SciFiReaders.readers.microscopy.spm.afm.AR_hdf5.ARhdf5Reader

SciFiReaders.readers.microscopy.spm.afm.AR_hdf5.ARhdf5Reader#

class SciFiReaders.readers.microscopy.spm.afm.AR_hdf5.ARhdf5Reader(file_path, *args, **kwargs)[source]#

Bases: Reader

Extracts data and metadata from ARhdf5 files These are Asylum Research files typically captured for force maps from their microscopes. The ARhdf5 file should be generated with the converter provided by Asylum Research called ARDFtoHDF5. Contact David Aue <David.Aue@oxinst.com> or Tommaso Costanzo <tommaso.costanzo01@gmail.com> to get a copy of the converter. NOTE: the AR converter works only under windows.

NOTE: At this point, the z dimension vector is not correctly captured Not immediately clear how to fix it. TODO: Check with Asylum

Parameters:

file_path (str) – Path to the file that needs to be read

self._input_file_path#

Path to the file that will be read

Type:

str

Notes

  • This method will check to make sure that the provided file_path is indeed a string and a valid file path.

  • Consider calling can_read() within __init__() for validating the provided file

Raises:

FileNotFoundError –

Methods

can_read

Tests whether or not the provided file has a .ibw extension

get_def_unit

Retrive the default unit from the channel name

note_value

Get the value of a single note entry with name "name"

read

Reads the file given in file_path into a sidpy dataset
can_read()[source]#

Tests whether or not the provided file has a .ibw extension

get_def_unit(chan_name)[source]#

Retrive the default unit from the channel name

Parameters:

chan_name (string) – Name of the channel to get the unit

Returns:

default_unit – Default unit of that channel

Return type:

string

note_value(name)[source]#

Get the value of a single note entry with name “name”

Parameters:

name (String / unicode) – Name of the parameter to get the value

Returns:

value – Value of the Note entry requested.

Return type:

String / unicode

read(verbose=False)[source]#

Reads the file given in file_path into a sidpy dataset

Parameters:

verbose (Boolean (Optional)) – Whether or not to show print statements for debugging

Returns:

sidpy.Dataset – Multi-channel inputs are separated into individual dataset objects

Return type:

List of sidpy.Dataset objects.

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