Full loader configuration

The example below combines the loader options described in the preceding sections. It assumes that:

• The input file contains a dataset of projections only.

• Image keys and rotation angles are not available in the input file.

• Dark and flat images are stored in separate HDF5 files.

Replace the file paths, dataset paths and rotation angle values with those appropriate for your data. The example angle values describe 2161 projections acquired from -49 to 59 degrees in steps of 0.05 degrees.

- method: standard_tomo
  module_path: httomo.data.hdf.loaders
  parameters:
    data_path: /path/to/data
    image_key_path: null # no keys in the file
    rotation_angles: # in degrees
      user_defined:
        start_angle: -49
        stop_angle: 59
        angles_total: 2161
    preview:
      detector_x:
        start: null
        stop: null
      detector_y:
        start: null
        stop: null
    darks:
      file: path/to/file_darks.h5
      image_key_path: null
      data_path: /path/to/darks
    flats:
      file: path/to/file_flats.h5
      image_key_path: null
      data_path: /path/to/flats
    continuous_scan_subset: null

Note

User-defined rotation angles are equally spaced and expressed in degrees. Both start_angle and stop_angle are included. angles_total must match the number of projections, excluding dark and flat images.

With image_key_path: null, every image in the projection dataset is treated as a projection. The dataset must therefore not contain interleaved dark or flat images.

Tip

Use file: input_data if the dark or flat dataset is stored in the main input file. Dataset paths such as /path/to/flats identify datasets inside an HDF5 file; they are not filesystem paths.

Null preview (null) bounds select the full detector extent. This example does not specify preview.angles and therefore retains all projections. continuous_scan_subset: null disables configuration-based selection of an individual scan from a continuous acquisition.