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nabu.resources.dataset_analyzer

source module nabu.resources.dataset_analyzer

Classes

Functions

source enum ImageKey(*args, **kwds)

Bases : Enum

Attributes

  • ALIGNMENT

  • PROJECTION

  • FLAT_FIELD

  • DARK_FIELD

  • INVALID

source class DatasetAnalyzer(location, extra_options=None, logger=None)

Initialize a Dataset analyzer.

Parameters

  • location : str — Dataset location (directory or file name)

  • extra_options : dict, optional — Extra options on how to interpret the dataset.

  • logger : logging object, optional — Logger. If not set, messages will just be printed in stdout.

Attributes

  • kind — Base class for datasets analyzers.

  • energy — Return the energy in kev.

  • distance — Return the sample-detector distance in meters.

  • pixel_size — Return the pixel size in microns.

  • rotation_angles — Return the rotation angles in radians.

  • is_halftomo — Indicates whether the current dataset was performed with half acquisition.

  • detector_tilt — Return the detector tilt in degrees

  • projections_srcurrent — Return the synchrotron electric current for each projection.

  • flats_srcurrent — Return the synchrotron electric current for each flat image.

  • flats — Return the REDUCED flat-field images. Either by reducing (median) the raw flats, or a user-defined reduced flats.

  • darks — Return the REDUCED flat-field images. Either by reducing (mean) the raw darks, or a user-defined reduced darks.

  • is_360 — Return True iff the scan is 360 degrees (regardless of half-tomo mode)

Methods

source property DatasetAnalyzer.energy

Return the energy in kev.

source property DatasetAnalyzer.distance

Return the sample-detector distance in meters.

source property DatasetAnalyzer.pixel_size

Return the pixel size in microns.

source property DatasetAnalyzer.rotation_angles

Return the rotation angles in radians.

source property DatasetAnalyzer.is_halftomo

Indicates whether the current dataset was performed with half acquisition.

source property DatasetAnalyzer.detector_tilt

Return the detector tilt in degrees

source property DatasetAnalyzer.projections

source property DatasetAnalyzer.projections_srcurrent

Return the synchrotron electric current for each projection.

source property DatasetAnalyzer.flats_srcurrent

Return the synchrotron electric current for each flat image.

source method DatasetAnalyzer.check_defined_attribute(name, error_msg=None)

Utility function to check that a given attribute is defined.

Raises

  • ValueError

source property DatasetAnalyzer.flats

Return the REDUCED flat-field images. Either by reducing (median) the raw flats, or a user-defined reduced flats.

source property DatasetAnalyzer.darks

Return the REDUCED flat-field images. Either by reducing (mean) the raw darks, or a user-defined reduced darks.

source property DatasetAnalyzer.scan_basename

source property DatasetAnalyzer.scan_dirname

source method DatasetAnalyzer.get_alignment_projections(image_sub_region=None)

Raises

  • NotImplementedError

source property DatasetAnalyzer.all_angles

source method DatasetAnalyzer.get_frame(idx)

source property DatasetAnalyzer.is_360

Return True iff the scan is 360 degrees (regardless of half-tomo mode)

source class EDFDatasetAnalyzer(location, extra_options=None, logger=None)

Bases : DatasetAnalyzer

EDF Dataset analyzer for legacy ESRF acquisitions

Initialize a Dataset analyzer.

Parameters

  • location : str — Dataset location (directory or file name)

  • extra_options : dict, optional — Extra options on how to interpret the dataset.

  • logger : logging object, optional — Logger. If not set, messages will just be printed in stdout.

Attributes

  • energy — Return the energy in kev.

  • distance — Return the sample-detector distance in meters.

  • pixel_size — Return the pixel size in microns.

  • rotation_angles — Return the rotation angles in radians.

  • is_halftomo — Indicates whether the current dataset was performed with half acquisition.

  • detector_tilt — Return the detector tilt in degrees

  • projections_srcurrent — Return the synchrotron electric current for each projection.

  • flats_srcurrent — Return the synchrotron electric current for each flat image.

  • flats — Return the REDUCED flat-field images. Either by reducing (median) the raw flats, or a user-defined reduced flats.

  • darks — Return the REDUCED flat-field images. Either by reducing (mean) the raw darks, or a user-defined reduced darks.

  • is_360 — Return True iff the scan is 360 degrees (regardless of half-tomo mode)

  • hdf5_entry — Return the HDF5 entry of the current dataset. Not applicable for EDF (return None)

Methods

source property EDFDatasetAnalyzer.hdf5_entry

Return the HDF5 entry of the current dataset. Not applicable for EDF (return None)

source method EDFDatasetAnalyzer.get_reduced_flats(**reader_kwargs)

Raises

  • FileNotFoundError

source method EDFDatasetAnalyzer.get_reduced_darks(**reader_kwargs)

Raises

  • FileNotFoundError

source property EDFDatasetAnalyzer.files

source method EDFDatasetAnalyzer.get_reader(**kwargs)

source property EDFDatasetAnalyzer.scan_basename

source property EDFDatasetAnalyzer.scan_dirname

source method EDFDatasetAnalyzer.get_excluded_projections_indices(including_other_frames_types=True)

Raises

  • NotImplementedError

source class HDF5DatasetAnalyzer(location, extra_options=None, logger=None)

Bases : DatasetAnalyzer

HDF5 dataset analyzer

Initialize a Dataset analyzer.

Parameters

  • location : str — Dataset location (directory or file name)

  • extra_options : dict, optional — Extra options on how to interpret the dataset.

  • logger : logging object, optional — Logger. If not set, messages will just be printed in stdout.

Attributes

  • energy — Return the energy in kev.

  • distance — Return the sample-detector distance in meters.

  • pixel_size — Return the pixel size in microns.

  • rotation_angles — Return the rotation angles in radians.

  • is_halftomo — Indicates whether the current dataset was performed with half acquisition.

  • detector_tilt — Return the detector tilt in degrees

  • projections_srcurrent — Return the synchrotron electric current for each projection.

  • flats_srcurrent — Return the synchrotron electric current for each flat image.

  • flats — Return the REDUCED flat-field images. Either by reducing (median) the raw flats, or a user-defined reduced flats.

  • darks — Return the REDUCED flat-field images. Either by reducing (mean) the raw darks, or a user-defined reduced darks.

  • is_360 — Return True iff the scan is 360 degrees (regardless of half-tomo mode)

  • hdf5_entry — Return the HDF5 entry of the current dataset

Methods

source property HDF5DatasetAnalyzer.z_translation

source property HDF5DatasetAnalyzer.x_translation

source property HDF5DatasetAnalyzer.dataset_hdf5_url

source property HDF5DatasetAnalyzer.hdf5_entry

Return the HDF5 entry of the current dataset

source method HDF5DatasetAnalyzer.get_data_slices(what)

Return indices in the data volume where images correspond to a given kind.

Parameters

  • what : str — Which keys to get. Can be "projections", "flats", "darks"

Returns

  • slices : list of slice — A list where each item is a slice.

source method HDF5DatasetAnalyzer.get_reduced_flats(method='median', force_reload=False, **reader_kwargs)

source method HDF5DatasetAnalyzer.get_reduced_darks(method='mean', force_reload=False, **reader_kwargs)

source method HDF5DatasetAnalyzer.frames_slices(frame_type)

Return a list of slice objects corresponding to the data corresponding to "frame_type". For example, if the dataset flats are located at indices [1, 2, ..., 99], then frame_slices("flats") will return [slice(0, 100)].

source method HDF5DatasetAnalyzer.get_reader(**kwargs)

source property HDF5DatasetAnalyzer.scan_basename

source property HDF5DatasetAnalyzer.scan_dirname

source method HDF5DatasetAnalyzer.get_alignment_projections(image_sub_region=None)

Get the extra projections (if any) that are used as "reference projections" for alignment. For certain scan, when completing a (half) turn, sometimes extra projections are acquired for alignment purpose.

Returns

  • projs : numpy.ndarray — Array with shape (n_projections, n_y, n_x)

  • angles : numpy.ndarray — Corresponding angles in degrees

  • indices — Indices of projections

source property HDF5DatasetAnalyzer.all_angles

source method HDF5DatasetAnalyzer.get_index_from_angle(angle, image_key=0, return_found_angle=False)

Return the index of the image taken at rotation angle 'angle'. By default look at the projections, i.e image_key = 0

source method HDF5DatasetAnalyzer.get_image_at_angle(angle_deg, image_type='projection', sub_region=None, return_angle_and_index=False)

source method HDF5DatasetAnalyzer.get_frame(idx)

source method HDF5DatasetAnalyzer.get_frames_indices(frame_type)

source method HDF5DatasetAnalyzer.index_to_proj_number(proj_index)

Return the projection number, from its frame index.

For example if there are 11 flats before projections, then projections will have indices [11, 12, .....] (possibly not contiguous) while their number is [0, 1, ..., ] (contiguous, starts from 0)

source method HDF5DatasetAnalyzer.get_excluded_projections_indices(including_other_frames_types=True)

source get_angle_at_index(all_angles, index)

Return the rotation angle corresponding to image index 'index'

source get_radio_pair(dataset_info, radio_angles: tuple, return_indices=False)

Get closest radios at radio_angles[0] and radio_angles[1] angles must be in angles

Parameters

  • dataset_info : [DatasetAnalyzer][__mkapi__.nabu.resources.dataset_analyzer.DatasetAnalyzer] instance — Data structure with the dataset information

  • radio_angles : tuple — tuple of two elements: angles (in radian) to get

  • return_indices : bool, optional — Whether to return radios indices along with the radios array.

Returns

  • res : array or tuple — If return_indices is True, return a tuple (radios, indices). Otherwise, return an array with the radios.

Raises

  • TypeError

source analyze_dataset(dataset_path, extra_options=None, logger=None)

Raises

  • ValueError