate.model.devices.stages.asi_MSTwoThousand import (
@@ -705,7 +711,10 @@ def start_stage(
         from navigate.model.devices.stages.tl_kcube_inertial import TLKIMStage
 
         return TLKIMStage(microscope_name, device_connection, configuration, id)
-
+    elif device_type == "KINESIS":
+        from navigate.model.devices.stages.tl_kinesis_steppermotor import TLKINStage
+
+        return TLKINStage(microscope_name, device_connection, configuration, id)
     elif device_type == "KST101":
         from navigate.model.devices.stages.tl_kcube_steppermotor import TLKSTStage
 
@@ -1265,7 +1274,6 @@ def start_lasers(
             modulation = "analog"
         elif digital == "NI":
             modulation = "digital"
-
         return LaserNI(
             microscope_name=microscope_name,
             device_connection=device_connection,

src/navigate/model/devices/APIs/asi/asi_MS2000_controller.py

@@ -34,6 +34,7 @@
 import threading
 import time
 import logging
+import platform
 
 # Third Party Imports
 from serial import Serial
@@ -79,6 +80,7 @@ def __init__(self, code: str):
             ":N-6": "Undefined Error (command is incorrect, but the controller does "
             "not know exactly why.",
             ":N-21": "Serial Command halted by the HALT command",
+            ":N-21\r\n": "Serial Command halted by the HALT command",
         }
         #: str: Error code received from MS2000 Console
         self.code = code
@@ -191,8 +193,9 @@ def connect_to_serial(
         self.serial_port.write_timeout = write_timeout
         self.serial_port.timeout = read_timeout
 
-        # set the size of the rx and tx buffers before calling open
-        self.serial_port.set_buffer_size(rx_size, tx_size)
+        if platform.system()=="Windows": 
+            # Only changed the buffer size in windows            
+            self.serial_port.set_buffer_size(rx_size, tx_size)
         try:
             self.serial_port.open()
         except SerialException:
@@ -216,8 +219,8 @@ def connect_to_serial(
                 "X",
                 "Y",
                 "Z",
-            ]  # self.get_default_motor_axis_sequence()
-
+            ]
+            
     def get_default_motor_axis_sequence(self) -> None:
         """Get the default motor axis sequence from the ASI device
 
@@ -374,7 +377,7 @@ def read_response(self) -> str:
         self.report_to_console(f"Received Response: {response.strip()}")
         if response.startswith(":N"):
             logger.error(f"Incorrect response received: {response}")
-            raise MS2000Exception(response)
+            raise MS2000Exception(response.strip())
 
         return response  # in case we want to read the response
 

src/navigate/model/devices/APIs/thorlabs/pykinesis_controller.py

@@ -0,0 +1,149 @@
+"""
+API for connection to Thorlabs.MotionControl.KCube.StepperMotor.dll.
+See Thorlabs.MotionControl.KCube.StepperMotor.h for more functions to implement.
+"""
+
+"""
+2024/10/23 Sheppard: Initialized to control Kinesis Stepper motor in Linux
+"""
+from pylablib.devices import Thorlabs
+import logging
+# Local Imports
+
+# Logger Setup
+p = __name__.split(".")[1]
+logger = logging.getLogger(p)
+
+class KinesisStage():
+    def __init__(self, dev_path: str, verbose: bool):
+        """_summary_
+
+        Args:
+            connection (_type_): _description_
+        """
+        connection = {"port":dev_path,"baudrate":115200,"rtscts":True} 
+        self.verbose = verbose
+        self.dev_path = dev_path
+        self.defualt_axes = ["f"]
+
+        self.move_params = {"min_velocity":None,
+                            "max_velocity":None,
+                            "acceleration":None}
+
+        self.open(connection)
+
+
+    def __str__(self) -> str:
+        """Returns the string representation of the MS2000 Controller class"""
+        return "KinesisController"
+
+    def open(self, connection):
+        """
+        Open the device for communications.
+
+        Parmeters
+        ---------
+        serial_number : str
+            Serial number of Thorlabs Kinesis Stepper Motor (KST) device.
+
+        Returns
+        -------
+        int
+            The error code or 0 if successful.
+        """
+        try:
+            self.stage = Thorlabs.KinesisMotor(("serial", connection), scale="step")
+            success = True
+        except Exception as e:
+            success = False
+            raise ConnectionError(f"KST101 stage connection failed! \nError: {e}")
+
+    def close(self):
+        """
+        Disconnect and close the device.
+
+        Parmeters
+        ---------
+        serial_number : str
+            Serial number of Thorlabs Kinesis Stepper Motor (KST) device.
+
+        Returns
+        -------
+        None
+        """
+        self.stage.stop()
+        self.stage.close()
+
+    def move_to_position(self, position, steps_per_um, wait_till_done):
+        """Move to position (um)
+        """
+        self.stage.get_position(channel=1, scale=False)
+        cur_pos = self.stage.get_position(channel=1, scale=False)
+        position_um = cur_pos / steps_per_um
+        # calculate the distance needed to move
+        distance = position - position_um
+        # convert total distance to steps
+        steps = steps_per_um * distance
+        self.stage.move_by(steps, channel=1, scale=False)
+        if wait_till_done:
+            self.stage.wait_move(channel=1)
+        return 0
+
+    def get_current_position(self, steps_per_um):
+        """Get the current position      
+
+        Parmeters
+        ---------
+        serial_number : str
+            Serial number of Thorlabs Kinesis Stepper Motor (KST) device.
+
+        Returns
+        -------
+        int
+            Current position.
+        """    
+        self.stage.get_position(channel=1, scale=False)
+        position = self.stage.get_position(channel=1, scale="False")
+        position_um = position / steps_per_um 
+        return round(position_um, 2)
+
+    def stop(self):
+        """
+        Halt motion
+
+        Parmeters
+        ---------
+        serial_number : str
+            Serial number of Thorlabs Kinesis Stepper Motor (KST) device.
+        channel : int
+            The device channel. One of SCC_Channels.
+
+        Returns
+        -------
+        int
+            The error code or 0 if successful.
+        """
+        self.stage.stop()
+        return 0
+
+    def home_stage(self):
+        """Home Device
+        """
+        self.stage.home()
+        return 0
+
+    def set_velocity_params(self,
+                            min_velocity, 
+                            max_velocity,
+                            acceleration,
+                            steps_per_um):
+        """Set velocity profile required for move
+        """        
+        min_velocity *= steps_per_um
+        max_velocity *= steps_per_um
+        acceleration *= steps_per_um
+        self.stage.set_move_params(min_velocity, max_velocity, acceleration)
+        self.move_params = {"min_velocity":min_velocity,
+                            "max_velocity":max_velocity,
+                            "acceleration":acceleration}
+        return 0

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

@@ -66,8 +66,8 @@ def build_photometrics_connection(camera_connection):
     """
     try:
         pvc.init_pvcam()
-        # camera_names = Camera.get_available_camera_names()
-        camera_to_open = Camera.select_camera(camera_connection)
+        camera_names = Camera.get_available_camera_names()
+        camera_to_open = Camera.select_camera(camera_names[0])
         camera_to_open.open()
         return camera_to_open
     except Exception as e:

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

@@ -172,12 +172,14 @@ def set_external_trigger(self, external_trigger=None) -> None:
                 self.analog_output_tasks[
                     board_name
                 ].triggers.start_trigger.cfg_dig_edge_start_trig(trigger_source)
-                try:
-                    self.analog_output_tasks[board_name].register_done_event(None)
-                except Exception:
-                    logger.debug(
-                        f"Error Registering Done Event: {traceback.format_exc()}"
-                    )
+                # NOTE: this was causing an error for me using PCIe-6343 in Linux. Not sure if it was board or OS related.
+                # try:
+                #     # print(board_name)
+                #     # self.analog_output_tasks[board_name].register_done_event(None)
+                # except Exception:
+                #     logger.debug(
+                #         f"Error Registering Done Event: {traceback.format_exc()}"
+                #     )
         else:
             # close master trigger task
             if self.master_trigger_task: