Quick Start

Before the program is started, the parameters in the config.yml should be adjusted.

Data Import

You can select the import of single files or complete folder structures (including subfolders). _folder and unsupported formats are ignored.

import:
    single file import: No      # select folders instead of single files

Labjournal

The optional xlsx-labjournal file can contain several measurement informations, e.g. type (stm, ecstm, afm, cv, peis, xps, image, sem, or raman), day, surface, or remark (see xlsx file in /tests). Each row must have an explicit ID corresponding to the file name of the measurement in order to read in the information properly.

Labjournal Example
date ID type surface atmosphere remark
2020-11-16 data01 stm carbon vacuum beautiful stm image
2020-11-16 data02 cv carbon H2SO4 beautiful cv

If you do not want to pass a labjournal set labjournal available and fallback method accordingly:

import:
    single file import: No,
    labjournal available: No,
    ask for labjournal: Yes,
    fallback method: stm

If no labjournal is available, only one measurement type can be processed at the same time.

SPM Processing

SPM data is processed with Gwyddion non-GUI instance.

How to change the SPM processing:

  1. Run the desired function on some data from within the Gwyddion GUI
  2. Right click on the image and select View Log
  3. Use the parameters found there to edit your config.yml file, for more information see module list
spm:
    immediate functions:
        - level
        - align_rows
        - fix_zero

The parameter for each function are passed as well in the yaml file.

align rows:
    max degree: 3
    do extract: No
    do plot: No
    method: 0
    masking: 2

Data Export

A html report can be created, which includes all the processed measurement data and the corresponding labjournal informations. Setting server path will create correct links in the html report for easy access to your raw data. The given path should overlap with the data path given during program runtime and will compensate for OS depending mounting (/media/server-data vs. H:\server-data).

export:
    create html report: Yes
    image export modification dialog: No
    server path: file://///nas.ads.mwn.de/tuch/pc1/Surface-Microscopy/SM-ECSTM
    move html to parent and rest in subfolder: Yes
    Force overwrite excisting files: Yes

Program execution

Run the proespm.py file with Python 2.7.

$ python2 proespm.py
  1. Prompts for files/folder
  2. Asks for labjournal file (optional)
  3. Files are matched with labjournal information if possible
  4. Data files are saved in non-proprietary file formats
  5. HTML report is generated
  6. Files are moved to final server destination incl. subfolder structure