pynxtools-apm

Harmonize atom probe tomography and related field-ion microscopy data and metadata for research data management using NeXus

https://github.com/fairmat-nfdi/pynxtools-apm

Science Score: 54.0%

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary

Keywords

area-b nexus nomad-plugin pynxtools-plugin

Last synced: 6 months ago · JSON representation ·

Repository

Harmonize atom probe tomography and related field-ion microscopy data and metadata for research data management using NeXus

Basic Info

Host: GitHub
Owner: FAIRmat-NFDI
License: apache-2.0
Language: Python
Default Branch: main
Homepage: https://fairmat-nfdi.github.io/pynxtools-apm/
Size: 1.31 MB

Statistics

Stars: 0
Watchers: 4
Forks: 0
Open Issues: 5
Releases: 8

Topics

area-b nexus nomad-plugin pynxtools-plugin

Created almost 2 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

Parse and normalize atom probe tomography and field-ion microscopy data

Installation

It is recommended to use python 3.12 with a dedicated virtual environment for this package. Learn how to manage python versions and virtual environments.

This package is a reader plugin for pynxtools and thus should be installed together with pynxtools: shell pip install pynxtools[apm]

for the latest release version from pypi.

If you are interested in the newest version, we recommend to work with a development installation instead.

Purpose

This reader plugin for pynxtools is used to translate diverse file formats from the scientific community and technology partners within the field of atom probe tomography and field-ion microscopy into a standardized representation using the NeXus application definition NXapm.

Supported file formats

This plugin supports the majority of the file formats that are currently used for atom probe research. A detailed summary is available in the reference section of the documentation.

Getting started

A getting started tutorial is offered that guides you on how to use the apm reader for converting your data to NeXus from a Jupyter notebook or command line calls. Note that not every combination of input from a supported file format and other input, such as from an electronic lab notebook, allows filling all required and recommended fields including their attributes of the NXapm application definition. Therefore, you may need to provide an ELN file that contains the missing values in order for the validation step of the EM reader to pass.

Contributing

We are continously working on improving the collection of parsers and their functionalities. If you would like to implement a parser for your data, feel free to get in contact.

Development install

Install the package with its dependencies:

shell git clone https://github.com/FAIRmat-NFDI/pynxtools-apm.git --branch main --recursive pynxtools_apm cd pynxtools_apm python -m pip install --upgrade pip python -m pip install -e ".[dev,docs]" pre-commit install

The last line installs a pre-commit hook which automatically formats (linting) and type checks the code before committing.

Test this software

Especially relevant for developers, there exists a basic test framework written in pytest which can be used as follows:

shell python -m pytest -sv tests

Contact person in FAIRmat for this reader

Markus Kühbach

Owner

Name: FAIRmat
Login: FAIRmat-NFDI
Kind: organization
Location: Germany

Website: https://www.fairmat-nfdi.eu/
Twitter: FAIRmat_NFDI
Repositories: 2
Profile: https://github.com/FAIRmat-NFDI

FAIR data infrastructure for condensed-matter physics and the chemical physics of solids

Citation (CITATION.cff)

cff-version: 1.2.0
title: 'pynxtools-apm: A pynxtools reader plugin for atom probe tomography and related field-ion microscopy (APM) data'
version: 0.4.0
message:
  If you use this software, please cite it using the metadata from this file.
type: software
authors:
  - given-names: Markus
    family-names: Kühbach
    orcid: 'https://orcid.org/0000-0002-7117-5196'
  - given-names: Sandor
    family-names: Brockhauser
    orcid: 'https://orcid.org/0000-0002-9700-4803'
  - given-names: Baptiste
    family-names: Gault
    orcid: 'https://orcid.org/0000-0002-4934-0458'
  - given-names: Dierk
    family-names: Raabe
    orcid: 'https://orcid.org/0000-0003-0194-6124'
  - given-names: Heiko B.
    family-names: Weber
    orcid: 'https://orcid.org/0000-0002-6403-9022'
  - given-names: Christoph
    family-names: Koch
    orcid: 'https://orcid.org/0000-0002-3984-1523'
  - given-names: Claudia
    family-names: Draxl
    orcid: 'https://orcid.org/0000-0003-3523-6657'
doi: 10.5281/zenodo.14263076
repository-code: https://github.com/FAIRmat-NFDI/pynxtools-apm
url: https://zenodo.org/records/14263076
keywords:
  - Atom probe tomography
  - Field ion microscopy
  - Microscopy
  - NOMAD
  - pynxtools
  - NeXus
abstract:
  pynxtools-apm is a reader plugin for pynxtools (https://github.com/FAIRmat-NFDI/pynxtools)
  written in Python. pynxtools-apm is a tool for reading and translating data from various proprietary
  and open-source data formats from technology partners and the wider atom probe community and
  standardizing it such that it is compliant with the NeXus application definition NXapm
  (https://fairmat-nfdi.github.io/nexus_definitions/).

  pynxtools-apm is developed both as a standalone reader and as a tool within NOMAD,
  an open-source research data management platform for Materials Science (https://nomad-lab.eu/nomad-lab/).

  The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat)
  (https://gepris.dfg.de/gepris/projekt/460197019?language=en).
license: Apache-2.0
funding:
  - name: Deutsche Forschungsgemeinschaft
    award-number: 460197019
    title: FAIRmat - FAIR Data Infrastructure for Condensed-Matter Physics and the Chemical Physics of Solids
    award-uri: https://gepris.dfg.de/gepris/projekt/460197019?language=en

GitHub Events

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Create event: 25
Issues event: 13
Release event: 3
Delete event: 21
Member event: 1
Issue comment event: 16
Push event: 88
Pull request review event: 1
Pull request event: 40

Last Year

Create event: 25
Issues event: 13
Release event: 3
Delete event: 21
Member event: 1
Issue comment event: 16
Push event: 88
Pull request review event: 1
Pull request event: 40

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Last synced: 6 months ago

All Time

Total issues: 9
Total pull requests: 20
Average time to close issues: 6 months
Average time to close pull requests: 13 days
Total issue authors: 2
Total pull request authors: 2
Average comments per issue: 0.67
Average comments per pull request: 0.15
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 5

Past Year

Issues: 7
Pull requests: 20
Average time to close issues: 9 days
Average time to close pull requests: 13 days
Issue authors: 2
Pull request authors: 2
Average comments per issue: 0.29
Average comments per pull request: 0.15
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 5

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Top Authors

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mkuehbach (12)
lukaspie (1)
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lukaspie (2)

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dependencies (4) python (4)

Packages

Total packages: 1
Total downloads:
- pypi 3,900 last-month

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 8
Total maintainers: 1

pypi.org: pynxtools-apm

A reader for transferring APM from vendor formats to NeXus and NOMAD.

Homepage: https://github.com/FAIRmat-NFDI/pynxtools-apm
Documentation: https://pynxtools-apm.readthedocs.io/
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Latest release: 0.4.0
published 6 months ago

Versions: 8
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 3,900 Last month

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Dependent packages count: 9.5%

Average: 36.0%

Dependent repos count: 62.6%

Maintainers (1)

mkuehbach