=============
IMAGIC plugin
=============
This plugin includes two protocols to provide wrappers around Multivariate Statistical Analysis (MSA) module of `IMAGIC <https://www.imagescience.de/imagic.html>`_ software suite. IMAGIC is a licensed software, not distributed with Scipion and has to be installed by user.
.. image:: https://img.shields.io/pypi/v/scipion-em-imagic.svg
:target: https://pypi.python.org/pypi/scipion-em-imagic
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-imagic.svg
:target: https://pypi.python.org/pypi/scipion-em-imagic
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-imagic.svg
:target: https://pypi.python.org/pypi/scipion-em-imagic
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-imagic?server=https%3A%2F%2Fsonarcloud.io
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:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-imagic
:target: https://pypi.python.org/pypi/scipion-em-imagic
: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-imagic
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-imagic.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-imagic --devel
Also, you need a working IMAGIC installation. Default installation path assumed is ``software/em/imagic-190830``, if you want to change it, set *IMAGIC_HOME* in ``scipion.conf`` file to the folder where the IMAGIC is installed (it is the same as *IMAGIC_ROOT* variable in your shell environment). If you want to use MPI-based parallel job execution, make sure you have `openmpi` directory inside IMAGIC installation folder.
To check the installation, simply run the following Scipion test:
``scipion tests tests.em.workflows.test_workflow_imagicMSA.TestImagicWorkflow``
Supported versions
------------------
* 190830
Since with every version of IMAGIC software user interaction with IMAGIC programs is changed, we came up with a way to provide multiple version support. In `imagic/scripts` directory you have a folder for each corresponding version, that contains batch scripts similar to those used by IMAGIC. This way one can create a similar script specific to a certain version. At the moment version 190830 (Aug 2019) is supported. If you experience any problems or need help with adapting scripts for your IMAGIC version, do not hesitate to `create an issue on Github <https://github.com/scipion-em/scipion-em-imagic/issues/new>`_. Besides editing scripts directory you would need to add version number to `_supportedVersions` list in file ``imagic/__init__.py`` and edit IMAGIC_HOME variable in ``scipion.conf``.
Protocols
---------
* imagic - msa
* imagic - msa-classify
References
----------
1. M van Heel and W Keegstra (1981). IMAGIC: A fast, flexible and friendly image analysis software system. Ultramicroscopy 7: 113-130.
2. M van Heel, G Harauz, EV Orlova, R Schmidt and M Schatz (1996). A new generation of the IMAGIC image processing system. J. Struct. Biol. 116: 17-24.
3. M van Heel, R Portugal, A Rohou, C Linnemayr, C Bebeacua, R Schmidt, T Grant and M Schatz (2012). Four-Dimensional Cryo Electron Microscopy at Quasi Atomic Resolution: "IMAGIC 4D”. International Tables for Crystallography, vol. F, ch. 19.9: 624-628.
4. M van Heel (1984). Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy 13(1-2): 165-183.
5. Lisa Borland and Marin van Heel (1990). Classification of image data in conjugate representation spaces. Journal of the Optical Society of America A 7(4): 601-610.
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