more integration and fixing

software/control/core/core.py

@@ -789,18 +789,6 @@ def update_pos(self, microcontroller):
             print('joystick button pressed')
             microcontroller.signal_joystick_button_pressed_event = False
 
-    # TODO(imo): This should be don in the CephlaStage init since we have the encoder info there already
-    def configure_encoder(self, axis, transitions_per_revolution,flip_direction):
-        self.microcontroller.configure_stage_pid(axis, transitions_per_revolution=int(transitions_per_revolution), flip_direction=flip_direction)
-
-    # TODO(imo): This should be done in the CephlaStage init
-    def set_pid_control_enable(self, axis, enable_flag):
-        self.pid_enable_flag[axis] = enable_flag
-        if self.pid_enable_flag[axis] is True:
-            self.microcontroller.turn_on_stage_pid(axis)
-        else:
-            self.microcontroller.turn_off_stage_pid(axis)
-
     # TODO(imo): This is only called from a closeEvent.  This isn't guaranteed to run - do we need to do this?
     def turnoff_axis_pid_control(self):
         for i in range(len(self.pid_enable_flag)):
@@ -814,16 +802,6 @@ def keep_scan_begin_position(self, x, y):
         self.scan_begin_position_x = x
         self.scan_begin_position_y = y
 
-    # TODO(imo): This is only called in an init, so it should be done in CephlaStage init via CephlaStage specific axis config
-    def set_axis_PID_arguments(self, axis, pid_p, pid_i, pid_d):
-        self.microcontroller.set_pid_arguments(axis, pid_p, pid_i, pid_d)
-
-    # TODO(imo): Can we just have this be a part of move_z and move_z_to?  Or does it need to be a separate axis concept?
-    def set_piezo_um(self, z_piezo_um):
-        dac = int(65535 * (z_piezo_um / OBJECTIVE_PIEZO_RANGE_UM))
-        dac = 65535 - dac if OBJECTIVE_PIEZO_FLIP_DIR else dac
-        self.microcontroller.analog_write_onboard_DAC(7, dac)
-
 
 class SlidePositionControlWorker(QObject):
 

software/control/gui_hcs.py

@@ -587,16 +587,6 @@ def setupMultiWindowLayout(self):
     def makeConnections(self):
         self.streamHandler.signal_new_frame_received.connect(self.liveController.on_new_frame)
         self.streamHandler.packet_image_to_write.connect(self.imageSaver.enqueue)
-        # self.streamHandler.packet_image_for_tracking.connect(self.trackingController.on_new_frame)
-        # TODO(imo): Fix ui position updates since removal of navigation controller
-        # self.navigationController.xPos.connect(lambda x: self.navigationWidget.label_Xpos.setText("{:.2f}".format(x) + " mm"))
-        # self.navigationController.yPos.connect(lambda x: self.navigationWidget.label_Ypos.setText("{:.2f}".format(x) + " mm"))
-        # self.navigationController.zPos.connect(lambda x: self.navigationWidget.label_Zpos.setText("{:.2f}".format(x) + " μm"))
-
-        # if SHOW_NAVIGATION_BAR:
-        #     self.navigationController.xPos.connect(self.navigationBarWidget.update_x_position)
-        #     self.navigationController.yPos.connect(self.navigationBarWidget.update_y_position)
-        #     self.navigationController.zPos.connect(self.navigationBarWidget.update_z_position)
 
         # TODO(imo): Fix joystick after removal of navigation controller
         # if ENABLE_TRACKING:
@@ -609,15 +599,13 @@ def makeConnections(self):
 
         if ENABLE_FLEXIBLE_MULTIPOINT:
             self.flexibleMultiPointWidget.signal_acquisition_started.connect(self.toggleAcquisitionStart)
-            # self.flexibleMultiPointWidget.signal_z_stacking.connect(self.multipointController.set_z_stacking_config)
             if ENABLE_STITCHER:
                 self.flexibleMultiPointWidget.signal_stitcher_widget.connect(self.toggleStitcherWidget)
                 self.flexibleMultiPointWidget.signal_acquisition_channels.connect(self.stitcherWidget.updateRegistrationChannels)
                 self.flexibleMultiPointWidget.signal_stitcher_z_levels.connect(self.stitcherWidget.updateRegistrationZLevels)
 
         if ENABLE_WELLPLATE_MULTIPOINT:
             self.wellplateMultiPointWidget.signal_acquisition_started.connect(self.toggleAcquisitionStart)
-            # self.wellplateMultiPointWidget.signal_z_stacking.connect(self.multipointController.set_z_stacking_config)
             if ENABLE_STITCHER:
                 self.wellplateMultiPointWidget.signal_stitcher_widget.connect(self.toggleStitcherWidget)
                 self.wellplateMultiPointWidget.signal_acquisition_channels.connect(self.stitcherWidget.updateRegistrationChannels)