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Readme
STMapy (previously STM_Data_Analysis and Scampy) is a Graphical User Interface (GUI) to analyse CITS recorded under Nanonis (.3ds), MATRIX (spip exported .asc or _mtrx) or RHK (.sm4). It is written in Python using PyQt for the GUI.
STMapy can also be installed using PyPI : pip install stmapy
STMapy can also be installed from its source code.
To do this:
git clone https://github.com/cea-lateqs/STMapy/
pip
:cd stmapy
pip install [-e] . [--user]
If needed, put -e
for an install in editable mode (useful for development as sources will be directly linked to package) and/or --user
to install it only for the current user (local installation).
You can test if the installation succedeed by importing stmapy in a Python console:
>>> import stmapy
>>> print(stmapy.__version__)
Requirements should automatically be installed when running the install with pip
. Using stmapy requires the following installations :
To start Stmapy, run stmapy
in the console:
stmapy
It should display the following interface.
If it is not working, run directly the main.py
file from Stmapy sources:
python3 stmapy/main.py
To load a CITS, click on the Open CITS button on top-left corner. A window will appear, prompting to select a CITS of supported format (either .3ds, .sm4 or .asc). The filenames can be filtered according to the format by selecting 3D binary file (.3ds) or RHK File (.sm4) or Ascii files (.asc) or mtrx files (_mtrx).
Once the CITS was selected, Stmapy will load the spectroscopic data and will attempt to read the topography to plot it in a seperate window.
This always succeeds for .3ds and .sm4 as it plots the topography contained in the file. For .asc and mtrx however, it will search for a file 'Topo.txt' in the same folder of the selected file. This 'Topo.txt' can be created by using the Export to TXT method of Gwyddion. If no topographic file is found, no topography will be plotted.
No checks are done to see if 'Topo.txt' corresponds to the loaded CITS. Always check that the topography file was taken at the same location as the CITS.
If the loading succeed, a 2D plot should appear on the bottom-left widget. If not, check the console for error messages and report them (see Further information at the end).
The following buttons add a new channel in the last position of the Displayed channel (dropdown).
Various parameters for the plotting can be adjusted in the stmapy.mplstyle
file located in the stmapy
folder.
It is possible to set various parameters in the config.json
file located in the stmapy
folder:
working_directory
: Name of a directory that will be taken as root when asking to load a CITS. Default: HOME directory.matplotlib_stylesheet
: Name of a valid stylesheet to be imported at launch to tune matplotlib aspect. Default: None.autoload
: Boolean to trigger the loading of a CITS at launch. Default: false.default_cmap
: Name of the colormap to use for the CITS map. Note that this is only at launch as the colormap can be changed afterwards in stmapy. Default: magma_r.topo_cmap
: Name of the colormap to use for the topography. This colormap cannot be changed after launch. Default: afm_hot.level_topo
: Type of leveling to use before plotting for the topo: can be line
, plane
or no
to deactivate leveling. Default: no.Any missing entry in config.json
will be set to its default value.
The code is available on the Git repo. Bugs can be reported as Issues on the repository. It includes use of the access2thematrix package developed by the Stephan J. M. Zevenhuizen.
Stmapy not found
issues : change spyder path. If it doesn't solve the problem, you can try to copy main.py
out of the stmapy folder.FAQs
Scanning tunneling microscopy analysis in Python
We found that stmapy demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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