Code Release

.gitignore

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+.vscode
+__pycache__
+
+Drivers/Motor_Driver/DLL_Files
+Drivers/Motor_Driver/Documentation
+# Drivers/Motor_Driver/Documentation
+# Drivers/Microscope_Driver/Documentation.*

Auto_Detect_Flakes.py

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+import json
+import os
+import shutil
+import sys
+import time
+import cv2
+
+import Utils.conversion_functions as conversion
+import Utils.etc_functions as etc
+import Utils.raster_functions as raster
+import Utils.stitcher_functions as stitcher
+import Utils.upload_functions as uploader
+from Drivers import CameraDriver, MicroscopeDriver, MotorDriver
+from GMMDetector import MaterialDetector
+
+START_TIME: float = time.time()
+
+# Constants
+SCAN_NAME: str = "SCAN_NAME"  # The Scan name for the Database
+SCAN_USER: str = "SCAN_USER"  # Your last name or Nickname
+EXFOLIATED_MATERIAL: str = "MATERIAL"  # The Material on the Wafer
+CHIP_THICKNESS: str = "THICKNESS"  # The Thickness of the Wafer
+MAGNIFICATION: int = 20  # Currently only 20x is supported
+USED_CHANNELS: str = "BGR"  # The Channels which are used for the detection
+STANDARD_DEVIATION_THRESHOLD: float = 5  # Maximum Mahalanobis Distance
+SIZE_THRESHOLD: float = 200  # Flake size threshold in square micrometers (μm²)
+COMMENT: str = ""  # The Comment for the Scan
+USE_AUTO_AF: bool = True  # Wheter the AF should be automatically calibrated
+SERVER_URL: str = "http://localhost:4999/upload"  # The URL of the Server where to send the POST Request to
+SCAN_DIRECTORY_ROOT: str = "C:/Path/to/the/scan/directory/root"  # The Root Directory where the Scans should be saved
+
+# Created Metadict
+META_DICT = {
+    "server_url": SERVER_URL,
+    "standard_deviation_threshold": STANDARD_DEVIATION_THRESHOLD,
+    "image_directory": SCAN_DIRECTORY_ROOT,
+    "scan_name": SCAN_NAME,
+    "scan_user": SCAN_USER,
+    "scan_exfoliated_material": EXFOLIATED_MATERIAL,
+    "chip_thickness": CHIP_THICKNESS,
+    "scan_magnification": MAGNIFICATION,
+    "chip_thickness": CHIP_THICKNESS,
+    "size_threshold": SIZE_THRESHOLD,
+    "scan_time": START_TIME,
+    "scan_comment": COMMENT,
+    "use_auto_AF": USE_AUTO_AF,
+}
+
+# File Paths
+FILE_PATH = os.path.dirname(os.path.abspath(__file__))
+SCAN_DIRECTORY = os.path.join(SCAN_DIRECTORY_ROOT, SCAN_NAME)
+scan_meta_path = os.path.join(SCAN_DIRECTORY, "meta.json")
+overview_path = os.path.join(SCAN_DIRECTORY, "overview.png")
+overview_compressed_path = os.path.join(SCAN_DIRECTORY, "overview_compressed.jpg")
+overview_mask_path = os.path.join(SCAN_DIRECTORY, "mask.png")
+scan_area_path = os.path.join(SCAN_DIRECTORY, "scan_area_map.png")
+
+(
+    contrast_params,
+    camera_settings,
+    microscope_settings,
+    magnification_params,
+    flatfield,
+) = etc.load_all_detection_parameters(
+    material=EXFOLIATED_MATERIAL,
+    magnification=MAGNIFICATION,
+    chip_thickness=CHIP_THICKNESS,
+)
+
+# Create the Scan Directory and save the flatfield and the meta.json
+if os.path.exists(SCAN_DIRECTORY):
+    sys.exit("Scan Directory already exists")
+else:
+    os.makedirs(SCAN_DIRECTORY)
+cv2.imwrite(os.path.join(SCAN_DIRECTORY, "flatfield.png"), flatfield)
+with open(scan_meta_path, "w") as fp:
+    json.dump(META_DICT, fp, sort_keys=True, indent=4)
+
+# Driver Initialization
+motor_driver = MotorDriver()
+camera_driver = CameraDriver()
+microscope_driver = MicroscopeDriver()
+
+# Detector Initialization
+model = MaterialDetector(
+    contrast_dict=contrast_params,
+    size_threshold=conversion.micrometers_to_pixels(SIZE_THRESHOLD, MAGNIFICATION),
+    standard_deviation_threshold=STANDARD_DEVIATION_THRESHOLD,
+    used_channels=USED_CHANNELS,
+)
+
+(
+    low_magification_image_directory,
+    low_magification_metadata_directory,
+) = raster.raster_plate_low_magnification(
+    scan_directory=SCAN_DIRECTORY,
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+)
+
+(
+    overview_image,
+    scan_area_map,
+) = stitcher.create_overview_image_and_map(
+    image_directory=low_magification_image_directory,
+    overview_path=overview_path,
+    overview_mask_path=overview_mask_path,
+    scan_area_path=scan_area_path,
+    overview_compressed_path=overview_compressed_path,
+    magnification_params=magnification_params,
+)
+
+# Remove the 2.5x images from memory as they are not needed anymore and take up a lot of space
+shutil.rmtree(os.path.dirname(low_magification_image_directory))
+
+formatted_time = time.strftime("%H:%M:%S", time.gmtime(time.time() - START_TIME))
+print(f"Time to create overview image and map: {formatted_time}")
+
+new_flatfield = etc.calibrate_scope(
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    magnification_index=conversion.magnification_to_magnification_index(MAGNIFICATION),
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+    scan_area_map=scan_area_map,
+    use_auto_AF=USE_AUTO_AF,
+    **magnification_params,
+)
+
+if new_flatfield is not None:
+    flatfield = new_flatfield.copy()
+    cv2.imwrite(os.path.join(SCAN_DIRECTORY, "flatfield.png"), flatfield)
+
+
+scan_area_time_start = time.time()
+print(f"Scanning for flakes in High Magnification...")
+raster.search_scan_area_map(
+    scan_directory=SCAN_DIRECTORY,
+    scan_area_map=scan_area_map,
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    model=model,
+    flatfield=flatfield,
+    magnification_index=conversion.magnification_to_magnification_index(MAGNIFICATION),
+    overview_image=overview_image,
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+    **magnification_params,
+)
+
+formatted_time = time.strftime(
+    "%H:%M:%S", time.gmtime(time.time() - scan_area_time_start)
+)
+print(f"Elapsed Time: {formatted_time}")
+
+revisit_time_start = time.time()
+print("Revisiting each Flake to take Pictures...")
+for current_magnification_index in [3, 4, 5, 1, 2]:
+    raster.read_meta_and_center_flakes(
+        scan_directory=SCAN_DIRECTORY,
+        motor_driver=motor_driver,
+        microscope_driver=microscope_driver,
+        camera_driver=camera_driver,
+        camera_settings=camera_settings,
+        microscope_settings=microscope_settings,
+        magnification_index=current_magnification_index,
+    )
+
+formatted_time = time.strftime(
+    "%H:%M:%S", time.gmtime(time.time() - revisit_time_start)
+)
+print(f"Elapsed Time during revisiting: {formatted_time}")
+
+print("Turning off the Lamp on the Microscope to conserve the Lifetime...")
+microscope_driver.lamp_off()
+
+print("Uploading the Scan Directory...")
+uploader.upload_directory(SCAN_DIRECTORY, SERVER_URL)
+
+formatted_time = time.strftime("%H:%M:%S", time.gmtime(time.time() - START_TIME))
+print(f"Total elapsed Time: {formatted_time}")

Auto_Detect_Flakes_GUI.py

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+import json
+import os
+import shutil
+import sys
+import time
+import cv2
+
+import Utils.conversion_functions as conversion
+import Utils.etc_functions as etc
+import Utils.raster_functions as raster
+import Utils.stitcher_functions as stitcher
+import Utils.upload_functions as uploader
+from Drivers import CameraDriver, MicroscopeDriver, MotorDriver
+from GMMDetector import MaterialDetector
+from GUI import ParameterPicker
+
+# getting the Parameters
+try:
+    parameter_picker = ParameterPicker()
+    parameter_dict = parameter_picker.take_input()
+except:
+    sys.exit("Parameter Picker was closed, exiting")
+
+START_TIME = time.time()
+
+# Constants
+SCAN_NAME: str = parameter_dict["scan_name"]
+SCAN_USER: str = parameter_dict["scan_user"]
+EXFOLIATED_MATERIAL: str = parameter_dict["scan_exfoliated_material"]
+CHIP_THICKNESS: str = parameter_dict["chip_thickness"]
+MAGNIFICATION: int = parameter_dict["scan_magnification"]
+USED_CHANNELS: str = parameter_dict["used_channels"]
+STANDARD_DEVIATION_THRESHOLD: float = parameter_dict["standard_deviation_threshold"]
+SIZE_THRESHOLD: float = parameter_dict["size_threshold"]
+USE_AUTO_AF: bool = parameter_dict["use_auto_AF"]
+SERVER_URL: str = parameter_dict["server_url"]
+SCAN_DIRECTORY_ROOT: str = parameter_dict["image_directory"]
+
+# Created Metadict
+META_DICT = {
+    **parameter_dict,
+    "scan_time": START_TIME,
+}
+
+# File Paths
+FILE_PATH = os.path.dirname(os.path.abspath(__file__))
+SCAN_DIRECTORY = os.path.join(SCAN_DIRECTORY_ROOT, SCAN_NAME)
+scan_meta_path = os.path.join(SCAN_DIRECTORY, "meta.json")
+overview_path = os.path.join(SCAN_DIRECTORY, "overview.png")
+overview_compressed_path = os.path.join(SCAN_DIRECTORY, "overview_compressed.jpg")
+overview_mask_path = os.path.join(SCAN_DIRECTORY, "mask.png")
+scan_area_path = os.path.join(SCAN_DIRECTORY, "scan_area_map.png")
+
+(
+    contrast_params,
+    camera_settings,
+    microscope_settings,
+    magnification_params,
+    flatfield,
+) = etc.load_all_detection_parameters(
+    material=EXFOLIATED_MATERIAL,
+    magnification=MAGNIFICATION,
+    chip_thickness=CHIP_THICKNESS,
+)
+
+# Create the Scan Directory and save the flatfield and the meta.json
+if os.path.exists(SCAN_DIRECTORY):
+    sys.exit("Scan Directory already exists")
+else:
+    os.makedirs(SCAN_DIRECTORY)
+cv2.imwrite(os.path.join(SCAN_DIRECTORY, "flatfield.png"), flatfield)
+with open(scan_meta_path, "w") as fp:
+    json.dump(META_DICT, fp, sort_keys=True, indent=4)
+
+# Driver Initialization
+motor_driver = MotorDriver()
+camera_driver = CameraDriver()
+microscope_driver = MicroscopeDriver()
+
+# Detector Initialization
+model = MaterialDetector(
+    contrast_dict=contrast_params,
+    size_threshold=conversion.micrometers_to_pixels(SIZE_THRESHOLD, MAGNIFICATION),
+    standard_deviation_threshold=STANDARD_DEVIATION_THRESHOLD,
+    used_channels=USED_CHANNELS,
+)
+
+(
+    low_magification_image_directory,
+    low_magification_metadata_directory,
+) = raster.raster_plate_low_magnification(
+    scan_directory=SCAN_DIRECTORY,
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+)
+
+(
+    overview_image,
+    scan_area_map,
+) = stitcher.create_overview_image_and_map(
+    image_directory=low_magification_image_directory,
+    overview_path=overview_path,
+    overview_mask_path=overview_mask_path,
+    scan_area_path=scan_area_path,
+    overview_compressed_path=overview_compressed_path,
+    magnification_params=magnification_params,
+)
+
+# Remove the 2.5x images from memory as they are not needed anymore and take up a lot of space
+shutil.rmtree(os.path.dirname(low_magification_image_directory))
+
+formatted_time = time.strftime("%H:%M:%S", time.gmtime(time.time() - START_TIME))
+print(f"Time to create overview image and map: {formatted_time}")
+
+new_flatfield = etc.calibrate_scope(
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    magnification_index=conversion.magnification_to_magnification_index(MAGNIFICATION),
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+    scan_area_map=scan_area_map,
+    use_auto_AF=USE_AUTO_AF,
+    **magnification_params,
+)
+
+if new_flatfield is not None:
+    flatfield = new_flatfield.copy()
+    cv2.imwrite(os.path.join(SCAN_DIRECTORY, "flatfield.png"), flatfield)
+
+
+scan_area_time_start = time.time()
+print(f"Scanning for flakes in High Magnification...")
+raster.search_scan_area_map(
+    scan_directory=SCAN_DIRECTORY,
+    scan_area_map=scan_area_map,
+    motor_driver=motor_driver,
+    microscope_driver=microscope_driver,
+    camera_driver=camera_driver,
+    model=model,
+    flatfield=flatfield,
+    magnification_index=conversion.magnification_to_magnification_index(MAGNIFICATION),
+    overview_image=overview_image,
+    camera_settings=camera_settings,
+    microscope_settings=microscope_settings,
+    **magnification_params,
+)
+
+formatted_time = time.strftime(
+    "%H:%M:%S", time.gmtime(time.time() - scan_area_time_start)
+)
+print(f"Elapsed Time: {formatted_time}")
+
+revisit_time_start = time.time()
+print("Revisiting each Flake to take Pictures...")
+for current_magnification_index in [3, 4, 5, 1, 2]:
+    raster.read_meta_and_center_flakes(
+        scan_directory=SCAN_DIRECTORY,
+        motor_driver=motor_driver,
+        microscope_driver=microscope_driver,
+        camera_driver=camera_driver,
+        camera_settings=camera_settings,
+        microscope_settings=microscope_settings,
+        magnification_index=current_magnification_index,
+    )
+
+formatted_time = time.strftime(
+    "%H:%M:%S", time.gmtime(time.time() - revisit_time_start)
+)
+print(f"Elapsed Time during revisiting: {formatted_time}")
+
+print("Turning off the Lamp on the Microscope to conserve the Lifetime...")
+microscope_driver.lamp_off()
+
+print("Uploading the Scan Directory...")
+uploader.upload_directory(SCAN_DIRECTORY, SERVER_URL)
+
+formatted_time = time.strftime("%H:%M:%S", time.gmtime(time.time() - START_TIME))
+print(f"Total elapsed Time: {formatted_time}")