Merge pull request #101 from Cephla-Lab/improve-laser-autofocus

feat: improve laser autofocus with robust spot detection and error handling

Major changes:

Add comprehensive error handling and logging to laser autofocus
Implement robust spot detection with multiple detection modes
Add type hints and docstrings throughout
Add class constants for configuration values
Add laser autofocus testing and plotting capabilities
Technical improvements:

Move SpotDetectionMode from utils.py to _def.py
Add image cross correlation-based error detection
Improve defensive programming practices
Remove obsolete variables

software/configurations/configuration_HCS_v2.ini

@@ -155,12 +155,8 @@ _support_laser_autofocus_options = [True, False]
 main_camera_model = MER2-1220-32U3M
 focus_camera_model = MER2-630-60U3M
 focus_camera_exposure_time_ms = 0.8
-
-use_glass_top = True
-_use_glass_top_options = [True, False]
-
-has_two_interfaces = True
-_has_two_interfaces_options = [True, False]
+laser_af_spot_detection_mode = "DUAL_LEFT"
+_laser_af_spot_detection_mode_options = [SINGLE, DUAL_LEFT, DUAL_RIGHT, MULTI_RIGHT, MULTI_SECOND_RIGHT]
 
 enable_flexible_multipoint = True
 _enable_flexible_multipoint_options = [True, False]

software/configurations/configuration_Squid+.ini

@@ -153,12 +153,8 @@ _support_laser_autofocus_options = [True, False]
 main_camera_model = MER2-1220-32U3M
 focus_camera_model = MER2-630-60U3M
 focus_camera_exposure_time_ms = 0.8
-
-use_glass_top = True
-_use_glass_top_options = [True, False]
-
-has_two_interfaces = True
-_has_two_interfaces_options = [True, False]
+laser_af_spot_detection_mode = "DUAL_LEFT"
+_laser_af_spot_detection_mode_options = [SINGLE, DUAL_LEFT, DUAL_RIGHT, MULTI_RIGHT, MULTI_SECOND_RIGHT]
 
 enable_flexible_multipoint = True
 _enable_flexible_multipoint_options = [True, False]

software/configurations/configuration_Squid+_H117_ORCA.ini

@@ -165,12 +165,8 @@ _support_laser_autofocus_options = [True, False]
 main_camera_model = C15440-20UP
 focus_camera_model = MER2-630-60U3M
 focus_camera_exposure_time_ms = 0.8
-
-use_glass_top = True
-_use_glass_top_options = [True, False]
-
-has_two_interfaces = True
-_has_two_interfaces_options = [True, False]
+laser_af_spot_detection_mode = "DUAL_LEFT"
+_laser_af_spot_detection_mode_options = [SINGLE, DUAL_LEFT, DUAL_RIGHT, MULTI_RIGHT, MULTI_SECOND_RIGHT]
 
 enable_flexible_multipoint = True
 _enable_flexible_multipoint_options = [True, False]

software/control/_def.py

@@ -5,7 +5,7 @@
 from configparser import ConfigParser
 import json
 import csv
-
+from control.utils import SpotDetectionMode
 import squid.logging
 
 log = squid.logging.get_logger(__name__)
@@ -525,13 +525,12 @@ class SOFTWARE_POS_LIMIT:
 FOCUS_CAMERA_MODEL = "MER2-630-60U3M"
 FOCUS_CAMERA_EXPOSURE_TIME_MS = 2
 FOCUS_CAMERA_ANALOG_GAIN = 0
-LASER_AF_AVERAGING_N = 5
+LASER_AF_AVERAGING_N = 3
 LASER_AF_DISPLAY_SPOT_IMAGE = True
 LASER_AF_CROP_WIDTH = 1536
 LASER_AF_CROP_HEIGHT = 256
-HAS_TWO_INTERFACES = True
+LASER_AF_SPOT_DETECTION_MODE = SpotDetectionMode.DUAL_LEFT
 LASER_AF_RANGE = 200
-USE_GLASS_TOP = True
 SHOW_LEGACY_DISPLACEMENT_MEASUREMENT_WINDOWS = False
 
 MULTIPOINT_REFLECTION_AUTOFOCUS_ENABLE_BY_DEFAULT = False
@@ -731,10 +730,10 @@ def load_formats():
     DEFAULT_DISPLAY_CROP = Tracking.DEFAULT_DISPLAY_CROP
 
 USE_XERYON = False
-XERYON_SERIAL_NUMBER = '95130303033351E02050'
+XERYON_SERIAL_NUMBER = "95130303033351E02050"
 XERYON_SPEED = 80
-XERYON_OBJECTIVE_SWITCHER_POS_1 = ['4x', '10x']
-XERYON_OBJECTIVE_SWITCHER_POS_2 = ['20x', '40x', '60x']
+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/camera.py

@@ -601,6 +601,12 @@ def send_trigger(self):
 
     def read_frame(self):
         return self.current_frame
+        '''
+        # read from disk for laser af debugging
+        image = cv2.imread("control/tests/data/laser_af_camera.png")[:, :, 0]
+        height, width = image.shape
+        return image + np.random.randint(0, 10, size=(height, width), dtype=np.uint8)
+        '''
 
     def _on_frame_callback(self, user_param, raw_image):
         pass