Creates 3d meshes from microscopy experimental data
Project description
nanomesh
Creates 3d meshes from microscopy experimental data.
Documentation: https://nanomesh.readthedocs.io/en/latest/
Installation
If you use conda, create a new environment:
conda create -n nanomesh python=3.8
conda activate nanomesh
Install nanomesh:
git clone https://github.com/hpgem/nanomesh.git
cd nanomesh
pip install .
Note, to enable the IPython widgets:
jupyter nbextension enable --py widgetsnbextension
Note, if you are using Jupyter lab:
jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets
With pygalmesh (linux only)
To use some of the additional functionality depending on pygalmesh, first install the dependencies for pygalmesh (CGAL and EIGEN3)
sudo apt-get install libcgal-dev libeigen3-dev
The instructions are the same as above, except specify with_pygalmesh
as option
to trigger the installation of pygalmesh. Currently this installs
our fork.
pip install .[with_pygalmesh]
Development
Install nanomesh
using the development dependencies:
pip install -e .[develop] -c constraints.txt
Running the tests:
pytest
Linting/checks:
pre-commit
Building the docs:
make html --directory docs
License
Copyright (c) 2020,
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Credits
This package was created with Cookiecutter and the NLeSC/python-template.
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