ceacosmic/pysap

PySAP will automatically install all of the required dependencies, however issues may arise on some operating systems. If you encounter any problems please ensure that you have all of the following dependencies installed before opening a new issue.

PySAP requires that the COSMIC package |link-to-modopt| be installed.

.. |link-to-modopt| raw:: html

ModOpt⁠

PySAP also requires the installation of the following third party software packages:

scipy [==1.5.4]
numpy [==1.19.5]
matplotlib [==3.3.4]
astropy [==4.1]
nibabel [==3.2.1]
pyqtgraph [==0.11.1]
progressbar2 [==3.53.1]
scikit-learn [==0.24.1]
pybind11 [==2.6.2]
pyqt5 [==5.15.4]
PyWavelets [==1.1.1]

⁠Plug-Ins

PySAP currently supports the following plug-ins:

|link-to-pysap-astro| [==0.0.1]
|link-to-pysap-mri| [==0.3.0]

.. |link-to-pysap-astro| raw:: html

PySAP-Astro⁠

.. |link-to-pysap-mri| raw:: html

PySAP-MRI⁠

⁠Installation

The installation of PySAP has been extensively tested on Ubuntu and macOS, however we cannot guarantee it will work on every operating system (e.g. Windows). A Docker image is available (see below) for those unable to install PySAP directly.

If you encounter any installation issues be sure to go through the following steps before opening a new issue:

Check that that all the dependencies listed above have been correctly installed.
Read through all of the documentation provided, including the troubleshooting suggestions.
Check if your problem has already been addressed in a previous issue.

Further instructions are available |link-to-install|.

.. |link-to-install| raw:: html

here⁠

⁠From PyPi

To install PySAP simply run:

.. code-block:: bash

$ pip install python-pysap

Depending on your Python setup you may need to provide the --user option.

.. code-block:: bash

$ pip install --user python-pysap

⁠Locally

To build PySAP locally, clone the repository:

.. code-block:: bash

$ git clone https://github.com/CEA-COSMIC/pysap.git⁠

and run:

.. code-block:: bash

$ python setup.py install

or:

.. code-block:: bash

$ python setup.py develop

As before, use the --user option if needed.

⁠Conda Environment

A a conda environment.yml file is provided to facilitate the installation of the required PySAP dependencies along with some optional dependencies that provide additional features. To build the environment run:

.. code-block:: bash

$ conda env create -f environment.yml

Then to activate the environment run:

.. code-block:: bash

$ conda activate pysap

Finally, install PySAP following the instructions above.

⁠Docker Image

A PySAP Docker image is available via DockerHub that includes the latest stable version of PySAP pre-installed. To install the image run:

.. code-block:: bash

$ docker pull ceacosmic/pysap

A Jupyter notebook can be launched using the Docker image as a backend and with access to the users current working directory as follows:

.. code-block:: bash

$ docker run -p 8888:8888 -v ${PWD}:/home ceacosmic/pysap

⁠macOS

Help with installation on macOS is available here_.

.. _here: ./doc/macos_install.rst

⁠Linux

Please refer to the |link-to-pyqt| for issues regarding the installation of pyqtgraph.

.. |link-to-pyqt| raw:: html

PyQtGraph homepage⁠

⁠Contributing

If you want to contribute to pySAP, be sure to review the contribution guidelines_ and follow to the code of conduct_.

.. _contribution guidelines: ./CONTRIBUTING.md

.. _code of conduct: ./CODE_OF_CONDUCT.md

⁠Citation

If you use PySAP in a scientific publication, we would appreciate citations to the following paper: |link-to-paper|

.. |link-to-paper| raw:: html

<a href="https://www.sciencedirect.com/science/article/pii/S2213133720300561⁠ "target="_blank"> PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing, S. Farrens et al., Astronomy and Computing 32, 2020

The bibtex citation is the following: k:: @Article{farrens2020pysap, title={{PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing}}, author={Farrens, S and Grigis, A and El Gueddari, L and Ramzi, Z and Chaithya, GR and Starck, S and Sarthou, B and Cherkaoui, H and Ciuciu, P and Starck, J-L}, journal={Astronomy and Computing}, volume={32}, pages={100402}, year={2020}, publisher={Elsevier} }

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Digest

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1.5 GB

Last updated

about 5 years ago

docker pull ceacosmic/pysap