===========
Warp plugin
===========
This plugin provides a wrapper for some of the programs of the `Warp <https://github.com/dtegunov/warp>`_ software.
.. image:: https://img.shields.io/pypi/v/scipion-em-warp.svg
:target: https://pypi.python.org/pypi/scipion-em-warp
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-warp.svg
:target: https://pypi.python.org/pypi/scipion-em-warp
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-warp.svg
:target: https://pypi.python.org/pypi/scipion-em-warp
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-warp?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-warp
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-warp
:target: https://pypi.python.org/pypi/scipion-em-warp
: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-warp
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-warp.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-warp --devel
Verifying
---------
To check the installation, simply run one of the following Scipion tests:
* scipion3 tests warp.tests.test_protocols.TestDeconvolveMics
* scipion3 tests warp.tests.test_protocols_tomo.TestDeconvolveTomo
Protocols
----------
* deconvolve micrographs
* deconvolve tomograms
* deconvolve tilt-series
References
-----------
1. Dimitry Tegunov and Patrick Cramer. Real-time cryo-electron microscopy data preprocessing with Warp. Nature Methods 16(11), 2019, p. 1146-1152.
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