api.rst

📖 API Reference

This section provides a categorized reference of SimBA's modules and methods, grouped by their functionality such as feature extraction, plotting, transformation, and modeling.

• |:mag:| Blob tracking tools
• |:package:| Bounding-box tools
• |:repeat:| Circular transformations
• |:wrench:| Config reader
• |:bulb:| Cue-light tools
• |:wrench:| Data processing tools
• |:straight_ruler:| Feature extraction mixins
• |:pencil:| Feature extraction wrappers
• |:triangular_ruler:| Geometry transformations
• |:frame_with_picture:| Image transformations
• |:label:| Labeling tools
• |:robot_face:| Model tools
• |:link:| Network transformations
• |:warning:| Outlier correction
• |:art:| Plotting and visualization tools
• |:package:| Pose-estimation import tools
• |:world_map:| ROI tools
• |:bar_chart:| Statistics transformations
• |:inbox_tray:| Third-party label appenders
• |:clock1:| Time-series transformations
• |:crystal_ball:| Unsupervised learning
• |:desktop_computer:| User Interface (UI) tools
• |:gear:| Utilities
• |:video_camera:| Video processing tools
• 👁️ YOLO Methods

|:mag:| Blob tracking tools

Track animals in videos using background subtraction and blob detection. Extract geometric features (center, nose, tail, left/right points) from detected blob shapes without requiring pose-estimation data.

.. toctree::
   :maxdepth: 5

   simba.blob

|:package:| Bounding-box tools

Detect animal interactions via overlapping bounding boxes.

See tutorial: Cue-light tutorial

.. toctree::
   :maxdepth: 2

   simba.bounding_box_tools
   simba.yolo

|:repeat:| Circular transformations

Statistical operations for circular data like head direction. Wraparound-aware, multi-animal capable, and based on body-part derived base angles.

.. toctree::
   :maxdepth: 4

   simba.circular_statistics

|:wrench:| Config reader

Parse SimBA config files and access project-specific metadata.

.. toctree::
   :maxdepth: 2

   simba.config_reader

|:bulb:| Cue-light tools

Link animal behavior to cue-light on/off states.

See tutorial: Cue-light tutorial

.. toctree::
   :maxdepth: 2

   simba.cue_light_tools

|:wrench:| Data processing tools

Transform classification, tracking, and image data.

.. toctree::
   :maxdepth: 1

   simba.data_processors

|:straight_ruler:| Feature extraction mixins

Core low-level feature methods used in SimBA's default extraction pipelines.

.. toctree::
   :maxdepth: 4

   simba.feature_extraction_mixins

|:pencil:| Feature extraction wrappers

Pre-configured "out-of-the-box" feature extraction modules for common pose-estimation schemas.

.. toctree::
   :maxdepth: 1

   simba.feature_extractors

|:triangular_ruler:| Geometry transformations

Transform pose-estimated body-part coordinates into geometric shapes (bounding boxes, polygons, circles), and compute spatial relationships like distance and intersection.

.. toctree::
   :maxdepth: 4

   simba.geometry_mixin

|:frame_with_picture:| Image transformations

Slice frames and extract visual information from tracking data; compare image features across time.

.. toctree::
   :maxdepth: 5

   simba.image_transformations

|:label:| Labeling tools

SimBA tools for annotating behavioral events.

.. toctree::
   :maxdepth: 2

   simba.labelling

|:robot_face:| Model tools

Create, train, and manage behavior classifiers in SimBA.

.. toctree::
   :maxdepth: 4

   simba.model_mixin

|:link:| Network transformations

Build and analyze graphs derived from pose-estimation time-series data.

.. toctree::
   :maxdepth: 5

   simba.networks

|:warning:| Outlier correction

Heuristic-based filtering of body-part tracking outliers.

.. toctree::
   :maxdepth: 5

   simba.outlier_tools

|:art:| Plotting and visualization tools

Visualize behavioral data and pose-tracking outputs.

.. toctree::
   :maxdepth: 5

   simba.plotting

|:package:| Pose-estimation import tools

Parse, load, and process pose-estimation data from common formats.

.. toctree::
   :maxdepth: 1

   simba.pose_importers

|:world_map:| ROI tools

Define and analyze regions-of-interest (ROIs) in relation to tracking data.

.. toctree::
   :maxdepth: 3

   simba.roi_tools

|:bar_chart:| Statistics transformations

Compute statistical features, drift, distances, and distribution comparisons in sliding or static time windows.

.. toctree::
   :maxdepth: 4

   simba.statistics_mixin

|:inbox_tray:| Third-party label appenders

Append labels from external annotation tools to pose-estimation outputs.

.. toctree::
   :maxdepth: 1

   simba.third_party_label_appenders

|:clock1:| Time-series transformations

Analyze time-series complexity using sliding window methods.

.. toctree::
   :maxdepth: 5

   simba.timeseries

|:crystal_ball:| Unsupervised learning

Clustering and dimensionality reduction methods for behavioral analysis.

.. toctree::
   :maxdepth: 2

   simba.unsupervised

|:desktop_computer:| User Interface (UI) tools

SimBA's GUI components and window-based interaction logic.

.. toctree::
   :maxdepth: 1

   simba.ui

|:gear:| Utilities

Helper methods for logging, CLI execution, argument checks, warnings, and I/O.

.. toctree::
   :maxdepth: 1

   simba.utils

|:video_camera:| Video processing tools

Video processing tools using OpenCV and FFmpeg.

.. toctree::
   :maxdepth: 5

   simba.video_processing

👁️ YOLO Methods

Methods for training YOLO models, creating training and validation datasets, and converting behavioral neuroscience-specific datasets to YOLO datasets.

Uses the Ultralytics package.

.. toctree::
   :maxdepth: 2

   simba.yolo