FEI TIA (SER & EMI)#
RosettaSciIO can read .ser and .emi files files created by the FEI (now
ThermoFisher) software TEM Imaging & Analysis (TIA), but the reading features are
not complete (and probably they will be unless FEI/ThermoFisher releases the specifications
of the format). That said we know that this is an important feature and if loading
a particular .ser or .emi file fails for you, please report it as an issue in the
issues tracker to make us
aware of the problem.
RosettaSciIO (unlike TIA) can read data directly from the .ser files. However,
by doing so, the information that is stored in the .emi file is lost.
Therefore, it is strongly recommended to load using the .emi file instead.
If several .ser files are associated to the .emi file being read,
all of them will be read and returned as a list.
API functions#
- rsciio.tia.file_reader(filename, lazy=False, only_valid_data=True)#
Read sets of
.serand.emifiles from the FEI/ThermoFisher software TIA (TEM Imaging & Analysis).- Parameters:
- filename
str,pathlib.Path Filename of the file to read or corresponding pathlib.Path.
- lazybool, default=False
Whether to open the file lazily or not.
- only_valid_databool, Default=True
For cases, where acquisition of series or linescan data stopped before the end. If True, load only the acquired data. If False, the empty data are filled with zeros.
- filename
- Returns:
listofdictList of dictionaries containing the following fields:
‘data’ – multidimensional
numpy.ndarrayordask.array.Array‘axes’ – list of dictionaries describing the axes containing the fields ‘name’, ‘units’, ‘index_in_array’, and either ‘size’, ‘offset’, and ‘scale’ or a numpy array ‘axis’ containing the full axes vector
‘metadata’ – dictionary containing the parsed metadata
‘original_metadata’ – dictionary containing the full metadata tree from the input file
When the file contains several datasets, each dataset will be loaded as separate dictionary.