===========
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.
Raw data
{
"_id": null,
"home_page": null,
"name": "scipion-em-warp",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3.0",
"author": null,
"author_email": "Grigory Sharov <sharov.grigory@gmail.com>, Yunior Fonseca <cfonseca@cnb.csic.es>, Pablo Conesa <pconesa@cnb.csic.es>",
"download_url": "https://files.pythonhosted.org/packages/68/b1/8c636a481cf176f62a4236c2ea382fb353e161e3b54c28c36d5818d0c7fa/scipion_em_warp-3.4.4.tar.gz",
"platform": null,
"description": "===========\nWarp plugin\n===========\n\nThis plugin provides a wrapper for some of the programs of the `Warp <https://github.com/warpem/warp>`_ software.\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-warp.svg\n :target: https://pypi.python.org/pypi/scipion-em-warp\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-warp.svg\n :target: https://pypi.python.org/pypi/scipion-em-warp\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-warp.svg\n :target: https://pypi.python.org/pypi/scipion-em-warp\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-warp?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-warp\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-warp\n :target: https://pypi.python.org/pypi/scipion-em-warp\n :alt: Downloads\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-warp\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-warp.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-warp --devel\n\n\nVerifying\n---------\n\nTo check the installation, simply run one of the following Scipion tests:\n\n* scipion3 tests warp.tests.protocols_tomo_tests.TestWarpEstimateCTFTomoReconstruction\n* scipion3 tests warp.tests.protocols_tomo_tests.TestDeconvolveTomo\n* scipion3 tests warp.tests.test_protocols.TestWarpMotionCorrection\n* scipion3 tests warp.tests.test_protocols.TestDeconvolveMics\n\nProtocols\n----------\n\n* deconvolve micrographs\n* deconvolve tomograms\n* deconvolve tilt-series\n* tomo reconstruction\n* motion correction (for SPA)\n* tilt-series motion and ctf estimation (includes ctf estimation and defocus handedness)\n\nReferences\n-----------\n\n1. Dimitry Tegunov and Patrick Cramer. Real-time cryo-electron microscopy data preprocessing with Warp. Nature Methods 16(11), 2019, p. 1146-1152.\n",
"bugtrack_url": null,
"license": "GNU General Public License v3 (GPLv3)",
"summary": "Plugin to use Warp within the Scipion framework",
"version": "3.4.4",
"project_urls": {
"Homepage": "https://github.com/scipion-em/scipion-em-warp",
"Issues": "https://github.com/scipion-em/scipion-em-warp/issues",
"Repository": "https://github.com/scipion-em/scipion-em-warp"
},
"split_keywords": [
"scipion",
" electron-microscopy",
" cryo-em",
" structural-biology",
" image-processing",
" scipion-3.0"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "48149388aa94c8270667a412ff2bc283fc18007c2e7870c4482dd96f4a449fc5",
"md5": "ff6d802b477a43ce94f1156d1bc8aafb",
"sha256": "9fe44db3fe998dbcb0fddbb1e48b96852ca46f3dd78547b30fb67114167aaf19"
},
"downloads": -1,
"filename": "scipion_em_warp-3.4.4-py3-none-any.whl",
"has_sig": false,
"md5_digest": "ff6d802b477a43ce94f1156d1bc8aafb",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 73687,
"upload_time": "2024-12-13T09:37:51",
"upload_time_iso_8601": "2024-12-13T09:37:51.892120Z",
"url": "https://files.pythonhosted.org/packages/48/14/9388aa94c8270667a412ff2bc283fc18007c2e7870c4482dd96f4a449fc5/scipion_em_warp-3.4.4-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "68b18c636a481cf176f62a4236c2ea382fb353e161e3b54c28c36d5818d0c7fa",
"md5": "df92b2a1ef67b871d83a487911445730",
"sha256": "c6346d76a026b30eac07675016fbea22efa2da4e805233cbf0a0f3631f70808f"
},
"downloads": -1,
"filename": "scipion_em_warp-3.4.4.tar.gz",
"has_sig": false,
"md5_digest": "df92b2a1ef67b871d83a487911445730",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 58665,
"upload_time": "2024-12-13T09:37:54",
"upload_time_iso_8601": "2024-12-13T09:37:54.228299Z",
"url": "https://files.pythonhosted.org/packages/68/b1/8c636a481cf176f62a4236c2ea382fb353e161e3b54c28c36d5818d0c7fa/scipion_em_warp-3.4.4.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-12-13 09:37:54",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-em-warp",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "scipion-em-warp"
}
JSON
