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File Image Stack

Source

ImageStack implementation for file-backed data.

FileImageStack

ImageStack implementation for file-backed data.

This implementation is aimed at representing a single file from a set of multi-file datasets, where the entire dataset cannot be loaded into memory at once.

Parameters:

  • source (Path) –

    Path to the file.

  • axes (str) –

    Axis order (e.g. STCZYX).

  • data_shape (tuple of int) –

    Shape in SC(Z)YX order.

  • data_dtype (DTypeLike) –

    Type of the data.

  • read_func (ReadFunc) –

    Function to read the file into an array.

  • read_kwargs (dict or Any, default: None ) –

    Extra keyword arguments for read_func.

  • original_data_shape (tuple of int or None, default: None ) –

    Shape in original axis order.

Notes

The data will not be loaded until the load method is called. The close method can be used to remove the internal reference to the data.

is_loaded property

True if the file has been loaded into memory.

Returns:

  • bool –

    True if the file has been loaded into memory, False otherwise.

original_axes property

Original axes of the data.

Returns:

  • str –

    Axis order string (e.g. STCZYX).

original_data_shape property

Original shape of the data.

Returns:

  • tuple of int –

    Shape in original axis order.

__init__(source, axes, data_shape, data_dtype, read_func, read_kwargs=None, original_data_shape=None)

Constructor.

This implementation is aimed at representing a single file from a set of multi-file datasets, where the entire dataset cannot be loaded into memory at once. The data is therefore only loaded when the load method is called, and internal reference is deleted upon calling the close method.

Parameters:

  • source (Path) –

    Path to the file.

  • axes (str) –

    Axis order (e.g. STCZYX).

  • data_shape (tuple of int) –

    Shape in SC(Z)YX order after transformation.

  • data_dtype (DTypeLike) –

    Type of the data.

  • read_func (ReadFunc) –

    Function to read the file into an array.

  • read_kwargs (dict or Any, default: None ) –

    Extra keyword arguments passed to read_func.

  • original_data_shape (tuple of int or None, default: None ) –

    Shape in original axis order before transformation.

close()

Remove the internal reference to the data to clear up memory.

extract_patch(sample_idx, channels, coords, patch_size)

Extract a patch for a given sample and channels within the image stack.

Parameters:

  • sample_idx (int) –

    Sample index.

  • channels (sequence of int or None) –

    Channel indices to extract. If None, all channels will be extracted.

  • coords (sequence of int) –

    Spatial coordinates of the top-left corner of the patch.

  • patch_size (sequence of int) –

    Size of the patch in each spatial dimension.

Returns:

  • ndarray –

    A patch of the image data from a particular sample with dimensions C(Z)YX.

from_tiff(path, axes) classmethod

Construct the ImageStack from a TIFF file.

Parameters:

  • path (Path) –

    Path to the TIFF file.

  • axes (str) –

    The original axes of the data, must be a subset of STCZYX.

Returns:

  • Self –

    The ImageStack with the underlying data being from a TIFF file.

load()

Load the data stored in a file.