microscope: fix simulated mode in microscope

software/control/gui_hcs.py

@@ -16,8 +16,7 @@
 import control.widgets as widgets
 import pyqtgraph.dockarea as dock
 import squid.logging
-
-import control.microscope as microscope
+import squid.microscope
 
 log = squid.logging.get_logger(__name__)
 
@@ -108,7 +107,7 @@ def __init__(self, is_simulation=False, live_only_mode=False, *args, **kwargs):
 
         self.makeConnections()
 
-        self.microscope = microscope.Microscope(self)
+        self.microscope = squid.microscope.Microscope(self)
 
         # Move to cached position
         if HOMING_ENABLED_X and HOMING_ENABLED_Y and HOMING_ENABLED_Z:

software/control/microscope.py → software/squid/microscope.py

@@ -1,29 +1,25 @@
+import serial
 import time
-import os
-import sys
-from control._def import *
+
+from PyQt5.QtCore import QObject
+
 import control.core as core
-# import control.camera as camera
+from control._def import *
+import control
+
 if CAMERA_TYPE == "Toupcam":
     import control.camera_toupcam as camera
 import control.microcontroller as microcontroller
 import control.serial_peripherals as serial_peripherals
-import control.utils as utils
-
-import numpy as np
-from scipy.interpolate import griddata
 
-from qtpy.QtCore import *
-from qtpy.QtWidgets import *
-from qtpy.QtGui import *
 
 class Microscope(QObject):
 
-    def __init__(self, microscope=None,is_simulation=False):
+    def __init__(self, microscope=None, is_simulation=False):
         super().__init__()
         if microscope is None:
-            self.initialize_camera()
-            self.initialize_microcontroller()
+            self.initialize_camera(is_simulation=is_simulation)
+            self.initialize_microcontroller(is_simulation=is_simulation)
             self.initialize_core_components()
             self.initialize_peripherals()
         else:
@@ -41,7 +37,7 @@ def __init__(self, microscope=None,is_simulation=False):
             elif USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
                 self.emission_filter_wheel = microscope.emission_filter_wheel
 
-    def initialize_camera(self,is_simulation):
+    def initialize_camera(self, is_simulation):
         if is_simulation:
             self.camera = camera.Camera_Simulation(rotate_image_angle=ROTATE_IMAGE_ANGLE, flip_image=FLIP_IMAGE)
         else:
@@ -52,9 +48,9 @@ def initialize_camera(self,is_simulation):
         self.camera.set_pixel_format(DEFAULT_PIXEL_FORMAT)
         self.camera.set_software_triggered_acquisition()
 
-    def initialize_microcontroller(self,is_simulation):
+    def initialize_microcontroller(self, is_simulation):
         if is_simulation:
-            self.microcontroller = microcontroller.Microcontroller_Simulation()
+            self.microcontroller = microcontroller.Microcontroller(existing_serial=control.microcontroller.SimSerial())
         else:
             self.microcontroller = microcontroller.Microcontroller(version=CONTROLLER_VERSION, sn=CONTROLLER_SN)
 

software/tests/squid/test_microscope.py

@@ -0,0 +1,4 @@
+import squid.microscope
+
+def test_create_simulated_microscope():
+    sim_scope = squid.microscope.Microscope(is_simulation=True)