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pixelflow

https://github.com/alan-turing-institute/pixelflow

Science Score: 62.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ✓
    Institutional organization owner
    Organization alan-turing-institute has institutional domain (turing.ac.uk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: alan-turing-institute
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Size: 14.2 MB
Statistics
  • Stars: 5
  • Watchers: 8
  • Forks: 4
  • Open Issues: 24
  • Releases: 0
Created over 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License Citation

README.md

Continuous integration status badge Licence badge (BSD 3 Clause)

Pixelflow is a tool for extracting information about the characteristics of objects in images. Segmentation models can be used to identify objects, but researchers typically then want to obtain more details about these objects, e.g. their number, size, shape etc. Pixelflow aims to simplify this process, working with a mask from 2D or 3D images and outputting a dataframe of the desired characteristics.

It is part of the scivision library of tools for working with computer vision models and data.

Installation

Pixelflow is not currently available through PyPI, but it can be installed directly from this github repo

bash pip install git+https://github.com/alan-turing-institute/pixelflow.git

Usage

``` python from pixelflow import pixelflow, pixelflow_custom import numpy.typing as npt

@pixelflowcustom def customfunc(x: npt.NDArray, y: npt.NDArray) -> float: return -np.sum(x * y)

pixelflow( mask, img, features=('label', 'bbox', 'centroid', 'area', 'majoraxislength', 'orientation', 'imageintensity'), custom=(customfunc,), dim_labels="YX", labelled=True ) ```

A more detailed example usecase of pixelflow, extracting information on seed size and shape, can be found in the scivision-gallery.

Contributing

Contributions of any kind welcome! Please feel free to open a pull request or raise an issue.

Owner

  • Name: The Alan Turing Institute
  • Login: alan-turing-institute
  • Kind: organization
  • Email: info@turing.ac.uk

The UK's national institute for data science and artificial intelligence.

Citation (CITATION.cff) 

cff-version: 1.2.0
title: pixelflow
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Evangeline Mae
    family-names: Corcoran
    orcid: 'https://orcid.org/0000-0003-0321-009X'
  - given-names: Isabel S.
    family-names: Fenton
    orcid: 'https://orcid.org/0000-0001-7174-0725'
  - given-names: J. Scott
    family-names: Hosking
    orcid: 'https://orcid.org/0000-0002-3646-3504'
  - given-names: Alan R.
    family-names: Lowe
    orcid: 'https://orcid.org/0000-0002-0558-3597'
repository-code: 'https://github.com/alan-turing-institute/pixelflow'
keywords:
  - image analysis
  - image processing
license: BSD-3-Clause

GitHub Events

Total
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 62
  • Total Committers: 3
  • Avg Commits per committer: 20.667
  • Development Distribution Score (DDS): 0.306
Past Year
  • Commits: 62
  • Committers: 3
  • Avg Commits per committer: 20.667
  • Development Distribution Score (DDS): 0.306
Top Committers
Name Email Commits
Isabel Fenton i****n@t****k 43
quantumjot c****e@a****k 15
Isabel Fenton I****n 4
Committer Domains (Top 20 + Academic)
arlowe.co.uk: 1 turing.ac.uk: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 47
  • Total pull requests: 26
  • Average time to close issues: 18 days
  • Average time to close pull requests: 9 days
  • Total issue authors: 10
  • Total pull request authors: 4
  • Average comments per issue: 1.17
  • Average comments per pull request: 0.35
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 14
  • Pull requests: 8
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 17 days
  • Issue authors: 5
  • Pull request authors: 3
  • Average comments per issue: 0.36
  • Average comments per pull request: 0.13
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • evangeline-corcoran (13)
  • IFenton (12)
  • quantumjot (7)
  • ots22 (5)
  • lupinthief (2)
  • asthanameghna (1)
  • crangelsmith (1)
  • acocac (1)
  • louisavz (1)
Pull Request Authors
  • IFenton (19)
  • quantumjot (5)
  • lupinthief (2)
  • jameswilsenach (2)
Top Labels
Issue Labels
enhancement (8) coworking (4) bug (2) idea (1)
Pull Request Labels

Dependencies

pyproject.toml pypi
  • matplotlib *
  • numpy *
  • pandas *
  • scikit-image *
.github/workflows/linting.yml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/tests.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite