# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (jmdelarosa@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 numpy as np
from pwem.objects import SetOfNormalModes
from pyworkflow.utils import removeBaseExt
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO
from pwem.protocols import *
from pwem.viewers.viewers_data import DataViewer
from pwem.viewers.plotter import EmPlotter
from pwem.viewers.views import CtfView, ObjectView
from pwem.viewers.showj import *
from pwem import Domain
TomoDataViewer = Domain.importFromPlugin('tomo.viewers.viewers_data',
'TomoDataViewer', doRaise=True)
SetOfClassesSubTomograms = Domain.importFromPlugin('tomo.objects',
'SetOfClassesSubTomograms')
from xmipp2.protocols.protocol_mltomo import Xmipp2ProtMLTomo
[docs]class XmippViewer(DataViewer):
""" Wrapper to visualize different type of objects
with the Xmipp program xmipp_showj
"""
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_targets = [
Xmipp2ProtMLTomo
]
def __createTemporaryCtfs(self, obj, setOfMics):
pwutils.cleanPath(obj._getPath("ctfs_temporary.sqlite"))
self.protocol._createFilenameTemplates()
ctfSet = self.protocol._createSetOfCTF("_temporary")
for mic in setOfMics:
micDir = obj._getExtraPath(removeBaseExt(mic.getFileName()))
ctfparam = self.protocol._getFileName('ctfparam', micDir=micDir)
if exists(ctfparam) or exists('xmipp_default_ctf.ctfparam'):
if not os.path.exists(ctfparam):
ctfparam = 'xmipp_default_ctf.ctfparam'
# ctfModel = readCTFModel(ctfparam, mic)
# self.protocol._setPsdFiles(ctfModel, micDir)
# ctfSet.append(ctfModel)
if not ctfSet.isEmpty():
ctfSet.write()
ctfSet.close()
return ctfSet
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, SetOfNormalModes):
fn = obj.getFileName()
# from .viewer_nma import OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD
# objCommands = "'%s' '%s'" % (OBJCMD_NMA_PLOTDIST, OBJCMD_NMA_VMD)
# self._views.append(ObjectView(self._project, self.protocol.strId(),
# fn, obj.strId(),
# viewParams={OBJCMDS: objCommands},
# **kwargs))
elif issubclass(cls, SetOfClassesSubTomograms):
self._views.append(v.ClassesSubTomogramsView(self._project, obj.strId(),
obj.getFileName()))
else:
# Use default visualization defined in base class
DataViewer._visualize(self, obj, **kwargs)
return self._views
[docs] def getCTFViews(self, ctfSet):
# This could be used by any CTF viewer to show CTF plus, phaseShift plot
# if applies.
# Return phaseShift plot if apply
firstCtf = ctfSet.getFirstItem()
if firstCtf.hasPhaseShift():
phase_shift = []
for ctf in ctfSet.iterItems():
phShift = ctf.getPhaseShift()
phase_shift.append(phShift)
plotter = EmPlotter()
plotter.createSubPlot("Phase Shift estimation",
"Number of CTFs", "Phase Shift")
plotter.plotData(np.arange(0, len(phase_shift)), phase_shift)
self._views.append(plotter)
# Return Standard CTF view (showJ)
self._views.append(CtfView(self._project, ctfSet))