=============
Spider plugin
=============
This plugin provides wrappers for several programs of `SPIDER <https://github.com/spider-em/SPIDER>`_ software suite.
.. image:: https://img.shields.io/pypi/v/scipion-em-spider.svg
:target: https://pypi.python.org/pypi/scipion-em-spider
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-spider.svg
:target: https://pypi.python.org/pypi/scipion-em-spider
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-spider.svg
:target: https://pypi.python.org/pypi/scipion-em-spider
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-spider?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-spider
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-spider
:target: https://pypi.python.org/pypi/scipion-em-spider
: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-spider
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-spider.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-spider --devel
SPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation.
Default installation path assumed is ``software/em/spider-26.06``, if you want to change it, set *SPIDER_HOME* in ``scipion.conf`` file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate `page <https://github.com/scipion-em/scipion-em-spider/wiki/How-to-Install-MPI>`_. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :(
Depending on you CPU type you might want to change the default binary from ``spider_linux_mp_intel64`` to a different one by explicitly setting *SPIDER* variable.
To check the installation, simply run one of the following Scipion tests:
.. code-block::
scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct
scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert
scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinement
A complete list of tests can also be seen by executing ``scipion test --show --grep spider``
Supported versions
------------------
26.06
Protocols
---------
* `Align AP SR <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignAPSR>`_
* `Align pairwise <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignPairwise>`_
* `CA PCA <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtCAPCA>`_
* `Classification protocols: Diday, K-means, Ward <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtClassify>`_
* Custom 2D mask
* Filter particles
* Reconstruct Fourier
* Refinement
References
----------
1. \J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.
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"description": "=============\nSpider plugin\n=============\n\nThis plugin provides wrappers for several programs of `SPIDER <https://github.com/spider-em/SPIDER>`_ software suite.\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-spider.svg\n :target: https://pypi.python.org/pypi/scipion-em-spider\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-spider.svg\n :target: https://pypi.python.org/pypi/scipion-em-spider\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-spider.svg\n :target: https://pypi.python.org/pypi/scipion-em-spider\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-spider?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-spider\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-spider\n :target: https://pypi.python.org/pypi/scipion-em-spider\n :alt: Downloads\n\n\nInstallation\n------------\n\nYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-spider\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-spider.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-spider --devel\n\nSPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation. \nDefault installation path assumed is ``software/em/spider-26.06``, if you want to change it, set *SPIDER_HOME* in ``scipion.conf`` file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate `page <https://github.com/scipion-em/scipion-em-spider/wiki/How-to-Install-MPI>`_. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :(\nDepending on you CPU type you might want to change the default binary from ``spider_linux_mp_intel64`` to a different one by explicitly setting *SPIDER* variable.\n\nTo check the installation, simply run one of the following Scipion tests:\n\n.. code-block::\n\n scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct\n scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign\n scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow\n scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert\n scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinement\n\n\nA complete list of tests can also be seen by executing ``scipion test --show --grep spider``\n\nSupported versions\n------------------\n\n26.06\n\nProtocols\n---------\n\n* `Align AP SR <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignAPSR>`_\n* `Align pairwise <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignPairwise>`_\n* `CA PCA <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtCAPCA>`_\n* `Classification protocols: Diday, K-means, Ward <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtClassify>`_\n* Custom 2D mask\n* Filter particles\n* Reconstruct Fourier\n* Refinement\n\nReferences\n----------\n\n1. \\J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.\n\n\n",
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