Fixing issue with Autofocus signals

.gitignore

@@ -84,3 +84,4 @@ imswitch/ImSwitch/recordings*
 locai/*
 conda/*
 conda-out/*
+imswitch/ImSwitch/ImSwitch/recordings/*

imswitch/imcontrol/controller/CommunicationChannel.py

@@ -92,7 +92,7 @@ class CommunicationChannel(SignalInterface):
 
     #sigSendScannersInScan = Signal(object)  # (scannerList)
 
-    sigAutoFocus =  Signal(float, float, float) # scanrange and stepsize and initialz
+    sigAutoFocus =  Signal(float, float) # scanrange and stepsize
     sigAutoFocusRunning = Signal(bool) # indicate if autofocus is running or not
 
     sigInitialFocalPlane = Signal(float) # initial focal plane for DeckScanController

imswitch/imcontrol/controller/controllers/AufofocusController.py

@@ -92,7 +92,7 @@ def doAutofocusBackground(self, rangez=100, resolutionz=10):
         # precompute values for Z-scan
         Nz = int(2 * rangez // resolutionz)
         allfocusvals = np.zeros(Nz)
-        allfocuspositions = np.linspace(-abs(rangez), abs(rangez), Nz) + initialPosition
+        allfocuspositions = np.int32(np.linspace(-abs(rangez), abs(rangez), Nz) + initialPosition)
         allfocusimages = []
 
         # 0 move focus to initial position

imswitch/imcontrol/controller/controllers/DeckScanController.py

@@ -313,8 +313,7 @@ def doAutofocus(self, params):
         self._widget.setNImages("Autofocusing...")
         slot, well, first_position_offset, first_z_focus, first_pos = self.get_first_row()
         self.positioner.move(value=first_pos, axis="XYZ", is_absolute=True, is_blocking=True)
-        self._commChannel.sigAutoFocus.emit(float(params["valueRange"]), float(params["valueSteps"]),
-                                            float(params["valueInitial"]))
+        self._commChannel.sigAutoFocus.emit(float(params["valueRange"]), float(params["valueSteps"]))#FIXME: float(params["valueInitial"]))
         self.isAutofocusRunning = True
         while self.isAutofocusRunning:
             time.sleep(0.1)

imswitch/imcontrol/controller/controllers/HistoScanController.py

@@ -220,8 +220,7 @@ def doScan(self):
 
     def doAutofocus(self, params):
         self._logger.info("Autofocusing...")
-        isRunInBackground = False
-        self._commChannel.sigAutoFocus.emit(int(params["valueRange"]), int(params["valueSteps"], isRunInBackground))
+        self._commChannel.sigAutoFocus.emit(int(params["valueRange"]), int(params["valueSteps"]))
 
     def doScanThread(self, coordinateList):
         # store initial stage position

imswitch/imcontrol/controller/controllers/OpentronsDeckScanController.py

@@ -247,7 +247,7 @@ def doAutofocus(self, params):
         slot, well, offset = self.get_first_position()
         self.scanner.moveToWell(well=well, slot=slot, is_blocking=True)
         self.scanner.shiftXY(xy_shift=offset, is_blocking=True)
-        self._commChannel.sigAutoFocus.emit(float(params["valueRange"]), float(params["valueSteps"]), float(params["valueInitial"]))
+        self._commChannel.sigAutoFocus.emit(float(params["valueRange"]), float(params["valueSteps"])) #FIXME:, float(params["valueInitial"]))
         self.isAutofocusRunning = True
         while self.isAutofocusRunning:
             time.sleep(0.1)

imswitch/imcontrol/controller/controllers/PositionerController.py

@@ -3,8 +3,8 @@
 from imswitch.imcommon.model import APIExport
 from ..basecontrollers import ImConWidgetController
 from imswitch.imcommon.model import initLogger
-
-
+import threading
+import time 
 class PositionerController(ImConWidgetController):
     """ Linked to PositionerWidget."""
 
@@ -67,7 +67,8 @@ def move(self, positionerName, axis, dist, isAbsolute=None, isBlocking=False):
             self._master.positionersManager[positionerName].move(dist, axis, isAbsolute, isBlocking)
         except:
             self._master.positionersManager[positionerName].move(dist, axis)
-        self.updatePosition(positionerName, axis)
+        self.updatePosition()
+
 
     def setPos(self, positionerName, axis, position):
         """ Moves the positioner to the specified position in the specified axis. """
@@ -92,9 +93,14 @@ def setSpeed(self, positionerName, axis, speed=(1000, 1000, 1000)):
         self._widget.setSpeedSize(positionerName, axis, speed)
 
     def updatePosition(self, positionerName, axis):
-        newPos = self._master.positionersManager[positionerName].position[axis]
-        self._widget.updatePosition(positionerName, axis, newPos)
-        self.setSharedAttr(positionerName, axis, _positionAttr, newPos)
+        #newPos = self._master.positionersManager[positionerName].position[axis]#FIXME: Is this always pulling the latest position from the device?
+        def grabPos():
+            for i in range(10):
+                newPos = self._master.positionersManager[positionerName].getPosition()[axis]
+                self._widget.updatePosition(positionerName, axis, newPos)
+                self.setSharedAttr(positionerName, axis, _positionAttr, newPos)
+                time.sleep(.3)
+        threading.Thread(target=grabPos).start()
 
     @APIExport(runOnUIThread=True)
     def homeAxis(self, positionerName, axis, isBlocking=False):

imswitch/imcontrol/model/managers/positioners/ESP32StageManager.py

@@ -5,7 +5,7 @@
 from imswitch.imcommon.model import APIExport, generateAPI, initLogger
 import threading
 
-        
+
 PHYS_FACTOR = 1
 gTIMEOUT = 100
 class ESP32StageManager(PositionerManager):
@@ -178,14 +178,7 @@ def __init__(self, positionerInfo, name, **lowLevelManagers):
         self.setupMotor(self.minT, self.maxT, self.stepsizeT, self.backlashT, "T")
 
         # get bootup position and write to GUI
-        self._position  = self.getPosition()
-
-        # force setting the position
-        self.setPosition(self._position['X'],"X")
-        self.setPosition(self._position['Y'],"X")
-        self.setPosition(self._position['Z'],"Z")
-        self.setPosition(self._position['T'],"T")
-
+        self._position = self.getPosition()
 
     def setAxisOrder(self, order=[0,1,2,3]):
         self._motor.setMotorAxisOrder(order=order)
@@ -231,11 +224,7 @@ def move(self, value=0, axis="X", is_absolute=False, is_blocking=True, accelerat
         elif axis == 'XYZ':
             self._motor.move_xyz(value, speed, acceleration=acceleration, is_absolute=is_absolute, is_enabled=isEnable, is_blocking=is_blocking, timeout=timeout)
         else:
-            print('Wrong axis, has to be "X" "Y" or "Z".')
-
-        # finally update positions 
-        threading.Thread(target=self.getPosition).start()
-
+            print('Wrong axis, has to be "X" "Y" or "Z".')        
 
     def measure(self, sensorID=0, NAvg=100):
         return self._motor.read_sensor(sensorID=sensorID, NAvg=NAvg)
@@ -271,7 +260,6 @@ def getPosition(self):
         # load position from device
         # t,x,y,z
         try:
-            time.sleep(0.5)
             allPositions = self._motor.get_position()
         except:
             allPositions = [0,0,0,0]