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https://github.com/seu-allen-codebase/v3d-py-helper

Make Vaa3D functions accessible for high-performance python computation.

https://github.com/seu-allen-codebase/v3d-py-helper

Science Score: 13.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

high-performance-computing image-processing neuron-morphology vaa3d
Last synced: 7 months ago · JSON representation

Repository

Make Vaa3D functions accessible for high-performance python computation.

Basic Info
  • Host: GitHub
  • Owner: SEU-ALLEN-codebase
  • License: mit
  • Language: Cython
  • Default Branch: main
  • Homepage:
  • Size: 170 KB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 1
  • Open Issues: 1
  • Releases: 5
Topics
high-performance-computing image-processing neuron-morphology vaa3d
Created about 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Vaa3D in Python Made Easy

Python library for Vaa3D functions.

Installation

shell $ pip install v3d-py-helper

By cloning the repo and test the Cyhton usages: shell $ python setup.py build_ext --inplace

Usage

Loading Vaa3D format data

```python from v3dpy.loaders import Raw, PBD

raw = Raw() img = raw.load('path.v3draw') raw.save('path.v3draw', img)

pbd = PBD() img = pbd.load('path.v3dpbd') pbd.save('path.v3dpbd', img) ```

Loading TeraFly format data

Currently only support Tiff 3D tiles.

```python from v3dpy.terafly import TeraflyInterface import numpy as np

t = TeraflyInterface('teraconvertpath') x, y, z, c = t.getdim()

center block

size = np.array(t.getdim()[:3]) halfblocksize = np.array([128, 128, 64]) // 2 start = size // 2 - halfblocksize end = size // 2 + halfblock_size - 1

4D image, indexed by c, z, y, x

img = t.getsubvolume(start[0], end[0], start[1], end[1], start[2], end[2]) ```

Toubleshooting

On Windows, MS BuildTool >= 16 is required to build the wheel.

Newer setuptools seem to be buggy.

Once successfully installed, the package can still report import error, which suggests some of the runtime libs, especially those related with compression, are missing in you machine.

Useful Links

Github project: https://github.com/SEU-ALLEN-codebase/v3d-py-helper

Vaa3D source: https://github.com/Vaa3D/v3d_external

Documentation: https://SEU-ALLEN-codebase.github.io/v3d-py-helper

Contact

Main Developer: Zuohan Zhao
My GitHub Page: https://github.com/zzhmark
Email: zzhmark@126.com

Owner

  • Name: SEU-ALLEN-codebase
  • Login: SEU-ALLEN-codebase
  • Kind: organization

GitHub Events

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

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 191 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
pypi.org: v3d-py-helper

Make Vaa3D functions available for high-performance python computation.

  • Versions: 7
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 191 Last month
Rankings
Dependent packages count: 7.1%
Average: 19.6%
Dependent repos count: 32.0%
Maintainers (1)
odehan
Last synced: 8 months ago

Dependencies

.github/workflows/static.yml actions
  • actions/checkout v3 composite
  • actions/deploy-pages v1 composite
  • actions/setup-python v4 composite
  • actions/upload-pages-artifact v1 composite
pyproject.toml pypi
  • numpy *
setup.py pypi
.github/workflows/release.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish v1.8.12 composite