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")))
def reconstruct(self):
iteration=1
fnDirCurrent=self._getExtraPath("Iter%03d"%iteration)
TsCurrent=self.readInfoField(fnDirCurrent,"sampling",xmipp.MDL_SAMPLINGRATE)
fnAngles=join(fnDirCurrent,"angles.xmd")
fnVol=join(fnDirCurrent,"volume.vol")
args="-i %s -o %s --sym %s --weight"%(fnAngles,fnVol,self.symmetryGroup)
row=getFirstRow(fnAngles)
if row.containsLabel(xmipp.MDL_CTF_DEFOCUSU) or row.containsLabel(xmipp.MDL_CTF_MODEL):
args+=" --useCTF --sampling %f"%TsCurrent
if self.phaseFlipped:
args+=" --phaseFlipped"
self.runJob("xmipp_reconstruct_fourier",args)
def reconstruct(self):
iteration = 1
fnDirCurrent = self._getExtraPath("Iter%03d" % iteration)
TsCurrent = self.readInfoField(fnDirCurrent, "sampling",
xmipp.MDL_SAMPLINGRATE)
fnAngles = join(fnDirCurrent, "angles.xmd")
fnVol = join(fnDirCurrent, "volume.vol")
args = "-i %s -o %s --sym %s --weight" % (fnAngles, fnVol,
self.symmetryGroup)
row = getFirstRow(fnAngles)
if row.containsLabel(xmipp.MDL_CTF_DEFOCUSU) or row.containsLabel(
xmipp.MDL_CTF_MODEL):
args += " --useCTF --sampling %f" % TsCurrent
if self.phaseFlipped:
args += " --phaseFlipped"
self.runJob("xmipp_reconstruct_fourier", args)
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")))
def globalAssignment(self):
iteration = 1
fnDirCurrent = self._getExtraPath("Iter%03d" % iteration)
makePath(fnDirCurrent)
fnGlobal = join(fnDirCurrent, "globalAssignment")
makePath(fnGlobal)
targetResolution = self.significantMaxResolution.get()
TsCurrent = max(self.TsOrig, targetResolution / 3)
self.prepareImages(fnGlobal, TsCurrent)
self.prepareReferences(fnGlobal, TsCurrent, targetResolution)
# Calculate angular step at this resolution
ResolutionAlignment = targetResolution
newXdim = self.readInfoField(fnGlobal, "size", xmipp.MDL_XSIZE)
angleStep = self.calculateAngStep(newXdim, TsCurrent,
ResolutionAlignment)
self.writeInfoField(fnGlobal, "angleStep", xmipp.MDL_ANGLE_DIFF,
float(angleStep))
# Significant alignment
alpha = 1 - 0.01 * self.significantSignificance.get()
fnDirSignificant = join(fnGlobal, "significant")
fnImgs = join(fnGlobal, "images.xmd")
makePath(fnDirSignificant)
# Create defocus groups
row = getFirstRow(fnImgs)
if row.containsLabel(xmipp.MDL_CTF_MODEL) or row.containsLabel(
xmipp.MDL_CTF_DEFOCUSU):
self.runJob("xmipp_ctf_group","--ctfdat %s -o %s/ctf:stk --pad 2.0 --sampling_rate %f --phase_flipped --error 0.1 --resol %f"%\
(fnImgs,fnDirSignificant,TsCurrent,targetResolution),numberOfMpi=1)
moveFile("%s/ctf_images.sel" % fnDirSignificant,
"%s/ctf_groups.xmd" % fnDirSignificant)
cleanPath("%s/ctf_split.doc" % fnDirSignificant)
md = xmipp.MetaData("numberGroups@%s" %
join(fnDirSignificant, "ctfInfo.xmd"))
fnCTFs = "%s/ctf_ctf.stk" % fnDirSignificant
numberGroups = md.getValue(xmipp.MDL_COUNT, md.firstObject())
ctfPresent = True
else:
numberGroups = 1
ctfPresent = False
# Generate projections
fnReferenceVol = join(fnGlobal, "volumeRef.vol")
fnGallery = join(fnDirSignificant, "gallery.stk")
fnGalleryMd = join(fnDirSignificant, "gallery.xmd")
args="-i %s -o %s --sampling_rate %f --sym %s --min_tilt_angle %f --max_tilt_angle %f"%\
(fnReferenceVol,fnGallery,angleStep,self.symmetryGroup,self.angularMinTilt.get(),self.angularMaxTilt.get())
self.runJob("xmipp_angular_project_library", args)
cleanPath(join(fnDirSignificant, "gallery_angles.doc"))
moveFile(join(fnDirSignificant, "gallery.doc"), fnGalleryMd)
fnAngles = join(fnGlobal, "anglesDisc.xmd")
for j in range(1, numberGroups + 1):
fnAnglesGroup = join(fnDirSignificant, "angles_group%02d.xmd" % j)
if not exists(fnAnglesGroup):
if ctfPresent:
fnGroup = "ctfGroup%06d@%s/ctf_groups.xmd" % (
j, fnDirSignificant)
fnGalleryGroup = join(fnDirSignificant,
"gallery_group%06d.stk" % j)
fnGalleryGroupMd = join(fnDirSignificant,
"gallery_group%06d.xmd" % j)
self.runJob("xmipp_transform_filter",
"-i %s -o %s --fourier binary_file %d@%s --save_metadata_stack %s --keep_input_columns"%\
(fnGalleryMd,fnGalleryGroup,j,fnCTFs,fnGalleryGroupMd))
else:
fnGroup = fnImgs
fnGalleryGroupMd = fnGalleryMd
args='-i %s --initgallery %s --odir %s --sym %s --iter 1 --alpha0 %f --alphaF %f --angularSampling %f --maxShift %d '\
'--minTilt %f --maxTilt %f --useImed --angDistance %f --dontReconstruct'%\
(fnGroup,fnGalleryGroupMd,fnDirSignificant,self.symmetryGroup,alpha,alpha,angleStep,\
round(self.angularMaxShift.get()*newXdim/100),self.angularMinTilt.get(),self.angularMaxTilt.get(),2*angleStep)
self.runJob('xmipp_reconstruct_significant',
args,
numberOfMpi=self.numberOfThreads.get())
moveFile(join(fnDirSignificant, "angles_iter001_00.xmd"),
join(fnDirSignificant, "angles_group%02d.xmd" % j))
self.runJob("rm -f",
fnDirSignificant + "/images_*iter00?_*.xmd",
numberOfMpi=1)
if j == 1:
copyFile(fnAnglesGroup, fnAngles)
else:
self.runJob("xmipp_metadata_utilities",
"-i %s --set union %s" %
(fnAngles, fnAnglesGroup),
numberOfMpi=1)
if ctfPresent:
self.runJob("rm -f", fnDirSignificant + "/gallery*", numberOfMpi=1)
def globalAssignment(self):
iteration=1
fnDirCurrent=self._getExtraPath("Iter%03d"%iteration)
makePath(fnDirCurrent)
fnGlobal=join(fnDirCurrent,"globalAssignment")
makePath(fnGlobal)
targetResolution=self.significantMaxResolution.get()
TsCurrent=max(self.TsOrig,targetResolution/3)
self.prepareImages(fnGlobal,TsCurrent)
self.prepareReferences(fnGlobal,TsCurrent,targetResolution)
# Calculate angular step at this resolution
ResolutionAlignment=targetResolution
newXdim=self.readInfoField(fnGlobal,"size",xmipp.MDL_XSIZE)
angleStep=self.calculateAngStep(newXdim, TsCurrent, ResolutionAlignment)
self.writeInfoField(fnGlobal,"angleStep",xmipp.MDL_ANGLE_DIFF,float(angleStep))
# Significant alignment
alpha=1-0.01*self.significantSignificance.get()
fnDirSignificant=join(fnGlobal,"significant")
fnImgs=join(fnGlobal,"images.xmd")
makePath(fnDirSignificant)
# Create defocus groups
row=getFirstRow(fnImgs)
if row.containsLabel(xmipp.MDL_CTF_MODEL) or row.containsLabel(xmipp.MDL_CTF_DEFOCUSU):
self.runJob("xmipp_ctf_group","--ctfdat %s -o %s/ctf:stk --pad 2.0 --sampling_rate %f --phase_flipped --error 0.1 --resol %f"%\
(fnImgs,fnDirSignificant,TsCurrent,targetResolution),numberOfMpi=1)
moveFile("%s/ctf_images.sel"%fnDirSignificant,"%s/ctf_groups.xmd"%fnDirSignificant)
cleanPath("%s/ctf_split.doc"%fnDirSignificant)
md = xmipp.MetaData("numberGroups@%s"%join(fnDirSignificant,"ctfInfo.xmd"))
fnCTFs="%s/ctf_ctf.stk"%fnDirSignificant
numberGroups=md.getValue(xmipp.MDL_COUNT,md.firstObject())
ctfPresent=True
else:
numberGroups=1
ctfPresent=False
# Generate projections
fnReferenceVol=join(fnGlobal,"volumeRef.vol")
fnGallery=join(fnDirSignificant,"gallery.stk")
fnGalleryMd=join(fnDirSignificant,"gallery.xmd")
args="-i %s -o %s --sampling_rate %f --sym %s --min_tilt_angle %f --max_tilt_angle %f"%\
(fnReferenceVol,fnGallery,angleStep,self.symmetryGroup,self.angularMinTilt.get(),self.angularMaxTilt.get())
self.runJob("xmipp_angular_project_library",args)
cleanPath(join(fnDirSignificant,"gallery_angles.doc"))
moveFile(join(fnDirSignificant,"gallery.doc"), fnGalleryMd)
fnAngles=join(fnGlobal,"anglesDisc.xmd")
for j in range(1,numberGroups+1):
fnAnglesGroup=join(fnDirSignificant,"angles_group%02d.xmd"%j)
if not exists(fnAnglesGroup):
if ctfPresent:
fnGroup="ctfGroup%06d@%s/ctf_groups.xmd"%(j,fnDirSignificant)
fnGalleryGroup=join(fnDirSignificant,"gallery_group%06d.stk"%j)
fnGalleryGroupMd=join(fnDirSignificant,"gallery_group%06d.xmd"%j)
self.runJob("xmipp_transform_filter",
"-i %s -o %s --fourier binary_file %d@%s --save_metadata_stack %s --keep_input_columns"%\
(fnGalleryMd,fnGalleryGroup,j,fnCTFs,fnGalleryGroupMd))
else:
fnGroup=fnImgs
fnGalleryGroupMd=fnGalleryMd
args='-i %s --initgallery %s --odir %s --sym %s --iter 1 --alpha0 %f --alphaF %f --angularSampling %f --maxShift %d '\
'--minTilt %f --maxTilt %f --useImed --angDistance %f --dontReconstruct'%\
(fnGroup,fnGalleryGroupMd,fnDirSignificant,self.symmetryGroup,alpha,alpha,angleStep,\
round(self.angularMaxShift.get()*newXdim/100),self.angularMinTilt.get(),self.angularMaxTilt.get(),2*angleStep)
self.runJob('xmipp_reconstruct_significant',args,numberOfMpi=self.numberOfThreads.get())
moveFile(join(fnDirSignificant,"angles_iter001_00.xmd"),join(fnDirSignificant,"angles_group%02d.xmd"%j))
self.runJob("rm -f",fnDirSignificant+"/images_*iter00?_*.xmd",numberOfMpi=1)
if j==1:
copyFile(fnAnglesGroup, fnAngles)
else:
self.runJob("xmipp_metadata_utilities","-i %s --set union %s"%(fnAngles,fnAnglesGroup),numberOfMpi=1)
if ctfPresent:
self.runJob("rm -f",fnDirSignificant+"/gallery*",numberOfMpi=1)