Metadata-Version: 1.0
Name: scipion-em-sphire
Version: 3.0.6
Summary: Cryolo picker, training and custom model importer. Janni denoising.
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
Description: Sphire Scipion plugin
        =====================
        
        This plugin allows to use cryolo within Scipion framework.
        So far we have implemented:
        
        - crYOLO particle picker
        - JANNI denoising
        
        This plugin is able to install cryolo (which includes janni) and the generic models for both picking
        and denoising.
        
        `crYOLO`_ is a pipeline for particle detection in cryo-electron
        microscopy images which is based on the deep learning object detection system "You Only Look Once" (YOLO).
        
        `JANNI`_ (Just Another Noise 2 Noise Implementation) implements a neural network denoising tool based on
        deep learning.
        
        Setup
        =====
        
        It is assumed that `Scipion3`_ is currently installed. If not, follow the instructions `here`_.
        
        Plugin scipion-em-sphire requires to have Conda (Anaconda or Miniconda) installed and not initialized in
        the shell.
        
        - **Install this plugin in user mode:**
        
            It can be installed in user mode via Scipion main window (**Configuration** >
            **Plugins**) or using the command line:
        
        .. code-block::
        
            scipion installp -p local/path/to/scipion-em-sphire
        
        - **Install this plugin in developer mode:**
        
        .. code-block::
        
            scipion installp -p local/path/to/scipion-em-sphire --devel
        
        
        Plugin integration
        ------------------
        
        The following steps presuppose that you have Anaconda or Miniconda installed on
        your computer.
        If you don't have the optional SCIPION_HOME/config/scipion.conf create it like this
        
        ::
        
         [PYWORKFLOW]
         CONDA_ACTIVATION_CMD = eval "$(/path/to/conda/bin/conda shell.bash hook)"
         
         
        This also should work . /anaconda2/etc/profile.d/conda.sh. Note the conda initialization is tricky with csh shell and might not work.
         
        If you wish to install the plugin with the default settings just go to plugin
        manager and install scipion-em-sphire. This will create the default environment
        named cryolo-x.x.x (where x.x.x is referred to the downloaded version of cryolo) for you.
        
        You are ready to use crYOLO and JANNI.
        If you wish to change the environment name you can introduce
        **CRYOLO_ENV_ACTIVATION** variable in the ``~/.config/scipion.conf`` variables section:
        
        For example:
        ::
        
         CRYOLO_ENV_ACTIVATION = conda activate cryoloenvname
        
        Downloaded crYOLO and JANNI general models can be found, respectively, in the following locations:
        
        ``<SCIPION_HOME>/software/em/cryolo_model-[model_version]``
        
        ``<SCIPION_HOME>/software/em/cryolo_negstain_model-[model_version]``
        
        ``<SCIPION_HOME>/software/em/janni_model-[model_version]``
        
        Running only with CPU
        ---------------------
        CrYOLO is able to `run in CPU <http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1#run_it_on_the_cpu>`_, however this is only recomended for predicting task, not trainning. For that reason, the CPU implementation is only enabled for the ``crYOLO-Picking protocol``. In this protocol, both implementation are possible and you must select one of them in the GPU section of the from.
        
        The CPU implementation of crYOLO **is not installed by default**. Therefore, to be able to run the CPU version of crYOLO-picking, you must install the `cryoloCPU-[version]` package in the ``Plugin Manager >> scipion-em-sphire`` or by running
        
        ``scipion3 installb cryoloCPU``
        
        The CPU integration of crYOLO is installed under a conda environment called ``cryoloCPU-[version]`` . If you want to modify this environ name, please set the following variable in the scipion's config file.
        
        ``CRYOLO_ENV_ACTIVATION_CPU = conda activate cryoloCPU-envName``
        
        Running plugin tests
        --------------------
        To check that everything is properly installed and configured, you might want
        to run some tests:
        
        .. code-block::
        
           scipion test --grep sphire --run
           
           
        .. _crYOLO: https://cryolo.readthedocs.io/en/latest/
        
        .. _JANNI: https://sphire.mpg.de/wiki/doku.php?id=janni
        
        .. _Scipion3: http://scipion.i2pc.es/
        
        .. _here: https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html
        
        .. _install: https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins
        
        .. _GitHub: https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#from-github
           
        
Keywords: scipion cryoem imageprocessing picking denoise scipion-3.0
Platform: UNKNOWN
