nOmicron

About

Python API for interacting with Scienta Omicron Matrix (via the MATE scripting language).

A fork of Stephan Zevenhuizen's MATE-for-Dummies, nOmicron allows for simple, easily extensible control of Matrix and running of common routines, and without the need to ever touch Matrix or compile MATE scripts!

All data channels are readable during experimentation, negating the need to finish experimenting and converting from the proprietary .mtrx file formats.

The package has been verified to work with Matrix 4.3.5 and Python 3.6.3 and the STM Spectroscopy experiment window.

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Installation

Recommended method is to install from PyPi with pip install nOmicron

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Citing

If you use nOmicron in your research, it would be appreciated if you could cite via DOI : 10.5281/zenodo.3368927

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Setting & Getting Parameters

After opening Matrix and initialising a connection to your SPM, initialise the code with

from nOmicron.microscope import IO
IO.connect

Experiment parameters are settable in their related packages. For example, you can change the scan position and angle, with

from nOmicron.microscope import xy_scanner
xy_scanner.set_scan_position(angle=10, xy_pos=[5e-9, 0])

It is also possible (but not preferable) to get and set parameters in the mate4dummies style, with

from nOmicron.mate import objects as mo

mo.mate.xy_scanner.Angle()    # Get the angle
mo.mate.xy_scanner.Angle(10)  # Set the angle
mo.mate.xy_scanner.Area([5e-9, 0])  

Although any sent parameter is first verified to be within the tolerable parameters of the object, you can also manually check the allowed values with

from nOmicron.utils import read_min_max
min_max = read_min_max("xy_scanner", "Angle")

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Getting Live Data

Data can only be acquired in pre-defined chunks, due to technical limitations of MATE. It is also not (yet) possible to acquire more than one data source at a time.

Pickable channels are those available in the Channel List window of Matrix. e.g

Z
I
Aux1
I(V)
I(Z)
Aux1(Z)
Z(t)
I(t)

Image channels can be captured and viewed on a line-by-line basis with

from nOmicron.microscope.xy_scanner import get_xy_scan
from nOmicron.utils.plotting import plot_xy

xydata = get_xy_scan("Z", x_direction="forward", y_direction="up")
plot_xy(xydata, view_count, pixel_scale=mo.xy_scanner.Width() * 1e9 / mo.xy_scanner.Points())

Spectroscopy is performable with the microscope.continuous_spectroscopy.get_point_spectra function

from nOmicron.microscope.continuous_spectroscopy import get_point_spectra
V, I = get_point_spectra("I(V)", start_end=(0, 4), target_position=[0, 1],
                          repeats=2, sample_points=50, sample_time=10e-3, 
                          forward_back=True)

Time series data can be captured with the microscope.continuous_spectroscopy.get_continuous_signal function

from nOmicron.microscope.continuous_spectroscopy import get_continuous_signal
t, I = get_continuous_signal("I(t)", sample_time=2, sample_points=50)

For ease of use, common routines are abstracted from the underlying MATE code

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Adding core MATE functions

Anything doable with MATE is doable in nOmicron. Individual elements can be determined from the Matrix window by selecting the ↖❓ button and clicking on a changeable element, or with the the MATE documentation in Tools -> Manage Scripts -> Help -> Script Documentation.

For example, the Points parameter of the XY Scanner window has:

Experiment Element: XYScanner Parameter Name: Points Type: boolean

We now go to mate.objects.py and look for the Class _XYScanner and make a function called Points, following the template from the other functions.

If we want to make a whole new Experiment Element, we can make this with a similar Class beginning with _, and then initialising it with name() at the bottom of the file.

If you do this, please submit a pull request :)