Refactor project settings and other code cleanup

src/jabs/__init__.py

@@ -1 +1 @@
-"""JABS Behavior Classifier"""
+"""JABS Behavior classifier"""

src/jabs/classifier/classifier.py

@@ -19,12 +19,12 @@
 )
 from sklearn.model_selection import LeaveOneGroupOut
 
-from jabs.project import Project, TrackLabels, load_training_data
-from jabs.types import (
+from jabs.enums import (
     DEFAULT_CV_GROUPING_STRATEGY,
     ClassifierType,
     CrossValidationGroupingStrategy,
 )
+from jabs.project import Project, TrackLabels, load_training_data
 from jabs.utils import hash_file
 
 _VERSION = 10

src/jabs/classifier/training_report.py

@@ -7,7 +7,7 @@
 import numpy as np
 from tabulate import tabulate
 
-from jabs.types import CrossValidationGroupingStrategy
+from jabs.enums import CrossValidationGroupingStrategy
 
 
 @dataclass

src/jabs/constants.py

@@ -2,12 +2,14 @@
 APP_NAME = "JABS"
 APP_NAME_LONG = f"{ORG_NAME} Animal Behavior System"
 
-# maximum number of recent projects to show in the File->Recent Projects menu
-RECENT_PROJECTS_MAX = 10
+# a hard coded random seed used for the final training
+# This is not used during cross-validation, but to ensure that final classifier is reproducible
+# we use this fixed seed when training the final model after cross validation.
+FINAL_TRAIN_SEED = 0xAB3BDB
 
 # some defaults for compressing hdf5 output
 COMPRESSION = "gzip"
 COMPRESSION_OPTS_DEFAULT = 6
 
-# settings keys
-SETTINGS_CV_GROUPING = "cv_grouping"
+# settings keys for project settings stored in the project.json file
+CV_GROUPING_KEY = "cv_grouping"

src/jabs/project/export_training.py

@@ -7,15 +7,15 @@
 
 import jabs.feature_extraction
 import jabs.version
+from jabs.constants import FINAL_TRAIN_SEED
 from jabs.project.project_utils import to_safe_name
-from jabs.utils import FINAL_TRAIN_SEED
 
 # these are used for type hints, but cause circular imports
 # TYPE_CHECKING is always false at runtime, so this gets around that
 # also requires enclosing Project and Classifier type hints in quotes
 if TYPE_CHECKING:
+    from jabs.enums import ClassifierType
     from jabs.project import Project
-    from jabs.types import ClassifierType
 
 
 def export_training_data(

src/jabs/project/feature_manager.py

@@ -1,12 +1,12 @@
 import jabs.feature_extraction as feature_extraction
+from jabs.enums import ProjectDistanceUnit
 from jabs.pose_estimation import (
     PoseEstimation,
     get_points_per_lixit,
     get_pose_file_major_version,
     get_pose_path,
     get_static_objects_in_file,
 )
-from jabs.types import ProjectDistanceUnit
 
 from .project_paths import ProjectPaths
 from .video_manager import VideoManager

src/jabs/project/project.py

@@ -15,8 +15,8 @@
 import pandas as pd
 
 import jabs.feature_extraction as fe
+from jabs.enums import CrossValidationGroupingStrategy, ProjectDistanceUnit
 from jabs.pose_estimation import PoseEstimation, get_pose_path, open_pose_file
-from jabs.types import CrossValidationGroupingStrategy, ProjectDistanceUnit
 
 from .feature_manager import FeatureManager
 from .parallel_workers import FeatureLoadJobSpec, collect_labeled_features
@@ -104,14 +104,6 @@ def __init__(
         # the session tracker.
         self._session_tracker.start_session()
 
-    def _ensure_executor(self) -> "ProcessPoolManager | None":
-        """Return the shared application-level ProcessPoolManager, or None if running single-threaded."""
-        return self._process_pool
-
-    def shutdown_executor(self) -> None:
-        """No-op: executor is owned by the application, not individual projects."""
-        pass
-
     def _validate_pose_files(self):
         """Ensure all videos have corresponding pose files."""
         err = False
@@ -619,7 +611,7 @@ def get_labeled_features(
             }
             jobs.append(job)
 
-        executor = self._ensure_executor()
+        executor = self._process_pool
         results_by_video: dict[str, dict] = {}
 
         if executor is not None:

src/jabs/project/read_training.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 
-from jabs.types import ClassifierType, ProjectDistanceUnit
+from jabs.enums import ClassifierType, ProjectDistanceUnit
 
 
 def read_project_settings(h5_file: h5py.Group) -> dict:

src/jabs/project/settings_manager.py

@@ -2,8 +2,8 @@
 import typing
 
 import jabs.feature_extraction as feature_extraction
-from jabs.constants import SETTINGS_CV_GROUPING
-from jabs.types.cv_grouping import DEFAULT_CV_GROUPING_STRATEGY, CrossValidationGroupingStrategy
+from jabs.constants import CV_GROUPING_KEY
+from jabs.enums.cv_grouping import DEFAULT_CV_GROUPING_STRATEGY, CrossValidationGroupingStrategy
 from jabs.version import version_str
 
 if typing.TYPE_CHECKING:
@@ -93,7 +93,7 @@ def cv_grouping_strategy(self) -> CrossValidationGroupingStrategy:
             CrossValidationGroupingStrategy: The CV grouping strategy.
         """
         grouping_str = self._project_info.get("settings", {}).get(
-            SETTINGS_CV_GROUPING, DEFAULT_CV_GROUPING_STRATEGY.value
+            CV_GROUPING_KEY, DEFAULT_CV_GROUPING_STRATEGY.value
         )
         try:
             return CrossValidationGroupingStrategy(grouping_str)

src/jabs/resources/docs/user_guide/gui.md

@@ -91,11 +91,11 @@ Clicking the Brightness or Contrast controls will reset the brightness or contra
 ## Menu
 
 - **JABS→About:** Display About Dialog
-- **JABS→Project Settings:** Display Project Settings Dialog
-- **JABS→User Guide:** Display User Guide
+- **JABS→JABS Preferences:** Open JABS Preferences Dialog
+- **JABS→Project Settings:** Open Project Settings Dialog
+- **JABS→User Guide:** Open User Guide
 - **JABS→Check for Updates:** Check PyPI for JABS updates
 - **JABS→View License Agreement:** Display License Agreement
-- **JABS→Enable Session Tracking:** Enable labeling session tracking
 - **JABS→Quit JABS:** Quit Program
 - **File→Open Project:** Select a project directory to open. If a project is already opened, it will be closed and the newly selected project will be opened.
 - **File→Open Recent:** Submenu to open recently opened projects.
@@ -125,10 +125,18 @@ Clicking the Brightness or Contrast controls will reset the brightness or contra
   - **Window→Bring All to Front:** Bring all JABS windows to the front
   - The Window menu also displays a list of all open JABS windows (main window, user guide, training reports, etc.) with a checkmark (✓) next to the currently active window. Click any window in the list to activate and bring it to the front.
 
+## JABS Preferences Dialog
+The **JABS Preferences Dialog**, available from the JABS menu, allows you to configure application-wide settings. These settings affect behavior of the JABS application and are not specific to any single project. These preferences are saved across application restarts, and apply regardless of which project is opened.
+
+Preferences are designed to be easily discoverable; preferences are grouped into logical sections, and each section includes built-in documentation, making it easy to understand the purpose and effect of each option directly within the dialog. Users should explore this dialog and customize preferences as needed.
+
+
 ## Project Settings Dialog
 
 The **Project Settings Dialog**, available from the JABS menu, allows you to configure project-wide settings. Settings are designed to be easily discoverable; each settings group includes built-in documentation, making it easy to understand the purpose and effect of each option directly within the dialog. Users should explore this dialog and customize project settings as needed.
 
+Project settings are saved within the project directory and apply only to the currently opened project.
+
 ### Settings Overview
 
 | Setting                        | Description                                                      |

src/jabs/scripts/cli.py

@@ -13,8 +13,8 @@
 from rich.console import Console
 
 from jabs.classifier import Classifier
+from jabs.enums import ClassifierType
 from jabs.project import Project, export_training_data, get_videos_to_prune
-from jabs.types import ClassifierType
 
 # find out which classifiers are supported in this environment
 CLASSIFIER_CHOICES: list[ClassifierType] = Classifier().classifier_choices()

src/jabs/scripts/generate_features.py

@@ -9,10 +9,10 @@
 import sys
 from pathlib import Path
 
+from jabs.enums import ProjectDistanceUnit
 from jabs.feature_extraction.features import IdentityFeatures
 from jabs.pose_estimation import open_pose_file
 from jabs.project import Project
-from jabs.types import ProjectDistanceUnit
 
 
 def generate_feature_cache(args):

src/jabs/scripts/initialize_project.py

@@ -18,9 +18,9 @@
 import jabs.feature_extraction
 import jabs.pose_estimation
 import jabs.project
+from jabs.enums import ProjectDistanceUnit
 from jabs.project.video_manager import VideoManager
 from jabs.schema.metadata import validate_metadata
-from jabs.types import ProjectDistanceUnit
 from jabs.video_reader import VideoReader
 
 DEFAULT_WINDOW_SIZE = 5

src/jabs/scripts/stats.py

@@ -5,9 +5,9 @@
 from tabulate import tabulate
 
 from jabs.classifier import Classifier
+from jabs.enums import ProjectDistanceUnit
 from jabs.project import load_training_data
 from jabs.scripts.classify import train
-from jabs.types import ProjectDistanceUnit
 
 
 def main():

src/jabs/ui/constants.py

@@ -0,0 +1,6 @@
+# these are settings keys stored in QSettings for the JABS GUI
+LICENSE_ACCEPTED_KEY = "license_accepted"
+LICENSE_VERSION_KEY = "license_version"
+RECENT_PROJECTS_KEY = "recent_projects"
+SESSION_TRACKING_ENABLED_KEY = "session_tracking_enabled"
+WINDOW_SIZE_KEY = "main_window_size"

src/jabs/ui/main_control_widget/main_control_widget.py

@@ -16,7 +16,7 @@
 from PySide6.QtGui import QIcon, QPainter, QPixmap
 
 from jabs.classifier import Classifier
-from jabs.types import ClassifierType
+from jabs.enums import ClassifierType
 
 from ..colors import (
     BEHAVIOR_BUTTON_COLOR_BRIGHT,
@@ -154,16 +154,7 @@ def __init__(self, *args, **kwargs):
         #  drop down to select type of classifier to use
         self._classifier_selection = QtWidgets.QComboBox()
         self._classifier_selection.currentIndexChanged.connect(self.classifier_changed)
-
-        classifier_types = Classifier().classifier_choices()
-        for classifier, name in classifier_types.items():
-            self._classifier_selection.addItem(name, userData=classifier)
-
-        # Set default classifier as the initial selection
-        for i in range(self._classifier_selection.count()):
-            if self._classifier_selection.itemData(i) == DEFAULT_CLASSIFIER:
-                self._classifier_selection.setCurrentIndex(i)
-                break
+        self.initialize_classifier_choices()
 
         #  slider to set number of times to train/test
         self._kslider = KFoldSliderWidget()
@@ -545,6 +536,25 @@ def set_window_size(self, size: int):
             self._add_window_size(size)
         self._window_size.setCurrentText(str(size))
 
+    def initialize_classifier_choices(self) -> None:
+        """populate the classifier selection combobox with available classifiers"""
+        # first, save the current selection so we can restore it after repopulating
+        current_classifier = self.classifier_type if self.classifier_type else DEFAULT_CLASSIFIER
+
+        # clear and repopulate the classifier selection combobox
+        self._classifier_selection.blockSignals(True)
+        self._classifier_selection.clear()
+        classifier_types = Classifier().classifier_choices()
+        for classifier, name in classifier_types.items():
+            self._classifier_selection.addItem(name, userData=classifier)
+
+        # now restore the previous selection if possible
+        for i in range(self._classifier_selection.count()):
+            if self._classifier_selection.itemData(i) == current_classifier:
+                self._classifier_selection.setCurrentIndex(i)
+                break
+        self._classifier_selection.blockSignals(False)
+
     def remove_behavior(self, behavior: str):
         """remove a behavior from the behavior selection box"""
         idx = self.behavior_selection.findText(behavior, QtCore.Qt.MatchFlag.MatchExactly)

src/jabs/ui/main_window/central_widget.py

@@ -12,9 +12,9 @@
 import jabs.feature_extraction
 from jabs.behavior_search import SearchHit
 from jabs.classifier import Classifier
+from jabs.enums import ClassifierType
 from jabs.pose_estimation import PoseEstimation, PoseEstimationV8
 from jabs.project import Project, TimelineAnnotations, TrackLabels, VideoLabels
-from jabs.types import ClassifierType
 
 from ..classification_thread import ClassifyThread
 from ..dialogs import AnnotationEditDialog, TrainingReportDialog

src/jabs/ui/main_window/constants.py

@@ -2,16 +2,12 @@
 
 from jabs.utils import get_bool_env_var
 
+# maximum number of recent projects to show in the File->Recent Projects menu
+RECENT_PROJECTS_MAX = 10
+
 # Environment variable flags
 USE_NATIVE_FILE_DIALOG = get_bool_env_var("JABS_NATIVE_FILE_DIALOG", True)
 
-# Settings keys
-RECENT_PROJECTS_KEY = "recent_projects"
-LICENSE_ACCEPTED_KEY = "license_accepted"
-LICENSE_VERSION_KEY = "license_version"
-WINDOW_SIZE_KEY = "main_window_size"
-SESSION_TRACKING_ENABLED_KEY = "session_tracking_enabled"
-
 # Default window dimensions
 DEFAULT_WINDOW_WIDTH = 1280
 DEFAULT_WINDOW_HEIGHT = 720