Cli Reference Tissue Models
===========================

.. py:module:: petpal.cli.cli_reference_tissue_models

.. autoapi-nested-parse::

   This module provides a command-line interface for running various reference tissue model (RTM) analyses.

   The module defines a set of command-line arguments for the input and output data, as well
   as the analysis specifics. Several types of RTM analyses, such as SRTM, FRTM, MRTM and its variants,
   are supported, each with its associated arguments.

   The primary function in the module is `main()`, which is responsible for parsing command-line
   arguments, running the selected analysis, and handling the results. The analysis is performed
   using the :class:`RTMAnalysis<petpal.reference_tissue_models.RTMAnalysis>` class.

   .. rubric:: Example

   Assuming that the package has been installed, we have:

   For running an FRTM analysis:

   .. code-block:: bash

       petpal-rtms frtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0 5.0

   For running an SRTM analysis:

   .. code-block:: bash

       petpal-rtms srtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0 5.0

   For running an FRTM2 analysis:

   .. code-block:: bash

       petpal-rtms frtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0

   For running an SRTM2 analysis:

   .. code-block:: bash

       petpal-rtms srtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0

   For running an MRTM analysis:

   .. code-block:: bash

       petpal-rtms mrtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0

   For running an MRTM2 analysis:

   .. code-block:: bash

       petpal-rtms mrtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0 --k2-prime 0.1


   For running the original MRTM analysis:

   .. code-block:: bash

       petpal-rtms mrtm-original --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0

   .. seealso:: * :mod:`petpal.reference_tissue_models`




Attributes
----------

.. autoapisummary::

   petpal.cli.cli_reference_tissue_models._RTM_EXAMPLES_


Functions
---------

.. toctree::
   :hidden:

   /autoapi/petpal/cli/cli_reference_tissue_models/add_common_args
   /autoapi/petpal/cli/cli_reference_tissue_models/parse_args
   /autoapi/petpal/cli/cli_reference_tissue_models/_generate_bounds
   /autoapi/petpal/cli/cli_reference_tissue_models/_pretty_print_results

.. autoapisummary::
   :nosignatures:

   petpal.cli.cli_reference_tissue_models.add_common_args
   petpal.cli.cli_reference_tissue_models.parse_args
   petpal.cli.cli_reference_tissue_models._generate_bounds
   petpal.cli.cli_reference_tissue_models._pretty_print_results


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

.. py:data:: _RTM_EXAMPLES_
   :value: Multiline-String

   .. raw:: html

      <details><summary>Show Value</summary>

   .. code-block:: python

      """
      Examples:
        - FRTM (4 parameters: R1, k2, k3, k4):
          petpal-rtms frtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0
        - SRTM (3 parameters: R1, k2, BP):
          petpal-rtms srtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0
        - FRTM2 (3 parameters: R1, k3, k4):
          petpal-rtms frtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 0.0 --upper-bounds 5.0 5.0 5.0 5.0
        - SRTM2 (2 parameters: R1, BP):
          petpal-rtms srtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --k2-prime 0.5 --prefix sub_001 --print --initial-guesses 0.1 0.1 0.1 0.1 --lower-bounds 0.0 0.0 0.0 --upper-bounds 5.0 5.0
        - MRTM (2 parameters: BP, k2_prime):
          petpal-rtms mrtm --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0
        - MRTM2 (2 parameters: BP):
          petpal-rtms mrtm2 --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0 --k2-prime 0.1
        - MRTM (Original) (2 parameters: BP, k2_prime):
          petpal-rtms mrtm-original --ref-tac-path /path/to/ref/tac --roi-tac-path /path/to/roi/tac --prefix sub_001 --print --t-thresh-in-mins 30.0
      """

   .. raw:: html

      </details>