Opening SPM Files

SPIEPy does not contain any functions to open SPM files. In this way SPIEPy can be used by all scanning probe microscopy systems. To open a SPM file you must write your own Python code or use code that is provided by others. There is a Python library available for accessing the result files of the Omicron NanoTechnology’s MATRIX Control System, the author is the very same as the author of this library. The library is called access2theMatrix. It can easily be installed with pip:

> pip install access2theMatrix

Opening Omicron NanoTechnology’s MATRIX Control System Result Files

In the example, below, the MATRIX Control System has stored the acquired data in the folder c:\data. In addition to the result data files the folder must also contain the result file chain, see the MATRIX Application Manual for SPM. The file 20140325-092702_AFM_NonContact_QPlus--51_1.Z_mtrx will be opened and the backward/up trace will be selected.

>>> import access2thematrix
>>> mtrx_data = access2thematrix.MtrxData()
>>> data_file = r'c:\data\20140325-092702_AFM_NonContact_QPlus--51_1.Z_mtrx'
>>> traces, message = mtrx_data.open(data_file)
>>> print message
Successfully opened and processed data file 20140325-092702_AFM_NonContact_QPlus--51_1.Z_mtrx.
>>> traces
{0: 'forward/up', 1: 'backward/up', 2: 'forward/down', 3: 'backward/down'}
>>> im, message = mtrx_data.select_image(traces[1])
>>> print message
Trace backward/up selected.
>>> im.data
array([[ -1.80605572e-08,  -1.80625201e-08,  -1.80663057e-08, ...,
         -1.82079808e-08,  -1.82142887e-08,  -1.82174186e-08],
       [ -1.80587456e-08,  -1.80613477e-08,  -1.80623131e-08, ...,
         -1.82091517e-08,  -1.82156607e-08,  -1.82195526e-08],
       [ -1.80513618e-08,  -1.80510353e-08,  -1.80531660e-08, ...,
         -1.82131799e-08,  -1.82177880e-08,  -1.82229330e-08],
       ...,
       [ -1.79789472e-08,  -1.79819920e-08,  -1.79856806e-08, ...,
         -1.81261956e-08,  -1.81293811e-08,  -1.81332706e-08],
       [ -1.79804649e-08,  -1.79810591e-08,  -1.79850527e-08, ...,
         -1.81223942e-08,  -1.81250894e-08,  -1.81293146e-08],
       [ -1.79775549e-08,  -1.79791702e-08,  -1.79830948e-08, ...,
         -1.81149155e-08,  -1.81181441e-08,  -1.81199908e-08]])
>>> im.data.shape
(240, 320)
>>> im.angle
122
>>> im.height
3.0000000000000004e-09
>>> im.width
4e-09
>>> im.x_offset
-8.7804110391206612e-08
>>> im.y_offset
1.86005503318584e-07
>>>

The image data and the metadata angle, height, width, x_offset and y_offset are stored in the object im which is an access2theMatrix Image Structure object.

Note

To use the object im with the SPIEPy library, im must change from access2theMatrix Image Structure object to SPIEPy Image Structure object.

Changing the class of im:

>>> import spiepy
>>> im.__class__ = spiepy.Im