BidsMetadataMender
========================================

.. py:class:: petpal.utils.metadata.BidsMetadataMender(json_filepath: str, decay_correction: bool = False)

   Class for repairing and filling in the gaps of BIDS metadata based on existing fields.

   For most use cases, just initialize a mender object, passing a string path to the .json file,
   and a boolean for whether the image was decay_corrected. Then, simply calling the object
   (i.e. 'mender()') will result in keys being added/updated where possible.

   The following checks are made:

   - If 'FrameDuration' is present, fill 'FrameTimesStart', assuming the first entry to be 0.
   - If 'TracerRadionuclide' is present, add 'RadionuclideHalfLife'.
       - Note that 'RadionuclideHalfLife' is not listed in BIDS, but we find it useful to store.
   - If all the previous keys were added, use them to calculate 'FrameReferenceTime'.
       - 'FrameReferenceTime' is not BIDS-required but it is useful.
   - If all the previous keys were added, add 'DecayCorrectionFactor' and 'ImageDecayCorrected'.
       - If decay_correction was set to False, 'DecayCorrectionFactor' is a list of ones of
         len(FrameDuration) and 'ImageDecayCorrected will be 'false', per BIDS.

   :ivar metadata: dictionary containing all the existing BIDS metadata
   :vartype metadata: dict
   :ivar filepath: path to .json file containing original BIDS metadata
   :vartype filepath: str
   :ivar decay_correction: whether or not the image is decay-corrected

   :vartype decay_correction: bool

   Initializes a new BidsMetadataMender object.

   :param json_filepath: path to .json file with original BIDS metadata.
   :type json_filepath: str
   :param decay_correction: Whether or not the image is decay-corrected. Defaults to False.
   :type decay_correction: bool


   .. py:method:: __call__(output_filepath: str | None = None)


   .. py:method:: _add_missing_keys()

      Repair/Fill missing keys where possible.



   .. py:method:: _add_half_life()

      Add "RadionuclideHalfLife" key to metadata.



   .. py:method:: _add_empty_decay_factors()

      Adds a list of ones for decay factors and sets 'ImageDecayCorrected' to False.



   .. py:method:: _add_decay_factors()

      Computes decay factors and adds 'DecayCorrectionFactor' to metadata.



   .. py:method:: _add_frame_times_start()

      Fill in frame starts from frame durations, assuming first frame starts at 0.



   .. py:method:: _add_frame_reference_times()

      Fill in frame reference times from frame starts and durations.



   .. py:method:: _to_file(filepath: str | None = None)

      Write metadata dictionary to a .json file; defaults to making a backup.