Image Operations 4d
===================

.. py:module:: petpal.preproc.image_operations_4d

.. autoapi-nested-parse::

   The 'image_operations_4d' module provides several functions used to do preprocessing
   on 4D PET imaging series. These functions typically take one or more paths to imaging
   data in NIfTI format, and save modified data to a NIfTI file, and may return the
   modified imaging array as output.

   .. todo::

      *   (weighted_series_sum) Refactor the DecayFactor key extraction into its own function
      *   (weighted_series_sum) Refactor verbose reporting into the class as it is unrelated to
          computation
      *   (extract_tac_from_4dnifty_using_mask) Write the number of voxels in the mask, or the
          volume of the mask. This is necessary for certain analyses with the resulting tacs,
          such as finding the average uptake encompassing two regions.
      *   Methods that create new images should copy over a previous metadata file, if one exists,
          and create a new one if it does not.
      *   (stitch_broken_scans) Separate 'add desc entity' section to its own function somewhere.
      *   (stitch_broken_scans) Assumes non-BIDS key 'DecayFactor' instead of BIDS-required 'DecayCorrectionFactor' for
          ease-of-use with NIL data. Should be changed in the future.
      *   (stitch_broken_scans) Currently writes intermediate files even if output_image_path is None.




Classes
-------

.. toctree::
   :hidden:

   /autoapi/petpal/preproc/image_operations_4d/SimpleAutoImageCropper

.. autoapisummary::

   petpal.preproc.image_operations_4d.SimpleAutoImageCropper


Functions
---------

.. toctree::
   :hidden:

   /autoapi/petpal/preproc/image_operations_4d/stitch_broken_scans
   /autoapi/petpal/preproc/image_operations_4d/crop_image
   /autoapi/petpal/preproc/image_operations_4d/rescale_image
   /autoapi/petpal/preproc/image_operations_4d/extract_mean_roi_tac_from_nifti_using_segmentation
   /autoapi/petpal/preproc/image_operations_4d/threshold
   /autoapi/petpal/preproc/image_operations_4d/binarize_image_with_threshold
   /autoapi/petpal/preproc/image_operations_4d/gauss_blur
   /autoapi/petpal/preproc/image_operations_4d/roi_tac

.. autoapisummary::
   :nosignatures:

   petpal.preproc.image_operations_4d.stitch_broken_scans
   petpal.preproc.image_operations_4d.crop_image
   petpal.preproc.image_operations_4d.rescale_image
   petpal.preproc.image_operations_4d.extract_mean_roi_tac_from_nifti_using_segmentation
   petpal.preproc.image_operations_4d.threshold
   petpal.preproc.image_operations_4d.binarize_image_with_threshold
   petpal.preproc.image_operations_4d.gauss_blur
   petpal.preproc.image_operations_4d.roi_tac