access2theMatrix 0.4.4

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

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, Phase/Amplitude Curve data and volume Continuous Imaging Tunneling Spectroscopy (CITS) Curves 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 SPM Image, SPS Curve, Phase/Amplitude Curve and volume CITS Curves result files, to select one out of the four possible traces (forward/up, backward/up, forward/down and backward/down) for images and volume CITS curves, and to select one out of the two possible traces (trace, retrace) for spectroscopy 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. The last example will open a volume CITS file CO_Cu-111-spectra-20191028--10_1.Aux1(V)_mtrx.

>>> import os
>>> os.chdir('c:/data')
>>> mtrx_data.open('CO_Cu-111-spectra-20191028--10_1.Aux1(V)_mtrx')
({0: 'trace', 1: 'retrace', 2: 'forward/up'}, 'Successfully opened and processed
 data file CO_Cu-111-spectra-20191028--10_1.Aux1(V)_mtrx.')
>>> mtrx_data.object_type
'volume CITS'
>>> im_3d = mtrx_data.volume_scan['forward/up']['trace']
>>> im_3d.shape
(3, 3, 251)
>>> mtrx_data.channel_name_and_unit
['Aux1(V)', 'V']
>>> mtrx_data.z_data_name_and_unit
['Spectroscopy Device 1', 'Volt']
>>>

The variable im_3d contains the 3-dimensional combined scan data of the ‘forward/up’ xy-scan with the ‘trace’ z-scan of Spectroscopy Device 1 with channel output Aux1. The order of the dimensions is y, x, z. The z-data is in mtrx_data.scan[0].

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.

New in version 0.4.4

The result file chain consist of several result file chain links. The file name is ending on _0001.mtrx for the first part of the chain. This library can now use more than one chain link. A small bugfix for Python 2.7 users.

New in version 0.4.3

This is a bugfix release. The bug that originated in the previous version.

New in version 0.4.2

‘Foreign Parameters’ can be added to an experiment using the MATRIX Automated Task Environment (MATE). These ‘Foreign Parameters’ can now be accessed and are treated as parameters of the pseudo-Experiment Element instance ‘-Foreign’.

Authors & affiliations

Stephan J. M. Zevenhuizen [1]

[1]

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