https://github.com/bluebrain/vascpy
Python library for reading, writing, and manipulating large-scale vasculature graphs.
https://github.com/bluebrain/vascpy
Last synced: about 1 year ago
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Python library for reading, writing, and manipulating large-scale vasculature graphs.
- Host: GitHub
- URL: https://github.com/bluebrain/vascpy
- Owner: BlueBrain
- License: apache-2.0
- Created: 2021-12-10T15:59:26.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-02-19T09:40:13.000Z (over 2 years ago)
- Last Synced: 2024-05-19T20:01:52.013Z (about 2 years ago)
- Language: Python
- Homepage:
- Size: 31.6 MB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Authors: AUTHORS.txt
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README
> [!WARNING]
> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
> Future development will take place at: https://github.com/openbraininstitute/vascpy
vascpy
======
`vascpy` is a python library for reading, writing, and manipulating large-scale vasculature graphs. There are two alternative graph representations available: a section-centered and an edge-centered one. It supports the following respective formats:
* H5 Morphology (see [specification](https://morphology-documentation.readthedocs.io/en/latest/h5-vasc-graph.html))
* SONATA node population of edges (see [specification](https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md))
The `vascpy` library provides two classes: `PointVasculature` and `SectionVasculature` that allow for reading and writing edge-centered and section-centered datasets respectively, as well as converting between them.
Documentation
-------------
vascpy documentation is built and hosted on [readthedocs](https://readthedocs.org/).
* [latest snapshot](http://vascpy.readthedocs.org/en/latest/)
Usage
-----
Load and write an h5 morphology file:
```python
from vascpy import SectionVasculature
v = SectionVasculature.load("sample.h5")
print(v.points)
print(v.diameters)
print(v.connectivity)
print(v.sections)
v.save("sample2.h5")
```
Load and write an h5 SONATA file:
```python
from vascpy import PointVasculature
v = PointVasculature.load_sonata("sample_sonata.h5")
print(v.node_properties)
print(v.edge_properties)
print(v.points)
print(v.edges)
print(v.edge_types)
print(v.segment_points)
print(v.segment_diameters)
print(v.area)
print(v.volume)
v.save_sonata("sample_sonata2.h5")
```
Representation conversions
-----------
`vascpy` allows the conversion between the two representations:
```python
from vascpy import PointVasculature
point_vasculature = PointVasculature.load_hdf5("sample_sonata.h5")
section_vasculature = point_vasculature.as_section_graph()
point_vasculature = section_vasculature.as_point_graph()
```
Create and save an edge-centered vascular graph
-----------------------------------------------
```python
import numpy as np
import pandas as pd
from vascpy import PointVasculature
node_properties = DataFrame({
'x': np.array([0., 1., 2.]),
'y': np.array([3., 4., 5.]),
'z': np.array([6., 7., 8.]),
'diameter': np.array([0.1, 0.2, 0.3])
})
edge_properties = pd.DataFrame({
'start_node': np.array([0, 0, 1]),
'end_node': np.array([1, 2, 2]),
'type': np.array([1, 1, 1])
})
v = PointVasculature(node_properties=node_properties, edge_properties=edge_properties)
v.save_sonata('my_vasculature.h5')
```
Funding & Acknowledgements
-------------------------
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
Copyright (c) 2022-2024 Blue Brain Project/EPFL