spatiomic.data
==============

.. py:module:: spatiomic.data

.. autoapi-nested-parse::

   Expose i/o functions from the data submodule.



Classes
-------

.. autoapisummary::

   spatiomic.data.read
   spatiomic.data.subsample


Functions
---------

.. autoapisummary::

   spatiomic.data.anndata_from_array
   spatiomic.data.subset


Package Contents
----------------

.. py:function:: anndata_from_array(data, channel_names, clusters = None, cluster_key = 'clusters', spatial_weights = None)

   Create an AnnData object from an image data array.

   :param data: The image data array.
   :type data: NDArray
   :param channel_names: The channel names.
   :type channel_names: List[str]
   :param clusters: The clusters. Defaults to None.
   :type clusters: Optional[NDArray], optional
   :param cluster_key: The cluster key. Defaults to "clusters".
   :type cluster_key: str, optional
   :param spatial_weights: The spatial weights. Defaults to None.
   :type spatial_weights: Optional[W], optional

   :returns: The AnnData object
   :rtype: AnnData


.. py:class:: read

   A class to read in microscopy files.


   .. py:method:: get_czi_image_channels(image, image_shape, ubyte = True)
      :staticmethod:


      Get the channels of an .czi image.

      :param image: The read CziFile of an image.
      :type image: NDArray
      :param image_shape: The shape of the CziFile.
                          Example format of the image shape:
                          [('B', 1), ('H', 1), ('T', 1), ('C', 3), ('Z', 1), ('Y', 2048), ('X', 2048)]
      :type image_shape: List[Tuple[str, int]]
      :param ubyte: Whether to interpret the data as np.uint8.. Defaults to True.
      :type ubyte: bool, optional

      :returns: An array containing the channels of the .czi file
      :rtype: NDArray



   .. py:method:: read_czi(file_path, input_dimension_order = 'XYC')
      :classmethod:


      Read a single czi file on a given path and returns it.

      :param file_path: Location of the file to be read.
      :type file_path: str

      :returns: An array containing the channels of the .czi file
      :rtype: NDArray



   .. py:method:: read_lif(file_path, image_idx = 0)
      :staticmethod:


      Read a single lif file on a given path and returns it.

      :param file_path: Location of the file to be read.
      :type file_path: str

      :returns: An array containing the channels of the .lif file
      :rtype: NDArray



   .. py:method:: read_tiff(file_path, input_dimension_order = 'XYC', precision = 'float32')
      :staticmethod:


      Read a single tiff file on a given path and returns it.

      :param file_path: Location of the file to be read.
      :type file_path: str
      :param input_dimension_order: The dimension order of the channels in the tiff file.
                                    Defaults to "XYC".
      :type input_dimension_order: str, optional
      :param precision: The precision of the data in the tiff file.
                        Defaults to "float32".
      :type precision: Literal["float32", "float64"], optional

      :returns: An array containing the channels of the .tiff file in XYC dimension order.
      :rtype: NDArray



   .. py:method:: split_multi_image_lif(file_path, save_folder, save_prefix)
      :staticmethod:


      Read a lif file with multiple images and save every image in a defined folder.

      :param file_path: [description]
      :type file_path: str
      :param save_folder: [description]
      :type save_folder: str
      :param save_prefix: [description]
      :type save_prefix: str



.. py:class:: subsample

   A class to subsample image data.


   .. py:method:: fit_transform(data, method = 'fraction', fraction = 0.1, count = 100000, *args, **kwargs)
      :staticmethod:


      Create a random subsample of some image data pixels, preserving channel dimensionality.

      :param data: Image data to take the subsample from.
      :type data: NDArray
      :param method: The method to use. Defaults to "fraction".
      :type method: Literal["fraction", "count"], optional
      :param fraction: The fraction of pixels to take when using the "fraction" method. When this
                       results in a non-integer number of pixels, the number of pixels is rounded down.
                       Defaults to 0.1.
      :type fraction: float, optional
      :param count: The number of pixels to take. Defaults to 10000 when using the "count" method.
                    Defaults to 100,000.
      :type count: int, optional
      :param seed: The seed to use for random number generation. Defaults to None.
      :type seed: Optional[int], optional

      :returns: A flattened, random subsample of the pixels in the provided image data.
      :rtype: NDArray



.. py:function:: subset(data, channel_names_data, channel_names_subset)

   Subset the data with the given channel names to the subset channel names in the given order.

   :param data: The image data, channel-last.
   :type data: NDArray
   :param channel_names_data: The channel names of the data.
   :type channel_names_data: List[str]
   :param channel_names_subset: The channel names to include in the subset.
   :type channel_names_subset: List[str]

   :returns: The subsetted data, with channel ordered according to the subset channel names.
   :rtype: NDArray