Introduction

A python package for processing Scanning Tunneling Microscopy (STM) data from RHK, based on the spym project. Source is available from GitHub.

To make the most of rhkpy, also consult the xarray documentation and check out plotting examples, with HoloViews. The HoloViews website has examples on how to customize plots, as well as tutorial notebooks.

Known issues

  • For line spectra, topography is loaded in the incorrect order. The topography data of line spectra should not be used at the moment.

  • The method: coord_to_absolute() doesn’t work for the image part of line spectra.

  • For the older version (RHK_MinorVer = 5) of the RHK software, the I(z) spectra seem to have the wrong RHK_LineTypeName field value. They show up as dI/dV spectra.

Notes

The “forward” scan direction in rhkpy is the “right” scan direction, when the file is opened in Gwyddion.

Installation

pip install rhkpy

# to upgrade to a new version, use
pip install --upgrade rhkpy

Specific example on a Windows machine

  • Download WinPython (3.xx), from GitHub or Sourceforge.

  • After installing, in the WinPython directory, start the WindowsPowerShell.exe. Here you can run the “pip” commands, to install rhkpy.

  • Start the “Jupyter Lab.exe” to run Jupyter notebooks.

Setting the notebook directory on Windows

You may wish to change the default directory holding the Jupyter notebook files. You can do this by the following steps.

  • In PowerShell, run this command to generate a Jupyter config file: “jupyter notebook –generate-config”

  • The config file will be located in the sub-directory of WinPython: “python-3.xx.x.amd64/etc/jupyter”

  • In the config file look for the option: “c.NotebookApp.notebook_dir”

  • Change this to the desired directory.

Examples

Take a look at the demo.ipynb and tutorial.ipynb Jupyter notebooks in the GitHub repository.

Below is a simple example.

import rhkpy

# Load an sm4 file
data = rhkpy.rhkdata('filename.sm4')

# "quick plot" of the data
data.qplot()

# make thumbnails of the sm4 files in the current working directory
rhkpy.genthumbs()