Methods to perform geometry transformation of pose-estimation data. This includes creating bounding boxes, line objects, polygons, circles etc. from pose-estimated body-parts and recording environment and computing metric representations of the relationships between created shapes or their attributes (sizes, distances, overlaps, intersection, etc.)
.. toctree:: :maxdepth: 4 simba.geometry_mixin
Unlike linear data, circular data wrap around in a circular or periodic manner such as two measurements of e.g., 360 vs. 1 are more similar than two measurements of 1 vs. 3. Thus, the minimum and maximum values are connected, forming a closed loop, and we therefore need specialized statistical methods.These methods have support for multiple animals and base radial directions derived from two or three body-parts.
.. toctree:: :maxdepth: 4 simba.circular_statistics
Statistics methods used for feature extraction, drift assessment, distance computations, distribution comparisons in sliding and static windows.
.. toctree:: :maxdepth: 4 simba.statistics_mixin
Methods to slice and compute attributes of images from tracking data and comparing those image attributes across sequential images.
.. toctree:: :maxdepth: 5 simba.image_transformations
Time-series methods focused on signal complexity in sliding windows.
.. toctree:: :maxdepth: 5 simba.timeseries
Methods for creating and analyze time-dependent graphs from pose-estimation data.
.. toctree:: :maxdepth: 5 simba.networks
Feature extraction methods used by "default" feature extraction wrappers. These methods are used by the "out-of-the-box" pre-defined pose-estimation schemas and compute - mainly - movement, distances and size features.
.. toctree:: :maxdepth: 4 simba.feature_extraction_mixins
Methods for processing videos (e.g., pre- or processing functions that typically depend on ffmpeg or opencv).
.. toctree:: :maxdepth: 5 simba.video_processing
Methods for visualizing behavior, tracking, and transformed data based on animal tracking.
.. toctree:: :maxdepth: 5 simba.plotting
Methods for removing outliers based on heuristic rules of movement and location of pose-estimated body-parts
.. toctree:: :maxdepth: 5 simba.outlier_tools
Methods for manipulating and transforming classification data, image data, and animal tracking data
.. toctree:: :maxdepth: 1 simba.data_processors
Methods for unsupervised learning in SimBA
.. toctree:: :maxdepth: 2 simba.unsupervised
SimBA methods and interfaces for annotating images for behavioral states.
.. toctree:: :maxdepth: 2 simba.labelling
SimBA methods for appending annotation data from dedicated annotation software to pose-estimation data.
.. toctree:: :maxdepth: 1 simba.third_party_label_appenders
Helper functions for lookups, terminal printing, argument validity checks, reading and writing to disk, warning / error handling, and helpers for executing functions through CLI
.. toctree:: :maxdepth: 1 simba.utils
Methods for drawing, defining, and analyzing tracking data in relation to ROIs
.. toctree:: :maxdepth: 3 simba.roi_tools
"Standard" feature extraction methods for input pose-estimation data. These methods are used by the "out-of-the-box" pre-defined pose-estimation schemas and compute - mainly - movement, distances and size features.
.. toctree:: :maxdepth: 1 simba.feature_extractors
Methods to import and manipulate pose-estimation data
.. toctree:: :maxdepth: 1 simba.pose_importers
Methods for SimBA graphical interfaces
.. toctree:: :maxdepth: 1 simba.ui
Methods for analyzing animal interactions through overlapping bounding boxes.
.. toctree:: :maxdepth: 2 simba.bounding_box_tools simba.yolo
Methods for creating behavior models
.. toctree:: :maxdepth: 4 simba.model_mixin
Methods for reading SimBA project config and associated project data
.. toctree:: :maxdepth: 2 simba.config_reader
Methods for analyzing animal behaviours associated with cue-light states through.
.. toctree:: :maxdepth: 2 simba.cue_light_tools