Metadata-Version: 1.2
Name: scipion-em-motioncorr
Version: 3.0.12
Summary: Plugin to use motioncorr programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-motioncorr
Author: Grigory Sharov, J.M. De la Rosa Trevin
Author-email: sharov.grigory@gmail.com, delarosatrevin@scilifelab.se
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-motioncorr/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-motioncorr/
Description: =================
        Motioncorr plugin
        =================
        
        This plugin allows to use motioncor2 program within the Scipion framework.
        
        Motioncor2 is a GPU-accelerated program for correction of electron beam-induced sample motion. It is developed by `Shawn Zheng <https://emcore.ucsf.edu/ucsf-motioncor2>`_.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-motioncorr.svg
                :target: https://pypi.python.org/pypi/scipion-em-motioncorr
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-motioncorr.svg
                :target: https://pypi.python.org/pypi/scipion-em-motioncorr
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-motioncorr.svg
                :target: https://pypi.python.org/pypi/scipion-em-motioncorr
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-motioncorr?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-motioncorr
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-motioncorr
                :target: https://pypi.python.org/pypi/scipion-em-motioncorr
                :alt: Downloads
        
        
        +--------------+----------------+--------------------+
        | prod: |prod| | devel: |devel| | support: |support| |
        +--------------+----------------+--------------------+
        
        .. |prod| image:: http://scipion-test.cnb.csic.es:9980/badges/motioncorr_prod.svg
        .. |devel| image:: http://scipion-test.cnb.csic.es:9980/badges/motioncorr_devel.svg
        .. |support| image:: http://scipion-test.cnb.csic.es:9980/badges/motioncorr_support.svg
        
        **IMPORTANT!**
        
            If you have imported movies with a gain file in **DM4** format, you need to **flip the gain reference upside-down** in the motioncor2 protocol! (`bug details <https://github.com/I2PC/xmippCore/issues/39>`_)
        
        Installation
        ------------
        
        You will need to use `3.0 <https://github.com/I2PC/scipion/releases/tag/V3.0.0>`_ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
        
        a) Stable version
        
        .. code-block::
        
           scipion installp -p scipion-em-motioncorr
        
        b) Developer's version
        
           * download repository 
           
           .. code-block::
           
              git clone https://github.com/scipion-em/scipion-em-motioncorr.git
        
           * install
           
           .. code-block::
        
              scipion installp -p path_to_scipion-em-motioncorr --devel
        
        Motioncor2 binaries will be installed automatically with the plugin, but you can also link an existing installation. 
        Default installation path assumed is ``software/em/motioncor2-1.4.0``, if you want to change it, set *MOTIONCOR2_HOME* in ``scipion.conf`` file to
        the folder where the Motioncor2 is installed. Depending on your CUDA version you might want to change the default binary from ``MotionCor2_1.4.0_Cuda101``
        to a different one by explicitly setting *MOTIONCOR2* variable. If you need to use CUDA different from the one used during Scipion installation
        (defined by CUDA_LIB), you can add *MOTIONCOR2_CUDA_LIB* variable to the config file. Various binaries can be downloaded from the official UCSF website.
        
        To check the installation, simply run the following Scipion test: 
        
        ``scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies``
        
        Supported versions
        ------------------
        
        1.2.6, 1.3.0, 1.3.1, 1.3.2, 1.4.0
        
        Protocols
        ---------
        
        * movie alignment
        
        References
        ----------
        
        1.  Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng & David A Agard. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods volume 14, pages 331–332 (2017).
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
