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https://github.com/kostrykin/carnapy
Real-time 3D visualization for biomedical data and beyond in Python
https://github.com/kostrykin/carnapy
3d data-visualization jupyter-notebook library opengl python virtual-reality
Last synced: 24 days ago
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Real-time 3D visualization for biomedical data and beyond in Python
- Host: GitHub
- URL: https://github.com/kostrykin/carnapy
- Owner: kostrykin
- License: bsd-3-clause
- Created: 2021-06-08T18:00:31.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2023-12-14T14:25:01.000Z (about 1 year ago)
- Last Synced: 2024-12-16T05:28:44.232Z (about 1 month ago)
- Topics: 3d, data-visualization, jupyter-notebook, library, opengl, python, virtual-reality
- Language: C++
- Homepage:
- Size: 4.72 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
CarnaPy
========
The aim of this package is to provide real-time 3D visualization in Python for specifically, but not limited to, biomedical data. The library is based on [Carna](https://github.com/kostrykin/Carna).
See [examples/kalinin2018.ipynb](examples/kalinin2018.ipynb) for an example.
[](https://anaconda.org/kostrykin/carnapy)
[](https://anaconda.org/kostrykin/carnapy)
[](https://anaconda.org/kostrykin/carnapy)
---
## Contents
* [Limitations](#1-limitations)
* [Dependencies](#2-dependencies)
* [Installation](#3-installation)
* [Build instructions](#4-build-instructions)
---
## 1. Limitations
* Only 8bit and 16bit volume data are supported at the moment.
* DRR renderings are not exposed to Python yet.
* Build process is currently limited to Linux-based systems.
---
## 2. Dependencies
Using the library requires the following dependencies:
* [numpy](https://numpy.org/) ≥ 1.16
* EGL driver support
* OpenGL 3.3
* Python ≥ 3.7
The following dependencies must be satisfied for the build process:
* [Carna](https://github.com/kostrykin/Carna) ≥ 3.1
* [Eigen](http://eigen.tuxfamily.org/) ≥ 3.0.5
* [libboost-iostreams](https://www.boost.org/doc/libs/1_76_0/libs/iostreams/doc/index.html)
* [pybind11](https://github.com/pybind/pybind11)
* EGL development files
In addition, the following dependencies are required to run the test suite:
* [matplotlib](https://matplotlib.org/)
* [scipy](https://www.scipy.org/)
---
## 3. Installation
The easiest way to install and use the library is to use one of the binary [Conda](https://docs.anaconda.com/anaconda/install/) packages:
```bash
conda install -c kostrykin carnapy
```
Conda packages are available for Python 3.7–3.9.
---
## 4. Build instructions
Assuming you are using a recent version of Ubuntu:
```bash
sudo apt-get -qq install libegl1-mesa-dev libboost-iostreams-dev
```
Create and activate a Conda environment to work in, then:
```bash
conda install -c conda-forge pybind11
```
Grab a recent version of [Eigen](http://eigen.tuxfamily.org), unpack it, and tell CMake where it is located:
```bash
wget https://gitlab.com/libeigen/eigen/-/archive/3.2.10/eigen-3.2.10.tar.gz
tar -vzxf eigen-3.2.10.tar.gz -C /tmp/
export CMAKE_PREFIX_PATH="/tmp/eigen-3.2.10:$CMAKE_PREFIX_PATH"
```
If you have not already, download, build, and install Carna:
```bash
git clone [email protected]:kostrykin/Carna.git build_carna
cd build_carna
sh linux_build.sh
```
Now it is time to build, package, and install CarnaPy:
```
cd ..
python setup.py build
python setup.py install
```