nabu.pipeline.helical.helical_reconstruction module

class nabu.pipeline.helical.helical_reconstruction.HelicalReconstructorRegridded(process_config, logger=None, extra_options=None, cuda_options=None)

Bases: object

A class for obtaining a full-volume reconstructions from helical-scan datasets.

Initialize a LocalReconstruction object. This class is used for managing pipelines

Parameters:

• process_config (ProcessConfig object) – Data structure with process configuration

• logger (Logger, optional) – logging object

• extra_options (dict, optional) – Dictionary with advanced options. Please see ‘Other parameters’ below

• cuda_options (dict, optional) – Dictionary with cuda options passed to nabu.cuda.processing.CudaProcessing

• be (Advanced options can be passed in the 'extra_options' dictionary. These can) –

  • “gpu_mem_fraction”: 0.9,

  • ”cpu_mem_fraction”: 0.9,

  • ”use_phase_margin”: True,

  • ”max_chunk_size”: None,

  • ”phase_margin”: None,

  • ”dry_run”: 0,

  • ”diag_zpro_run”: 0,

reading_granularity = 100

The data angular span which needs to be read for a reconstruction is read step by step, reading each time a maximum of reading_granularity radios, and doing the preprocessing till phase retrieval for each of these angular groups

get_relative_files(files=None)

merge_histograms(output_file=None, force_merge=False)

Merge the partial histograms

merge_data_dumps(axis=1)

estimate_chunk_size(available_memory_GB, process_config, chunk_step=1, user_max_chunk_size=None)

Estimate the maximum chunk size given an avaiable amount of memory.

Parameters:

• available_memory_GB (float) – available memory in Giga Bytes (GB - not GiB !).

• process_config (ProcessConfig) – ProcessConfig object

reconstruct()

merge_hdf5_reconstructions(output_file=None, prefix=None, files=None, process_name=None, axis=0, merge_histograms=True, output_dir=None)

Merge existing hdf5 files by creating a HDF5 virtual dataset.

Parameters:

output_file (str, optional) – Output file name. If not given, the file prefix in section “output” of nabu config will be taken.

merge_hdf5_files(output_file=None, prefix=None, files=None, process_name=None, axis=0, merge_histograms=True, output_dir=None)

Merge existing hdf5 files by creating a HDF5 virtual dataset.

Parameters:

output_file (str, optional) – Output file name. If not given, the file prefix in section “output” of nabu config will be taken.