def start(self):
### get stack data
notstackdata = apStack.getOnlyStackData(self.params['notstackid'])
tiltstackdata = apStack.getOnlyStackData(self.params['tiltstackid'])
### get good particle numbers
includeParticle, tiltParticlesData = self.getGoodAlignParticles()
self.numpart = len(includeParticle)
### make doc file of Euler angles
eulerfile = self.makeEulerDoc(tiltParticlesData)
### write kept particles to file
self.params['keepfile'] = os.path.join(
self.params['rundir'], "keepfile" + self.timestamp + ".lst")
apDisplay.printMsg("writing to keepfile " + self.params['keepfile'])
kf = open(self.params['keepfile'], "w")
for partnum in includeParticle:
kf.write(str(partnum) + "\n")
kf.close()
### make new stack of tilted particle from that run
tiltstackfile = os.path.join(tiltstackdata['path']['path'],
tiltstackdata['name'])
rctstackfile = os.path.join(self.params['rundir'],
"rctstack" + self.timestamp + ".hed")
apFile.removeStack(rctstackfile, warn=False)
apStack.makeNewStack(tiltstackfile, rctstackfile,
self.params['keepfile'])
spiderstack = self.convertStackToSpider(rctstackfile)
#self.mirrorParticles(tiltParticlesData, spiderstack)
### iterations over volume creation
### back project particles into filter volume
volfile = os.path.join(self.params['rundir'],
"volume%s-%03d.spi" % (self.timestamp, 0))
backproject.backprojectCG(spiderstack,
eulerfile,
volfile,
numpart=self.numpart,
pixrad=self.params['radius'])
alignstack = spiderstack
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, 0)
for i in range(self.params['numiters']):
looptime = time.time()
iternum = i + 1
apDisplay.printMsg("running backprojection iteration " +
str(iternum))
### xy-shift particles to volume projections
alignstack = backproject.rctParticleShift(
volfile,
alignstack,
eulerfile,
iternum,
numpart=self.numpart,
pixrad=self.params['radius'],
timestamp=self.timestamp)
apFile.removeFile(volfile)
### back project particles into better volume
volfile = os.path.join(
self.params['rundir'],
"volume%s-%03d.spi" % (self.timestamp, iternum))
backproject.backproject3F(alignstack,
eulerfile,
volfile,
numpart=self.numpart)
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, iternum)
apDisplay.printColor(
"finished volume refinement loop in " +
apDisplay.timeString(time.time() - looptime), "cyan")
### optimize Euler angles
#NOT IMPLEMENTED YET
### perform eotest
if self.params['eotest'] is True:
self.runEoTest(alignstack, eulerfile)
self.runRmeasure()
### insert volumes into DB
self.insertRctRun(mrcvolfile)
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 start(self):
### get stack data
notstackdata = apStack.getOnlyStackData(self.params['notstackid'])
tiltstackdata = apStack.getOnlyStackData(self.params['tiltstackid'])
### get good particle numbers
includeParticle, tiltParticlesData = self.getGoodAlignParticles()
self.numpart = len(includeParticle)
### make doc file of Euler angles
eulerfile = self.makeEulerDoc(tiltParticlesData)
### write kept particles to file
self.params['keepfile'] = os.path.join(self.params['rundir'], "keepfile"+self.timestamp+".lst")
apDisplay.printMsg("writing to keepfile "+self.params['keepfile'])
kf = open(self.params['keepfile'], "w")
for partnum in includeParticle:
kf.write(str(partnum)+"\n")
kf.close()
### make new stack of tilted particle from that run
tiltstackfile = os.path.join(tiltstackdata['path']['path'], tiltstackdata['name'])
rctstackfile = os.path.join(self.params['rundir'], "rctstack"+self.timestamp+".hed")
apFile.removeStack(rctstackfile, warn=False)
apStack.makeNewStack(tiltstackfile, rctstackfile, self.params['keepfile'])
spiderstack = self.convertStackToSpider(rctstackfile)
#self.mirrorParticles(tiltParticlesData, spiderstack)
### iterations over volume creation
### back project particles into filter volume
volfile = os.path.join(self.params['rundir'], "volume%s-%03d.spi"%(self.timestamp, 0))
backproject.backprojectCG(spiderstack, eulerfile, volfile,
numpart=self.numpart, pixrad=self.params['radius'])
alignstack = spiderstack
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, 0)
for i in range(self.params['numiters']):
looptime = time.time()
iternum = i+1
apDisplay.printMsg("running backprojection iteration "+str(iternum))
### xy-shift particles to volume projections
alignstack = backproject.rctParticleShift(volfile, alignstack, eulerfile, iternum,
numpart=self.numpart, pixrad=self.params['radius'], timestamp=self.timestamp)
apFile.removeFile(volfile)
### back project particles into better volume
volfile = os.path.join(self.params['rundir'], "volume%s-%03d.spi"%(self.timestamp, iternum))
backproject.backproject3F(alignstack, eulerfile, volfile,
numpart=self.numpart)
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, iternum)
apDisplay.printColor("finished volume refinement loop in "
+apDisplay.timeString(time.time()-looptime), "cyan")
### optimize Euler angles
#NOT IMPLEMENTED YET
### perform eotest
if self.params['eotest'] is True:
self.runEoTest(alignstack, eulerfile)
self.runRmeasure()
### insert volumes into DB
self.insertRctRun(mrcvolfile)
def start(self):
### get stack data
notstackdata = apStack.getOnlyStackData(self.params['notstackid'])
tiltstackdata = apStack.getOnlyStackData(self.params['tiltstackid'])
for cnum in self.classlist:
print "\n"
apDisplay.printMsg("###########################")
apDisplay.printMsg("Processing stack of class "+str(cnum)+"")
apDisplay.printMsg("###########################")
print "\n"
### get good particle numbers
includeParticle, tiltParticlesData = self.getGoodAlignParticles(cnum)
self.numpart = len(includeParticle)
### write kept particles to file
apParam.createDirectory(os.path.join(self.params['rundir'], str(cnum)))
self.params['keepfile'] = os.path.join(self.params['rundir'], str(cnum), "keepfile"+self.timestamp+".lst")
apDisplay.printMsg("writing to keepfile "+self.params['keepfile'])
kf = open(self.params['keepfile'], "w")
for partnum in includeParticle:
kf.write(str(partnum)+"\n")
kf.close()
### make new stack of tilted particle from that run
tiltstackfile = os.path.join(tiltstackdata['path']['path'], tiltstackdata['name'])
otrstackfile = os.path.join(self.params['rundir'], str(cnum), "otrstack"+self.timestamp+".hed")
apFile.removeStack(otrstackfile)
apStack.makeNewStack(tiltstackfile, otrstackfile, self.params['keepfile'])
spiderstack = self.convertStackToSpider(otrstackfile, cnum)
### make doc file of Euler angles
eulerfile = self.makeEulerDoc(tiltParticlesData, cnum)
### iterations over volume creation
looptime = time.time()
### back project particles into volume
volfile = os.path.join(self.params['rundir'], str(cnum), "volume%s-%03d.spi"%(self.timestamp, 0))
self.initialBPRP(cnum, volfile, spiderstack, eulerfile, len(includeParticle), self.params['radius'])
### RCT backproject method
#backproject.backprojectCG(spiderstack, eulerfile, volfile, numpart=len(includeParticle), pixrad=self.params['radius'])
### filter the volume (low-pass Butterworth)
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])
backproject.butterworthLP(volfile, apix)
### need work... filtered volume overwrites on the existing volume
backproject.normalizeVol(volfile)
alignstack = spiderstack
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, cnum, 0)
for i in range(self.params['numiters']):
iternum = i+1
apDisplay.printMsg("running backprojection iteration "+str(iternum))
### xy-shift particles to volume projections
alignstack = backproject.otrParticleShift(volfile, alignstack, eulerfile, iternum,
numpart=len(includeParticle), pixrad=self.params['radius'], timestamp=self.timestamp, classnum=cnum)
apDisplay.printColor("finished volume refinement in "
+apDisplay.timeString(time.time()-looptime), "cyan")
### back project particles into better volume
volfile = os.path.join(self.params['rundir'], str(cnum), "volume%s-%03d.spi"%(self.timestamp, iternum))
backproject.backproject3F(alignstack, eulerfile, volfile, numpart=len(includeParticle))
### filter the volume (low-pass Butterworth)
backproject.butterworthLP(volfile, apix)
### need work... filtered volume has a different name
backproject.normalizeVol(volfile)
### center/convert the volume file
mrcvolfile = self.processVolume(volfile, cnum, iternum)
###############################
# #
# Andres's refinement steps #
# #
###############################
print "\n"
apDisplay.printMsg("##################################")
apDisplay.printMsg("Starting Andres' refinement steps")
apDisplay.printMsg("##################################")
print "\n"
for j in range(self.params['refineiters']):
iternum = j+1
appiondata.ApPathData.direct_query(1)
apDisplay.printMsg("Starting projection-matching refinement/XMIPP iteration "+str(iternum))
boxsize = self.getBoxSize()
### projection-matching refinement/XMIPP
apshout, apshstack, apsheuler = self.projMatchRefine(cnum, volfile, alignstack, eulerfile, boxsize, len(includeParticle), self.params['radius'], iternum)
apDisplay.printMsg("Calculating weighted cross-correlation coefficients")
### calculation of weighted cross-correlation coefficients
apshout_weighted = self.cccAPSH(apshout, cnum, iternum)
apDisplay.printMsg("Creating select files based on weighted cross-correlation coefficients")
### create select files based on calculated weighted-cross-correlation
corrSelect = self.makecccAPSHselectFile(apshout_weighted, cnum, iternum, factor=0.1)
### create volume file names
apshVolfile = os.path.join(self.params['rundir'], str(cnum), "apshVolume-%03d.spi"%(iternum))
### run BPRP on selected particles
self.APSHbackProject(apshstack, apsheuler, apshVolfile, cnum, corrSelect)
### center volume
filename = os.path.splitext(apshVolfile)[0]
apshVolFileCentered = filename+"_centered.spi"
backproject.centerVolume(apshVolfile, apshVolFileCentered)
### calculate FSC
### generate odd and even select files for FSC calculation
corrSelectOdd, corrSelectEven = self.splitOddEven(cnum, corrSelect, iternum)
fscout = self.runEoTest(corrSelectOdd, corrSelectEven, cnum, apshstack, apsheuler, iternum)
self.runRmeasure(apshVolFileCentered)
### filter volume
backproject.butterworthFscLP(apshVolFileCentered, fscout)
### reset file names for next round
volfile = apshVolFileCentered
eulerfile = apsheuler
mrcvolfile = self.processVolume(volfile, cnum, iternum)
print "\n"
apDisplay.printMsg("###########################")
apDisplay.printMsg("Done with iteration "+str(j+1)+"")
apDisplay.printMsg("###########################")
print "\n"
#if len(self.classlist) > 1:
#get a list of all unique combinations of volumes
# pairlist = self.computeClassVolPair()
### insert volumes into DB
self.insertOtrRun(mrcvolfile)