Metadata-Version: 2.1
Name: nipet
Version: 2.0.1
Summary: CUDA-accelerated Python utilities for high-throughput PET/MR image reconstruction and analysis
Home-page: https://github.com/NiftyPET/NIPET
Author: Pawel Markiewicz
Author-email: p.markiewicz@ucl.ac.uk
Maintainer: Casper da Costa-Luis
Maintainer-email: casper.dcl@physics.org
License: Apache 2.0
Project-URL: Changelog, https://github.com/NiftyPET/NIPET/releases
Project-URL: Documentation, https://niftypet.readthedocs.io
Description: ===========================================================
        NIPET: high-throughput Neuro-Image PET reconstruction
        ===========================================================
        
        |Docs| |Version| |Downloads| |Py-Versions| |DOI| |Licence| |Tests|
        
        NIPET is a Python sub-package of NiftyPET_, offering high-throughput PET image reconstruction as well as image processing and analysis (``nimpa``: https://github.com/NiftyPET/NIMPA) for PET/MR imaging with high quantitative accuracy and precision. The software is written in CUDA C and embedded in Python C extensions.
        
        .. _NiftyPET: https://github.com/NiftyPET/NiftyPET
        
        The scientific aspects of this software are covered in two open-access publications:
        
        * *NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis* Neuroinformatics (2018) 16:95. https://doi.org/10.1007/s12021-017-9352-y
        
        * *Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis* Physics in Medicine & Biology (2016). https://doi.org/10.1088/0031-9155/61/13/N322
        
        Although, the two stand-alone and independent packages, ``nipet`` and ``nimpa``, are dedicated to brain imaging, they can equally well be used for whole body imaging.  Strong emphasis is put on the data, which are acquired using positron emission tomography (PET) and magnetic resonance (MR), especially the hybrid and simultaneous PET/MR scanners.
        
        This software platform and Python name-space *NiftyPET* covers the entire processing pipeline, from the raw list-mode (LM) PET data through to the final image statistic of interest (e.g., regional SUV), including LM bootstrapping and multiple reconstructions to facilitate voxel-wise estimation of uncertainties.
        
        In order to facilitate all the functionality, *NiftyPET* relies on third-party software for image conversion from DICOM to NIfTI (dcm2niix) and image registration (NiftyReg).  The additional software is installed automatically to a user specified location.
        
        **Documentation with installation manual and tutorials**: https://niftypet.readthedocs.io/
        
        Quick Install
        ~~~~~~~~~~~~~
        
        Note that installation prompts for setting the path to ``NiftyPET_tools`` and
        hardware attenuation maps. This can be avoided by setting the environment
        variables ``PATHTOOLS`` and ``HMUDIR``, respectively.
        It's also recommended (but not required) to use `conda`.
        
        .. code:: sh
        
            # optional (Linux syntax) to avoid prompts
            export PATHTOOLS=$HOME/NiftyPET_tools
            export HMUDIR=$HOME/mmr_hardwareumaps
            # cross-platform install
            conda install -c conda-forge python=3 \
              ipykernel numpy scipy scikit-image matplotlib ipywidgets
            pip install "nipet>=2"
        
        External CMake Projects
        ~~~~~~~~~~~~~~~~~~~~~~~
        
        The raw C/CUDA libraries may be included in external projects using ``cmake``.
        Simply build the project and use ``find_package(NiftyPETnipet)``.
        
        .. code:: sh
        
            # print installation directory (after `pip install nipet`)...
            python -c "from niftypet.nipet import cmake_prefix; print(cmake_prefix)"
        
            # ... or build & install directly with cmake
            mkdir build && cd build
            cmake ../niftypet && cmake --build . && cmake --install . --prefix /my/install/dir
        
        At this point any external project may include NIPET as follows
        (Once setting ``-DCMAKE_PREFIX_DIR=<installation prefix from above>``):
        
        .. code:: cmake
        
            cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
            project(myproj)
            find_package(NiftyPETnipet COMPONENTS mmr_auxe mmr_lmproc petprj nifty_scatter REQUIRED)
            add_executable(myexe ...)
            target_link_libraries(myexe PRIVATE
              NiftyPET::mmr_auxe NiftyPET::mmr_lmproc NiftyPET::petprj NiftyPET::nifty_scatter)
        
        Licence
        ~~~~~~~
        
        |Licence| |DOI|
        
        Copyright 2018-21
        
        - `Pawel J. Markiewicz <https://github.com/pjmark>`__ @ University College London
        - `Casper O. da Costa-Luis <https://github.com/casperdcl>`__ @ King's College London
        - `Contributors <https://github.com/NiftyPET/NIPET/graphs/contributors>`__
        
        .. |Docs| image:: https://readthedocs.org/projects/niftypet/badge/?version=latest
           :target: https://niftypet.readthedocs.io/en/latest/?badge=latest
        .. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4417680.svg
           :target: https://doi.org/10.5281/zenodo.4417680
        .. |Licence| image:: https://img.shields.io/pypi/l/nipet.svg?label=licence
           :target: https://github.com/NiftyPET/NIPET/blob/master/LICENCE
        .. |Tests| image:: https://img.shields.io/github/workflow/status/NiftyPET/NIPET/Test?logo=GitHub
           :target: https://github.com/NiftyPET/NIPET/actions
        .. |Downloads| image:: https://img.shields.io/pypi/dm/nipet.svg?logo=pypi&logoColor=white&label=PyPI%20downloads
           :target: https://pypi.org/project/nipet
        .. |Version| image:: https://img.shields.io/pypi/v/nipet.svg?logo=python&logoColor=white
           :target: https://github.com/NiftyPET/NIPET/releases
        .. |Py-Versions| image:: https://img.shields.io/pypi/pyversions/nipet.svg?logo=python&logoColor=white
           :target: https://pypi.org/project/nipet
        
Keywords: PET,image reconstruction,analysis
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: dev
Provides-Extra: examples
