DecayFix
========================================

.. py:class:: petpal.preproc.decay_correction.DecayFix(image_loader: Optional[petpal.io.image.ImageLoader] = None)

   Bases: :py:obj:`DecayCorrect`


   Special case for decay correction where the dynamic PET image was scaled with the wrong
   isotope but JSON metadata retains accurate decay correction factors.


   .. py:method:: fix_factor(input_image_path: str, isotope_to_remove: str) -> numpy.ndarray[float]

      Get ratio of the expected decay correction factor to the factor that was incorrectly
      applied to PET image.

      :param input_image_path: Path to dynamic PET image.
      :type input_image_path: str
      :param isotope_to_remove: Name of the isotope that was incorrectly used to scale dynamic
                                PET image, such as 'o15' or 'c11'.
      :type isotope_to_remove: str

      :returns: *fix_factor (np.ndarray[float])* --

                Scalar array with the correction factor to apply to
                    each frame in dynamic PET.



   .. py:method:: __call__(input_image_path: str, output_image_path: str, isotope_to_remove: str)

      Calculate correction factor based on the accurate metadata and name of the isotope
      incorrectly used to scale image data.

      :param input_image_path: Path to dynamic PET image.
      :type input_image_path: str
      :param output_image_path: Path to where corrected image is saved.
      :type output_image_path: str
      :param isotope_to_remove: Name of the isotope that was incorrectly used to scale dynamic
                                PET image, such as 'o15' or 'c11'.
      :type isotope_to_remove: str



   .. py:method:: apply_factor(input_image_path: str, correction_factor: numpy.ndarray[float])

      Apply fix factor to image and write output.

      :param input_image_path: Path to dynamic PET image.
      :type input_image_path: str
      :param correction_factor_path: Path to file with correction factors, one per frame.
                                     File must have exactly one column, with a header followed by one scalar per
                                     line.
      :type correction_factor_path: str



   .. py:method:: save_modified_pet(input_image_path: str, output_image_path: str)

      Save the modified PET image

      :param input_image_path: Path to dynamic PET image.
      :type input_image_path: str
      :param output_image_path: Path to where corrected image is saved.
      :type output_image_path: str



   .. py:method:: decay_correct_factor_from_file(input_image_path: str, output_image_path: str, correction_factor_path: str)

      Apply a set of correction factors to each frame in a PET image.

      Provide path to dynamic PET image, path to where corrected image is saved, and path to a
      file containing factors for each frame. File containing correction factors must have
      exactly one column, with a header followed by one scalar per line to apply to the
      corresponding frame in the PET. Reads image and correction factors, applies them, and saves
      result.

      :param input_image_path: Path to dynamic PET image.
      :type input_image_path: str
      :param output_image_path: Path to where corrected image is saved.
      :type output_image_path: str
      :param correction_factor_path: Path to file with correction factors, one per frame.
                                     File must have exactly one column, with a header followed by one scalar per
                                     line.
      :type correction_factor_path: str