Graphical Analysis
==================

.. py:module:: petpal.kinetic_modeling.graphical_analysis

.. autoapi-nested-parse::

   This module provides functions and a key class, :class:`GraphicalAnalysis`, for performing
   graphical analysis on Time Activity Curve (TAC) data. It heavily utilizes Numpy and supports
   various analysis methods like Patlak, Logan, and alternative Logan analysis.

   The :class:`GraphicalAnalysis` class encapsulates the main functionality of the module. It provides
   an organized way to perform graphical analysis where it initializes with paths to input data and
   output details, runs an analysis using a specific method, calculates the best fit parameters,
   computes properties related to the fitting process, and stores the analysis results. All these
   properties and results are stored within an instance's 'analysis_props' dictionary, providing an
   organized storage of result of an analysis task.

   .. todo::

      * Check if it makes more sense to lift out the more mathy methods out into a separate module.
      * Add references for the TCMs and Patlak. Could maybe rely on Turku PET Center.
      * Handle cases when tac_vals = 0.0. Might be able to use t_thresh so that we are past the 0-values.
      * Add more detailed documentation to patlak analysis.




Classes
-------

.. toctree::
   :hidden:

   /autoapi/petpal/kinetic_modeling/graphical_analysis/GraphicalAnalysis
   /autoapi/petpal/kinetic_modeling/graphical_analysis/MultiTACGraphicalAnalysis

.. autoapisummary::

   petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis
   petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis


Functions
---------

.. toctree::
   :hidden:

   /autoapi/petpal/kinetic_modeling/graphical_analysis/_line_fitting_make_rhs_matrix_from_xdata
   /autoapi/petpal/kinetic_modeling/graphical_analysis/fit_line_to_data_using_lls
   /autoapi/petpal/kinetic_modeling/graphical_analysis/fit_line_to_data_using_lls_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/linear_least_squares_fit_with_stats
   /autoapi/petpal/kinetic_modeling/graphical_analysis/cumulative_trapezoidal_integral
   /autoapi/petpal/kinetic_modeling/graphical_analysis/calculate_patlak_x
   /autoapi/petpal/kinetic_modeling/graphical_analysis/get_index_from_threshold
   /autoapi/petpal/kinetic_modeling/graphical_analysis/patlak_analysis
   /autoapi/petpal/kinetic_modeling/graphical_analysis/patlak_analysis_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/logan_analysis
   /autoapi/petpal/kinetic_modeling/graphical_analysis/logan_analysis_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/logan_ref_region_analysis
   /autoapi/petpal/kinetic_modeling/graphical_analysis/logan_ref_region_analysis_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/alternative_logan_analysis
   /autoapi/petpal/kinetic_modeling/graphical_analysis/alternative_logan_analysis_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/get_graphical_analysis_method
   /autoapi/petpal/kinetic_modeling/graphical_analysis/get_graphical_analysis_method_with_rsquared
   /autoapi/petpal/kinetic_modeling/graphical_analysis/km_multifit_analysis_to_tsv
   /autoapi/petpal/kinetic_modeling/graphical_analysis/km_multifit_analysis_to_jsons

.. autoapisummary::
   :nosignatures:

   petpal.kinetic_modeling.graphical_analysis._line_fitting_make_rhs_matrix_from_xdata
   petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls
   petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.linear_least_squares_fit_with_stats
   petpal.kinetic_modeling.graphical_analysis.cumulative_trapezoidal_integral
   petpal.kinetic_modeling.graphical_analysis.calculate_patlak_x
   petpal.kinetic_modeling.graphical_analysis.get_index_from_threshold
   petpal.kinetic_modeling.graphical_analysis.patlak_analysis
   petpal.kinetic_modeling.graphical_analysis.patlak_analysis_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.logan_analysis
   petpal.kinetic_modeling.graphical_analysis.logan_analysis_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis
   petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis
   petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method
   petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method_with_rsquared
   petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_tsv
   petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_jsons