Standard tomography loader

HTTomo provides the standard_tomo loader for parallel-beam tomography data stored in HDF5/NeXus files. A basic configuration specifies the projection data, image key, and rotation angles:

- method: standard_tomo
  module_path: httomo.data.hdf.loaders
  parameters:
    data_path: /entry1/tomo_entry/data/data
    image_key_path: /entry1/tomo_entry/instrument/detector/image_key
    rotation_angles:
      data_path: /entry1/tomo_entry/data/rotation_angle

data_path

The dataset containing the projection data. It commonly also contains the dark and flat images.

image_key_path

The dataset identifying each image as a projection (0), flat (1), or dark (2).

rotation_angles

The location or definition of the rotation angles. See Rotation angles when the input does not contain a usable angle dataset.

See Darks and flats for other dark and flat layouts, and Previewing for loading only part of the dataset.

Automatic NXtomo discovery

If the input contains a valid NXtomo entry, set the following parameters to auto:

- method: standard_tomo
  module_path: httomo.data.hdf.loaders
  parameters:
    data_path: auto
    image_key_path: auto
    rotation_angles: auto

HTTomo then discovers the projection data, image keys and rotation angles. Use the script in Creating an NXtomo file to create compatible NXtomo data.

Note

Automatic NXtomo discovery is unavailable when darks or flats are loaded from separate files.