# **************************************************************************
# *
# * 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