Metadata-Version: 1.2
Name: scipion-em-tomotwin
Version: 3.0b4
Summary: Plugin to use TomoTwin within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-tomotwin
Author: Grigory Sharov
Author-email: sharov.grigory@gmail.com
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-tomotwin/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-tomotwin/
Description: ===============
        TomoTwin plugin
        ===============
        
        This plugin provides a wrapper for `TomoTwin <https://github.com/MPI-Dortmund/tomotwin-cryoet>`_ software: Particle picking in Tomograms using triplet networks and metric learning
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-tomotwin.svg
                :target: https://pypi.python.org/pypi/scipion-em-tomotwin
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-tomotwin.svg
                :target: https://pypi.python.org/pypi/scipion-em-tomotwin
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomotwin.svg
                :target: https://pypi.python.org/pypi/scipion-em-tomotwin
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-tomotwin?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-tomotwin
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-tomotwin
                :target: https://pypi.python.org/pypi/scipion-em-tomotwin
                :alt: Downloads
        
        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-tomotwin
        
        b) Developer's version
        
           * download repository
        
            .. code-block::
        
                git clone -b devel https://github.com/scipion-em/scipion-em-tomotwin.git
        
           * install
        
            .. code-block::
        
               scipion installp -p /path/to/scipion-em-tomotwin --devel
        
        TomoTwin software will be installed automatically with the plugin but you can also use an existing installation by providing *TOMOTWIN_ENV_ACTIVATION* (see below).
        
        **Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
        
        Configuration variables
        -----------------------
        *CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the
        PATH (not recommended), which can lead to execution problems mixing scipion
        python with conda ones. One example of this could can be seen below but
        depending on your conda version and shell you will need something different:
        CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
        
        *TOMOTWIN_ENV_ACTIVATION* (default = conda activate tomotwin-0.2.1.6):
        Command to activate the TomoTwin environment.
        
        *TOMOTWIN_MODEL* (default = software/em/tomotwin_model-052022/tomotwin_model_p120_052022_loss.pth):
        Path to the pre-trained model.
        
        *NAPARI_ENV_ACTIVATION* (default = conda activate napari):
        Command to activate the Napari viewer (boxmanager) environment.
        
        Verifying
        ---------
        To check the installation, simply run the following Scipion test:
        
        ``scipion test tomotwin.tests.test_protocols_tomotwin.TestTomoTwinRefPicking``
        
        Supported versions
        ------------------
        
        0.1.2, 0.2.1.6
        
        Protocols
        ----------
        
        * reference-based picking
        
        References
        -----------
        
        1. TomoTwin: Generalized 3D Localization of Macromolecules in Cryo-electron Tomograms with Structural Data Mining. Gavin Rice, Thorsten Wagner, Markus Stabrin, Stefan Raunser. https://www.biorxiv.org/content/10.1101/2022.06.24.497279v1
        
Keywords: scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
