API reference
=============

Configuration
-------------

.. automodule:: tadpose.config
   :members:

.. automodule:: tadpose.cli
   :members:

Acquisition and pose estimation
--------------------------------

.. automodule:: tadpose.well_detection
   :members:

.. automodule:: tadpose.video_segmentation
   :members:

.. automodule:: tadpose.video_info
   :members:

.. automodule:: tadpose.dlc_runner
   :members:

Feature extraction
------------------

.. automodule:: tadpose.feature_extraction
   :members:

.. automodule:: tadpose.feature_cleaning
   :members:

.. automodule:: tadpose.normalisation
   :members:

Clustering
----------

.. automodule:: tadpose.clustering
   :members:

.. automodule:: tadpose.cluster_meta
   :members:

.. automodule:: tadpose.centroid_matching
   :members:

Cluster validation (choosing k)
-------------------------------

.. automodule:: tadpose.analysis.internal_metrics
   :members:

Post-clustering analysis
------------------------

.. automodule:: tadpose.analysis.proportions
   :members:

.. automodule:: tadpose.analysis.stats
   :members:

.. automodule:: tadpose.analysis.cluster_map
   :members:

.. automodule:: tadpose.analysis.markov_chain
   :members:

.. automodule:: tadpose.analysis.markov_chain_groups
   :members:

.. automodule:: tadpose.analysis.assign_new_data_to_clusters
   :members:

.. automodule:: tadpose.analysis.generate_new_labelling
   :members:

Visualisation
-------------

.. automodule:: tadpose.viz_constants
   :members:

.. automodule:: tadpose.analysis.viz_centroids
   :members:

.. automodule:: tadpose.analysis.viz_proportions
   :members:

Database and experiment management
----------------------------------

.. automodule:: tadpose.database
   :members:

.. automodule:: tadpose.file_manager
   :members:

.. automodule:: tadpose.plate_manager
   :members:

.. automodule:: tadpose.experiment_manager
   :members:

.. automodule:: tadpose.preset_manager
   :members:

.. automodule:: tadpose.result_manager
   :members:

.. automodule:: tadpose.slurm_jobs
   :members:

.. automodule:: tadpose.frame_getter
   :members: