Source code for cryosparc2.viewers.viewer_partsubtract


# **************************************************************************
# *
# * Authors: Yunior C. Fonseca Reyna    (cfonseca@cnb.csic.es)
# *
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

import sys
import webbrowser

import pwem.viewers.showj as showj
from pyworkflow.protocol.params import LabelParam
from pyworkflow.viewer import ProtocolViewer, DESKTOP_TKINTER
from pwem.viewers import ObjectView

from ..protocols import (ProtCryoSparcSubtract,
                         ProtCryoSparcGlobalCtfRefinement,
                         ProtCryoSparcLocalCtfRefinement,
                         ProtCryoSparcSymmetryExpansion)
from ..utils import *
from .. import Plugin


[docs]class CryosPARCViewerPartSubtract(ProtocolViewer): """ Visualization tools for cryosPARC results. CryoSPARC is a backend and frontend software system that provides data processing and image analysis capabilities for single particle cryo-EM, along with a browser based user interface and command line tools. Please find the documentation at https://cryosparc.com """ _environments = [DESKTOP_TKINTER] _targets = [ProtCryoSparcSubtract, ProtCryoSparcGlobalCtfRefinement, ProtCryoSparcLocalCtfRefinement, ProtCryoSparcSymmetryExpansion] _label = 'viewer cryosPARC' def __init__(self, *args, **kwargs): ProtocolViewer.__init__(self, **kwargs) sys.path.append(Plugin.getVar(CRYOSPARC_HOME)) def _defineParams(self, form): self._env = os.environ.copy() form.addSection(label='Visualization') group = form.addGroup('Particles') group.addParam('displayDataViewer', LabelParam, label='Display particle with Scipion') group.addParam('displayCryosPARC2D', LabelParam, label='Display particle with cryosPARC GUI') def _getVisualizeDict(self): self._load() visualizeDict = {'displayDataViewer': self._showOutputParticles, 'displayCryosPARC2D': self._showCryoSPARCClasses} # If the is some error during the load, just show that instead # of any viewer if self._errors: for k in visualizeDict.keys(): visualizeDict[k] = self._showErrors return visualizeDict def _showErrors(self, param=None): views = [] self.errorList(self._errors, views) return views def _showOutputParticles(self, paramName=None): views = [] if getattr(self.protocol, 'outputParticles', None) is not None: fn = self.protocol.outputParticles.getFileName() v = self.createScipionPartView(fn) views.append(v) return views
[docs] def createScipionPartView(self, filename, viewParams={}): inputParticlesId = self.protocol.inputParticles.get().strId() labels = 'enabled id _size _filename _transform._matrix' viewParams = {showj.ORDER: labels, showj.VISIBLE: labels, showj.RENDER: '_filename', 'labels': 'id', } return ObjectView(self._project, self.protocol.strId(), filename, other=inputParticlesId, env=self._env, viewParams=viewParams)
def _showCryoSPARCClasses(self, paramName=None): views = [] system_info = getSystemInfo() status_errors = system_info[0] if not status_errors: system_info = eval(system_info[1]) master_hostname = system_info.get('master_hostname') port_webapp = system_info.get('port_webapp') projectId = self.protocol.projectName.get() workspaceId = self.protocol.workSpaceName.get() jobId = self.protocol.currenJob.get() url = os.path.join("http://", master_hostname + ':' + port_webapp, "projects", projectId, workspaceId, jobId) browser = webbrowser.get() browser.open(url) return views def _load(self): self._errors = [] self.protocol._createFilenameTemplates()