tomwer.core.scan.edfscan.EDFTomoScan#
- class tomwer.core.scan.edfscan.EDFTomoScan(scan, overwrite_proc_file=False, update=True)#
Class used to represent a tomography acquisition with hdf5 files.
- Parameters:
scan (Union[str, None]) – path of the scan
- clear_caches()#
clear caches. Might be call if some data changed after first read of data or metadata
- data_flat_field_correction(data, index=None)#
Apply the flat field correction on the given data.
- Parameters:
data (numpy.ndarray) – radio to correct
- Return numpy.ndarray:
corrected data
- static directory_contains_scan(directory, src_pattern, dest_pattern)#
Check if the given directory is holding an acquisition
- Parameters:
directory (str) – directory we want to check
src_pattern (str) – buffer name pattern (‘lbsram’)
dest_pattern – output pattern (‘’). Needed because some acquisition can split the file produce between two directories. This is the case for edf, where .info file are generated in /data/dir instead of /lbsram/data/dir
- Returns:
does the given directory contains any acquisition
- Return type:
bool
- static from_identifier(identifier)#
Return the Dataset from a identifier
- getDark()#
For now only deal with one existing dark file.
- Returns:
image of the dark if existing. Else None
- getFlat(index=None)#
If projectionI is not requested then return the mean value. Otherwise return the interpolated value for the requested projection.
- Parameters:
index (Union[int,None]) – index of the projection for which we want the flat
- Returns:
Flat field value or None if can’t deduce it
- get_identifier()#
return the dataset identifier of the scan. The identifier is insure to be unique for each scan and allow the user to store the scan as a string identifier and to retrieve it later from this single identifier.
- static get_index_reconstructed(reconstructionFile, scanID)#
Return the slice reconstructed of a file from her name
- Parameters:
reconstructionFile (str) – the name of the file
- get_nabu_dataset_info(binning=1, binning_z=1, proj_subsampling=1)#
- Returns:
nabu dataset descriptor
- Return type:
dict
- 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
- static get_reconstructions_paths(scanID, withIndex=False)#
Return the dict of files: * fitting with a reconstruction pattern and ending by .edf * .vol files
- Parameters:
scanID – is the path to the folder of acquisition
withIndex (bool) – if False then return a list of slices otherwise return a dict with the index of the slice reconstructed.
- 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
- static guess_index_frm_EDFFile_name(_file)#
- static is_tomoscan_dir(directory, dataset_basename=None, src_pattern=None, dest_pattern=None, **kwargs)#
Check if the given directory is holding an acquisition
- Parameters:
directory (str) –
- Returns:
does the given directory contains any acquisition
- Return type:
bool
- load_from_dict(desc)#
Load properties contained in the dictionnary.
- Parameters:
_dict (dict) – dictionary to load
- Returns:
self
- Raises:
ValueError if dict is invalid
- projections_with_angle()#
- 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]
- to_dict()#
- Returns:
convert the TomoScanBase object to a dictionary. Used to serialize the object for example.
- Return type:
dict
- to_nabu_dataset_analyser()#
Return the equivalent DatasetAnalyzer for nabu
- update()#
update list of radio and reconstruction by parsing the scan folder
- property working_directory#
working directory to use for this scan (for launching reconstruction for example)