Reader Structure

pynxtools-spm hosts multiple readers for STS, STM and AFM experiments. It is envisioned that in the future more and more readers for other SPM techniques will be included in this package. The reader structure is designed in a modular way to make it easy to add new readers for other new techniques (e.g., Spin-Polarized STM) and extend the existing readers.

parsers Subpackage

The aim of the parser module is to read the raw data files from various SPM file formats and convert the raw data path into a slash-separated hierarchical path. This allows to build common function for all the file formats to read the raw data from the files. For reading the raw data into slash separated hierarchical path, we used third party python package e.g., spym python package for reading .sm4 file from Omicron or code from third party open source package like nanonispy. Module structure of parsers subpackage:

pynxtools_spm/parsers
├── __init__.py
├── base_parser.py
├── helpers.py
├── nanonis_dat.py
├── nanonis_sxm.py
├── nanonispy
│   ├── README.md
│   ├── __init__.py
│   ├── constants.py
│   ├── read.py
│   └── utils.py
└── omicron_sm4.py

2 directories, 11 files

nxformatters Subpackage

The aim of the formatter modules to curate the data from various SPM file formats, and convert and store them in pynxtools Template. pynxtools writer can write the data from Template to NeXus format according to the NeXus application definitions for SPM techniques.

The nxformatter hosts modules base_formatter, helpers and nested subpackages for each SPM vendors (e.g., nanonis, omicron) with corresponding formatter modules for STS, STM and AFM.

Module structure of nxformatters subpackage:

pynxtools_spm/nxformatters
├── __init__.py
├── base_formatter.py
├── helpers.py
├── nanonis
│   ├── __init__.py
│   ├── nanonis_base.py
│   ├── nanonis_dat_sts.py
│   ├── nanonis_sxm_afm.py
│   └── nanonis_sxm_stm.py
└── omicron
    ├── __init__.py
    ├── omicron_base.py
    └── omicron_sm4_stm.py

3 directories, 11 files

The class SPMformatter in module base_formatter holds the common interface and methods for all the formatters, whereas the vendor-specific base formatters (e.g., NanonisBase, omicronBase in the modules nanonis_base and omicron_base respectively) holds common methods and variables for its species. On top of this base classes, we developed specific methods to curate the unstructured data coming from the raw files and ELN yaml file following the instruction given in the config file.

config subpackage

The config subpackage hosts some config files for running the readers without providing user-specific configurations (not recommended because user may need to modify some of the concepts according to the requirements of experiment labs). These config files can be considered as a source of writing the custom config files for specific use cases.

Module structure of config subpackage:

pynxtools_spm/configs
├── __init__.py
├── nanonis
│   ├── nanonis_dat_generic_sts.json
│   ├── nanonis_sxm_generic_afm.json
│   └── nanonis_sxm_generic_stm.json
└── omicron
    └── omicron_sm4_stm.json

3 directories, 5 files

nomad subpackage

The nomad subpackage hosts module for nomad entry points in the entrypoints module and examples in the examples directory. The modules nomad_example_paths keep the example paths to be used in entrypoints module.

Module structure of nomad subpackage:

pynxtools_spm/nomad
├── entrypoints.py
├── examples
│   ├── afm
│   ├── stm
│   └── sts
└── nomad_example_paths.py

5 directories, 2 files