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Scienta Omicron (NanoScience) (NanoTechnology) MATRIX Control System result file accessing tool

Project description

access2theMatrix is a Python library for accessing Scienta Omicron (NanoScience) (NanoTechnology) MATRIX Control System result files. Scanning Probe Microscopy (SPM) Image data, Single Point Spectroscopy (SPS) Curve data and Phase/Amplitude Curve data will be accessed by this library. access2theMatrix is pure Python.

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 SPM Image, SPS Curve and Phase/Amplitude Curve result files, to select one out of the four possible traces (forward/up, backward/up, forward/down and backward/down) for images and to select one out of the two possible traces (trace, retrace) for curves. Includes method for experiment element parameters overview.

Dependencies

access2theMatrix requires the NumPy (http://www.numpy.org) and the six (https://pypi.python.org/pypi/six/) library.

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 image file Au(111) bbik fe-20151110-112314--3_1.Z_mtrx will be opened and the forward/up trace will be selected.

>>> import access2thematrix
>>> mtrx_data = access2thematrix.MtrxData()
>>> data_file = r'c:\data\Au(111) bbik fe-20151110-112314--3_1.Z_mtrx'
>>> traces, message = mtrx_data.open(data_file)
>>> traces
{0: 'forward/up', 1: 'backward/up'}
>>> im, message = mtrx_data.select_image(traces[0])
>>>

The variable im will contain the data and the metadata of the selected image and the im object has the initial attributes data, width, height, y_offset, x_offset, angle and channel_name_and_unit. We will continue the example by opening de curve file Au(111) bbik fe-20151110-112314--2_1.Aux2(V)_mtrx and selecting the retrace trace.

>>> data_file = r'c:\data\Au(111) bbik fe-20151110-112314--2_1.Aux2(V)_mtrx'
>>> traces, message = mtrx_data.open(data_file)
>>> traces
{0: 'trace', 1: 'retrace'}
>>> cu, message = mtrx_data.select_curve(traces[1])
>>>

The variable cu will contain the data and the metadata of the selected curve and the cu object has the initial attributes data, referenced_by, x_data_name_and_unit and y_data_name_and_unit.

To get a list and a printable sorted text list of the experiment element parameters with their values and units, use the method get_experiment_element_parameters.

Authors & affiliations

Stephan J. M. Zevenhuizen [1]

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

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