add auto offset adjustment for objective switching

software/control/_def.py

@@ -857,3 +857,4 @@ def load_formats():
 XERYON_SPEED = 80
 XERYON_OBJECTIVE_SWITCHER_POS_1 = ['4x', '10x']
 XERYON_OBJECTIVE_SWITCHER_POS_2 = ['20x', '40x', '60x']
+XERYON_OBJECTIVE_SWITCHER_POS_2_OFFSET_MM = 2

software/control/gui_hcs.py

@@ -434,7 +434,7 @@ def loadHardwareObjects(self):
 
         if USE_XERYON:
             try:
-                self.objective_changer = ObjectiveChanger2PosController(sn=XERYON_SERIAL_NUMBER)
+                self.objective_changer = ObjectiveChanger2PosController(sn=XERYON_SERIAL_NUMBER,stage=self.stage)
             except Exception:
                 self.log.error("Error initializing Xeryon objective switcher")
                 raise

software/control/objective_changer_2_pos_controller.py

@@ -3,31 +3,46 @@
 import time
 import serial
 
-from control.Xeryon import *
+from control.Xeryon import Xeryon
+from control._def import * # to remove once we create ObjectiveChangerConfig
+import squid.abc
 
 class ObjectiveChanger2PosController:
-    def __init__(self, sn: str):
+    def __init__(self, sn: str, stage: Optional[squid.abc.AbstractStage] = None):
         super().__init__()
         port = [p.device for p in serial.tools.list_ports.comports() if sn == p.serial_number]
         self.controller = Xeryon(port[0], 115200)
         self.axisX = self.controller.addAxis(Stage.XLA_1250_3N, "Z")
         self.controller.start()
         self.controller.reset()
 
+        self.stage = stage
+
         self.position1 = -19
         self.position2 = 19
 
         self.current_position = None
+        self.retracted = False # moved down by self.position2_offset for position 2
+
+        self.position2_offset = XERYON_OBJECTIVE_SWITCHER_POS_2_OFFSET_MM
 
     def home(self):
         self.axisX.findIndex()
 
     def moveToPosition1(self):
         self.axisX.setDPOS(self.position1)
+        if self.stage is not None and self.current_position == 2 and self.retracted:
+            # revert retracting z by self.position2_offset
+            self.stage.move_z(self.position2_offset)
+            self.retracted = False
         self.current_position = 1
 
     def moveToPosition2(self):
         self.axisX.setDPOS(self.position2)
+        if self.stage is not None and self.current_position == 1:
+            # retract z by self.position2_offset
+            self.stage.move_z(-self.position2_offset)
+            self.retracted = True
         self.current_position = 2
 
     def currentPosition(self) -> int: