Package: access2theMatrix
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.Dependenciesaccess2theMatrix requires the NumPy (http://www.numpy.org) and the six
(https://pypi.python.org/pypi/six/) library.InstallationUsing pip:> pip install access2theMatrixExample usageIn this example the MATRIX Control System has stored the acquired data in the
folderc:\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 fileAu(111) bbikfe-20151110-112314--3_1.Z_mtrxwill be opened
and theforward/uptrace will be selected.>>>importaccess2thematrix>>>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 variableimwill contain the data and the metadata of the selected
image and theimobject has the initial attributesdata,width,height,y_offset,x_offset,angleandchannel_name_and_unit.
We will continue the example by opening de curve fileAu(111) bbikfe-20151110-112314--2_1.Aux2(V)_mtrxand selecting theretracetrace.>>>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 variablecuwill contain the data and the metadata of the selected
curve and thecuobject has the initial attributesdata,referenced_by,x_data_name_and_unitandy_data_name_and_unit.
The last example will open a volume CITS fileCO_Cu-111-spectra-20191028--10_1.Aux1(V)_mtrx.>>>importos>>>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 variableim_3dcontains 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 inmtrx_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 methodget_experiment_element_parameters.New in version 0.4.4The result file chain consist of several result file chain links. The file name
is ending on_0001.mtrxfor 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 0.4.3This 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 & affiliationsStephan J. M. Zevenhuizen[1][1]Condensed Matter and Interfaces, Debye Institute for Nanomaterials
Science, Utrecht University, Utrecht, The Netherlands.