afmformats.afm_data
¶
Classes¶
AFMData
: General base class for AFM data
- class afmformats.afm_data.AFMData(data, metadata, diskcache=False)[source]¶
General base class for AFM data
Initialization
Inheritance
- export_data(out, metadata=True, fmt='tab')[source]¶
Export all data columns to a file
- Parameters
out (str, pathlib.Path, writable io.IOBase, or h5py.Group) – Output path, open file, or h5py object
metadata (bool or list) – If True, all available metadata are stored. If False, no metadata are stored. If a list, only the given metadata keys are stored.
fmt (str) – “tab” for the tab separated values format and “hdf5” / “h5” for the HDF5 file format
Notes
If you wish to append HDF5 data to an existing file, please open the file first and call this function with the h5py.File object, i.e.
with h5py.File(path, "a") as h5: fdist.export(out=h5, fmt="hdf5")
Otherwise the file will be overridden.
The column “index” is not exported in the HDF5 file format
- property columns¶
Available data columns
- property enum¶
Unique index of self in self.path
Indexing starts at “0”
- property metadata¶
Unique index of self in self.path
- abstract property modality¶
Imaging modality (e.g. force-distance)
- property path¶
Path to the measurement file
Variables¶
- afmformats.afm_data.column_dtypes¶
Data types of all known columns (all other columns are assumed to be float)
{'force': <class 'float'>, 'height (measured)': <class 'float'>, 'height (piezo)': <class 'float'>, 'index': <class 'int'>, 'segment': <class 'bool'>, 'time': <class 'float'>, 'tip position': <class 'float'>}
- afmformats.afm_data.column_units¶
Units of all known columns
{'force': 'N', 'height (measured)': 'm', 'height (piezo)': 'm', 'index': '', 'segment': '', 'time': 's', 'tip position': 'm'}
- afmformats.afm_data.known_columns¶
Known data columns
['force', 'height (measured)', 'height (piezo)', 'index', 'segment', 'time', 'tip position']