Metadata-Version: 2.1
Name: scipion-em-warp
Version: 3.6.1
Summary: Plugin to use Warp within the Scipion framework
Author-email: Grigory Sharov <sharov.grigory@gmail.com>, Yunior Fonseca <cfonseca@cnb.csic.es>, Pablo Conesa <pconesa@cnb.csic.es>
License: GNU General Public License v3 (GPLv3)
Project-URL: Homepage, https://github.com/scipion-em/scipion-em-warp
Project-URL: Repository, https://github.com/scipion-em/scipion-em-warp
Project-URL: Issues, https://github.com/scipion-em/scipion-em-warp/issues
Keywords: scipion,electron-microscopy,cryo-em,structural-biology,image-processing,scipion-3.0
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: scipion-em>=3.9.3
Requires-Dist: scipion-pyworkflow>=3.10.6
Requires-Dist: scipion-em-reliontomo>=4.0.2

===========
Warp plugin
===========

This plugin provides a wrapper for some of the programs of the `Warp <https://github.com/warpem/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.protocols_tomo_tests.TestWarpEstimateCTFTomoReconstruction
* scipion3 tests warp.tests.protocols_tomo_tests.TestDeconvolveTomo
* scipion3 tests warp.tests.test_protocols.TestWarpMotionCorrection
* scipion3 tests warp.tests.test_protocols.TestDeconvolveMics

Protocols
----------

* deconvolve micrographs
* deconvolve tomograms
* deconvolve tilt-series
* tomo reconstruction
* motion correction (for SPA)
* tilt-series motion and ctf estimation (includes ctf estimation and defocus handedness)

References
-----------

1. Dimitry Tegunov and Patrick Cramer. Real-time cryo-electron microscopy data preprocessing with Warp. Nature Methods 16(11), 2019, p. 1146-1152. 
