def projMatchRefine(self, volfile, alignstack, boxsize, numpart, pixrad, iternum):
APSHout, projstack, numprojs = backprojectPWL.alignAPSH(volfile, alignstack, boxsize, numpart, pixrad, self.timestamp, iternum)
### check APSH output
if (os.path.isfile(APSHout) is False):
apDisplay.printError("AP SH alignment did not generate a valid output file. Please check parameters and rerun!")
apsh = open(APSHout, "r")
neweulerdoc = os.path.join(self.params['rundir'],"newEulersdoc-%03d.spi"%(iternum))
neweulerfile = open(neweulerdoc, "w")
rotshiftdoc = os.path.join(self.params['rundir'],"rotShiftdoc-%03d.spi"%(iternum))
rotshiftfile = open(rotshiftdoc, "w")
starttime = time.time()
count = 0
for line in apsh.readlines():
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
continue
key = int(float(value[6]))
rot = float(value[7])
cumX = float(value[14]) #float(value[8])
cumY = float(value[15]) #float(value[9])
psi = float(value[2])
theta = float(value[3])
phi = float(value[4])
mirror = int(float(value[16]))
### write out new euler file
eulerline = operations.spiderOutLine(key, [psi, theta, phi])
neweulerfile.write(eulerline)
### write out new rotate-shift-mirror file
rotshiftline = operations.spiderOutLine(key, [key, rot, 1.00, cumX, cumY, mirror])
rotshiftfile.write(rotshiftline)
count+=1
#if (count%20) == 0:
# apDisplay.printColor(str(numpart-count)+" particles left", "cyan")
# apDisplay.printColor("Estimated time left is "+apDisplay.timeString(((time.time()-starttime)/count)*(numpart-count)), "cyan")
neweulerfile.close()
rotshiftfile.close()
### rotate and shift particle
APSHstack = backprojectPWL.rotshiftParticle(alignstack, rotshiftdoc, iternum, self.timestamp)
#APSHstack = backprojectPWL.rotshiftParticle(alignstack, key, rot, cumX, cumY, mirror, iternum, self.timestamp)
apDisplay.printColor("finished rotating and shifting particles "+apDisplay.timeString(time.time()-starttime), "cyan")
return APSHout, APSHstack, neweulerdoc, projstack, numprojs
def appendEulerDoc(self, eulerfile, tiltpartnum, count):
eulerf = open(eulerfile, "a")
stackpartdata = apStack.getStackParticle(self.params['tiltstackid'], tiltpartnum)
gamma, theta, phi, tiltangle = apTiltPair.getParticleTiltRotationAngles(stackpartdata)
line = operations.spiderOutLine(count, [phi, tiltangle, -1.0*gamma])
eulerf.write(line)
eulerf.close()
def makeEulerDoc(self, parttree):
count = 0
eulerfile = os.path.join(self.params['rundir'],
"eulersdoc" + self.timestamp + ".spi")
eulerf = open(eulerfile, "w")
apDisplay.printMsg("creating Euler doc file")
starttime = time.time()
for partdict in parttree:
stackpartdata = apStack.getStackParticle(
self.params['tiltstackid'], partdict['tilt'])
count += 1
if count % 100 == 0:
sys.stderr.write(".")
eulerf.flush()
gamma, theta, phi, tiltangle = apTiltPair.getParticleTiltRotationAngles(
stackpartdata)
if gamma is None:
apDisplay.printWarning("Skipping " + str(stackpartdata))
continue
line = operations.spiderOutLine(count, [phi, tiltangle, gamma])
eulerf.write(line)
eulerf.close()
apDisplay.printColor(
"finished Euler doc file in " +
apDisplay.timeString(time.time() - starttime), "cyan")
return eulerfile
def getPartcileLists(self):
#first query
query1 = self.queryParticles(swap=False)
self.cursor.execute(query1)
results1 = self.cursor.fetchall()
apDisplay.printMsg("Found "+str(len(results1))+" particle pairs in forward order")
#if len(results1) < 2:
# apDisplay.printError("Failed to find any particles")
#swap particle1 and particle2 in ApTiltParticlePairData
query2 = self.queryParticles(swap=True)
self.cursor.execute(query2)
results2 = self.cursor.fetchall()
apDisplay.printMsg("Found "+str(len(results2))+" particle pairs in reverse order")
#if len(results2) < 2:
# apDisplay.printError("Failed to find any particles")
parttree = self.parseResults(results1, results2)
f = open("tiltsync-"+self.timestamp+".dat", "w")
count = 0
for partdict in parttree:
count += 1
emannotnum = partdict['not']-1
emantiltnum = partdict['tilt']-1
line = operations.spiderOutLine(count, (emannotnum,emantiltnum))
f.write(line)
f.close()
apDisplay.printMsg("Writing "+str(len(parttree))+" particle pairs")
if len(parttree) < 2:
apDisplay.printError("Failed to find any particle pairs")
return parttree
def appendEulerDoc(self, eulerfile, tiltpartnum, count):
eulerf = open(eulerfile, "a")
stackpartdata = apStack.getStackParticle(self.params['tiltstackid'], tiltpartnum)
gamma, theta, phi, tiltangle = apTiltPair.getParticleTiltRotationAngles(stackpartdata)
if gamma is None:
apDisplay.printWarning("Skipping "+str(stackpartdata))
return
line = operations.spiderOutLine(count, [phi, tiltangle, -1.0*gamma])
eulerf.write(line)
eulerf.close()
def generateRandomAngles(numpart, dataext=".spi"):
i = 0
randdocfile = "randomeulerdoc"+dataext
f.open(randdocfile)
while(i < numpart):
eulerlist = randomEuler()
spiline = operations.spiderOutLine(i+1, eulerlist)
f.write(spiline)
i+=1
f.close()
return randdocfile
def generateRandomAngles(numpart, dataext=".spi"):
i = 0
randdocfile = "randomeulerdoc" + dataext
f.open(randdocfile)
while (i < numpart):
eulerlist = randomEuler()
spiline = operations.spiderOutLine(i + 1, eulerlist)
f.write(spiline)
i += 1
f.close()
return randdocfile
def splitOddEven(self, classnum, select, iternum):
if (os.path.isfile(select) is False):
apDisplay.printError("File " + select + " does not exist!")
selectFile = open(select, "r")
selectFilename = os.path.splitext(os.path.basename(select))[0]
selectOdd = os.path.join(self.params['rundir'], str(classnum),
selectFilename + "Odd.spi")
selectOddFile = open(selectOdd, "w")
selectEven = os.path.join(self.params['rundir'], str(classnum),
selectFilename + "Even.spi")
selectEvenFile = open(selectEven, "w")
countOdd = 1
countEven = 1
for line in selectFile.readlines():
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
continue
if float(value[0]) % 2.0 == 1.0:
sline = operations.spiderOutLine(countOdd, [int(value[0])])
selectOddFile.write(line)
countOdd += 1
else:
sline = operations.spiderOutLine(countEven, [int(value[0])])
selectEvenFile.write(line)
countEven += 1
selectOddFile.close()
selectEvenFile.close()
return selectOdd, selectEven
def appendEulerDoc(self, eulerfile, tiltpartnum, count):
eulerf = open(eulerfile, "a")
stackpartdata = apStack.getStackParticle(self.params['tiltstackid'],
tiltpartnum)
gamma, theta, phi, tiltangle = apTiltPair.getParticleTiltRotationAngles(
stackpartdata)
if gamma is None:
apDisplay.printWarning("Skipping " + str(stackpartdata))
return
line = operations.spiderOutLine(count, [phi, tiltangle, -1.0 * gamma])
eulerf.write(line)
eulerf.close()
def splitOddEven(self, classnum, select, iternum):
if (os.path.isfile(select) is False):
apDisplay.printError("File "+ select +" does not exist!")
selectFile = open(select, "r")
selectFilename = os.path.splitext(os.path.basename(select))[0]
selectOdd = os.path.join(self.params['rundir'], str(classnum), selectFilename+"Odd.spi")
selectOddFile = open(selectOdd, "w")
selectEven = os.path.join(self.params['rundir'], str(classnum), selectFilename+"Even.spi")
selectEvenFile = open(selectEven, "w")
countOdd=1
countEven=1
for line in selectFile.readlines():
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
continue
if float(value[0])%2.0 == 1.0:
sline = operations.spiderOutLine(countOdd, [int(value[0])])
selectOddFile.write(line)
countOdd+=1
else:
sline = operations.spiderOutLine(countEven, [int(value[0])])
selectEvenFile.write(line)
countEven+=1
selectOddFile.close()
selectEvenFile.close()
return selectOdd, selectEven
def writePartDocFile(self, partlist):
docfile = "finalshifts_"+self.params['timestamp']+".doc"
f = open(docfile, "w")
dlist = ['inplane', 'xshift', 'yshift', 'refnum', 'mirror', 'spread']
f.write(" ; partnum ... "+str(dlist)+"\n")
for partdict in partlist:
floatlist = []
for key in dlist:
floatlist.append(partdict[key])
line = operations.spiderOutLine(partdict['partnum'], floatlist)
f.write(line)
f.write(" ; partnum ... "+str(dlist)+"\n")
f.close()
apDisplay.printMsg("wrote rotation and shift parameters to "+docfile+" for "+str(len(partlist))+" particles")
return
def makeEulerDoc(self, tiltParticlesData, cnum):
count = 0
eulerfile = os.path.join(self.params['rundir'], str(cnum),
"eulersdoc" + self.timestamp + ".spi")
eulerf = open(eulerfile, "w")
apDisplay.printMsg("Creating Euler angles doc file")
starttime = time.time()
tiltParticlesData.sort(self.sortTiltParticlesData)
startmem = mem.active()
for stackpartdata in tiltParticlesData:
count += 1
if count % 50 == 0:
sys.stderr.write(".")
eulerf.flush()
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 3:
apDisplay.printColor(
"Memory increase: %d MB/part" % (memdiff), "red")
tiltrot, theta, notrot, tiltangle = apTiltPair.getParticleTiltRotationAnglesOTR(
stackpartdata)
### Hack for OTR to work ( bad tilt axis angle from tilt picker )
tiltrot = -7.0
notrot = -7.0
inplane, mirror = self.getParticleInPlaneRotation(stackpartdata)
totrot = -1.0 * (notrot + inplane)
if mirror is True:
#theta flips to the back
tiltangle = -1.0 * tiltangle + 180 #tiltangle = tiltangle + 180.0 #theta
totrot = -1.0 * totrot - 180.0 #phi
tiltrot = tiltrot + 180 #tiltrot = -1.0 * tiltrot + 180.0 #psi
while totrot < 0:
totrot += 360.0
### this is the original eman part num; count is new part num
partnum = stackpartdata['particleNumber'] - 1
line = operations.spiderOutLine(count,
[tiltrot, tiltangle, totrot])
eulerf.write(line)
eulerf.close()
apDisplay.printColor(
"\nFinished Euler angle doc file in " +
apDisplay.timeString(time.time() - starttime), "cyan")
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 0.1:
apDisplay.printColor("Memory increase: %.2f MB/part" % (memdiff),
"red")
return eulerfile
def makecccAPSHselectFile(self, APSHout, classnum, iternum, factor):
if (os.path.isfile(APSHout) is False):
apDisplay.printError("File "+ APSHout +" does not exist!")
apshFile = open(APSHout, "r")
corrValues = []
for line in apshFile.readlines():
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
continue
corrValues.append(float(value[12]))
apshFile.close()
corrmean = (numpy.array(corrValues)).mean()
corrvar = (numpy.array(corrValues)).var()
corrstd = (numpy.array(corrValues)).std()
threshold = corrmean + (factor*corrstd)
count = 1
part = 1
corrSelect = os.path.join(self.params['rundir'], str(classnum), "apshCorrSelect-%03d.spi"%(iternum))
corrSelectFile = open(corrSelect, "w")
for i,corrValue in enumerate(corrValues):
if corrValue >= threshold:
line = operations.spiderOutLine(count, [i+1])
corrSelectFile.write(line)
count+=1
corrSelectFile.close()
if count == 0:
apDisplay.printError("no correlation value is above threshold!")
return corrSelect
def makeEulerDoc(self, parttree):
count = 0
eulerfile = os.path.join(self.params['rundir'], "eulersdoc"+self.timestamp+".spi")
eulerf = open(eulerfile, "w")
apDisplay.printMsg("creating Euler doc file")
starttime = time.time()
for partdict in parttree:
stackpartdata = apStack.getStackParticle(self.params['tiltstackid'], partdict['tilt'])
count += 1
if count%100 == 0:
sys.stderr.write(".")
eulerf.flush()
gamma, theta, phi, tiltangle = apTiltPair.getParticleTiltRotationAngles(stackpartdata)
line = operations.spiderOutLine(count, [phi, tiltangle, gamma])
eulerf.write(line)
eulerf.close()
apDisplay.printColor("finished Euler doc file in "+apDisplay.timeString(time.time()-starttime), "cyan")
return eulerfile
def makeEulerDoc(self, tiltParticlesData, cnum):
count = 0
eulerfile = os.path.join(self.params["rundir"], str(cnum), "eulersdoc" + self.timestamp + ".spi")
eulerf = open(eulerfile, "w")
apDisplay.printMsg("Creating Euler angles doc file")
starttime = time.time()
tiltParticlesData.sort(self.sortTiltParticlesData)
startmem = mem.active()
for stackpartdata in tiltParticlesData:
count += 1
if count % 50 == 0:
sys.stderr.write(".")
eulerf.flush()
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 3:
apDisplay.printColor("Memory increase: %d MB/part" % (memdiff), "red")
tiltrot, theta, notrot, tiltangle = apTiltPair.getParticleTiltRotationAnglesOTR(stackpartdata)
### Hack for OTR to work ( bad tilt axis angle from tilt picker )
tiltrot = -7.0
notrot = -7.0
inplane, mirror = self.getParticleInPlaneRotation(stackpartdata)
totrot = -1.0 * (notrot + inplane)
if mirror is True:
# theta flips to the back
tiltangle = -1.0 * tiltangle + 180 # tiltangle = tiltangle + 180.0 #theta
totrot = -1.0 * totrot - 180.0 # phi
tiltrot = tiltrot + 180 # tiltrot = -1.0 * tiltrot + 180.0 #psi
while totrot < 0:
totrot += 360.0
### this is the original eman part num; count is new part num
partnum = stackpartdata["particleNumber"] - 1
line = operations.spiderOutLine(count, [tiltrot, tiltangle, totrot])
eulerf.write(line)
eulerf.close()
apDisplay.printColor(
"\nFinished Euler angle doc file in " + apDisplay.timeString(time.time() - starttime), "cyan"
)
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 0.1:
apDisplay.printColor("Memory increase: %.2f MB/part" % (memdiff), "red")
return eulerfile
def test(rdata):
radialsize = rdata.shape[0]
envshape = (4096, 4096)
### write data out
f = open('radial-envelope.dat', 'w')
spi = open('radial-envelope.spi', 'w')
for i in range(radialsize):
f.write('%d\t%.8f\n'%(i, rdata[i]))
spi.write(operations.spiderOutLine(i, [i, rdata[i]]))
f.close()
spi.close()
### create new mrc
xdata = numpy.arange(0, radialsize, 1.0, dtype=numpy.float64)
### fixed end values
#print 0, rdata[0], "-->", 265.20575
#print 2896, rdata[2896], "-->", 185.45721
rdata[0] = 265.20575
rdata[2896] = 185.45721
envcalc = fromRadialFunc(funcrad, envshape, xdata=xdata, rdata=rdata)
mrc.write(envcalc, 'calcualted-envelope.mrc')
def test(rdata):
radialsize = rdata.shape[0]
envshape = (4096, 4096)
### write data out
f = open('radial-envelope.dat', 'w')
spi = open('radial-envelope.spi', 'w')
for i in range(radialsize):
f.write('%d\t%.8f\n' % (i, rdata[i]))
spi.write(operations.spiderOutLine(i, [i, rdata[i]]))
f.close()
spi.close()
### create new mrc
xdata = numpy.arange(0, radialsize, 1.0, dtype=numpy.float64)
### fixed end values
#print 0, rdata[0], "-->", 265.20575
#print 2896, rdata[2896], "-->", 185.45721
rdata[0] = 265.20575
rdata[2896] = 185.45721
envcalc = fromRadialFunc(funcrad, envshape, xdata=xdata, rdata=rdata)
mrc.write(envcalc, 'calcualted-envelope.mrc')
def runEoTest(self, alignstack, eulerfile):
evenvolfile = os.path.join(self.params['rundir'],
"evenvolume%s.spi" % (self.timestamp))
oddvolfile = os.path.join(self.params['rundir'],
"oddvolume%s.spi" % (self.timestamp))
eveneulerfile = os.path.join(self.params['rundir'],
"eveneulers%s.spi" % (self.timestamp))
oddeulerfile = os.path.join(self.params['rundir'],
"oddeulers%s.spi" % (self.timestamp))
evenpartlist = os.path.join(self.params['rundir'],
"evenparts%s.lst" % (self.timestamp))
oddpartlist = os.path.join(self.params['rundir'],
"oddparts%s.lst" % (self.timestamp))
### Create New Doc Files
of = open(oddeulerfile, "w")
ef = open(eveneulerfile, "w")
op = open(oddpartlist, "w")
ep = open(evenpartlist, "w")
inf = open(eulerfile, "r")
evenpart = 0
oddpart = 0
for line in inf:
spidict = operations.spiderInLine(line)
if spidict:
partnum = spidict['row']
if partnum % 2 == 0:
ep.write("%d\n" % (partnum - 1))
evenpart += 1
outline = operations.spiderOutLine(evenpart,
spidict['floatlist'])
ef.write(outline)
elif partnum % 2 == 1:
op.write("%d\n" % (partnum - 1))
oddpart += 1
outline = operations.spiderOutLine(oddpart,
spidict['floatlist'])
of.write(outline)
inf.close()
of.close()
ef.close()
op.close()
ep.close()
### Create stacks
evenstack = os.path.join(self.params['rundir'],
"evenstack%s.spi" % (self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap" % (alignstack, evenstack,
evenpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
oddstack = os.path.join(self.params['rundir'],
"oddstack%s.spi" % (self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap" % (alignstack, oddstack,
oddpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
### Create Volumes
backproject.backproject3F(evenstack, eveneulerfile, evenvolfile,
evenpart)
backproject.backproject3F(oddstack, oddeulerfile, oddvolfile, oddpart)
if not os.path.isfile(evenvolfile) or not os.path.isfile(oddvolfile):
apDisplay.printError("Even-Odd volume creation failed")
### Calculate FSC
apix = apStack.getStackPixelSizeFromStackId(
self.params['tiltstackid']) * self.params['tiltbin']
emancmd = "proc3d %s %s" % (evenvolfile, evenvolfile + ".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
emancmd = "proc3d %s %s" % (oddvolfile, oddvolfile + ".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
fscfile = os.path.join(self.params['rundir'],
"fscdata%s.fsc" % (self.timestamp))
emancmd = "proc3d %s %s fsc=%s" % (evenvolfile + ".mrc",
oddvolfile + ".mrc", fscfile)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
if not os.path.isfile(fscfile):
apDisplay.printError("Even-Odd fsc calculation failed")
boxsize = self.getBoxSize()
self.fscresolution = apRecon.getResolutionFromFSCFile(fscfile,
boxsize,
apix,
msg=True)
apDisplay.printColor(
("Final FSC resolution: %.5f" % (self.fscresolution)), "cyan")
for fname in (evenvolfile, oddvolfile, evenstack, oddstack,
eveneulerfile, oddeulerfile, evenpartlist, oddpartlist):
apFile.removeFile(fname)
def runEoTest(self, alignstack, eulerfile):
evenvolfile = os.path.join(self.params['rundir'], "evenvolume%s.spi"%(self.timestamp))
oddvolfile = os.path.join(self.params['rundir'], "oddvolume%s.spi"%(self.timestamp))
eveneulerfile = os.path.join(self.params['rundir'], "eveneulers%s.spi"%(self.timestamp))
oddeulerfile = os.path.join(self.params['rundir'], "oddeulers%s.spi"%(self.timestamp))
evenpartlist = os.path.join(self.params['rundir'], "evenparts%s.lst"%(self.timestamp))
oddpartlist = os.path.join(self.params['rundir'], "oddparts%s.lst"%(self.timestamp))
### Create New Doc Files
of = open(oddeulerfile, "w")
ef = open(eveneulerfile, "w")
op = open(oddpartlist, "w")
ep = open(evenpartlist, "w")
inf = open(eulerfile, "r")
evenpart = 0
oddpart = 0
for line in inf:
spidict = operations.spiderInLine(line)
if spidict:
partnum = spidict['row']
if partnum % 2 == 0:
ep.write("%d\n"%(partnum-1))
evenpart += 1
outline = operations.spiderOutLine(evenpart, spidict['floatlist'])
ef.write(outline)
elif partnum % 2 == 1:
op.write("%d\n"%(partnum-1))
oddpart += 1
outline = operations.spiderOutLine(oddpart, spidict['floatlist'])
of.write(outline)
inf.close()
of.close()
ef.close()
op.close()
ep.close()
### Create stacks
evenstack = os.path.join(self.params['rundir'], "evenstack%s.spi"%(self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap"%(alignstack,evenstack,evenpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
oddstack = os.path.join(self.params['rundir'], "oddstack%s.spi"%(self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap"%(alignstack,oddstack,oddpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
### Create Volumes
backproject.backproject3F(evenstack, eveneulerfile, evenvolfile, evenpart)
backproject.backproject3F(oddstack, oddeulerfile, oddvolfile, oddpart)
if not os.path.isfile(evenvolfile) or not os.path.isfile(oddvolfile):
apDisplay.printError("Even-Odd volume creation failed")
### Calculate FSC
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
emancmd = "proc3d %s %s"%(evenvolfile, evenvolfile+".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
emancmd = "proc3d %s %s"%(oddvolfile, oddvolfile+".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
fscfile = os.path.join(self.params['rundir'], "fscdata%s.fsc"%(self.timestamp))
emancmd = "proc3d %s %s fsc=%s"%(evenvolfile+".mrc", oddvolfile+".mrc", fscfile)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
if not os.path.isfile(fscfile):
apDisplay.printError("Even-Odd fsc calculation failed")
boxsize = self.getBoxSize()
self.fscresolution = apRecon.getResolutionFromFSCFile(fscfile, boxsize, apix, msg=True)
apDisplay.printColor( ("Final FSC resolution: %.5f" % (self.fscresolution)), "cyan")
for fname in (evenvolfile, oddvolfile, evenstack, oddstack, eveneulerfile, oddeulerfile, evenpartlist, oddpartlist):
apFile.removeFile(fname)
def cccAPSH(self, APSHout, classnum, iternum):
### Calculate absolute shifts
absshifts=[]
if not os.path.isfile(APSHout):
apDisplay.printError("APSH output file not found: "+APSHout)
apsh = open(APSHout, "r")
for line in apsh.readlines():
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
continue
### absshift = sqrt(x^2 + y^2)
absshift = math.sqrt((float(value[8])*float(value[8]))+(float(value[9])*float(value[9])))
absshifts.append(absshift)
apsh.close()
### calculate the mean, variance and stdev of the absolute shift of the dataset
APSHmean = (numpy.array(absshifts)).mean()
APSHvar = (numpy.array(absshifts)).var()
APSHstd = (numpy.array(absshifts)).std()
### calculate the weighted cross correlation values
####################################################################
##
## 1
## prob(shift) = ------------------ * e^[-1/2*(shift-mean)/stdev]**2
## stdev*sqrt(2*pi)
##
####################################################################
const = APSHstd*math.sqrt(2*math.pi)
probs=[]
for absshift in absshifts:
### probability for each particle
prob = (1/const)*math.exp((-1/2)*((absshift-APSHmean)/APSHstd)*((absshift-APSHmean)/APSHstd))
probs.append(prob)
### output file for APSH with weighted CC values
APSHout_weighted = os.path.join(self.params['rundir'], str(classnum), "apshOut_weighted-%03d.spi"%(iternum))
apsh = open(APSHout, "r")
apshCCC = open(APSHout_weighted, "w")
notline=0
for i,line in enumerate(apsh.readlines()):
value = line.split()
try:
int(value[0])
except:
#apDisplay.printMsg(line)
notline+=1
continue
key = int(float(value[6]))
weightedCCvalue = float(value[12])*probs[i-notline]
psi = float(value[2])
theta = float(value[3])
phi = float(value[4])
ref = float(value[5])
partnum = float(value[6])
rot = float(value[7])
cumX = float(value[8])
cumY = float(value[9])
proj = float(value[10])
diff = float(value[11])
inplane = float(value[13])
sx = float(value[14])
sy = float(value[15])
mirror = float(value[16])
### write out new APSH file
APSHline = operations.spiderOutLine(key, [psi, theta, phi, ref, partnum, rot, cumX, cumY, proj, diff, weightedCCvalue, inplane, sx, sy, mirror])
apshCCC.write(APSHline)
apshCCC.close()
apsh.close()
return APSHout_weighted
