def reconstructStep(self, fnRoot):
from pyworkflow.em.metadata.utils import getSize
if os.path.exists(fnRoot+".xmd"):
Nimages=getSize(fnRoot+".xmd")
if Nimages>0:
self.runJob("xmipp_reconstruct_fourier","-i %s.xmd -o %s.vol --sym %s " %(fnRoot,fnRoot,self.symmetryGroup.get()))
self.runJob("xmipp_transform_mask","-i %s.vol --mask circular -%d "%(fnRoot,self.Xdim2/2))
else:
print fnRoot+".xmd is empty. The corresponding volume is not generated."
def _createAngDistChimera(self, it):
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
view=None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir,"angles.sqlite")
from pyworkflow.em.metadata.utils import getSize
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles), itemDataIterator=self._iterAngles(fnAngles))
view = ChimeraClientView(join(fnDir,"volumeAvg.mrc"), showProjection=True, angularDistFile=fnAnglesSqLite, spheresDistance=self.spheresScale.get())
return view
def _createAngDist2D(self, it):
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
view=None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir,"angles.sqlite")
from pyworkflow.em.metadata.utils import getSize
from pyworkflow.em.plotter import EmPlotter
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles), itemDataIterator=self._iterAngles(fnAngles))
view = EmPlotter(x=1, y=1, mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
view.plotAngularDistributionFromMd(fnAnglesSqLite, 'iter %d' % it)
return view
def split(self,i):
from pyworkflow.em.metadata.utils import getSize
from math import ceil
from random import randint
from time import sleep
sleep(randint(1,10))
fnDirCurrent=self._getExtraPath("Iter001")
fnAngles=self._getExtraPath("Iter001/angles.xmd")
fnSplit=self._getExtraPath('split%05d.xmd'%i)
Nimages=getSize(fnAngles)
Nsplit=ceil(Nimages*self.splitFraction.get())
self.runJob("xmipp_metadata_utilities","-i %s -o %s --operate random_subset %d"%(fnAngles,fnSplit,Nsplit),numberOfMpi=1)
fnVol=self._getExtraPath('split%05d.vol'%i)
args="-i %s -o %s --sym %s --weight"%(fnSplit,fnVol,self.symmetryGroup)
row=getFirstRow(fnAngles)
if row.containsLabel(xmipp.MDL_CTF_DEFOCUSU) or row.containsLabel(xmipp.MDL_CTF_MODEL):
TsCurrent=self.readInfoField(fnDirCurrent,"sampling",xmipp.MDL_SAMPLINGRATE)
args+=" --useCTF --sampling %f"%TsCurrent
if self.phaseFlipped:
args+=" --phaseFlipped"
self.runJob("xmipp_reconstruct_fourier",args,numberOfMpi=1)
self.runJob("xmipp_image_operate","-i %s --minus %s"%(fnVol,join(fnDirCurrent,"volume.vol")))
