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nabu.stitching.stitcher.dumper

source package nabu.stitching.stitcher.dumper

Classes

  • PostProcessingStitchingDumper — dumper to be used when save data during post-processing stitching (on reconstructed volume). Output is expected to be an NXtomo

  • PostProcessingStitchingDumperNoDD — same as PostProcessingStitchingDumper but prevent to do data duplication. In this case we need to work on HDF5 file only

  • PostProcessingStitchingDumperWithCache — PostProcessingStitchingDumper with intermediate cache in order to speed up writting. The cache is save to disk when full or when closing the dumper. Mostly convenient for HDF5

  • PreProcessingStitchingDumper — dumper to be used when save data durint pre-processing stitching (on projections). Output is expected to be an NXtomo

source class PostProcessingStitchingDumper(configuration)

Bases : DumperBase

dumper to be used when save data during post-processing stitching (on reconstructed volume). Output is expected to be an NXtomo

Methods

source method PostProcessingStitchingDumper.save_configuration()

source property PostProcessingStitchingDumper.output_identifier: VolumeIdentifier

source method PostProcessingStitchingDumper.create_output_dataset()

function called at the beginning of the stitching to prepare output dataset

source class PostProcessingStitchingDumperNoDD(configuration)

Bases : PostProcessingStitchingDumper

same as PostProcessingStitchingDumper but prevent to do data duplication. In this case we need to work on HDF5 file only

Attributes

  • stitching_regions_hdf5_dataset : Optional[tuple] — hdf5 dataset storing the stitched regions

  • raw_regions_hdf5_dataset : Optional[tuple] — hdf5 raw dataset

Methods

source method PostProcessingStitchingDumperNoDD.create_output_dataset()

function called at the beginning of the stitching to prepare output dataset

source staticmethod PostProcessingStitchingDumperNoDD.create_subset_selection(dataset: h5py.Dataset, slices: tuple) → h5py.VirtualSource

source method PostProcessingStitchingDumperNoDD.output_dataset(dataset: Optional[h5py.VirtualLayout])

Raises

  • TypeError

source property PostProcessingStitchingDumperNoDD.stitching_regions_hdf5_dataset: Optional[tuple]

hdf5 dataset storing the stitched regions

source property PostProcessingStitchingDumperNoDD.raw_regions_hdf5_dataset: Optional[tuple]

hdf5 raw dataset

source method PostProcessingStitchingDumperNoDD.save_stitched_frame(stitched_frame: numpy.ndarray, composition_cls: dict, i_frame: int, axis: int)

Save the full stitched frame to disk

Raises

  • ValueError

source class PostProcessingStitchingDumperWithCache(configuration)

Bases : PostProcessingStitchingDumper

PostProcessingStitchingDumper with intermediate cache in order to speed up writting. The cache is save to disk when full or when closing the dumper. Mostly convenient for HDF5

Methods

source method PostProcessingStitchingDumperWithCache.init_cache(dump_axis, size, dtype)

Raises

  • ValueError

source method PostProcessingStitchingDumperWithCache.reset_cache()

source method PostProcessingStitchingDumperWithCache.set_final_volume_shape(shape)

source method PostProcessingStitchingDumperWithCache.save_stitched_frame(stitched_frame: numpy.ndarray, composition_cls: dict, i_frame: int, axis: int)

save the frame to the volume. In this use case save the frame to the buffer. Waiting to be dump later. We expect 'save_stitched_frame' to be called with contiguous frames (in the output volume space)

Raises

  • RuntimeError

source method PostProcessingStitchingDumperWithCache.dump_cache(nb_frames)

dump the first nb_frames to disk

Raises

  • RuntimeError

source class PreProcessingStitchingDumper(configuration)

Bases : DumperBase

dumper to be used when save data durint pre-processing stitching (on projections). Output is expected to be an NXtomo

Methods

source method PreProcessingStitchingDumper.save_frame_to_disk(output_dataset: h5py.Dataset, index: int, stitched_frame: numpy.ndarray, **kwargs)

source method PreProcessingStitchingDumper.save_configuration()

dump configuration used for stitching at the NXtomo entry

source property PreProcessingStitchingDumper.output_identifier: ScanIdentifier

source method PreProcessingStitchingDumper.create_output_dataset()

function called at the beginning of the stitching to prepare output dataset

Raises

  • NotImplementedError