access2theMatrix 0.4.4

Description:

access2theMatrix 0.4.4

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.