Cli Tac Fitting
===============

.. py:module:: petpal.cli.cli_tac_fitting

.. autoapi-nested-parse::

   Command-line interface (CLI) for fitting Tissue Compartment Models (TCM) to PET Time-Activity Curves (TACs).

   This module provides a CLI to interact with the tac_fitting module. It utilizes argparse to handle command-line
   arguments.

   The user must provide:
       * Input TAC file path
       * Region of Interest (ROI) TAC file path
       * Compartment model name for fitting. Supported models are '1tcm', '2tcm-k4zero', or 'serial-2tcm'.
       * Filename prefix for the output files
       * Output directory where the analysis results will be saved
       * Whether to ignore blood volume contributions while fitting
       * Threshold in minutes (input fitting threshold)

   User can optionally provide:
       * Initial guesses for the fitting parameters
       * Lower and upper bounds for the fitting parameters
       * Maximum number of function iterations
       * Decay constant (in minutes) for per-frame weighting

   This script utilizes the :class:`TCMAnalysis<petpal.tac_fitting.TCMAnalysis>` class to perform the TAC fitting and save
    the results accordingly.

   .. rubric:: Examples

   In the proceeding example, we assume that we have an input TAC named 'input_tac.txt', and an ROI TAC named
   'roi_tac.tsv'. We want to try fitting a serial 2TCM to the ROI tac.

   .. code-block:: bash

       petpal-tcm-fit interp -i "input_tac.tsv"\
       -r "roi_tac.tsv"\
       -m "serial-2tcm"\
       -o "./" -p "cli_"\
       -t 35.0\
       -g 0.1 0.1 0.1 0.1 0.1\
       -l 0.0 0.0 0.0 0.0 0.0\
       -u 5.0 5.0 5.0 5.0 5.0\
       -f 2500 -n 4096 -b --print

   In this next example, we assume that we have an input TAC named 'input_tac.txt', an ROI TACs directory
    named './roi_tas/' which contains TACs for different ROIs, and a scan/image metadata file called 'scan_info.json'.
    We want to try fitting serial 2TCM to the ROI tacs, with the default bounds.

   .. code-block:: bash

       petpal-tcm-fit frame_avgd -i "input_tac.tsv"\
       -r "./roi_tacs/"\
       -s "scan_info.json"\
       -m "serial-2tcm"\
       -o "./" -p "cli_"\
       -f 2500 -n 4096 -b --print

   .. seealso:: :mod:`petpal.tac_fitting` - module for fitting TACs with TCMs.




Attributes
----------

.. autoapisummary::

   petpal.cli.cli_tac_fitting._EXAMPLE_


Functions
---------

.. toctree::
   :hidden:

   /autoapi/petpal/cli/cli_tac_fitting/add_common_io_args
   /autoapi/petpal/cli/cli_tac_fitting/add_common_analysis_args
   /autoapi/petpal/cli/cli_tac_fitting/add_common_print_args
   /autoapi/petpal/cli/cli_tac_fitting/_generate_args
   /autoapi/petpal/cli/cli_tac_fitting/_generate_bounds
   /autoapi/petpal/cli/cli_tac_fitting/fit_props_printer

.. autoapisummary::
   :nosignatures:

   petpal.cli.cli_tac_fitting.add_common_io_args
   petpal.cli.cli_tac_fitting.add_common_analysis_args
   petpal.cli.cli_tac_fitting.add_common_print_args
   petpal.cli.cli_tac_fitting._generate_args
   petpal.cli.cli_tac_fitting._generate_bounds
   petpal.cli.cli_tac_fitting.fit_props_printer


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

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

   .. raw:: html

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

   .. code-block:: python

      """Fitting a TAC to the serial 2TCM using the interpolation strategy:
      	petpal-tcm-fit interp -i "input_tac.txt" -r "2tcm_tac.txt" -m "serial-2tcm" -o "./" -p "cli_" -t 35.0 -g 0.1 0.1 0.1 0.1 0.1 -l 0.0 0.0 0.0 0.0 0.0 -u 5.0 5.0 5.0 5.0 5.0 -f 2500 -n 4096 -b --print
      
      Fitting a TAC to the serial 2TCM using the frame averaged strategy:
      	petpal-tcm-fit frame_avgd -i "input_tac.txt" -r "2tcm_tac.txt" -s scan_metadata.json -m "serial-2tcm" -o "./" -p "cli_" -g 0.1 0.1 0.1 0.1 0.1 -l 0.0 0.0 0.0 0.0 0.0 -u 5.0 5.0 5.0 5.0 5.0 -f 2500 -n 4096 -b --print"""

   .. raw:: html

      </details>