Metadata-Version: 1.2
Name: scipion-em-motioncorr
Version: 3.6
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
        
        **IMPORTANT!**
        
            1. 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! (`see details <https://github.com/I2PC/xmippCore/issues/39>`_)
            2. When importing EER movies, you should specify dose per single EER frame during import step.
            3. If you are processing EER movies and providing \*.gain reference file camera defects will be automatically extracted from the gain file header and converted to Motioncor2 format. This step is omitted if you provide a defects file yourself.
        
        Installation
        ------------
        
        You will need to use 3.0+ 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/motioncor2-1.4.7``, 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_1.4.7_Cuda102_12-09-2021``
        to a different one by explicitly setting *MOTIONCOR2_BIN* 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``
        
        Licensing
        ---------
        
        Motioncor2 is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:
        
            * agard@msg.ucsf.edu
            * Yifan.Cheng@ucsf.edu
        
        Supported versions
        ------------------
        
        1.4.0, 1.4.2, 1.4.4, 1.4.5, 1.4.7
        
        Protocols
        ---------
        
        * movie alignment
        * align tilt-series movies
        
        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
