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PIVA Submission #231

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pudeIko opened this issue Jan 4, 2025 · 0 comments
Open
20 of 32 tasks

PIVA Submission #231

pudeIko opened this issue Jan 4, 2025 · 0 comments

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@pudeIko
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pudeIko commented Jan 4, 2025

Submitting Author: Wojciech Radoslaw Pudelko (@pudeIko)
All current maintainers: Wojciech Radoslaw Pudelko (@pudeIko)
Package Name: PIVA
One-Line Description of Package: Visualization and analysis toolkit for experimental data from Angle-Resolved Photoemission Spectroscopy (ARPES)
Repository Link: https://github.com/pudeIko/piva
Version submitted: v2.3.1
EiC: TBD
Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
JOSS DOI: TBD
Version accepted: TBD
Date accepted (month/day/year): TBD


Code of Conduct & Commitment to Maintain Package

Description

  • Include a brief paragraph describing what your package does:

PIVA (Photoemission Interface for Visualization and Analysis) is a GUI application designed for the interactive and intuitive exploration of large, image-like datasets. While it accommodates the visualization of any multidimensional data, its features are specifically optimized for researchers conducting Angle-Resolved Photoemission Spectroscopy (ARPES) experiments. In addition to numerous image processing tools and the ability to apply technique-specific corrections, PIVA includes an expanding library of functions and methods for detailed fitting and advanced spectral analysis.

Scope

  • Please indicate which category or categories.
    Check out our package scope page to learn more about our
    scope. (If you are unsure of which category you fit, we suggest you make a pre-submission inquiry):

    • Data retrieval
    • Data extraction
    • Data processing/munging
    • Data deposition
    • Data validation and testing
    • Data visualization1
    • Workflow automation
    • Citation management and bibliometrics
    • Scientific software wrappers
    • Database interoperability

Domain Specific

  • Geospatial
  • Education

Community Partnerships

If your package is associated with an
existing community please check below:

  • For all submissions, explain how and why the package falls under the categories you indicated above. In your explanation, please address the following points (briefly, 1-2 sentences for each):

Data extraction: Within the ARPES community, it is common for each beamline and lab to use their own file formats and conventions, which means one often need a custom script to get everything into a common format. To handle these discrepancies, PIVA comes with a data_loaders module that converts them into a standardized Dataset object. The current version includes specific Dataloader classes implemented for numerous sources and beamlines around the world.

Data visualization: The package enables efficient and intuitive exploration of large, image-like datasets. It includes specialized interactive viewers designed to handle 2D, 3D, and 4D datasets, depending on the experimental mode or conditions under which they were collected.

  • Who is the target audience and what are scientific applications of this package?

Experimental physicists conducting ARPES measurements. The package provides a comprehensive framework addressing most of the experimenter's needs, including data extraction, inspection, validation, and detailed analysis.

  • Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Regarding software tailored for ARPES, two notable packages are ARPES Python Tools and PyARPES. However, they differ significantly from PIVA.

The visualization module in the former is limited to generating static plots and lacks any interactive features.

The latter is focused on post-processing and detailed analysis of the spectra, and is different in the following respects:

  • interactive exploration and browsing through data is either restricted to 2D data, or conducted inside the Jupyter environment, which highly affects efficiency and makes working with multiple datasets simultaneously difficult.
  • Viewers designed for 4D datasets are not implemented.
  • PIVA's data_loader module contains richer library of data loading scripts for different light sources around the world.

Furthermore, PyARPES has not been maintained for several years.

  • If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted:

#223 (@SimonMolinsky)

Technical checks

For details about the pyOpenSci packaging requirements, see our packaging guide. Confirm each of the following by checking the box. This package:

  • does not violate the Terms of Service of any service it interacts with.
  • uses an OSI approved license.
  • contains a README with instructions for installing the development version.
  • includes documentation with examples for all functions.
  • contains a tutorial with examples of its essential functions and uses.
  • has a test suite.
  • has continuous integration setup, such as GitHub Actions CircleCI, and/or others.

Publication Options

JOSS Checks
  • The package has an obvious research application according to JOSS's definition in their submission requirements. Be aware that completing the pyOpenSci review process does not guarantee acceptance to JOSS. Be sure to read their submission requirements (linked above) if you are interested in submitting to JOSS.
  • The package is not a "minor utility" as defined by JOSS's submission requirements: "Minor ‘utility’ packages, including ‘thin’ API clients, are not acceptable." pyOpenSci welcomes these packages under "Data Retrieval", but JOSS has slightly different criteria.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI: 10.5281/zenodo.14599024

Note: JOSS accepts our review as theirs. You will NOT need to go through another full review. JOSS will only review your paper.md file. Be sure to link to this pyOpenSci issue when a JOSS issue is opened for your package. Also be sure to tell the JOSS editor that this is a pyOpenSci reviewed package once you reach this step.

Are you OK with Reviewers Submitting Issues and/or pull requests to your Repo Directly?

This option will allow reviewers to open smaller issues that can then be linked to PR's rather than submitting a more dense text based review. It will also allow you to demonstrate addressing the issue via PR links.

  • Yes I am OK with reviewers submitting requested changes as issues to my repo. Reviewers will then link to the issues in their submitted review.

Confirm each of the following by checking the box.

  • I have read the author guide.
  • I expect to maintain this package for at least 2 years and can help find a replacement for the maintainer (team) if needed.

Please fill out our survey

P.S. Have feedback/comments about our review process? Leave a comment here

Editor and Review Templates

The editor template can be found here.

The review template can be found here.

Footnotes

  1. Please fill out a pre-submission inquiry before submitting a data visualization package.

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