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main_hcs: start converting code reachable via main_hcs.py to use native python logging instead of print #2

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Merged
ianohara merged 5 commits into from
Oct 25, 2024
Merged

main_hcs: start converting code reachable via main_hcs.py to use native python logging instead of print #2

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d4ef990
Start converting files reachable from main_hcs to logging framework
ianohara Oct 17, 2024
8d6173f
control/serial_peripherals.py: convert to using logging framework
ianohara Oct 17, 2024
a483a34
fix missing raise and log calls
ianohara Oct 17, 2024
04a202f
octopi -> squid
ianohara Oct 24, 2024
220fa05
make ctrl+c work for the gui
ianohara Oct 24, 2024
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90 changes: 48 additions & 42 deletions software/control/gui_hcs.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,8 @@
# set QT_API environment variable
import os
import sys
import time
os.environ["QT_API"] = "pyqt5"
import qtpy
import serial
import time

# qt libraries
from qtpy.QtCore import *
Expand All @@ -14,37 +13,40 @@

# app specific libraries
import control.widgets as widgets
import serial
import pyqtgraph.dockarea as dock
import squid.logging

log = squid.logging.get_logger(__name__)

if CAMERA_TYPE == "Toupcam":
try:
import control.camera_toupcam as camera
except:
print("Problem importing Toupcam, defaulting to default camera")
log.warning("Problem importing Toupcam, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "FLIR":
try:
import control.camera_flir as camera
except:
print("Problem importing FLIR camera, defaulting to default camera")
log.warning("Problem importing FLIR camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "Hamamatsu":
try:
import control.camera_hamamatsu as camera
except:
print("Problem importing Hamamatsu camera, defaulting to default camera")
log.warning("Problem importing Hamamatsu camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "iDS":
try:
import control.camera_ids as camera
except:
print("Problem importing iDS camera, defaulting to default camera")
log.warning("Problem importing iDS camera, defaulting to default camera")
import control.camera as camera
elif CAMERA_TYPE == "Tucsen":
try:
import control.camera_tucsen as camera
except:
print("Problem importing Tucsen camera, defaulting to default camera")
log.warning("Problem importing Tucsen camera, defaulting to default camera")
import control.camera as camera
else:
import control.camera as camera
Expand All @@ -53,13 +55,13 @@
try:
import control.camera_toupcam as camera_fc
except:
print("Problem importing Toupcam for focus, defaulting to default camera")
log.warning("Problem importing Toupcam for focus, defaulting to default camera")
import control.camera as camera_fc
elif FOCUS_CAMERA_TYPE == "FLIR":
try:
import control.camera_flir as camera_fc
except:
print("Problem importing FLIR camera for focus, defaulting to default camera")
log.warning("Problem importing FLIR camera for focus, defaulting to default camera")
import control.camera as camera_fc
else:
import control.camera as camera_fc
Expand All @@ -78,15 +80,10 @@
if SUPPORT_LASER_AUTOFOCUS:
import control.core_displacement_measurement as core_displacement_measurement

import pyqtgraph.dockarea as dock
import serial
import time

SINGLE_WINDOW = True # set to False if use separate windows for display and control


class OctopiGUI(QMainWindow):

fps_software_trigger = 100

def __init__(self, is_simulation=False, performance_mode=False, *args, **kwargs):
Expand Down Expand Up @@ -125,11 +122,9 @@ def loadObjects(self, is_simulation):
else:
try:
self.loadHardwareObjects()
except Exception as e:
print("\n---- !! ERROR CONNECTING TO HARDWARE !! ----")
print(e)
print("Falling back to simulation mode\n")
self.loadSimulationObjects()
except Exception:
log.error("---- !! ERROR CONNECTING TO HARDWARE !! ----", stack_info=True, exc_info=True)
raise

# Common object initialization
self.objectiveStore = core.ObjectiveStore(parent=self)
Expand Down Expand Up @@ -164,6 +159,7 @@ def loadObjects(self, is_simulation):
self.laserAutofocusController = core.LaserAutofocusController(self.microcontroller,self.camera_focus,self.liveController_focus_camera,self.navigationController,has_two_interfaces=HAS_TWO_INTERFACES,use_glass_top=USE_GLASS_TOP,look_for_cache=False)

def loadSimulationObjects(self):
log.debug("Loading simulated hardware objects...")
# Initialize simulation objects
if ENABLE_SPINNING_DISK_CONFOCAL:
self.xlight = serial_peripherals.XLight_Simulation()
Expand All @@ -187,73 +183,83 @@ def loadHardwareObjects(self):
if ENABLE_SPINNING_DISK_CONFOCAL:
try:
self.xlight = serial_peripherals.XLight(XLIGHT_SERIAL_NUMBER, XLIGHT_SLEEP_TIME_FOR_WHEEL)
except Exception as e:
raise Exception(f"Error initializing Spinning Disk Confocal: {e}")
except Exception:
log.error("Error initializing Spinning Disk Confocal")
raise

if ENABLE_NL5:
try:
import control.NL5 as NL5
self.nl5 = NL5.NL5()
except Exception as e:
raise Exception(f"Error initializing NL5: {e}")
except Exception:
log.error("Error initializing NL5")
raise

if ENABLE_CELLX:
try:
self.cellx = serial_peripherals.CellX(CELLX_SN)
for channel in [1,2,3,4]:
self.cellx.set_modulation(channel, CELLX_MODULATION)
self.cellx.turn_on(channel)
except Exception as e:
raise Exception(f"Error initializing CellX: {e}")
except Exception:
log.error("Error initializing CellX")
raise

if USE_LDI_SERIAL_CONTROL:
try:
self.ldi = serial_peripherals.LDI()
self.ldi.run()
self.ldi.set_intensity_mode(LDI_INTENSITY_MODE)
self.ldi.set_shutter_mode(LDI_SHUTTER_MODE)
except Exception as e:
raise Exception(f"Error initializing LDI: {e}")
except Exception:
log.error("Error initializing LDI")
raise

if SUPPORT_LASER_AUTOFOCUS:
try:
sn_camera_focus = camera_fc.get_sn_by_model(FOCUS_CAMERA_MODEL)
self.camera_focus = camera_fc.Camera(sn=sn_camera_focus)
self.camera_focus.open()
self.camera_focus.set_pixel_format('MONO8')
except Exception as e:
raise Exception(f"Error initializing Laser Autofocus Camera: {e}")
except Exception:
log.error(f"Error initializing Laser Autofocus Camera")
raise

try:
sn_camera_main = camera.get_sn_by_model(MAIN_CAMERA_MODEL)
self.camera = camera.Camera(sn=sn_camera_main, rotate_image_angle=ROTATE_IMAGE_ANGLE, flip_image=FLIP_IMAGE)
self.camera.open()
self.camera.set_pixel_format(DEFAULT_PIXEL_FORMAT)
except Exception as e:
raise Exception(f"Error initializing Main Camera: {e}")
except Exception:
log.error("Error initializing Main Camera")
raise

if USE_ZABER_EMISSION_FILTER_WHEEL:
try:
self.emission_filter_wheel = serial_peripherals.FilterController(FILTER_CONTROLLER_SERIAL_NUMBER, 115200, 8, serial.PARITY_NONE, serial.STOPBITS_ONE)
except Exception as e:
raise Exception(f"Error initializing Zaber Emission Filter Wheel: {e}")
except Exception:
log.error("Error initializing Zaber Emission Filter Wheel")
raise

if USE_OPTOSPIN_EMISSION_FILTER_WHEEL:
try:
self.emission_filter_wheel = serial_peripherals.Optospin(SN=FILTER_CONTROLLER_SERIAL_NUMBER)
except Exception as e:
raise Exception(f"Error initializing Optospin Emission Filter Wheel: {e}")
except Exception:
log.error("Error initializing Optospin Emission Filter Wheel")
raise

if USE_PRIOR_STAGE:
try:
self.priorstage = PriorStage(PRIOR_STAGE_SN, parent=self)
except Exception as e:
raise Exception(f"Error initializing Prior Stage: {e}")
except Exception:
log.error("Error initializing Prior Stage")
raise

try:
self.microcontroller = microcontroller.Microcontroller(version=CONTROLLER_VERSION, sn=CONTROLLER_SN)
except Exception as e:
raise Exception(f"Error initializing Microcontroller: {e}")
except Exception:
log.error(f"Error initializing Microcontroller")
raise

def setupHardware(self):
# Setup hardware components
Expand Down Expand Up @@ -335,7 +341,7 @@ def waitForMicrocontroller(self, timeout=None, error_message=None):
while self.microcontroller.is_busy():
time.sleep(0.005)
if timeout and time.time() - start_time > timeout:
print(error_message or 'Microcontroller operation timed out')
self.log.error(error_message or 'Microcontroller operation timed out')
sys.exit(1)

def loadWidgets(self):
Expand Down
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