7.1.1. algotom.io.converter

Module for converting data type:

  • Convert a list of tif files to a hdf/nxs file.

  • Extract tif images from a hdf/nxs file.

  • Emulate an HDF5-like interface for TIF files in a folder.

Functions:

convert_tif_to_hdf(input_path, output_path)

Convert a folder of tif files to a hdf/nxs file.

extract_tif_from_hdf(input_path, ...[, ...])

Extract tif images from a hdf/nxs file.
algotom.io.converter.convert_tif_to_hdf(input_path, output_path, key_path='entry/data', crop=(0, 0, 0, 0), pattern=None, **options)[source]

Convert a folder of tif files to a hdf/nxs file.

Parameters

  • input_path (str) – Folder path to the tif files.

  • output_path (str) – Path to the hdf/nxs file.

  • key_path (str, optional) – Key path to the dataset.

  • crop (tuple of int, optional) – Crop the images from the edges, i.e. crop = (crop_top, crop_bottom, crop_left, crop_right).

  • pattern (str, optional) – Used to find tif files with names matching the pattern.

  • options (dict, optional) – Add metadata. E.g options={“entry/angles”: angles, “entry/energy”: 53}.

Returns

str – Path to the hdf/nxs file.

algotom.io.converter.extract_tif_from_hdf(input_path, output_path, key_path, index=(0, -1, 1), axis=0, crop=(0, 0, 0, 0), prefix='img')[source]

Extract tif images from a hdf/nxs file.

Parameters

  • input_path (str) – Path to the hdf/nxs file.

  • output_path (str) – Output folder.

  • key_path (str) – Key path to the dataset in the hdf/nxs file.

  • index (tuple of int or int.) – Indices of extracted images. A tuple corresponds to (start,stop,step).

  • axis (int) – Axis which the images are extracted.

  • crop (tuple of int, optional) – Crop the images from the edges, i.e. crop = (crop_top, crop_bottom, crop_left, crop_right).

  • prefix (str, optional) – Prefix of names of tif files.

Returns

str – Folder path to the tif files.

class algotom.io.converter.HdfEmulatorFromTif(folder_path, ncore=1)[source]

Bases: object

Emulate an HDF5-like interface for TIF files in a folder, allowing indexed and sliced data access.

Parameters

  • folder_path (str) – Path to the folder containing TIFF files.

  • ncore (int, optional) – Number of cores to use for parallel processing. The default is 1 (sequential processing).

Examples

>>> hdf_emulator = HdfEmulatorFromTif('/path/to/tif/files', ncore=4)
>>> print(hdf_emulator.shape)
>>> last_image = hdf_emulator[-1]
>>> image_stack = hdf_emulator[:, 0:4, :]
property shape
property dtype