PyGwy repository

This repository is intended as a collection of Gwyddion PyGwy scripts: some that I made and those that I found on GitHub.

If you want to contribute by adding suggestions, scripts, or in any other form, or simply would like your link added/removed, you can file an Issue or contact me at: emmegamma [at] inventati dot org.

For more information about Gwyddion and PyGwy, see the official documentation. See below for Pygwy installation instructions.

Scripts in this repository

Currently the scripts available are: SXM_searchFiles, batch_export_to_image, and export_profiles.

SXM_searchFiles

This script is intended for searching files and filtering according to some properties (filename, real image size, setpoint, scantime, comments) through one or multiple folders. It can be useful e.g. when scraping through old data.

It is designed for Nanonis .SXM files, also after saving them as .gwy, but can be easily adapted to other formats (in this case, you can email me to ask or send the final result: I'd love to make a full search function of this)

It can also:

• Search recursively through folders (by using \* and escape characters in the folder search)
• Copy the files to a target folder (this can be useful when searching recursively, to collect all files/images in one place for a later check)
• Customize output (print filename, setpoint, size/speed, etc.)

The first part of the file contains the options/customizations available, with comments that should make them understandable:

### Folder and filetype ###
# Set folder(s) to search (use *\* for recursive searches) 
# and filetype (uncomment as needed)
folder = r'C:\Users\Myuser\DATA\STM\2024-10-*'
#filetype = '.gwy' 
filetype = '.sxm' 
#filetype = 'both' 

The script can also run as standalone in Python, the required libraries are loaded in the first lines of the file (make sure Gwyddion's install folder corresponds in your system)

batch_export_to_image

A script to batch export .gwy (or .sxm) files in a folder to images, inspired by kugatomodai/gwyddion_convert_many_files (see below in the repo list).

The filetype/extension of the images is .jpg by default but can be changed in variable imagefile, line 76.

It can filter filenames (similar to the script above), and has options to overwrite/not overwrite and for dry run (ultrasafe).

export_profiles

My very first script: to export all the profiles (Graphs) in open files to ASCII .txt files. Intended for import in another program (IgorPro or similar).

It works with open files only, either recursively (all open files) or the active one. The profiles are exported as OriginaleFilename_prof_xx.txt

Scripts available on GitHub

I've collected some links here for ease of use, with no intention to steal anyone's credits. You can also do a 'pygwy' search in GitHub, but I filtered out the unfinished/unclear projects. Note that, unless otherwise stated, they are untested.

• harripj/pygwy: a series of scripts, seemingly to batch-apply 'basic' Gwyddion operations (Median level, Gaussian filter, etc.)
• Madhavanlabcode/Gwyddion-Scripts: three-fold symmetrization of an image (intended for FFT)
• onakanob/PyGwyBatch: a batch handler to apply a single PyGwy/Python function to multiple files
• Drilack7/Python-Scripts-for-Gwyddion: different scripts for
  • batch flattening and mean depth calculation
  • creating a collage of images
  • simple batch operations (change Color scale, Scale min/max, or Level)
  • file actions (Open all files in a folder, Save all files in a folder to .gwy, etc.)
• kugatomodai/gwyddion_convert_many_files: batch conversion of files in a folder to png (not working and using deprecated methods, use only for inspiration)
• wampiter/gwyscripts: batch image processing scripts to
  • export files in a folder to .gwy+png, sorted by channel
  • stitch images in a line
  • save all open files to a folder, with a png too
• TomVincentUK/gwy2py: a script to export Gwyddion data to numpy (.npy) files

If you want your script removed from this list (or added!), please contact me

PyGwy installation

Windows

To install PyGwy correctly on Windows, follow the official documentation. You can also find the needed installers and short instructions in the Python 2 dependencies folder. The installers are also available on gwyddion's repository.

Linux

Instructions vary depending on the distribution, especially since Python 2 is outdated. The easiest way (and at least in latest Ubuntu versions, the only one I know of) is to install Gwyddion's FlatPak (see forum discussion)

If you have instructions for a specific distribution, file an Issue or drop an email at the address indicated above and I'll add them.