dcnum.read.cache

Exceptions

EmptyDatasetWarning

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

Classes

BaseImageChunkCache	Helper class that provides a standard way to create an ABC using
HDF5ImageCache	An HDF5 image cache
ImageCorrCache	Helper class that provides a standard way to create an ABC using

Functions

md5sum(path[, blocksize, count])

Compute (partial) MD5 sum of a file

Module Contents

exception dcnum.read.cache.EmptyDatasetWarning

Bases: UserWarning

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

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

Bases: abc.ABC

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

shape

_dtype = None

_len

cache

This is a FILO cache for the chunks

image_shape

chunk_shape

chunk_size

cache_size = 2

num_chunks

__getitem__(index)

__len__()

property dtype

data type of the image data

abstractmethod _get_chunk_data(chunk_slice)

Implemented in subclass to obtain actual data

_get_chunk_index_for_index(index)

get_chunk(chunk_index)

Return one chunk of images

get_chunk_size(chunk_index)

Return the number of images in this chunk

get_chunk_slice(chunk_index)

Return the slice corresponding to the chunk index

iter_chunks()

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

Bases: 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.

h5ds

boolean = False

_get_chunk_data(chunk_slice)

Implemented in subclass to obtain actual data

class dcnum.read.cache.ImageCorrCache(image: HDF5ImageCache, image_bg: HDF5ImageCache)

Bases: BaseImageChunkCache

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

image

image_bg

_get_chunk_data(chunk_slice)

Implemented in subclass to obtain actual data

dcnum.read.cache.md5sum(path, blocksize=65536, count=0)

Compute (partial) MD5 sum of a file

Parameters:

• path (str or pathlib.Path) – path to the file

• blocksize (int) – block size in bytes read from the file (set to 0 to hash the entire file)

• count (int) – number of blocks read from the file