.. NeuroPAL_ID documentation master file, created by
   sphinx-quickstart on Fri Apr 25 12:49:21 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

=======================================
NeuroPAL_ID Program
=======================================

.. toctree::
   :maxdepth: 2

`Back to overview <../../../_html/index.html>`_

Core ZephIR Calls
---------------------------------------

.. collapse:: recommend_frames

   .. automodule:: Wrapper::recommend_frames
      :members:
      :private-members:
      :undoc-members:

.. collapse:: track_all

   .. automodule:: Wrapper::track_all
      :members:
      :private-members:
      :undoc-members:

.. collapse:: extract_traces

   .. automodule:: Wrapper::extract_traces
      :members:
      :private-members:
      :undoc-members:


Native ZephIR Components
---------------------------------------

.. collapse:: main

   .. automodule:: zephir.main
      :members:
      :private-members:
      :undoc-members:

.. collapse:: annotator

   .. automodule:: zephir.annotator.main
      :members:
      :private-members:
      :undoc-members:

.. collapse:: models

   .. automodule:: zephir.models.container
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.models.losses
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.models.zephir
      :members:
      :private-members:
      :undoc-members:

.. collapse:: methods

   .. automodule:: zephir.methods.auto_annotate
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.build_annotations
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.build_models
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.build_springs
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.get_optimization_trajectory
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.overwrite_checkpoint
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.plot_loss_maps
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.save_annotations
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.methods.track_frame
      :members:
      :private-members:
      :undoc-members:

.. collapse:: zephod

   .. automodule:: zephir.zephod.main
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.zephod.augment
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.zephod.channels
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.zephod.model
      :members:
      :private-members:
      :undoc-members:

   .. automodule:: zephir.zephod.train
      :members:
      :private-members:
      :undoc-members:


Customized ZephIR Classes
---------------------------------------

.. collapse:: build_pdists

   .. automodule:: Wrapper::build_pdists
      :members:
      :private-members:
      :undoc-members:

.. collapse:: build_tree

   .. automodule:: Wrapper::build_tree
      :members:
      :private-members:
      :undoc-members:

.. collapse:: n_io

   .. automodule:: Wrapper::n_io
      :members:
      :private-members:
      :undoc-members:

.. collapse:: save_movie

   .. automodule:: Wrapper::save_movie
      :members:
      :private-members:
      :undoc-members:

Helper Scripts
---------------------------------------

.. collapse:: vddiag

   .. automodule:: Wrapper::vddiag
      :members:
      :private-members:
      :undoc-members:

.. collapse:: annotation_converter

   .. automodule:: Wrapper::annotation_converter
      :members:
      :private-members:
      :undoc-members:

.. collapse:: converter

   .. automodule:: Wrapper::converter
      :members:
      :private-members:
      :undoc-members: