def calcResolution(self, level):
self.resdict = {}
D=self.getClassificationAtLevel(level)
for classref in D:
stack=[]
for partnum in D[classref]:
stack.append(apImagicFile.readSingleParticleFromStack("alignedStack.hed",int(partnum)+1,msg=False))
apImagicFile.writeImagic(stack,"tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def calcResolution(self, level):
self.resdict = {}
D=self.getClassificationAtLevel(level)
for classref in D:
stack=[]
for partnum in D[classref]:
stack.append(apImagicFile.readSingleParticleFromStack("alignedStack.hed",int(partnum)+1,msg=False))
apImagicFile.writeImagic(stack,"tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def calcResolution(self, level):
self.resdict = {}
D=self.getClassificationAtLevel(level)
for classref in D:
stack=[]
for partnum in D[classref]:
### NOTE: RESOLUTION WILL NOT BE CALCULATED IF ALIGNED STACK IS NOT CREATED
stack.append(apImagicFile.readSingleParticleFromStack(self.params['timestamp']+".hed",int(partnum),msg=False))
apImagicFile.writeImagic(stack,"tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def calcResolution(self, level):
self.resdict = {}
D=self.getClassificationAtLevel(level)
for classref in D:
stack=[]
for partnum in D[classref]:
### NOTE: RESOLUTION WILL NOT BE CALCULATED IF ALIGNED STACK IS NOT CREATED
stack.append(apImagicFile.readSingleParticleFromStack(self.params['timestamp']+".hed",int(partnum),msg=False))
apImagicFile.writeImagic(stack,"tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def calcResolution(self, alignedStack):
self.resdict = {}
for classref, partlist in self.classD.iteritems():
if len(partlist) == 0:
continue
stack=[]
for partnum in partlist:
### NOTE: RESOLUTION WILL NOT BE CALCULATED IF ALIGNED STACK IS NOT CREATED
stack.append(apImagicFile.readSingleParticleFromStack(alignedStack,int(partnum),msg=False))
apImagicFile.writeImagic(stack,"tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def calcResolution(self, alignedStack):
self.resdict = {}
for classref, partlist in self.classD.iteritems():
if len(partlist) == 0:
continue
stack = []
for partnum in partlist:
### NOTE: RESOLUTION WILL NOT BE CALCULATED IF ALIGNED STACK IS NOT CREATED
stack.append(
apImagicFile.readSingleParticleFromStack(alignedStack,
int(partnum),
msg=False))
apImagicFile.writeImagic(stack, "tmp.hed")
frcdata = apFourier.spectralSNRStack("tmp.hed", self.apix)
self.resdict[classref] = apFourier.getResolution(
frcdata, self.apix, self.boxsize)
apFile.removeStack("tmp.hed")
def makeNewStacks(self, parttree):
### untilted stack
self.notstackdata = apStack.getOnlyStackData(self.params['notstackid'])
notstackfile = os.path.join(self.notstackdata['path']['path'], self.notstackdata['name'])
### tilted stack
if not self.tiltstackdata:
self.tiltstackdata = apStack.getOnlyStackData(self.params['tiltstackid'])
tiltstackfile = os.path.join(self.tiltstackdata['path']['path'], self.tiltstackdata['name'])
### make doc file of Euler angles
#eulerfile = self.makeEulerDoc(parttree)
eulerfile = os.path.join(self.params['rundir'], "eulersdoc"+self.timestamp+".spi")
if os.path.isfile(eulerfile):
apFile.removeFile(eulerfile)
count = 0
notstacklist = []
tiltstacklist = []
sizelimit = 2048
notbox = apImagicFile.getBoxsize(notstackfile)
tiltbox = apImagicFile.getBoxsize(tiltstackfile)
tiltstacks = []
notstacks = []
t0 = time.time()
for partdict in parttree:
### print friendly message
if count % 100 == 0:
backs = "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"
sys.stderr.write(backs+backs+backs+backs)
if count > sizelimit:
esttime = (len(parttree)/float(count)-1.0)*(time.time()-t0)
sys.stderr.write(str(count)+" particles of "+str(len(parttree))
+", "+apDisplay.timeString(esttime)+" remaining")
else:
sys.stderr.write(str(count)+" particles of "+str(len(parttree)))
### save stacks to file to save memory
if count%sizelimit == 0:
if count > 1:
apDisplay.printMsg("Writing stacks to file")
t1 = time.time()
tiltname = os.path.join(self.params['rundir'], "tiltstack%d.hed"%(count))
apFile.removeStack(tiltname)
apImagicFile.writeImagic(tiltstacklist, tiltname, msg=False)
tiltstacks.append(tiltname)
apDisplay.printMsg("finished tilted stack in "+apDisplay.timeString(time.time()-t1))
t1 = time.time()
notname = os.path.join(self.params['rundir'], "notstack%d.hed"%(count))
apFile.removeStack(notname)
apImagicFile.writeImagic(notstacklist, notname, msg=False)
notstacks.append(notname)
apDisplay.printMsg("finished untilted stack in "+apDisplay.timeString(time.time()-t1))
### reset stacks
apDisplay.printMsg("Reset stacks in memory")
notstacklist = []
tiltstacklist = []
### increment count
count += 1
### write to Euler doc
self.appendEulerDoc(eulerfile, partdict['tilt'], count)
### untilted stack
notpartarray = apImagicFile.readSingleParticleFromStack(notstackfile, partdict['not'], notbox, False)
notstacklist.append(notpartarray)
### tilted stack
tiltpartarray = apImagicFile.readSingleParticleFromStack(tiltstackfile, partdict['tilt'], tiltbox, False)
tiltstacklist.append(tiltpartarray)
### write remaining particles to stack
if len(notstacklist) > 0:
apDisplay.printMsg("Writing stacks to file")
t1 = time.time()
tiltname = os.path.join(self.params['rundir'], "tiltstack%d.hed"%(count))
apFile.removeStack(tiltname)
apImagicFile.writeImagic(tiltstacklist, tiltname, msg=False)
tiltstacks.append(tiltname)
apDisplay.printMsg("finished tilted stack in "+apDisplay.timeString(time.time()-t1))
t1 = time.time()
notname = os.path.join(self.params['rundir'], "notstack%d.hed"%(count))
apFile.removeStack(notname)
apImagicFile.writeImagic(notstacklist, notname, msg=False)
notstacks.append(notname)
apDisplay.printMsg("finished untilted stack in "+apDisplay.timeString(time.time()-t1))
### merge NOT stack
notname = os.path.join(self.params['rundir'], "notstack.hed")
apImagicFile.mergeStacks(notstacks, notname)
for stackname in notstacks:
apFile.removeStack(stackname, warn=False)
### merge TILT stack
tiltname = os.path.join(self.params['rundir'], "tiltstack.hed")
apImagicFile.mergeStacks(tiltstacks, tiltname)
for stackname in tiltstacks:
apFile.removeStack(stackname, warn=False)
### upload results
if self.params['commit'] is True:
self.uploadResults()
