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npy2bdv

Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.

https://github.com/nvladimus/npy2bdv

Science Score: 33.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

bigdataviewer h5 hdf5 numpy
Last synced: 9 months ago · JSON representation

Repository

Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.

Basic Info
  • Host: GitHub
  • Owner: nvladimus
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 4.13 MB
Statistics
  • Stars: 34
  • Watchers: 5
  • Forks: 12
  • Open Issues: 2
  • Releases: 2
Topics
bigdataviewer h5 hdf5 numpy
Created almost 7 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

npy2bdv

A library for writing/reading HDF5/XML datasets of Fiji BigDataViewer/BigStitcher format as numpy arrays.

Python 3.6 License: GPL v3

## Installation Run pip install npy2bdv in the command line. Use import npy2bdv in the code.

## Documentation For a quick start, see examples in the Jupyter notebook.

API documentation.

## Supported H5/XML writing options * compression methods None, gzip, lzf (None by default). * downsampling options: - any number of mipmap levels - computed via averaging, compatible with BigDataViewer/BigStitcher convention. * user-defined block sizes for H5 storage (default 4,256,256) * any number of time points, illuminations, channels, tiles, angles. * arbitrary affine transformation for each individual view (e.g. translation, rotation, shear). * arbitrary voxel calibration for each view, to account for spatial anisotropy. * individual views can differ in dimensions, voxel size, voxel units, exposure time, and exposure units. * missing views are labeled in XML automatically. * support of additional meta-information: - camera properties: name, exposureTime, exposureUnits - microscope (name and version), user * writing virtual stacks of arbitrary size, by plane or sub-stack. Handy when your stack is larger than your RAM. - virtual stacks can be written with multiple subsampling levels and compression.

## New features See Recent changes

## Writing speed Currently speeds betewen 150 - 320 MB/s were achieved with confidence. Speeds of up to 2300 MB/s reported in earlier versions are likely due to bugs in testing methods in notebook examples_h5writing.ipynb. More tesing is underway.

## Acknowledgements This code was inspired by Talley Lambert's code and improved by generous input from Adam Glaser, VolkerH, Doug Shepherd, Peter H, Mike Taormina and Pradeep Rajasekhar.

To report issues or bugs please use the issues tool.

## Citation You can cite it like so

DOI

Support

If you find this library useful, send me some love :blush:

It will give me some dopamine and motivation to keep improving it :heart:

Owner

  • Name: Nikita Vladimirov
  • Login: nvladimus
  • Kind: user
  • Location: Zürich
  • Company: @HelmchenLabSoftware

GitHub Events

Total
  • Fork event: 1
Last Year
  • Fork event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 112
  • Total Committers: 4
  • Avg Commits per committer: 28.0
  • Development Distribution Score (DDS): 0.063
Past Year
  • Commits: 15
  • Committers: 2
  • Avg Commits per committer: 7.5
  • Development Distribution Score (DDS): 0.267
Top Committers
Name Email Commits
Nikita Vladimirov n****s@g****m 105
Pradeep Rajasekhar p****r@g****m 4
Peter Hirsch a****d 2
Mike Taormina m****t@a****g 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 9
  • Total pull requests: 5
  • Average time to close issues: 9 days
  • Average time to close pull requests: 4 months
  • Total issue authors: 7
  • Total pull request authors: 4
  • Average comments per issue: 3.89
  • Average comments per pull request: 1.8
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 1
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
  • VolkerH (3)
  • dpshepherd (1)
  • pr4deepr (1)
  • Eddymorphling (1)
  • adamkglaser (1)
  • rharkes (1)
  • Sh4zKh4n (1)
Pull Request Authors
  • pr4deepr (2)
  • dependabot[bot] (1)
  • abred (1)
  • miketaormina (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 98 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 3
  • Total versions: 8
  • Total maintainers: 1
pypi.org: npy2bdv

Package for writing/reading 3d numpy arrays to/from HDF5 files (for Fiji/BigDataViewer/BigStitcher).

  • Versions: 8
  • Dependent Packages: 1
  • Dependent Repositories: 3
  • Downloads: 98 Last month
Rankings
Dependent packages count: 4.8%
Dependent repos count: 8.9%
Forks count: 10.5%
Average: 10.7%
Stargazers count: 11.5%
Downloads: 17.7%
Maintainers (1)
nvladimus
Last synced: 10 months ago

Dependencies

requirements-dev.txt pypi
  • pdoc3 * development
  • twine * development
  • wheel * development
requirements.txt pypi
  • h5py ==2.10.0
  • numpy ==1.19.2
  • scikit-image ==0.17.2
setup.py pypi
  • h5py *
  • numpy *
  • scikit-image *
  • tqdm *