microcorrelate.stitching
========================

.. py:module:: microcorrelate.stitching

.. autoapi-nested-parse::

   This module contains functions for stitching together microscopy images



Classes
-------

.. autoapisummary::

   microcorrelate.stitching.StitchConfig


Functions
---------

.. autoapisummary::

   microcorrelate.stitching.read_metadata
   microcorrelate.stitching.stitch_images


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

.. py:class:: StitchConfig

   Custom TIFF tag IDs used to store acquisition metadata in stitched images.

   .. attribute:: tag_metadata_common

      TIFF tag ID for the JSON-encoded metadata common to all acquired tiles.
      Default is 65000.

      :type: int

   .. attribute:: tag_metadata_all

      TIFF tag ID for the JSON-encoded per-tile acquisition metadata.
      Default is 65001.

      :type: int


.. py:function:: read_metadata(stitch_path: pathlib.Path) -> tuple[dict, dict]

   Read acquisition metadata from a stitched TIFF image.

   :param stitch_path: Path to the stitched TIFF file produced by :func:`stitch_images`.
   :type stitch_path: Path

   :returns: * **metadata_common** (*dict*) -- Metadata keys and values shared across all acquired tiles.
             * **metadata_all** (*dict*) -- Per-tile metadata, keyed by original filename.


.. py:function:: stitch_images(tileset_path: pathlib.Path | str, dest_path: pathlib.Path | str, compression: bool = True, group_path: str | None = None, pyramid_levels: int = 1, verbose: bool = False) -> None

   Stitch together tiled images from a tileset acquired via the Thermo Fisher Maps
   software and save the stitched image as a single TIFF file or Zarr file.
   The tileset is expected to be in the directory structure produced by Maps, and have
   been already stitched by the acquisition software
   (that is, there's no overlap or gaps between tiles).

   :param tileset_path: Path to the tileset directory.
   :type tileset_path: Path | str
   :param dest_path: Path to save the stitched image. It can be either a .tif file or a .zarr store.
   :type dest_path: Path | str
   :param compression: Save Tiff image with compression (zlib). This parameter is only used when
                       output is TIff. Zarr files are always compressed. (default = True).
   :type compression: bool
   :param group_path: Path to the group in the Zarr array where images should be saved. If None, save
                      in root. This parameter is only used if output is Zarr. (default = None).
   :type group_path: str | None
   :param pyramid_levels: Number or pyramid levels used when saving to Zarr multiscales. If 1, no
                          downscaled levels are calculated. (default = 1).
   :type pyramid_levels: int
   :param verbose: Enable verbose output (default = False).
   :type verbose: bool

   :rtype: None