Metadata-Version: 1.2
Name: scipion-em-sphire
Version: 3.1.1
Summary: Plugin to use Sphire programs within the Scipion framework
Home-page: https://github.com/scipion-em/scipion-em-sphire
Author: I2PC, Jose Miguel de La Rosa, Jorge Jiménez
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-sphire/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-sphire/
Description: =============
        Sphire plugin
        =============
        
        This plugin provides a wrapper for some programs of `SPHIRE <https://sphire.mpg.de/>`_ software suite:
        
            - JANNI (Just Another Noise 2 Noise Implementation): a neural network denoising tool
            - crYOLO: a fast and accurate particle picking procedure. It's based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-sphire.svg
                :target: https://pypi.python.org/pypi/scipion-em-sphire
                :alt: PyPI release
        
        .. image:: https://img.shields.io/pypi/l/scipion-em-sphire.svg
                :target: https://pypi.python.org/pypi/scipion-em-sphire
                :alt: License
        
        .. image:: https://img.shields.io/pypi/pyversions/scipion-em-sphire.svg
                :target: https://pypi.python.org/pypi/scipion-em-sphire
                :alt: Supported Python versions
        
        .. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-sphire?server=https%3A%2F%2Fsonarcloud.io
                :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-sphire
                :alt: SonarCloud quality gate
        
        .. image:: https://img.shields.io/pypi/dm/scipion-em-sphire
                :target: https://pypi.python.org/pypi/scipion-em-sphire
                :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
        
            It can be installed in user mode via Scipion plugin manager (**Configuration** > **Plugins**) or using the command line:
        
            .. code-block::
        
                scipion installp -p scipion-em-sphire
        
        b) Developer's version
        
            * download repository
        
            .. code-block::
        
                git clone -b devel https://github.com/scipion-em/scipion-em-sphire.git
        
            * install
        
            .. code-block::
        
                scipion installp -p /path/to/scipion-em-sphire --devel
        
        crYOLO software will be installed automatically with the plugin but you can also use an existing installation by providing *CRYOLO_ENV_ACTIVATION* (see below).
        
        **Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
        
        To check the installation you can run the plugin's tests:
        
        ``scipion test --grep sphire --run``
        
        
        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)"
        
        **CRYOLO_ENV_ACTIVATION** (default = conda activate cryolo-1.8.5):
        Command to activate the crYOLO environment.
        
        Downloaded crYOLO and JANNI general models can be found in the following locations:
        
        * ``<SCIPION_HOME>/software/em/cryolo_model-[model_version]``
        * ``<SCIPION_HOME>/software/em/cryolo_negstain_model-[model_version]`` (not installed by default)
        * ``<SCIPION_HOME>/software/em/janni_model-[model_version]``
        
        Running on CPU
        --------------
        
        crYOLO can run on CPU, however this is only recommended for picking protocol and not training.
        For that reason the CPU implementation is only available for the *crYOLO-Picking protocol*.
        
        The CPU implementation of crYOLO **is not installed by default**. Therefore you must install the *cryoloCPU-[version]* package in the **Configuration** > **Plugins** >> **scipion-em-sphire** or by running:
        
        ``scipion installb cryoloCPU``
        
        The CPU version of crYOLO is installed under a separate conda environment called *cryoloCPU-[version]*. If you already have a cryoloCPU environment pre-installed, then modify the following variable in the Scipion config file:
        
        ``CRYOLO_ENV_ACTIVATION_CPU = conda activate envName``
        
        
        Supported versions
        ------------------
        
        1.8.2, 1.8.4, 1.8.5
        
        Protocols
        ---------
        
            * import crYOLO training model
            * crYOLO picking
            * crYOLO tomo picking
            * crYOLO training
            * JANNI denoising
           
        References
        ----------
        
            * Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology 2, (2019).
        
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
