Metadata-Version: 2.1
Name: scipion-em-gapstop
Version: 3.3.0
Summary: Plugin to use gapstop within the Scipion framework
Author-email: Scipion Team <scipion@cnb.csic.es>
License: GNU General Public License v3 (GPLv3)
Project-URL: Homepage, https://github.com/scipion-em/scipion-em-gapstop
Project-URL: Issues, https://github.com/scipion-em/scipion-em-gapstop/issues
Keywords: scipion,cryoem,cryoet,imageprocessing,scipion-3.0
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: scipion-pyworkflow>=3.11.6
Requires-Dist: scipion-em-tomo>=3.11.3

=============================
Scipion plugin for GAPSTOP_TM
=============================

.. image:: https://img.shields.io/pypi/v/scipion-em-gapstop.svg
        :target: https://pypi.python.org/pypi/scipion-em-gapstop
        :alt: PyPI release

.. image:: https://img.shields.io/pypi/l/scipion-em-gapstop.svg
        :target: https://pypi.python.org/pypi/scipion-em-gapstop
        :alt: License

.. image:: https://img.shields.io/pypi/pyversions/scipion-em-gapstop.svg
        :target: https://pypi.python.org/pypi/scipion-em-gapstop
        :alt: Supported Python versions

.. image:: https://img.shields.io/pypi/dm/scipion-em-gapstop
        :target: https://pypi.python.org/pypi/scipion-em-gapstop
        :alt: Downloads

This plugin provides a wrapper around the program `GAPSTOP_TM <https://bturo.pages.mpcdf.de/gapstop_tm/index.html>`_
(GPU-Accelerated Python STOPgap for Template Matching) to use it within
`Scipion <https://scipion-em.github.io/docs/release-3.0.0/index.html>`_ framework. The library
`cryoCAT <https://cryocat.readthedocs.io/latest/index.html>`_ is also integrated as part of the plugin.

Installation
------------

You will need to use `3.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_
version of Scipion to run these protocols. To install the plugin, you have two options:


a) Stable version:

.. code-block::

    scipion3 installp -p scipion-em-gapstop

b) Developer's version

    * download the repository from github:

    .. code-block::

        git clone -b devel https://github.com/scipion-em/scipion-em-gapstop.git

    * install:

    .. code-block::

        scipion3 installp -p /path/to/scipion-em-gapstop --devel

To check the installation, simply run the following Scipion test for the plugin:

    .. code-block::

        scipion3 tests gapstop.tests.tests_gapstop.Testgapstop

To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing

    .. code-block::

        scipion3 tests --grep gapstop --show

Protocols
-----------

* **Template matching** : Generate score and angular maps from the introduced tomograms from which the coordinates can be extracted with the protocol 'Extract coordinates'.
* **Extract coordinates** : Extracts coordinates from score maps produced by template matching with GAPSTOP(TM).

Latest plugin versions
----------------------

If you want to check the latest version and release history go to `CHANGES <https://github.com/scipion-em-reliotomo/gapstop/blob/master/CHANGES.txt>`_

References
----------

1. Cruz-León, S., Majtner, T., Hoffmann, P.C. et al. Nat Commun 15, 3992 (2024).


