[{"_1":2,"_180":-5,"_181":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_159":160},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_89":90,"_110":111,"_148":-5,"_149":11,"_150":21,"_151":11,"_152":-5,"_153":11,"_154":-5,"_155":156,"_157":112,"_158":-7},"canonicalUrl","https://hub.docker.com/r/ceacosmic/pysap/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","ceacosmic","reponame","pysap","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":73,"_74":75,"_80":11,"_81":82,"_86":33,"_87":88},"categories",[],"content_types",[44],"image","date_registered","2021-04-22T18:11:03.652173Z","description","PySAP Docker Image","is_private","last_updated","2021-04-24T12:13:57.656176Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",299,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","\n|CI|_ |Codecov|_ |Python36|_ |Python37|_ |Python38|_ |Python39|_ |PyPi|_ |Doc|_ |Docker|_\n\n.. |CI| image:: https://github.com/CEA-COSMIC/pysap/workflows/CI/badge.svg\n.. _CI: https://github.com/CEA-COSMIC/pysap/actions?query=workflow%3ACI\n\n.. |Codecov| image:: https://codecov.io/gh/CEA-COSMIC/pysap/branch/master/graph/badge.svg?token=XHJIQXV7AX\n.. _Codecov: https://codecov.io/gh/CEA-COSMIC/pysap\n\n.. |Python36| image:: https://img.shields.io/badge/python-3.6-blue.svg\n.. _Python36: https://badge.fury.io/py/python-pySAP\n\n.. |Python37| image:: https://img.shields.io/badge/python-3.7-blue.svg\n.. _Python37: https://badge.fury.io/py/python-pySAP\n\n.. |Python38| image:: https://img.shields.io/badge/python-3.8-blue.svg\n.. _Python38: https://badge.fury.io/py/python-pySAP\n\n.. |Python39| image:: https://img.shields.io/badge/python-3.9-blue.svg\n.. _Python39: https://badge.fury.io/py/python-pySAP\n\n.. |PyPi| image:: https://badge.fury.io/py/python-pySAP.svg\n.. _PyPi: https://badge.fury.io/py/python-pySAP\n\n.. |Doc| image:: https://readthedocs.org/projects/python-pysap/badge/?version=latest\n.. _Doc: https://python-pysap.readthedocs.io/en/latest/?badge=latest\n\n.. |Docker| image:: https://img.shields.io/docker/cloud/build/ceacosmic/pysap\n.. _Docker: https://hub.docker.com/r/ceacosmic/pysap\n\nPySAP\n======\n\nPySAP (Python Sparse data Analysis Package) is a Python module for **sparse data analysis** that offers:\n\n* A common API for astronomical and neuroimaging datasets.\n* Access to |link-to-sparse2d| executables with both wrappers and bindings.\n* Access to application specific plug-ins.\n* A graphical user interface to play with the provided functions.\n\n.. |link-to-sparse2d| raw:: html\n\n Sparse2D\n\n.. raw:: html\n\n

\n\nThis package is the result of the |link-to-cosmic| project, which is a collaboration between\nthe CEA Neurospin UNATI and CEA CosmoStat laboratories.\n\n.. |link-to-cosmic| raw:: html\n\n COSMIC\n\nImportant links\n===============\n\n- Official source code repo: https://github.com/cea-cosmic/pysap\n- API documentation (last stable release): https://python-pysap.readthedocs.io/\n- PySAP paper: https://arxiv.org/abs/1910.08465\n\nDependencies\n============\n\nPySAP will automatically install all of the required dependencies, however\nissues may arise on some operating systems. If you encounter any problems please\nensure that you have all of the following dependencies installed before opening a\nnew issue.\n\n1. PySAP requires that the COSMIC package |link-to-modopt| be installed.\n\n.. |link-to-modopt| raw:: html\n\n ModOpt\n\n2. PySAP also requires the installation of the following third party software packages:\n\n* scipy [==1.5.4]\n* numpy [==1.19.5]\n* matplotlib [==3.3.4]\n* astropy [==4.1]\n* nibabel [==3.2.1]\n* pyqtgraph [==0.11.1]\n* progressbar2 [==3.53.1]\n* scikit-learn [==0.24.1]\n* pybind11 [==2.6.2]\n* pyqt5 [==5.15.4]\n* PyWavelets [==1.1.1]\n\nPlug-Ins\n========\n\nPySAP currently supports the following plug-ins:\n\n* |link-to-pysap-astro| [==0.0.1]\n* |link-to-pysap-mri| [==0.3.0]\n\n.. |link-to-pysap-astro| raw:: html\n\n PySAP-Astro\n\n.. |link-to-pysap-mri| raw:: html\n\n PySAP-MRI\n\nInstallation\n============\n\nThe installation of PySAP has been extensively tested on Ubuntu and macOS, however\nwe cannot guarantee it will work on every operating system (e.g. Windows). A Docker\nimage is available (see below) for those unable to install PySAP directly.\n\nIf you encounter any installation issues be sure to go through the following steps before opening a new issue:\n\n1. Check that that all the dependencies listed above have been correctly installed.\n2. Read through all of the documentation provided, including the troubleshooting suggestions.\n3. Check if your problem has already been addressed in a previous issue.\n\nFurther instructions are available |link-to-install|.\n\n.. |link-to-install| raw:: html\n\n here\n\nFrom PyPi\n---------\n\nTo install PySAP simply run:\n\n.. code-block:: bash\n\n $ pip install python-pysap\n\nDepending on your Python setup you may need to provide the ``--user`` option.\n\n.. code-block:: bash\n\n $ pip install --user python-pysap\n\nLocally\n-------\n\nTo build PySAP locally, clone the repository:\n\n.. code-block:: bash\n\n $ git clone https://github.com/CEA-COSMIC/pysap.git\n\nand run:\n\n.. code-block:: bash\n\n $ python setup.py install\n\nor:\n\n.. code-block:: bash\n\n $ python setup.py develop\n\nAs before, use the ``--user`` option if needed.\n\nConda Environment\n-----------------\n\nA a conda ``environment.yml`` file is provided to facilitate the installation of\nthe required PySAP dependencies along with some optional dependencies that\nprovide additional features. To build the environment run:\n\n.. code-block:: bash\n\n $ conda env create -f environment.yml\n\nThen to activate the environment run:\n\n.. code-block:: bash\n\n $ conda activate pysap\n\nFinally, install PySAP following the instructions above.\n\nDocker Image\n------------\n\nA PySAP Docker image is available via DockerHub that includes the latest stable\nversion of PySAP pre-installed. To install the image run:\n\n.. code-block:: bash\n\n $ docker pull ceacosmic/pysap\n\nA Jupyter notebook can be launched using the Docker image as a backend and with\naccess to the users current working directory as follows:\n\n.. code-block:: bash\n\n $ docker run -p 8888:8888 -v ${PWD}:/home ceacosmic/pysap\n\nmacOS\n-----\n\nHelp with installation on macOS is available `here`_.\n\n.. _here: ./doc/macos_install.rst\n\nLinux\n-----\n\nPlease refer to the |link-to-pyqt| for issues regarding the installation of\n``pyqtgraph``.\n\n.. |link-to-pyqt| raw:: html\n\n PyQtGraph homepage\n\nContributing\n============\n\nIf you want to contribute to pySAP, be sure to review the `contribution guidelines`_ and follow to the `code of conduct`_.\n\n.. _contribution guidelines: ./CONTRIBUTING.md\n\n.. _code of conduct: ./CODE_OF_CONDUCT.md\n\n\nCitation\n========\n\nIf you use PySAP in a scientific publication, we would appreciate citations to the following paper:\n|link-to-paper|\n\n.. |link-to-paper| raw:: html\n\n \n PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing, S. Farrens et al., Astronomy and Computing 32, 2020 \n\nThe bibtex citation is the following:\nk::\n @Article{farrens2020pysap,\n title={{PySAP: Python Sparse Data Analysis Package for multidisciplinary image processing}},\n 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},\n journal={Astronomy and Computing},\n volume={32},\n pages={100402},\n year={2020},\n publisher={Elsevier}\n }\n","has_starred","hub_user","sfarrens","immutable_tags_settings",{"_76":11,"_77":78},"enabled","rules",[79],".*","is_automated","permissions",{"_83":21,"_84":11,"_85":11},"read","write","admin","user","storage_size",1624264248,"orgData",{"_91":92,"_93":94,"_95":96,"_97":33,"_98":99,"_100":99,"_101":102,"_103":99,"_104":105,"_106":99,"_107":99,"_108":99,"_109":21},"id","4f2ab5bda4ce42d4917d6d2e0b09f043","uuid","4f2ab5bd-a4ce-42d4-917d-6d2e0b09f043","type","organization","orgname","full_name","","location","company","CEA COSMIC Project","profile_url","date_joined","2021-04-22T16:14:01.377582Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[112],{"_113":44,"_114":115,"_116":117,"_91":118,"_119":120,"_50":137,"_138":115,"_139":33,"_140":56,"_57":141,"_142":143,"_144":128,"_145":137,"_146":66,"_147":21},"content_type","creator",12664359,"full_size",1624255499,146881947,"images",[121],{"_122":123,"_124":125,"_126":99,"_127":128,"_129":130,"_131":132,"_133":99,"_134":-5,"_135":117,"_63":66,"_136":-5},"architecture","amd64","digest","sha256:e40ff6beb634a549c723dc3251a4facb30caf43af2d234c9ff51035c0f3a3d1f","features","last_pulled","2026-09-30T03:51:06.765038302Z","last_pushed","2021-04-23T15:29:09Z","os","linux","os_features","os_version","size","variant","2021-04-24T12:13:57.327057Z","last_updater","last_updater_username","media_type","latest","repository",12628570,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":161,"_168":169,"_155":178,"_179":11},{"_40":162,"_42":163,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":164,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":73,"_74":165,"_80":11,"_81":167,"_86":33,"_87":88},[],[44],[56],{"_76":11,"_77":166},[79],{"_83":21,"_84":11,"_85":11},"tags",{"_170":64,"_171":-5,"_172":-5,"_173":174},"count","next","previous","results",[175],{"_113":44,"_114":115,"_116":117,"_91":118,"_119":176,"_50":137,"_138":115,"_139":33,"_140":56,"_57":141,"_142":143,"_144":128,"_145":137,"_146":66,"_147":21},[177],{"_122":123,"_124":125,"_126":99,"_127":128,"_129":130,"_131":132,"_133":99,"_134":-5,"_135":117,"_63":66,"_136":-5},[],"canDeleteTags","actionData","errors"]

ceacosmic/pysap

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