# **************************************************************************
# *
# * 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_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()