access2theMatrix 0.1.3

Omicron NanoTechnology's MATRIX Control System result file accessing tool

access2theMatrix is a Python library for accessing Omicron NanoTechnology’s MATRIX Control System result files. Only topography image data will be accessed by this library.

The library access2theMatrix has the package access2thematrix which in turn contains the module access2thematrix. The class MtrxData in the access2thematrix module has the methods to open result files and to select one out of the four traces (forward/up, backward/up, forward/down and backward/down).

Dependencies

access2theMatrix requires the NumPy library (http://www.numpy.org). You must install it manually.

Installation

Using pip:

> pip install access2theMatrix

Example usage

In this example 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
>>>

Authors & affiliations

Stephan J. M. Zevenhuizen [1]

[1]

Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.