Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: koenderinklab
- License: apache-2.0
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://koenderinklab.github.io/OpenDDM/
- Size: 50.9 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 2
- Open Issues: 16
- Releases: 0
Metadata Files
README.md
OpenDDM
A Python package to analyse an image sequence and measure diffusion properties through Fourier techniques.
This package is under active development and currently in a pre-alpha state.
Additional information as well as API references can be found on our webpage.
Installation for users
Required dependencies
- Python 3.8 or 3.9
- Anaconda (recommended)
- Optional: Nvidia CUDA GPU
Instructions
OpenDDM is under development and not (yet) available through PyPI. We recommend installing the package in a conda environment. To install the software locally:
bash
conda env create -n ddm_env python=3.8
conda activate ddm_env
pip install git+https://github.com/koenderinklab/openddm
In order to make use of a CUDA-enabled GPU with cupy, you can install the additional dependencies with
```bash
conda env create -n ddm_env python=3.8
conda activate ddm_env
pip install git+https://github.com/koenderinklab/openddm#egg=ddm[cuda] ```
Please look at the CuPy requirements for more info on suitable GPUs.
Installation for developers
bash
git clone git@github.com:koenderinklab/openddm.git ddm
cd ddm
conda env create -f environment.yml
conda activate ddm_env
pip install -e .[dev]
Running tests
To run the test suite after installing OpenDDM with the development depednencies, run pytest in the root directory of the openddm repository.
License
Copyright 2022 Technische Universiteit Delft
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.
Owner
- Name: Biological Soft Matter
- Login: koenderinklab
- Kind: organization
- Website: https://www.tudelft.nl/tnw/over-faculteit/afdelingen/bionanoscience/research/research-labs/koenderink-lab
- Repositories: 1
- Profile: https://github.com/koenderinklab
GitHub Events
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Dependencies
- actions/checkout v2 composite
- actions/setup-python v1 composite
- codecov/codecov-action v3 composite
- JamesIves/github-pages-deploy-action v4 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- dask
- dask-image
- ipympl
- ipywidgets
- jpype1 >0.6.1*
- matplotlib
- nd2reader
- notebook
- numba
- numpy
- pims
- pip
- psutil
- pyfftw
- python 3.8.*
- python-graphviz
- readlif
- scikit-image
- scipy
- tqdm
- xarray