Source code for cryosparc2.viewers.viewer_2Dclassify

# **************************************************************************
# *
# * 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 ClassesView, Classes3DView

from ..protocols import ProtCryo2D
from ..utils import *
from .. import Plugin

AX_X = 0
AX_Y = 1
AX_Z = 2


[docs]class CryosPARCViewer2D(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 = [ProtCryo2D] _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('displayClass2D', LabelParam, label='Display particle classes with Scipion') group.addParam('displayCryosPARC2D', LabelParam, label='Display particle classes with cryosPARC GUI') def _getVisualizeDict(self): self._load() visualizeDict = {'displayClass2D': self._showScipionClasses, '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 _getZoom(self): # Ensure that classes are shown at least at 128 px to # properly see the rlnClassDistribution label. dim = self.protocol.inputParticles.get().getDim()[0] if dim < 128: zoom = int(128*100/dim) else: zoom = 100 return zoom def _showScipionClasses(self, paramName=None): views = [] if getattr(self.protocol, 'outputClasses', None) is not None: fn = self.protocol.outputClasses.getFileName() v = self.createScipionView(fn) views.append(v) return views 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._defineFileNames()
[docs] def createScipionView(self, filename): labels = 'enabled id _size _representative._filename ' labels += '_rlnclassDistribution _rlnAccuracyRotations _rlnAccuracyTranslations' viewParams = {showj.ORDER: labels, showj.VISIBLE: labels, showj.RENDER: '_representative._filename', showj.SORT_BY: '_size desc', showj.ZOOM: str(self._getZoom()) } inputParticlesId = self.protocol.inputParticles.get().strId() ViewClass = ClassesView if self.protocol.IS_2D else Classes3DView view = ViewClass(self._project, self.protocol.strId(), filename, other=inputParticlesId, env=self._env, viewParams=viewParams) return view