cibrrig.preprocess.preproc_pipeline
===================================

.. py:module:: cibrrig.preprocess.preproc_pipeline

.. autoapi-nested-parse::

   This module runs the preprocessing pipeline for a session.
   It extracts sync, video frame, opto, and physiology information from the session.



Attributes
----------

.. autoapisummary::

   cibrrig.preprocess.preproc_pipeline._log


Functions
---------

.. autoapisummary::

   cibrrig.preprocess.preproc_pipeline.plot_QC
   cibrrig.preprocess.preproc_pipeline.run_ephys_qc_session
   cibrrig.preprocess.preproc_pipeline.run
   cibrrig.preprocess.preproc_pipeline.cli
   cibrrig.preprocess.preproc_pipeline.runQC


Module Contents
---------------

.. py:data:: _log

.. py:function:: plot_QC(ephysQC)

   Plot the quality control figures for the ephys data.
   Saves images to the raw ephys folder

   :param ephysQC: EphysQC object containing the quality control data computed by IBL
   :type ephysQC: EphysQC


.. py:function:: run_ephys_qc_session(session_path)

   Run ephysQC on all probes in the session.

   :param session_path: Path to the session directory.
   :type session_path: str or Path

   :returns: None


.. py:function:: run(session_path, skip_ephysqc=False)

   Run the preprocessing pipeline for a session.
   1) Extract sync times (digital signals from the SpikeGLX NIDQ signal)
   2) Extract video frame times (from the digital line on the NIDQ input)
   3) Extract opto times (From either digital or analog signals, looks for "laser" in the wiring dictionary)
   4) Extract physiology data (emgs, ekgs, pressure differential, temperature)
   5) Run ephysQC (optional)

   :param session_path: Path to the session directory.
   :type session_path: str or Path
   :param skip_ephysqc: If True, skip the ephysQC step. Defaults to False.
   :type skip_ephysqc: bool, optional

   :returns: None


.. py:function:: cli(session_path, skip_ephysqc)

   Command-line interface for running the preprocessing pipeline.

   :param session_path: Path to the session directory.
   :type session_path: str
   :param skip_ephysqc: If True, skip the ephysQC step.
   :type skip_ephysqc: bool

   :returns: None


.. py:function:: runQC(session_path)