def projectInitialVolume(log,WorkingDir,InitialVolume,RemainingClasses,Xdim2,AngularSampling,SymmetryGroup):
fnOutputInitVolume=os.path.join(WorkingDir,"tmp/initialVolume.vol")
runJob(log,'xmipp_image_convert',"-i %s -o %s"%(removeFilenamePrefix(InitialVolume),fnOutputInitVolume))
runJob(log,"xmipp_image_resize","-i %s --dim %d %d"%(fnOutputInitVolume,Xdim2,Xdim2))
fnGallery=os.path.join(WorkingDir,'tmp/gallery_InitialVolume.stk')
runJob(log,"xmipp_angular_project_library", "-i %s -o %s --sampling_rate %f --sym %s --method fourier 1 0.25 bspline --compute_neighbors --angular_distance -1 --experimental_images %s"\
%(fnOutputInitVolume,fnGallery,float(AngularSampling),SymmetryGroup,RemainingClasses))
def defineSteps(self):
fnOutputClass=self.workingDirPath('classes.xmd')
self.insertStep('createDir',path=self.ExtraDir)
self.insertStep("linkAcquisitionInfo",InputFile=self.Classes,dirDest=self.WorkingDir)
if self.trueClass:
self.insertStep("copyFile",source=removeFilenamePrefix(self.Classes),dest=fnOutputClass)
else:
self.insertRunJobStep("xmipp_metadata_utilities","-i %s -o classes@%s"%(self.Classes,fnOutputClass),NumberOfMpi=1,NumberOfThreads=1)
# Projection Matching
fnAngles=self.extraPath('angles.xmd')
self.insertStep("projMatch",Volume=self.Volume,AngularSampling=self.AngularSampling,SymmetryGroup=self.SymmetryGroup,
Images="classes@%s"%fnOutputClass,ExtraDir=self.ExtraDir,fnAngles=fnAngles,NumberOfMpi=self.NumberOfMpi)
# Reorganize output and produce difference images
self.insertStep("runJob",programname="xmipp_metadata_utilities", params="-i classes@%s --set join %s --mode append"%(fnOutputClass,fnAngles),NumberOfMpi=1)
fnIn='classes@'+fnOutputClass
self.insertStep("produceAlignedImages",fnIn=fnIn, fnOut='classes_aligned@'+fnOutputClass, fnDiff=self.extraPath("diff.stk"),
volumeIsCTFCorrected=False)
self.insertStep("runJob",programname="xmipp_metadata_utilities", params="-i classes_aligned@%s --operate sort maxCC desc --mode append"%(fnOutputClass),NumberOfMpi=1)
self.insertStep("runJob",programname="xmipp_metadata_utilities", params="-i classes_aligned@%s --set join %s image --mode append"%(fnOutputClass,fnIn),NumberOfMpi=1)
