def calcResolution(self, partlist, stackfile, apix):
### group particles by refnum
reflistsdict = {}
for partdict in partlist:
refnum = partdict['template']
partnum = partdict['num']
if not refnum in reflistsdict:
reflistsdict[refnum] = []
reflistsdict[refnum].append(partnum)
### get resolution
self.resdict = {}
boxsizetuple = apFile.getBoxSize(stackfile)
boxsize = boxsizetuple[0]
for refnum in reflistsdict.keys():
partlist = reflistsdict[refnum]
esttime = 3e-6 * len(partlist) * boxsize**2
apDisplay.printMsg("Ref num %d; %d parts; est time %s"
%(refnum, len(partlist), apDisplay.timeString(esttime)))
frcdata = apFourier.spectralSNRStack(stackfile, apix, partlist, msg=False)
frcfile = "frcplot-%03d.dat"%(refnum)
apFourier.writeFrcPlot(frcfile, frcdata, apix, boxsize)
res = apFourier.getResolution(frcdata, apix, boxsize)
self.resdict[refnum] = res
return
def calcResolution(self, partlist, stackfile, apix):
### group particles by refnum
reflistsdict = {}
for partdict in partlist:
refnum = partdict['template']
partnum = partdict['num']
if not refnum in reflistsdict:
reflistsdict[refnum] = []
reflistsdict[refnum].append(partnum)
### get resolution
self.resdict = {}
boxsizetuple = apFile.getBoxSize(stackfile)
boxsize = boxsizetuple[0]
for refnum in reflistsdict.keys():
partlist = reflistsdict[refnum]
esttime = 3e-6 * len(partlist) * boxsize**2
apDisplay.printMsg("Ref num %d; %d parts; est time %s"
%(refnum, len(partlist), apDisplay.timeString(esttime)))
frcdata = apFourier.spectralSNRStack(stackfile, apix, partlist, msg=False)
frcfile = "frcplot-%03d.dat"%(refnum)
apFourier.writeFrcPlot(frcfile, frcdata, apix, boxsize)
res = apFourier.getResolution(frcdata, apix, boxsize)
self.resdict[refnum] = res
return
def getResolutionFromGenericFSCFile(fscfile,
boxsize,
apix,
filtradius=3,
criterion=0.5,
msg=False):
"""
parses standard 2-column FSC file with 1) spatial frequency and 2) FRC, returns resolution
"""
if not os.path.isfile(fscfile):
apDisplay.printError("fsc file does not exist")
if msg is True:
apDisplay.printMsg("box: %d, apix: %.3f, file: %s" %
(boxsize, apix, fscfile))
f = open(fscfile, 'r')
fscfileinfo = f.readlines()
f.close()
fscdata = numpy.zeros((int(boxsize) / 2), dtype=numpy.float32)
for i, info in enumerate(fscfileinfo): # skip commented out lines
if info[0] == "#":
pass
else:
fscfileinfo = fscfileinfo[i:]
break
for j, info in enumerate(fscfileinfo):
frc = float(info.split()[1])
fscdata[j] = frc
res = apFourier.getResolution(fscdata,
apix,
boxsize,
filtradius=filtradius,
crit=criterion)
return res
def getResolutionFromGenericFSCFile(fscfile, boxsize, apix, filtradius=3, criterion=0.5, msg=False):
"""
parses standard 2-column FSC file with 1) spatial frequency and 2) FRC, returns resolution
"""
if not os.path.isfile(fscfile):
apDisplay.printError("fsc file does not exist")
if msg is True:
apDisplay.printMsg("box: %d, apix: %.3f, file: %s" % (boxsize, apix, fscfile))
f = open(fscfile, "r")
fscfileinfo = f.readlines()
f.close()
fscdata = numpy.zeros((int(boxsize) / 2), dtype=numpy.float32)
for i, info in enumerate(fscfileinfo): # skip commented out lines
if info[0] == "#":
pass
else:
fscfileinfo = fscfileinfo[i:]
break
for j, info in enumerate(fscfileinfo):
frc = float(info.split()[1])
fscdata[j] = frc
res = apFourier.getResolution(fscdata, apix, boxsize, filtradius=filtradius, crit=criterion)
return res
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")