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stemdiff

Convert a 4D-STEM dataset to a 2D-powder diffractogram.

https://github.com/mirekslouf/stemdiff

Science Score: 44.0%

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    DOI references
    Found 8 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (13.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Convert a 4D-STEM dataset to a 2D-powder diffractogram.

Basic Info
  • Host: GitHub
  • Owner: mirekslouf
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 5.27 MB
Statistics
  • Stars: 8
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 0
Created over 4 years ago · Last pushed 9 months ago
Metadata Files
Readme Citation

README.md

STEMDIFF :: 4D-STEM dataset to 2D-diffractogram

  • The STEMDIFF package converts...
    ... a 4D-STEM dataset from a SEM microscope (huge and complex)
    ... to a 2D-powder diffraction pattern (simple and easy to work with).
  • The STEMDIFF package is a key part of our 4D-STEM/PNBD method,
    which was described (together with the package) in open-access publications:
    1. Nanomaterials 11 (2021) 962. https://doi.org/10.3390/nano11040962
    2. Materials 14 (2021) 7550. https://doi.org/10.3390/ma14247550
  • If you use STEMDIFF package, please cite the 2nd publication (or both :-)

Principle

STEMDIFF principle

Installation

  • Requirement: Python with sci-modules = numpy, matplotlib, scipy, pandas
  • pip install scikit-image = 3rd party package for advanced image processing
  • pip install tqdm = to show progress meter during long summations
  • pip install idiff = to improve diffractograms (remove noise, background ...)
  • pip install stemdiff = STEMDIFF package itself (uses all packages above)

Quick start

Documentation, help and examples

Versions of STEMDIFF

  • Version 1.0 = Matlab: just a simple summation of 4D-dataset
  • Version 2.0 = like v.1.0 + post-processing in Jupyter
  • Version 3.0 = Python scripts: summation + S-filtering
  • Version 4.0 = Python package: summation + S-filtering + deconvolution
    • summation = summation of all 2D-diffractograms
    • S-filtering = sum only diffractograms with strong diffractions = high S
    • deconvolution = reduce the primary beam spread effect ⇒ better resolution
  • Version 4.2 = like v.4.0 + a few important improvements, such as:
    • sum just the central region with the strongest diffractions ⇒ higher speed
    • 3 centering types: (0) geometry, (1) center of 1st, (2) individual centers
    • better definition of summation and centering parameters
    • better documentation strings + demo data + improved master script
  • Version 5.0 = complete rewrite of v.4.2
    • all key features of v.4.2 (summation, filtering, deconvolution)
    • conversion 2D-diffractogram → 1D-profile moved to package EDIFF
    • several generalizations and improvements, namely:
      • possibility to define and use more detectors/datafile formats
      • better filtering (including estimated number of diffractions)
      • more types of deconvolution (experimental; to be finished in v.6.0)
  • Version 5.1 = (beta) support for parallel processing
  • Version 5.2 = (beta) improvement of diff.patterns in sister package idiff

Acknowledgement

The development was co-funded by TACR, program NCK, project TN02000020.

Owner

  • Login: mirekslouf
  • Kind: user

Citation (CITATION) 

If you use stemdiff package in your research, please cite:

Slouf M, Skoupy R, Pavlova E, Krzyzanek V:
High Resolution Powder Electron Diffraction in Scanning Electron Microscopy
Materials 14 (2021) 7550. https://doi.org/10.3390/ma14247550

GitHub Events

Total
  • Watch event: 1
  • Delete event: 2
  • Push event: 11
  • Create event: 2
Last Year
  • Watch event: 1
  • Delete event: 2
  • Push event: 11
  • Create event: 2

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 68
  • Total Committers: 1
  • Avg Commits per committer: 68.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
mirekslouf m****f@g****m 68

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 6
  • Total pull requests: 5
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.33
  • Average comments per pull request: 0.4
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mirekslouf (6)
Pull Request Authors
  • bubak4 (3)
  • mirekslouf (1)
  • rskoupy (1)
Top Labels
Issue Labels
enhancement (5) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 29 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 22
  • Total maintainers: 1
pypi.org: stemdiff

Convert 4D-STEM data to 2D-powder diffraction pattern.

  • Versions: 22
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 29 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 16.9%
Average: 18.1%
Forks count: 19.1%
Dependent repos count: 21.6%
Stargazers count: 23.1%
Maintainers (1)
MirekS
Last synced: 7 months ago

Dependencies

pyproject.toml pypi
setup.py pypi
  • numpy *