remove dead code

software/README.md

@@ -10,32 +10,6 @@ Reboot the computer to finish the installation.
 
 ## Optional or Hardware-specific dependencies
 
-<details>
-<summary>image stitching dependencies (optional)</summary>
-For optional image stitching using ImageJ, additionally run the following:
-
-```
-sudo apt-get update
-sudo apt-get install openjdk-11-jdk
-sudo apt-get install maven
-pip3 install pyimagej
-pip3 instlal scyjava
-pip3 install tifffile
-pip3 install imagecodecs
-```
-
-Then, add the following line to the top of `/etc/environment` (needs to be edited with `sudo [your text editor]`):
-```
-JAVA_HOME=/usr/lib/jvm/default-java
-```
-Then, add the following lines to the top of `~/.bashrc` (or whichever file your terminal sources upon startup):
-```
-source /etc/environment
-export JAVA_HOME = $JAVA_HOME
-export PATH=$JAVA_HOME/bin:$PATH
-```
-</details>
-
 <details>
 <summary>Installing drivers and libraries for FLIR camera support</summary>
 Go to FLIR's page for downloading their Spinnaker SDK (https://www.flir.com/support/products/spinnaker-sdk/) and register.

software/control/_def.py

@@ -7,7 +7,7 @@
 import json
 import csv
 import squid.logging
-from enum import Enum, auto
+from enum import Enum
 
 log = squid.logging.get_logger(__name__)
 
@@ -225,10 +225,6 @@ class ILLUMINATION_CODE:
     ILLUMINATION_SOURCE_730NM = 15
 
 
-class VOLUMETRIC_IMAGING:
-    NUM_PLANES_PER_VOLUME = 20
-
-
 class CMD_EXECUTION_STATUS:
     COMPLETED_WITHOUT_ERRORS = 0
     IN_PROGRESS = 1
@@ -443,15 +439,6 @@ def convert_to_enum(option: Union[str, "FocusMeasureOperator"]) -> "FocusMeasure
 FILE_ID_PADDING = 0
 
 
-class PLATE_READER:
-    NUMBER_OF_ROWS = 8
-    NUMBER_OF_COLUMNS = 12
-    ROW_SPACING_MM = 9
-    COLUMN_SPACING_MM = 9
-    OFFSET_COLUMN_1_MM = 20
-    OFFSET_ROW_A_MM = 20
-
-
 CAMERA_PIXEL_SIZE_UM = {
     "IMX290": 2.9,
     "IMX178": 2.4,
@@ -467,11 +454,6 @@ class PLATE_READER:
 
 TUBE_LENS_MM = 50
 CAMERA_SENSOR = "IMX226"
-TRACKERS = ["csrt", "kcf", "mil", "tld", "medianflow", "mosse", "daSiamRPN"]
-DEFAULT_TRACKER = "csrt"
-
-ENABLE_TRACKING = False
-TRACKING_SHOW_MICROSCOPE_CONFIGURATIONS = False  # set to true when doing multimodal acquisition
 
 
 class CAMERA_CONFIG:
@@ -499,15 +481,6 @@ class AF:
     CROP_HEIGHT = 800
 
 
-class Tracking:
-    SEARCH_AREA_RATIO = 10  # @@@ check
-    CROPPED_IMG_RATIO = 10  # @@@ check
-    BBOX_SCALE_FACTOR = 1.2
-    DEFAULT_TRACKER = "csrt"
-    INIT_METHODS = ["roi"]
-    DEFAULT_INIT_METHOD = "roi"
-
-
 SHOW_DAC_CONTROL = False
 
 
@@ -543,9 +516,6 @@ class SOFTWARE_POS_LIMIT:
     Z_NEGATIVE = 0.05
 
 
-SHOW_AUTOLEVEL_BTN = False
-AUTOLEVEL_DEFAULT_SETTING = False
-
 MULTIPOINT_AUTOFOCUS_CHANNEL = "BF LED matrix full"
 # MULTIPOINT_AUTOFOCUS_CHANNEL = 'BF LED matrix left half'
 MULTIPOINT_AUTOFOCUS_ENABLE_BY_DEFAULT = False
@@ -559,7 +529,6 @@ class SOFTWARE_POS_LIMIT:
 ENABLE_FLEXIBLE_MULTIPOINT = True
 USE_OVERLAP_FOR_FLEXIBLE = True
 ENABLE_WELLPLATE_MULTIPOINT = True
-ENABLE_RECORDING = False
 
 RESUME_LIVE_AFTER_ACQUISITION = True
 
@@ -569,7 +538,6 @@ class SOFTWARE_POS_LIMIT:
 
 CAMERA_SN = {"ch 1": "SN1", "ch 2": "SN2"}  # for multiple cameras, to be overwritten in the configuration file
 
-ENABLE_STROBE_OUTPUT = False
 
 ACQUISITION_PATTERN = "S-Pattern"  # 'S-Pattern', 'Unidirectional'
 FOV_PATTERN = "Unidirectional"  # 'S-Pattern', 'Unidirectional'
@@ -613,7 +581,6 @@ class SOFTWARE_POS_LIMIT:
 LASER_AF_MIN_PEAK_DISTANCE = 10
 LASER_AF_MIN_PEAK_PROMINENCE = 0.20
 LASER_AF_SPOT_SPACING = 100
-SHOW_LEGACY_DISPLACEMENT_MEASUREMENT_WINDOWS = False
 LASER_AF_FILTER_SIGMA = None
 LASER_AF_INITIALIZE_CROP_WIDTH = 1200
 LASER_AF_INITIALIZE_CROP_HEIGHT = 800
@@ -624,20 +591,11 @@ class SOFTWARE_POS_LIMIT:
 RETRACT_OBJECTIVE_BEFORE_MOVING_TO_LOADING_POSITION = True
 OBJECTIVE_RETRACTED_POS_MM = 0.1
 
-TWO_CLASSIFICATION_MODELS = False
-CLASSIFICATION_MODEL_PATH = "models/resnet18_en/version1/best.pt"
-CLASSIFICATION_MODEL_PATH2 = "models/resnet18_en/version2/best.pt"
-CLASSIFICATION_TEST_MODE = False
-CLASSIFICATION_TH = 0.3
-
 SEGMENTATION_MODEL_PATH = "models/m2unet_model_flat_erode1_wdecay5_smallbatch/model_4000_11.pth"
 ENABLE_SEGMENTATION = True
 USE_TRT_SEGMENTATION = False
 SEGMENTATION_CROP = 1500
 
-DISP_TH_DURING_MULTIPOINT = 0.95
-SORT_DURING_MULTIPOINT = False
-
 INVERTED_OBJECTIVE = False
 
 ILLUMINATION_INTENSITY_FACTOR = 0.6
@@ -687,7 +645,6 @@ class SOFTWARE_POS_LIMIT:
 
 # Napari integration
 USE_NAPARI_FOR_LIVE_VIEW = False
-USE_NAPARI_FOR_MULTIPOINT = True
 USE_NAPARI_FOR_MOSAIC_DISPLAY = True
 USE_NAPARI_WELL_SELECTION = False
 USE_NAPARI_FOR_LIVE_CONTROL = False
@@ -708,10 +665,7 @@ class SOFTWARE_POS_LIMIT:
 # Navigation Settings
 ENABLE_CLICK_TO_MOVE_BY_DEFAULT = True
 
-# Stitcher
 IS_HCS = False
-DYNAMIC_REGISTRATION = False
-STITCH_COMPLETE_ACQUISITION = False
 
 # Pseudo color settings
 CHANNEL_COLORS_MAP = {

software/control/core/channel_configuration_mananger.py

@@ -75,12 +75,6 @@ def save_configurations(self, objective: str) -> None:
             # Save only channel configurations
             self._save_xml_config(objective, ConfigType.CHANNEL)
 
-    def save_current_configuration_to_path(self, objective: str, path: Path) -> None:
-        """Only used in TrackingController. Might be temporary."""
-        config = self.all_configs[self.active_config_type][objective]
-        xml_str = config.to_xml(pretty_print=True, encoding="utf-8")
-        path.write_bytes(xml_str)
-
     def get_configurations(self, objective: str) -> List[ChannelMode]:
         """Get channel modes for current active type"""
         config = self.all_configs[self.active_config_type].get(objective)