dcnum.read.cache
================

.. py:module:: dcnum.read.cache


Exceptions
----------

.. autoapisummary::

   dcnum.read.cache.EmptyDatasetWarning


Classes
-------

.. autoapisummary::

   dcnum.read.cache.BaseImageChunkCache
   dcnum.read.cache.HDF5ImageCache
   dcnum.read.cache.ImageCorrCache


Functions
---------

.. autoapisummary::

   dcnum.read.cache.md5sum


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

.. py:exception:: EmptyDatasetWarning

   Bases: :py:obj:`UserWarning`


   Initialize self.  See help(type(self)) for accurate signature.


.. py:class:: BaseImageChunkCache(shape: tuple[int], chunk_size: int = 1000, cache_size: int = 2)

   Bases: :py:obj:`abc.ABC`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: shape


   .. py:attribute:: _dtype
      :value: None



   .. py:attribute:: _len


   .. py:attribute:: cache

      This is a FILO cache for the chunks


   .. py:attribute:: image_shape


   .. py:attribute:: chunk_shape


   .. py:attribute:: chunk_size


   .. py:attribute:: cache_size
      :value: 2



   .. py:attribute:: num_chunks


   .. py:method:: __getitem__(index)


   .. py:method:: __len__()


   .. py:property:: dtype

      data type of the image data


   .. py:method:: _get_chunk_data(chunk_slice)
      :abstractmethod:


      Implemented in subclass to obtain actual data



   .. py:method:: _get_chunk_index_for_index(index)


   .. py:method:: get_chunk(chunk_index)

      Return one chunk of images



   .. py:method:: get_chunk_size(chunk_index)

      Return the number of images in this chunk



   .. py:method:: get_chunk_slice(chunk_index)

      Return the slice corresponding to the chunk index



   .. py:method:: iter_chunks()


.. py:class:: HDF5ImageCache(h5ds: dcnum.common.h5py.Dataset | dcnum.read.mapped.MappedHDF5Dataset, chunk_size: int = 1000, cache_size: int = 2, boolean: bool = False)

   Bases: :py:obj:`BaseImageChunkCache`


   An HDF5 image cache

   Deformability cytometry data files commonly contain image stacks
   that are chunked in various ways. Loading just a single image
   can be time-consuming, because an entire HDF5 chunk has to be
   loaded, decompressed and from that one image extracted. The
   `HDF5ImageCache` class caches the chunks from the HDF5 files
   into memory, making single-image-access very fast.


   .. py:attribute:: h5ds


   .. py:attribute:: boolean
      :value: False



   .. py:method:: _get_chunk_data(chunk_slice)

      Implemented in subclass to obtain actual data



.. py:class:: ImageCorrCache(image: HDF5ImageCache, image_bg: HDF5ImageCache)

   Bases: :py:obj:`BaseImageChunkCache`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: image


   .. py:attribute:: image_bg


   .. py:method:: _get_chunk_data(chunk_slice)

      Implemented in subclass to obtain actual data



.. py:function:: md5sum(path, blocksize=65536, count=0)

   Compute (partial) MD5 sum of a file

   :param path: path to the file
   :type path: str or pathlib.Path
   :param blocksize: block size in bytes read from the file
                     (set to `0` to hash the entire file)
   :type blocksize: int
   :param count: number of blocks read from the file
   :type count: int