def setupVolumes(self, boxsize, apix):
voldocfile = "volumelist"+self.timestamp+".doc"
f = open(voldocfile, "w")
if self.params['modelstr'] is not None:
for i, modelid in enumerate(self.params['modelids']):
### Scale volume
mrcvolfile = os.path.join(self.params['rundir'], "volume%s_%02d_%05d.mrc"%(self.timestamp, i+1, modelid))
apModel.rescaleModel(modelid, mrcvolfile, boxsize, apix)
### Convert volume to spider
spivolfile = os.path.join(self.params['rundir'], "volume%s_%02d_%05d.spi"%(self.timestamp, i+1, modelid))
emancmd = "proc3d %s %s spidersingle"%(mrcvolfile, spivolfile)
apEMAN.executeEmanCmd(emancmd, verbose=False)
### Normalize volume
normalvolfile = self.normalizeVolume(spivolfile)
### Write to selection file
f.write(normalvolfile+" 1\n")
else:
for i in range(self.params['nvol']):
### Create Gaussian sphere
spivolfile = os.path.join(self.params['rundir'], "volume%s_%02d.spi"%(self.timestamp, i+1))
self.createGaussianSphere(spivolfile, boxsize)
### Normalize volume
normalvolfile = self.normalizeVolume(spivolfile)
### Write to selection file
f.write(normalvolfile+" 1\n")
f.close()
return voldocfile
def setupVolumes(self, boxsize, apix): voldocfile = "volumelist"+self.timestamp+".doc" f = open(voldocfile, "w") if self.params['modelstr'] is not None: for i, modelid in enumerate(self.params['modelids']): ### Scale volume mrcvolfile = os.path.join(self.params['rundir'], "volume%s_%02d_%05d.mrc"%(self.timestamp, i+1, modelid)) apModel.rescaleModel(modelid, mrcvolfile, boxsize, apix) ### Convert volume to spider spivolfile = os.path.join(self.params['rundir'], "volume%s_%02d_%05d.spi"%(self.timestamp, i+1, modelid)) emancmd = "proc3d %s %s spidersingle"%(mrcvolfile, spivolfile) apEMAN.executeEmanCmd(emancmd, verbose=False) ### Normalize volume normalvolfile = self.normalizeVolume(spivolfile) ### Write to selection file f.write(normalvolfile+" 1\n") else: for i in range(self.params['nvol']): ### Create Gaussian sphere spivolfile = os.path.join(self.params['rundir'], "volume%s_%02d.spi"%(self.timestamp, i+1)) self.createGaussianSphere(spivolfile, boxsize) ### Normalize volume normalvolfile = self.normalizeVolume(spivolfile) ### Write to selection file f.write(normalvolfile+" 1\n") f.close() return voldocfile
def start(self):
self.stack = {}
self.stack['data'] = apStack.getOnlyStackData(self.params['stackid'])
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(self.params['stackid'])
self.stack['boxsize'] = apStack.getStackBoxsize(self.params['stackid'])
self.stack['file'] = os.path.join(self.stack['data']['path']['path'], self.stack['data']['name'])
# symmetry info
if self.params['sym']=='Icos':
self.params['symtype']='I'
self.params['symfold']=None
else:
self.params['symtype']=self.params['sym'][0]
self.params['symfold']=int(self.params['sym'][1:])
# eman "d" symmetry is spider "ci"
if self.params['symtype'].upper()=="D":
self.params['symtype'] = "CI"
# create symmetry doc file
sydoc="sym.spi"
refine.symmetryDoc(self.params['symtype'],self.params['symfold'],sydoc)
# convert incr to array of increments
ang_inc=self.params['incr'].split(',')
self.params['numiter'] = len(ang_inc)
self.params['increments']=[]
for i in range(0,self.params['numiter']):
self.params['increments'].append(int(ang_inc[i]))
# convert stack to spider stack
spiderstack=os.path.join(self.params['rundir'],'start.spi')
operations.stackToSpiderStack(
self.stack['file'],
spiderstack,
apix=self.stack['apix'],
boxsize=self.stack['boxsize'],
numpart=self.params['numpart']
)
# create filtered stack
spiderstackfilt=spiderstack
if (self.params['lowpass']+self.params['highpass']) > 0:
spiderstackfilt=os.path.join(self.params['rundir'],'start_filt.spi')
operations.stackToSpiderStack(
self.stack['file'],
spiderstackfilt,
apix=self.stack['apix'],
boxsize=self.stack['boxsize'],
lp=self.params['lowpass'],
hp=self.params['highpass'],
numpart=self.params['numpart']
)
# rescale initial model if necessary
outvol = os.path.join(self.params['rundir'],"vol000.spi")
apModel.rescaleModel(self.params['modelid'], outvol, self.stack['boxsize'], self.stack['apix'], spider=True)
self.params['itervol']=outvol
for iter in range(1,self.params['numiter']+1):
# create projections for projection matching
apDisplay.printMsg("creating reference projections of volume: %s" % self.params['itervol'])
projs,numprojs,ang,sel = refine.createProjections(
incr=self.params['increments'][iter-1],
boxsz=self.stack['boxsize'],
symfold=self.params['symfold'],
invol=self.params['itervol'],
rad=self.params['rad'],
)
# run reference-based alignment
apDisplay.printMsg("running reference-based alignment (AP MQ)")
apmqfile = "apmq%03d.spi" % iter
outang = "angular%03d.spi" % iter
shf = "shifts%03d.spi" % iter
shiftedStack="parts_shifted.spi"
apFile.removeFile(shf)
refine.spiderAPMQ(
projs=projs,
numprojs=numprojs,
tsearch=self.params['xysearch'],
tstep=self.params['xystep'],
firstRing=self.params['firstring'],
lastRing=self.params['lastring'],
stackfile=spiderstackfilt,
nump=self.params['numpart'],
ang=ang,
apmqfile=apmqfile,
outang=outang,
nproc=self.params['proc'],
)
# use cross-correlation to find the sub-pixel alignment
# of the particles,
# results will be saved in "peakfile.spi"
apFile.removeFile(shiftedStack)
# don't use MPI here - for some reason slower?
mySpi=spyder.SpiderSession(dataext=".spi", logo=False, log=False)
apmqlist = refine.readDocFile(apmqfile)
avgccrot = 0
apDisplay.printMsg("creating shifted stack")
for p in range(0,self.params['numpart']):
ref=int(float(apmqlist[p][2]))
ccrot=float(apmqlist[p][3])
inplane=float(apmqlist[p][4])
avgccrot+=ccrot
# invert the sign - ref projs will be rotated
inplane*=-1
# get corresponding projection
if (ref <= 0):
# mirror projection if necessary
ref*=-1
refimg=spyder.fileFilter(projs)+"@"+str(ref)
refine.mirrorImg(refimg,"_3",inMySpi=mySpi)
img="_3"
else:
img=spyder.fileFilter(projs)+"@"+str(ref)
refine.rotAndShiftImg(img,"_2",inplane,inMySpi=mySpi)
refine.maskImg("_2","_3",self.params['rad'],"D","E",
center=int((self.stack['boxsize']/2)+1),
inMySpi=mySpi)
# pad ref image & stack image to twice the size
refine.padImg("_3","_2",2*self.stack['boxsize'],"N",1,1,0,inMySpi=mySpi)
stackimg=spyder.fileFilter(spiderstack)+"@"+str(p+1)
refine.padImg(stackimg,"_1",2*self.stack['boxsize'],"B",1,1,inMySpi=mySpi)
# calculate cross-correlation
refine.getCC("_1","_2","_1",inMySpi=mySpi)
# crop the correllation image to allowable shift amount
shift=int(self.params['allowedShift']*self.stack['boxsize'])
dim=2*shift+1
topleftx=self.stack['boxsize']-shift+1
refine.windowImg("_1","_2",dim,topleftx,topleftx,inMySpi=mySpi)
# find the sub-pixel location of cc peak
mySpi.toSpiderQuiet("PK x11,x12,x13,x14,x15,x16,x17","_2","0")
# create new stack of shifted particles
shpos=spyder.fileFilter(shiftedStack)+"@"+str(p+1)
mySpi.toSpiderQuiet("IF(x17.EQ.0.0) THEN")
mySpi.toSpiderQuiet("GP x17","_2",str(shift+1)+","+str(shift+1))
refine.copyImg(stackimg,shpos,inMySpi=mySpi)
mySpi.toSpiderQuiet("ELSE")
#mySpi.toSpiderQuiet("RT SQ",stackimg,shpos,inplane*-1,"-x15,-x16")
mySpi.toSpiderQuiet("SH F",stackimg,shpos,"-x15,-x16")
mySpi.toSpiderQuiet("ENDIF")
# save shifts to file
mySpi.toSpiderQuiet("SD "+str(p+1)+",x15,x16,x17",spyder.fileFilter(shf))
mySpi.toSpiderQuiet("SD E",spyder.fileFilter(shf))
mySpi.close()
# create class average images
refine.createClassAverages(
shiftedStack,
projs,
apmqfile,
numprojs,
self.stack['boxsize'],
shifted=True,
)
# rename class averages & variacnes for iteration
cmd="/bin/mv classes.hed classes.%d.hed;" % iter
cmd+="/bin/mv classes.img classes.%d.img;" % iter
cmd+="/bin/mv variances.hed variances.%d.hed;" % iter
cmd+="/bin/mv variances.img variances.%d.img;" % iter
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
# calculate the stddev for the apmq cc's for throwing out particles
avgccrot/=self.params['numpart']
stdccrot = 0
for p in range(0,self.params['numpart']):
stdccrot+=abs(float(apmqlist[p][3])-avgccrot)
stdccrot/=self.params['numpart']
cccutoff=avgccrot+(stdccrot*self.params['keepsig'])
apDisplay.printMsg("average cc: %f" %avgccrot)
apDisplay.printMsg("setting cutoff to: %f" %cccutoff)
# create new selection file that only has particles with good cc's
selectfile="select%03d.spi" % iter
apFile.removeFile(selectfile)
mySpi = spyder.SpiderSession(nproc=self.params['proc'],dataext=".spi", logo=False, log=False)
i=1
for p in range(0,self.params['numpart']):
ccrot=float(apmqlist[p][3])
if ccrot>=cccutoff:
mySpi.toSpiderQuiet("x11=%d" % (p+1))
mySpi.toSpiderQuiet("SD %d,x11" % i,spyder.fileFilter(selectfile))
i+=1
mySpi.close()
# calculate the new 3d structure using centered projections
# and the corrected angles from the angular doc file
apDisplay.printMsg("creating 3d volume")
out_rawvol="vol_raw%03d.spi" % iter
if self.params['voliter'] is not None:
refine.iterativeBackProjection(
shiftedStack,
selectfile,
rad=self.params['rad'],
ang=outang,
out=out_rawvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['bpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc'],
)
else:
refine.backProjection(
shiftedStack,
selectfile,
ang=outang,
out=out_rawvol,
sym=sydoc,
nproc=self.params['proc']
)
# create even & odd select files
apDisplay.printMsg("creating even/odd volumes")
oddfile="selectodd%03d.spi" % iter
evenfile="selecteven%03d.spi" % iter
refine.docSplit(selectfile,oddfile,evenfile)
# get the even & odd volumesa
oddvol="vol1%03d.spi" % iter
evenvol="vol2%03d.spi" % iter
if self.params['voliter'] is not None:
refine.iterativeBackProjection(
shiftedStack,
oddfile,
rad=self.params['rad'],
ang=outang,
out=oddvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['eobpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc']
)
refine.iterativeBackProjection(
shiftedStack,
evenfile,
rad=self.params['rad'],
ang=outang,
out=evenvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['eobpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc']
)
else:
refine.backProjection(
shiftedStack,
oddfile,
ang=outang,
out=oddvol,
sym=sydoc,
nproc=self.params['proc'],
)
refine.backProjection(
shiftedStack,
evenfile,
ang=outang,
out=evenvol,
sym=sydoc,
nproc=self.params['proc'],
)
# calculate the FSC
apDisplay.printMsg("calculating FSC")
fscfile="fsc%03d.spi" % iter
emanfsc="fsc.eotest.%d" % iter
refine.calcFSC(oddvol,evenvol,fscfile)
# convert to eman-style fscfile
refine.spiderFSCtoEMAN(fscfile,emanfsc)
# calculate the resolution at 0.5 FSC & write to file
res=apRecon.calcRes(emanfsc,self.stack['boxsize'],self.stack['apix'])
restxt="resolution.txt"
if iter==1 and os.path.isfile(restxt):
os.remove(restxt)
resfile=open(restxt,"a")
resfile.write("iter %d:\t%.3f\n" % (iter,res))
resfile.close()
# filter & normalize the volume to be used as a reference in the next round
outvol="vol%03d.spi" % iter
emancmd="proc3d %s %s apix=%.3f lp=%.3f mask=%d norm spidersingle" % (out_rawvol,outvol,self.stack['apix'],res,self.params['rad'])
if self.params['imask'] is not None:
emancmd+=" imask=%d" % self.params['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
# create mrc files of volumes
emancmd="proc3d %s %s apix=%.3f mask=%d norm" % (out_rawvol,"threed.%da.mrc" % iter, self.stack['apix'],self.params['rad'])
if self.params['imask'] is not None:
emancmd+=" imask=%d" % self.params['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
emancmd="proc3d %s %s apix=%.3f lp=%.3f mask=%d norm" % (out_rawvol,"threed.%da.lp.mrc" % iter, self.stack['apix'],res, self.params['rad'])
if self.params['imask'] is not None:
emancmd+=" imask=%d" % self.param['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
# set this model as start for next iteration, remove previous
os.remove(self.params['itervol'])
os.remove(out_rawvol)
self.params['itervol']=outvol
# clean up directory
apDisplay.printMsg("cleaning up directory")
if os.path.isfile(oddvol):
os.remove(oddvol)
if os.path.isfile(evenvol):
os.remove(evenvol)
if os.path.isfile(ang):
os.remove(ang)
if os.path.isfile(sel):
os.remove(sel)
if os.path.isfile(projs):
os.remove(projs)
if os.path.isfile(oddfile):
os.remove(oddfile)
if os.path.isfile(evenfile):
os.remove(evenfile)
if os.path.isfile(emanfsc) and os.path.isfile(fscfile):
os.remove(fscfile)
if os.path.isfile(shiftedStack):
os.remove(shiftedStack)
os.remove(self.params['itervol'])
def start(self):
self.stack = {}
self.stack['data'] = apStack.getOnlyStackData(self.params['stackid'])
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(
self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(
self.params['stackid'])
self.stack['boxsize'] = apStack.getStackBoxsize(self.params['stackid'])
self.stack['file'] = os.path.join(self.stack['data']['path']['path'],
self.stack['data']['name'])
# symmetry info
if self.params['sym'] == 'Icos':
self.params['symtype'] = 'I'
self.params['symfold'] = None
else:
self.params['symtype'] = self.params['sym'][0]
self.params['symfold'] = int(self.params['sym'][1:])
# eman "d" symmetry is spider "ci"
if self.params['symtype'].upper() == "D":
self.params['symtype'] = "CI"
# create symmetry doc file
sydoc = "sym.spi"
refine.symmetryDoc(self.params['symtype'], self.params['symfold'],
sydoc)
# convert incr to array of increments
ang_inc = self.params['incr'].split(',')
self.params['numiter'] = len(ang_inc)
self.params['increments'] = []
for i in range(0, self.params['numiter']):
self.params['increments'].append(int(ang_inc[i]))
# convert stack to spider stack
spiderstack = os.path.join(self.params['rundir'], 'start.spi')
operations.stackToSpiderStack(self.stack['file'],
spiderstack,
apix=self.stack['apix'],
boxsize=self.stack['boxsize'],
numpart=self.params['numpart'])
# create filtered stack
spiderstackfilt = spiderstack
if (self.params['lowpass'] + self.params['highpass']) > 0:
spiderstackfilt = os.path.join(self.params['rundir'],
'start_filt.spi')
operations.stackToSpiderStack(self.stack['file'],
spiderstackfilt,
apix=self.stack['apix'],
boxsize=self.stack['boxsize'],
lp=self.params['lowpass'],
hp=self.params['highpass'],
numpart=self.params['numpart'])
# rescale initial model if necessary
outvol = os.path.join(self.params['rundir'], "vol000.spi")
apModel.rescaleModel(self.params['modelid'],
outvol,
self.stack['boxsize'],
self.stack['apix'],
spider=True)
self.params['itervol'] = outvol
for iter in range(1, self.params['numiter'] + 1):
# create projections for projection matching
apDisplay.printMsg("creating reference projections of volume: %s" %
self.params['itervol'])
projs, numprojs, ang, sel = refine.createProjections(
incr=self.params['increments'][iter - 1],
boxsz=self.stack['boxsize'],
symfold=self.params['symfold'],
invol=self.params['itervol'],
rad=self.params['rad'],
)
# run reference-based alignment
apDisplay.printMsg("running reference-based alignment (AP MQ)")
apmqfile = "apmq%03d.spi" % iter
outang = "angular%03d.spi" % iter
shf = "shifts%03d.spi" % iter
shiftedStack = "parts_shifted.spi"
apFile.removeFile(shf)
refine.spiderAPMQ(
projs=projs,
numprojs=numprojs,
tsearch=self.params['xysearch'],
tstep=self.params['xystep'],
firstRing=self.params['firstring'],
lastRing=self.params['lastring'],
stackfile=spiderstackfilt,
nump=self.params['numpart'],
ang=ang,
apmqfile=apmqfile,
outang=outang,
nproc=self.params['proc'],
)
# use cross-correlation to find the sub-pixel alignment
# of the particles,
# results will be saved in "peakfile.spi"
apFile.removeFile(shiftedStack)
# don't use MPI here - for some reason slower?
mySpi = spyder.SpiderSession(dataext=".spi", logo=False, log=False)
apmqlist = refine.readDocFile(apmqfile)
avgccrot = 0
apDisplay.printMsg("creating shifted stack")
for p in range(0, self.params['numpart']):
ref = int(float(apmqlist[p][2]))
ccrot = float(apmqlist[p][3])
inplane = float(apmqlist[p][4])
avgccrot += ccrot
# invert the sign - ref projs will be rotated
inplane *= -1
# get corresponding projection
if (ref <= 0):
# mirror projection if necessary
ref *= -1
refimg = spyder.fileFilter(projs) + "@" + str(ref)
refine.mirrorImg(refimg, "_3", inMySpi=mySpi)
img = "_3"
else:
img = spyder.fileFilter(projs) + "@" + str(ref)
refine.rotAndShiftImg(img, "_2", inplane, inMySpi=mySpi)
refine.maskImg("_2",
"_3",
self.params['rad'],
"D",
"E",
center=int((self.stack['boxsize'] / 2) + 1),
inMySpi=mySpi)
# pad ref image & stack image to twice the size
refine.padImg("_3",
"_2",
2 * self.stack['boxsize'],
"N",
1,
1,
0,
inMySpi=mySpi)
stackimg = spyder.fileFilter(spiderstack) + "@" + str(p + 1)
refine.padImg(stackimg,
"_1",
2 * self.stack['boxsize'],
"B",
1,
1,
inMySpi=mySpi)
# calculate cross-correlation
refine.getCC("_1", "_2", "_1", inMySpi=mySpi)
# crop the correllation image to allowable shift amount
shift = int(self.params['allowedShift'] *
self.stack['boxsize'])
dim = 2 * shift + 1
topleftx = self.stack['boxsize'] - shift + 1
refine.windowImg("_1",
"_2",
dim,
topleftx,
topleftx,
inMySpi=mySpi)
# find the sub-pixel location of cc peak
mySpi.toSpiderQuiet("PK x11,x12,x13,x14,x15,x16,x17", "_2",
"0")
# create new stack of shifted particles
shpos = spyder.fileFilter(shiftedStack) + "@" + str(p + 1)
mySpi.toSpiderQuiet("IF(x17.EQ.0.0) THEN")
mySpi.toSpiderQuiet("GP x17", "_2",
str(shift + 1) + "," + str(shift + 1))
refine.copyImg(stackimg, shpos, inMySpi=mySpi)
mySpi.toSpiderQuiet("ELSE")
#mySpi.toSpiderQuiet("RT SQ",stackimg,shpos,inplane*-1,"-x15,-x16")
mySpi.toSpiderQuiet("SH F", stackimg, shpos, "-x15,-x16")
mySpi.toSpiderQuiet("ENDIF")
# save shifts to file
mySpi.toSpiderQuiet("SD " + str(p + 1) + ",x15,x16,x17",
spyder.fileFilter(shf))
mySpi.toSpiderQuiet("SD E", spyder.fileFilter(shf))
mySpi.close()
# create class average images
refine.createClassAverages(
shiftedStack,
projs,
apmqfile,
numprojs,
self.stack['boxsize'],
shifted=True,
)
# rename class averages & variacnes for iteration
cmd = "/bin/mv classes.hed classes.%d.hed;" % iter
cmd += "/bin/mv classes.img classes.%d.img;" % iter
cmd += "/bin/mv variances.hed variances.%d.hed;" % iter
cmd += "/bin/mv variances.img variances.%d.img;" % iter
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
# calculate the stddev for the apmq cc's for throwing out particles
avgccrot /= self.params['numpart']
stdccrot = 0
for p in range(0, self.params['numpart']):
stdccrot += abs(float(apmqlist[p][3]) - avgccrot)
stdccrot /= self.params['numpart']
cccutoff = avgccrot + (stdccrot * self.params['keepsig'])
apDisplay.printMsg("average cc: %f" % avgccrot)
apDisplay.printMsg("setting cutoff to: %f" % cccutoff)
# create new selection file that only has particles with good cc's
selectfile = "select%03d.spi" % iter
apFile.removeFile(selectfile)
mySpi = spyder.SpiderSession(nproc=self.params['proc'],
dataext=".spi",
logo=False,
log=False)
i = 1
for p in range(0, self.params['numpart']):
ccrot = float(apmqlist[p][3])
if ccrot >= cccutoff:
mySpi.toSpiderQuiet("x11=%d" % (p + 1))
mySpi.toSpiderQuiet("SD %d,x11" % i,
spyder.fileFilter(selectfile))
i += 1
mySpi.close()
# calculate the new 3d structure using centered projections
# and the corrected angles from the angular doc file
apDisplay.printMsg("creating 3d volume")
out_rawvol = "vol_raw%03d.spi" % iter
if self.params['voliter'] is not None:
refine.iterativeBackProjection(
shiftedStack,
selectfile,
rad=self.params['rad'],
ang=outang,
out=out_rawvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['bpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc'],
)
else:
refine.backProjection(shiftedStack,
selectfile,
ang=outang,
out=out_rawvol,
sym=sydoc,
nproc=self.params['proc'])
# create even & odd select files
apDisplay.printMsg("creating even/odd volumes")
oddfile = "selectodd%03d.spi" % iter
evenfile = "selecteven%03d.spi" % iter
refine.docSplit(selectfile, oddfile, evenfile)
# get the even & odd volumesa
oddvol = "vol1%03d.spi" % iter
evenvol = "vol2%03d.spi" % iter
if self.params['voliter'] is not None:
refine.iterativeBackProjection(
shiftedStack,
oddfile,
rad=self.params['rad'],
ang=outang,
out=oddvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['eobpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc'])
refine.iterativeBackProjection(
shiftedStack,
evenfile,
rad=self.params['rad'],
ang=outang,
out=evenvol,
lam=self.params['lambda'],
iterlimit=self.params['voliter'],
mode=self.params['eobpmode'],
smoothfac=self.params['smoothfac'],
sym=sydoc,
nproc=self.params['proc'])
else:
refine.backProjection(
shiftedStack,
oddfile,
ang=outang,
out=oddvol,
sym=sydoc,
nproc=self.params['proc'],
)
refine.backProjection(
shiftedStack,
evenfile,
ang=outang,
out=evenvol,
sym=sydoc,
nproc=self.params['proc'],
)
# calculate the FSC
apDisplay.printMsg("calculating FSC")
fscfile = "fsc%03d.spi" % iter
emanfsc = "fsc.eotest.%d" % iter
refine.calcFSC(oddvol, evenvol, fscfile)
# convert to eman-style fscfile
refine.spiderFSCtoEMAN(fscfile, emanfsc)
# calculate the resolution at 0.5 FSC & write to file
res = apRecon.calcRes(emanfsc, self.stack['boxsize'],
self.stack['apix'])
restxt = "resolution.txt"
if iter == 1 and os.path.isfile(restxt):
os.remove(restxt)
resfile = open(restxt, "a")
resfile.write("iter %d:\t%.3f\n" % (iter, res))
resfile.close()
# filter & normalize the volume to be used as a reference in the next round
outvol = "vol%03d.spi" % iter
emancmd = "proc3d %s %s apix=%.3f lp=%.3f mask=%d norm spidersingle" % (
out_rawvol, outvol, self.stack['apix'], res,
self.params['rad'])
if self.params['imask'] is not None:
emancmd += " imask=%d" % self.params['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
# create mrc files of volumes
emancmd = "proc3d %s %s apix=%.3f mask=%d norm" % (
out_rawvol, "threed.%da.mrc" % iter, self.stack['apix'],
self.params['rad'])
if self.params['imask'] is not None:
emancmd += " imask=%d" % self.params['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
emancmd = "proc3d %s %s apix=%.3f lp=%.3f mask=%d norm" % (
out_rawvol, "threed.%da.lp.mrc" % iter, self.stack['apix'],
res, self.params['rad'])
if self.params['imask'] is not None:
emancmd += " imask=%d" % self.param['imask']
apEMAN.executeEmanCmd(emancmd, verbose=True)
# set this model as start for next iteration, remove previous
os.remove(self.params['itervol'])
os.remove(out_rawvol)
self.params['itervol'] = outvol
# clean up directory
apDisplay.printMsg("cleaning up directory")
if os.path.isfile(oddvol):
os.remove(oddvol)
if os.path.isfile(evenvol):
os.remove(evenvol)
if os.path.isfile(ang):
os.remove(ang)
if os.path.isfile(sel):
os.remove(sel)
if os.path.isfile(projs):
os.remove(projs)
if os.path.isfile(oddfile):
os.remove(oddfile)
if os.path.isfile(evenfile):
os.remove(evenfile)
if os.path.isfile(emanfsc) and os.path.isfile(fscfile):
os.remove(fscfile)
if os.path.isfile(shiftedStack):
os.remove(shiftedStack)
os.remove(self.params['itervol'])
