def runEoTest(self, corrSelectOdd, corrSelectEven, cnum, apshstack, apsheuler, iternum):
apshOddVolfile = os.path.join(self.params['rundir'], str(cnum), "apshVolume_Odd-%03d.spi"%(iternum))
apshEvenVolfile = os.path.join(self.params['rundir'], str(cnum), "apshVolume_Even-%03d.spi"%(iternum))
self.APSHbackProject(apshstack, apsheuler, apshOddVolfile, cnum, corrSelectOdd)
self.APSHbackProject(apshstack, apsheuler, apshEvenVolfile, cnum, corrSelectEven)
fscout = os.path.join(self.params['rundir'], str(cnum), "FSCout-%03d.spi"%(iternum))
backproject.calcFSC(apshOddVolfile, apshEvenVolfile, fscout)
### Calculate FSC - taken from Neil's RCT script
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
emancmd = "proc3d %s %s"%(apshEvenVolfile, apshEvenVolfile+".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
emancmd = "proc3d %s %s"%(apshOddVolfile, apshOddVolfile+".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"%(apshEvenVolfile+".mrc", apshOddVolfile+".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")
return fscout
def start(self):
res = apRecon.getResolutionFromFSCFile(self.params['fscfile'],
self.params['boxsize'],
self.params['apix'],
self.params['criteria'])
apDisplay.printColor(("resolution: %.5f at criteria %.3f" %
(res, self.params['criteria'])), "cyan")
sys.stdout.write(
"%s resolution %.5f (%.3f)\n" %
(self.params['fscfile'], res, self.params['criteria']))
def start(self):
res = apRecon.getResolutionFromFSCFile(self.params['fscfile'],
self.params['boxsize'], self.params['apix'], self.params['criteria'])
apDisplay.printColor( ("resolution: %.5f at criteria %.3f" % (res, self.params['criteria'])), "cyan")
sys.stdout.write("%s resolution %.5f (%.3f)\n"%(self.params['fscfile'], res, self.params['criteria']))
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):
self.rootname = self.params['stackname'].split(".")[0]
self.params['outputstack'] = os.path.join(self.params['rundir'],
self.params['stackname'])
if os.path.isfile(self.params['outputstack']):
apFile.removeStack(self.params['outputstack'])
if self.params['eotest'] is True:
self.params['evenstack'] = os.path.splitext(
self.params['outputstack'])[0] + '.even.hed'
if os.path.isfile(self.params['evenstack']):
apFile.removeStack(self.params['evenstack'])
self.params['oddstack'] = os.path.splitext(
self.params['outputstack'])[0] + '.odd.hed'
if os.path.isfile(self.params['oddstack']):
apFile.removeStack(self.params['oddstack'])
classes = self.getClassData(self.params['reconid'],
self.params['iter'])
stackid = apStack.getStackIdFromRecon(self.params['reconid'])
stackdata = apStack.getOnlyStackData(stackid)
stackpath = os.path.join(stackdata['path']['path'], stackdata['name'])
classkeys = classes.keys()
classkeys.sort()
classnum = 0
keeplist = self.procKeepList()
finallist = []
apDisplay.printMsg("Processing " + str(len(classes)) + " classes")
#loop through classes
for key in classkeys:
classnum += 1
if classnum % 10 == 1:
sys.stderr.write("\b\b\b\b\b\b\b\b\b\b\b\b\b\b")
sys.stderr.write(
str(classnum) + " of " + (str(len(classkeys))))
# loop through particles in class
classfile = self.rootname + "-class.lst"
classf = open(classfile, 'w')
classf.write('#LST\n')
nptcls = 0
for ptcl in classes[key]['particles']:
# translate DB into EMAN
partnum = ptcl['particle']['particleNumber'] - 1
if partnum in keeplist:
if ptcl['mirror']:
mirror = 1
else:
mirror = 0
rot = ptcl['euler3'] * math.pi / 180.0
classf.write("%d\t%s\t%f,\t%f,%f,%f,%d\n" %
(partnum, stackpath, ptcl['quality_factor'],
rot, ptcl['shiftx'], ptcl['shifty'], mirror))
nptcls += 1
finallist.append(partnum)
classf.close()
if nptcls < 1:
continue
self.makeClassAverages(classfile, self.params['outputstack'],
classes[key], self.params['mask'])
if self.params['eotest'] is True:
self.makeEvenOddClasses(classfile, self.params['outputstack'],
classes[key], self.params['mask'])
apFile.removeFile(classfile)
sys.stderr.write("\n")
finalfilename = self.rootname + "-keep.lst"
finalf = open(finalfilename, 'w')
finallist.sort()
for partnum in finallist:
finalf.write('%d\n' % (partnum, ))
finalf.close()
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
### recon 3d volumes
threedname = os.path.join(
self.params['rundir'],
self.rootname + "." + str(self.params['iter']) + "a.mrc")
emancmd = ("make3d " + self.params['outputstack'] + " out=" +
threedname + " hard=50 sym=" + self.params['symmname'] +
" pad=240 mask=" + str(self.params['mask']) + "; echo ''")
#print emancmd
apEMAN.executeEmanCmd(emancmd,
verbose=False,
showcmd=True,
logfile=self.rootname + "-eman.log")
threednameb = os.path.join(
self.params['rundir'],
self.rootname + "." + str(self.params['iter']) + "b.mrc")
emancmd = ("proc3d " + threedname + " " + threednameb +
" apix=1.63 norm=0,1 lp=8 origin=0,0,0 mask=" +
str(self.params['mask']) + "; echo '' ")
apEMAN.executeEmanCmd(emancmd,
verbose=False,
showcmd=True,
logfile=self.rootname + "-eman.log")
if self.params['eotest'] is True:
# even
evenname = os.path.join(
self.params['rundir'],
self.rootname + "-even." + str(self.params['iter']) + "a.mrc")
if os.path.isfile(self.params['evenstack']):
evenemancmd = ("make3d " + self.params['evenstack'] + " out=" +
evenname + " hard=50 sym=" +
self.params['symmname'] + " pad=240 mask=" +
str(self.params['mask']) + "; echo ''")
#print evenemancmd
apEMAN.executeEmanCmd(evenemancmd,
verbose=False,
showcmd=True,
logfile=self.rootname + "-eveneman.log")
else:
apDisplay.printWarning("file " + self.params['evenstack'] +
" does not exist")
# odd
oddname = os.path.join(
self.params['rundir'],
self.rootname + "-odd." + str(self.params['iter']) + "a.mrc")
if os.path.isfile(self.params['oddstack']):
oddemancmd = ("make3d " + self.params['oddstack'] + " out=" +
oddname + " hard=50 sym=" +
self.params['symmname'] + " pad=240 mask=" +
str(self.params['mask']) + "; echo ''")
#print oddemancmd
apEMAN.executeEmanCmd(oddemancmd,
verbose=False,
showcmd=True,
logfile=self.rootname + "-oddeman.log")
else:
apDisplay.printWarning("file " + self.params['oddstack'] +
" does not exist")
#eotest
fscout = os.path.join(self.params['rundir'],
self.rootname + "-fsc.eotest")
if os.path.isfile(oddname) and os.path.isfile(evenname):
eotestcmd = "proc3d " + oddname + " " + evenname + " fsc=" + fscout
apEMAN.executeEmanCmd(eotestcmd, verbose=True, showcmd=True)
else:
apDisplay.printWarning("could not perform eotest")
if os.path.isfile(fscout):
res = apRecon.getResolutionFromFSCFile(fscout, 160.0, 1.63)
apDisplay.printColor(("resolution: %.5f" % (res)), "cyan")
resfile = self.rootname + "-res.txt"
f = open(resfile, 'a')
f.write("[ %s ]\nresolution: %.5f\n" % (time.asctime(), res))
f.close()
def start(self):
res = apRecon.getResolutionFromFSCFile(self.params['fscfile'],
self.params['boxsize'],
self.params['apix'])
apDisplay.printColor(("resolution: %.5f" % (res)), "cyan")
def start(self):
res = apRecon.getResolutionFromFSCFile(self.params['fscfile'], self.params['boxsize'], self.params['apix'])
apDisplay.printColor( ("resolution: %.5f" % (res)), "cyan")
def start(self):
self.params['outputstack'] = os.path.join(self.params['rundir'],
self.params['stackname'])
particles, self.params['refineiter'] = getParticleInfo(
self.params['reconid'], self.params['iter'])
stackdata = particles[0]['particle']['stack']
stack = os.path.join(stackdata['path']['path'], stackdata['name'])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params['sigma'] is not None:
cutoff = cstats[
'meanquality'] + self.params['sigma'] * cstats['stdquality']
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(
particles, rejectlst, cutoff)
if self.params['avgjump'] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params['rejectlst']:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open('keep.lst', 'w')
keepfile.write('#LST\n')
reject = open('reject.lst', 'w')
reject.write('#LST\n')
apDisplay.printMsg("Processing classes")
#loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open('clstmp.lst', 'w')
clsfile.write('#LST\n')
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(
str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
#loop through particles in class
nptcls = 0
for ptcl in classes[key]['particles']:
if ptcl['mirror']:
mirror = 1
else:
mirror = 0
rot = ptcl['euler3']
rot = rot * math.pi / 180
if ptcl['particle']['particleNumber'] not in rejectlst:
l = '%d\t%s\t%f,\t%f,%f,%f,%d\n' % (
ptcl['particle']['particleNumber'] - 1, stack,
ptcl['quality_factor'], rot, ptcl['shiftx'],
ptcl['shifty'], mirror)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' %
(ptcl['particle']['particleNumber'] - 1,
stack, ptcl['quality_factor'], rot,
ptcl['shiftx'], ptcl['shifty'], mirror))
#if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params['skipavg'] is False:
makeClassAverages('clstmp.lst', self.params['outputstack'],
classes[key], self.params)
if self.params['eotest'] is True:
self.makeEvenOddClasses('clstmp.lst', classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove('clstmp.lst')
# make 3d density file if specified:
if self.params['make3d'] is not None:
self.params['make3d'] = os.path.basename(self.params['make3d'])
outfile = os.path.join(self.params['rundir'],
self.params['make3d'])
apEMAN.make3d(self.params['stackname'],
outfile,
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" %
(outfile, outfile, self.params['mask']))
if self.params['eotest'] is True:
apEMAN.make3d(self.params['oddstack'],
"odd.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.make3d(self.params['evenstack'],
"even.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg('inserting density into database')
symdata = apSymmetry.findSymmetry(self.params['sym'])
if not symdata:
apDisplay.printError('no symmetry associated with this model')
modq = appiondata.Ap3dDensityData()
modq['session'] = apStack.getSessionDataFromStackId(
self.params['stackid'])
modq['name'] = self.params['make3d']
modq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
modq['boxsize'] = box
modq['mask'] = self.params['mask']
modq['pixelsize'] = apix
fscres = apRecon.getResolutionFromFSCFile('fsc.eotest',
box,
apix,
msg=True)
modq['resolution'] = fscres
modq['rmeasure'] = apRecon.runRMeasure(apix, outfile)
modq['md5sum'] = apFile.md5sumfile(outfile)
modq['maxjump'] = self.params['avgjump']
modq['sigma'] = self.params['sigma']
modq['hard'] = self.params['hard']
modq['symmetry'] = symdata
modq['refineIter'] = self.params['refineiter']
if self.params['commit'] is True:
modq.insert()
apChimera.filterAndChimera(outfile,
res=fscres,
apix=apix,
box=box,
chimtype='snapshot',
zoom=self.params['zoom'],
sym=self.params['sym'],
mass=self.params['mass'])
else:
apDisplay.printError(
'no 3d volume was generated - check the class averages:')
apDisplay.printError(self.params['stackname'])
apDisplay.printError(
'hard may be set too high, or avg euler jump set too low for the # of particles'
)
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n" +
"subStack.py --projectid=" + str(self.params['projectid']) +
" -s " + stackstr + " \\\n " + " -k " +
os.path.join(self.params['rundir'], "keep.lst") + " \\\n " +
" -d 'recon " + reconstr + " sitters' -n sitters" + reconstr +
" -C ", "purple")
def start(self):
self.params["outputstack"] = os.path.join(self.params["rundir"], self.params["stackname"])
particles, self.params["refineiter"] = getParticleInfo(self.params["reconid"], self.params["iter"])
stackdata = particles[0]["particle"]["stack"]
stack = os.path.join(stackdata["path"]["path"], stackdata["name"])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params["sigma"] is not None:
cutoff = cstats["meanquality"] + self.params["sigma"] * cstats["stdquality"]
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(particles, rejectlst, cutoff)
if self.params["avgjump"] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params["rejectlst"]:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open("keep.lst", "w")
keepfile.write("#LST\n")
reject = open("reject.lst", "w")
reject.write("#LST\n")
apDisplay.printMsg("Processing classes")
# loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open("clstmp.lst", "w")
clsfile.write("#LST\n")
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
# loop through particles in class
nptcls = 0
for ptcl in classes[key]["particles"]:
if ptcl["mirror"]:
mirror = 1
else:
mirror = 0
rot = ptcl["euler3"]
rot = rot * math.pi / 180
if ptcl["particle"]["particleNumber"] not in rejectlst:
l = "%d\t%s\t%f,\t%f,%f,%f,%d\n" % (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write(
"%d\t%s\t%f,\t%f,%f,%f,%d\n"
% (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
)
# if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params["skipavg"] is False:
makeClassAverages("clstmp.lst", self.params["outputstack"], classes[key], self.params)
if self.params["eotest"] is True:
self.makeEvenOddClasses("clstmp.lst", classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove("clstmp.lst")
# make 3d density file if specified:
if self.params["make3d"] is not None:
self.params["make3d"] = os.path.basename(self.params["make3d"])
outfile = os.path.join(self.params["rundir"], self.params["make3d"])
apEMAN.make3d(
self.params["stackname"],
outfile,
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" % (outfile, outfile, self.params["mask"]))
if self.params["eotest"] is True:
apEMAN.make3d(
self.params["oddstack"],
"odd.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.make3d(
self.params["evenstack"],
"even.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params["stackid"])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg("inserting density into database")
symdata = apSymmetry.findSymmetry(self.params["sym"])
if not symdata:
apDisplay.printError("no symmetry associated with this model")
modq = appiondata.Ap3dDensityData()
modq["session"] = self.params["sessionname"]
modq["name"] = self.params["make3d"]
modq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
modq["boxsize"] = box
modq["mask"] = self.params["mask"]
modq["pixelsize"] = apix
fscres = apRecon.getResolutionFromFSCFile("fsc.eotest", box, apix, msg=True)
modq["resolution"] = fscres
modq["rmeasure"] = apRecon.runRMeasure(apix, outfile)
modq["md5sum"] = apFile.md5sumfile(outfile)
modq["maxjump"] = self.params["avgjump"]
modq["sigma"] = self.params["sigma"]
modq["hard"] = self.params["hard"]
modq["symmetry"] = symdata
modq["refineIter"] = self.params["refineiter"]
if self.params["commit"] is True:
modq.insert()
apChimera.filterAndChimera(
outfile,
res=fscres,
apix=apix,
box=box,
chimtype="snapshot",
zoom=self.params["zoom"],
sym=self.params["sym"],
mass=self.params["mass"],
)
else:
apDisplay.printError("no 3d volume was generated - check the class averages:")
apDisplay.printError(self.params["stackname"])
apDisplay.printError("hard may be set too high, or avg euler jump set too low for the # of particles")
stackstr = str(stackdata.dbid)
reconstr = str(self.params["reconid"])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n"
+ "subStack.py --projectid="
+ str(self.params["projectid"])
+ " -s "
+ stackstr
+ " \\\n "
+ " -k "
+ os.path.join(self.params["rundir"], "keep.lst")
+ " \\\n "
+ " -d 'recon "
+ reconstr
+ " sitters' -n sitters"
+ reconstr
+ " -C ",
"purple",
)
def start(self):
self.rootname = self.params['stackname'].split(".")[0]
self.params['outputstack'] = os.path.join(self.params['rundir'], self.params['stackname'])
if os.path.isfile(self.params['outputstack']):
apFile.removeStack(self.params['outputstack'])
if self.params['eotest'] is True:
self.params['evenstack'] = os.path.splitext(self.params['outputstack'])[0]+'.even.hed'
if os.path.isfile(self.params['evenstack']):
apFile.removeStack(self.params['evenstack'])
self.params['oddstack'] = os.path.splitext(self.params['outputstack'])[0]+'.odd.hed'
if os.path.isfile(self.params['oddstack']):
apFile.removeStack(self.params['oddstack'])
classes = self.getClassData(self.params['reconid'], self.params['iter'])
stackid = apStack.getStackIdFromRecon(self.params['reconid'])
stackdata = apStack.getOnlyStackData(stackid)
stackpath = os.path.join(stackdata['path']['path'], stackdata['name'])
classkeys = classes.keys()
classkeys.sort()
classnum=0
keeplist = self.procKeepList()
finallist = []
apDisplay.printMsg("Processing "+str(len(classes))+" classes")
#loop through classes
for key in classkeys:
classnum+=1
if classnum%10 == 1:
sys.stderr.write("\b\b\b\b\b\b\b\b\b\b\b\b\b\b")
sys.stderr.write(str(classnum)+" of "+(str(len(classkeys))))
# loop through particles in class
classfile = self.rootname+"-class.lst"
classf = open(classfile, 'w')
classf.write('#LST\n')
nptcls=0
for ptcl in classes[key]['particles']:
# translate DB into EMAN
partnum = ptcl['particle']['particleNumber'] - 1
if partnum in keeplist:
if ptcl['mirror']:
mirror=1
else:
mirror=0
rot = ptcl['euler3']*math.pi/180.0
classf.write(
"%d\t%s\t%f,\t%f,%f,%f,%d\n" %
(partnum, stackpath, ptcl['quality_factor'],
rot, ptcl['shiftx'], ptcl['shifty'], mirror))
nptcls+=1
finallist.append(partnum)
classf.close()
if nptcls<1:
continue
self.makeClassAverages(classfile, self.params['outputstack'], classes[key], self.params['mask'])
if self.params['eotest'] is True:
self.makeEvenOddClasses(classfile, self.params['outputstack'], classes[key], self.params['mask'])
apFile.removeFile(classfile)
sys.stderr.write("\n")
finalfilename = self.rootname+"-keep.lst"
finalf = open(finalfilename, 'w')
finallist.sort()
for partnum in finallist:
finalf.write('%d\n' % (partnum,) )
finalf.close()
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
### recon 3d volumes
threedname = os.path.join(self.params['rundir'], self.rootname+"."+str(self.params['iter'])+"a.mrc")
emancmd = ( "make3d "+self.params['outputstack']+" out="
+threedname+" hard=50 sym="+self.params['symmname']+" pad=240 mask="+str(self.params['mask'])+"; echo ''" )
#print emancmd
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True, logfile=self.rootname+"-eman.log")
threednameb = os.path.join(self.params['rundir'], self.rootname+"."+str(self.params['iter'])+"b.mrc")
emancmd = ( "proc3d "+threedname+" "+threednameb
+" apix=1.63 norm=0,1 lp=8 origin=0,0,0 mask="+str(self.params['mask'])+"; echo '' " )
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True, logfile=self.rootname+"-eman.log")
if self.params['eotest'] is True:
# even
evenname = os.path.join(self.params['rundir'], self.rootname+"-even."+str(self.params['iter'])+"a.mrc")
if os.path.isfile(self.params['evenstack']):
evenemancmd = ( "make3d "+self.params['evenstack']+" out="
+evenname+" hard=50 sym="+self.params['symmname']+" pad=240 mask="+str(self.params['mask'])+"; echo ''" )
#print evenemancmd
apEMAN.executeEmanCmd(evenemancmd, verbose=False, showcmd=True, logfile=self.rootname+"-eveneman.log")
else:
apDisplay.printWarning("file "+self.params['evenstack']+" does not exist")
# odd
oddname = os.path.join(self.params['rundir'], self.rootname+"-odd."+str(self.params['iter'])+"a.mrc")
if os.path.isfile(self.params['oddstack']):
oddemancmd = ( "make3d "+self.params['oddstack']+" out="
+oddname+" hard=50 sym="+self.params['symmname']+" pad=240 mask="+str(self.params['mask'])+"; echo ''" )
#print oddemancmd
apEMAN.executeEmanCmd(oddemancmd, verbose=False, showcmd=True, logfile=self.rootname+"-oddeman.log")
else:
apDisplay.printWarning("file "+self.params['oddstack']+" does not exist")
#eotest
fscout = os.path.join(self.params['rundir'], self.rootname+"-fsc.eotest")
if os.path.isfile(oddname) and os.path.isfile(evenname):
eotestcmd = "proc3d "+oddname+" "+evenname+" fsc="+fscout
apEMAN.executeEmanCmd(eotestcmd, verbose=True, showcmd=True)
else:
apDisplay.printWarning("could not perform eotest")
if os.path.isfile(fscout):
res = apRecon.getResolutionFromFSCFile(fscout, 160.0, 1.63)
apDisplay.printColor( ("resolution: %.5f" % (res)), "cyan")
resfile = self.rootname+"-res.txt"
f = open(resfile, 'a')
f.write("[ %s ]\nresolution: %.5f\n" % (time.asctime(), res))
f.close()