Source code for cryosparc2.viewers.viewer_initialmodel

# **************************************************************************
# *
# * 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 webbrowser

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

from ..constants import *
from ..utils import *
from ..protocols import ProtCryoSparcInitialModel, ProtCryoSparc3DClassification


[docs]class CryosPARCViewerInitialModel(ProtocolViewer): """ Wrapper to visualize different type of objects with the Xmipp program xmipp_showj """ _environments = [DESKTOP_TKINTER, WEB_DJANGO] _targets = [ProtCryoSparcInitialModel, ProtCryoSparc3DClassification] def _defineParams(self, form): self._env = os.environ.copy() form.addSection(label='Results') group = form.addGroup('3D Classes') group.addParam('show3DClasses', LabelParam, label='Initial model output classes') group = form.addGroup('Volume') group.addParam('displayVol', EnumParam, choices=['dataViewer', 'cryoSPARC'], default=DATA_VIEWER, display=EnumParam.DISPLAY_HLIST, label='Display volume with', help='*dataViewer*: display volumes as surface with Scipion.\n' '*cryoSPARC: display volumes as surface with cryoSPARC') # '*slices*: display volumes as 2D slices along z axis.\n' def _getVisualizeDict(self): self._load() return {'show3DClasses': self._visualizeClasses, 'displayVol': self._visualizeVolumes, } def _visualizeClasses(self, paramName=None): view = [] obj = self.protocol.outputClasses fn = obj.getFileName() labels = 'enabled id _size _representative._filename ' view.append(ObjectView(self._project, obj.strId(), fn, viewParams={showj.MODE: showj.MODE_MD, showj.VISIBLE: labels, showj.RENDER: '_representative._filename'})) return view def _visualizeVolumes(self, paramName=None): if self.displayVol == DATA_VIEWER: return self._showVolumesDataViewer() # elif self.displayVol == VOLUME_SLICES: # return self._createVolumesSqlite() elif self.displayVol == VOLUME_CRYOSPARC: return self._showCryoSPARVolume() def _showCryoSPARVolume(self, paramName=None): views = [] system_info = getSystemInfo() status_errors = system_info[0] print(status_errors) 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 _showVolumesDataViewer(self): """ Visualize the volumes with the Scipion dataViewer. """ view = [] obj = self.protocol.outputVolumes fn = obj.getFileName() labels = 'id enabled comment _filename ' objCommands = "'%s' '%s' '%s'" % (OBJCMD_CLASSAVG_PROJS, OBJCMD_PROJS, OBJCMD_INITVOL) view.append(ObjectView(self._project, obj.strId(), fn, viewParams={showj.MODE: showj.MODE_MD, showj.VISIBLE: labels, showj.RENDER: '_filename', showj.OBJCMDS: objCommands})) return view def _load(self): """ Load the 3D classes and volumes for visualization mode. """ self.protocol._defineFileNames()