tomwer.core.scan.scanbase.TomwerScanBase#
- class tomwer.core.scan.scanbase.TomwerScanBase(overwrite_proc_file=False)#
Simple interface to extend the tomoscan.TomwerScanBase with specific functions
- VALID_RECONS_EXTENSION = ('.edf', '.npy', '.npz', '.hdf5', '.tiff', '.jp2', '.vol')#
- acquire_process_file_lock()#
create a FileLocker context manager to insure safe write to the process file
- add_latest_reconstructions(urls)#
- add_latest_vol_reconstructions(volume_identifiers)#
- add_reconstruction_path(path)#
- property axis_params#
- clear_caches()#
- clear_latest_reconstructions()#
- clear_latest_vol_reconstructions()#
- data_flat_field_correction(data, index=None)#
Apply flat field correction on the given data
- Parameters:
data (numpy.ndarray) – the data to apply correction on
index (Uion[int, None]) – index of the data in the acquisition sequence
- Returns:
corrected data
- Return type:
numpy.ndarray
- equal(other)#
- Parameters:
other – instance to compare with
- Returns:
True if instance are equivalent
- Note:
we cannot use the __eq__ function because this object need to be pickable
- getReconsParamList()#
- Returns:
reconstruction parameters
- Return type:
ReconsParamList
- getReconstructedFilesFromParFile(with_index)#
- get_nabu_dataset_info(binning=1, binning_z=1, proj_subsampling=1)#
- Returns:
nabu dataset descriptor
- Return type:
dict
- get_normed_sinogram(line, subsampling=1)#
Util to get the sinogram normed with settings currently defined on the ‘intensity_normalization’ property
- Parameters:
line –
subsampling –
- Returns:
- get_opposite_projections(mode)#
Return the radios for axis calculation and the requested mode.
- Param:
angles we want to use for COR calculation. Can be 0-180, 90-180 or manual. If manual will return the ‘most’ appropriate
- Type:
- Parameters:
nearest – if True then, pick the closest angle from the requested one. If False, return (None, None) if the the angles does not exists.
- Type:
bool
- Returns:
couple of opposite radios that can be used for axis calculation.
- Return type:
tuple(Optional[AxisResource], Optional[AxisResource])
- static get_process_file_name(scan)#
- get_proj_angle_url(use_cache=True, *args, **kwargs)#
retrieve the url for each projections (including the alignement / return one) and associate to each (if possible) the angle. Alignment angle are set as angle (1) to specify that this is an alignment one. :param bool use_cache: :return: dictionary with angle (str or int) as key and url as value :rtype: dict
- get_proposal_name()#
- Return type:
Optional[str]
- static get_pyhst_recons_file(scanID)#
Return the .par file used for the current reconstruction if any. Otherwise return None
- get_reconstructions_urls()#
- Returns:
list of urls that contains reconstruction from nabu
- Return type:
list
- get_reconstructions_urls_from_path(path, check_url=False)#
- get_sinogram(line, subsampling=1, norm_method=None, **kwargs)#
extract the sinogram from projections
- Parameters:
line – which sinogram we want
subsampling – subsampling to apply on the sinogram
- Type:
int
- Returns:
sinogram from the radio lines
- Return type:
numpy.array
- get_url_proj_index(url)#
Return the index in the acquisition from the url
- property latest_reconstructions#
List of latest slices reconstructions (as VolumeIdentifier) - single slice volume
- property latest_vol_reconstructions#
List of latest volume reconstructions (as VolumeIdentifier)
- load_from_dict(desc)#
- property nabu_recons_params#
- pop_process_index()#
Return and lock the next free process index
- Return type:
int
- property process_file: str#
- Returns:
file used to store the processes launch by tomwer
- property process_file_url: DataUrl#
- Returns:
DataUrl of the process file
- projections_with_angle()#
- property reconstruction_paths#
- property reconstructions#
list of reconstruction files
- property sa_delta_beta_params#
- property saaxis_params#
- scan_basename()#
return basename of the directory containing the acquisition
- Return type:
Optional[str]
- scan_dir_name()#
return name of the directory containing the acquisition
- Return type:
Optional[str]
- scan_parent_dir_basename()#
return parent basename of the directory containing the acquisition
- Return type:
Optional[str]
- set_latest_reconstructions(urls)#
- set_latest_vol_reconstructions(volume_identifiers)#
- set_process_index_frm_tomwer_process_file()#
Set the process_index to the last index find in the tomwer_process_file + 1
- set_proposal_name(proposal_name)#
- Return type:
None
- to_dict()#
- to_nabu_dataset_analyser()#
Return the equivalent DatasetAnalyzer for nabu
- property working_directory: str | None#
working directory to use for this scan (for launching reconstruction for example)