def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['start'] is None:
apDisplay.printError("a number of starting classes was not provided")
if self.params['end'] is None:
apDisplay.printError("a number of ending classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] is None:
self.params['numpart'] = npart
elif self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
self.boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.workingboxsize = math.floor(self.boxsize/self.params['bin'])
if not self.params['mask']:
self.params['mask'] = (self.boxsize/2)-2
self.workingmask = math.floor(self.params['mask']/self.params['bin'])
if self.params['mramethod'] == 'imagic':
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
self.stackdata = apStack.getOnlyStackData(self.params['stackid'],
msg=False)
stackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(
self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(
boxsize / float(self.params['bin'] * 2))) * 2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d" %
(self.params['clipsize'], self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
self.mpirun = self.checkMPI()
if self.mpirun is None:
apDisplay.printError("There is no MPI installed")
if self.params['nproc'] is None:
self.params['nproc'] = self.params['nodes'] * self.params['ppn']
if self.params['nproc'] < 2:
apDisplay.printError(
"Only the MPI version of CL2D is currently supported, must run with > 1 CPU"
)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
#if self.params['description'] is None:
# apDisplay.printError("run description was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: " +
str(self.fastmodes))
if not self.params['converge'] in self.convergemodes:
apDisplay.printError("converge mode must be on of: " +
str(self.convergemodes))
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
self.stackdata = apStack.getOnlyStackData(self.params['stackid'],
msg=False)
stackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(
self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(
boxsize / float(self.params['bin'] * 2))) * 2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d" %
(self.params['clipsize'], self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
#if self.params['description'] is None:
# apDisplay.printError("run description was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: "+str(self.fastmodes))
if not self.params['converge'] in self.convergemodes:
apDisplay.printError("converge mode must be on of: "+str(self.convergemodes))
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
self.mpirun = self.checkMPI()
if self.mpirun is None:
apDisplay.printError("There is no MPI installed")
if self.params['nproc'] is None:
self.params['nproc'] = self.params['nodes']*self.params['ppn']
if self.params['nproc'] < 2:
apDisplay.printError("Only the MPI version of CL2D is currently supported, must run with > 1 CPU")
if __name__ == "__main__":
params = parseOptions()
apProject.setDBfromProjectId(params["projectid"])
stackdata = apStack.getOnlyStackData(params["stackid"])
stackpath = stackdata["path"]["path"]
# generate stack if it doesn't exist.
if not os.path.isdir(stackpath):
os.makedirs(stackpath)
fname = os.path.join(stackpath, stackdata["name"])
# check if stack file already exists
if os.path.isfile(fname):
apDisplay.printError("file: '%s' already exists" % fname)
vstackdata = apStack.getVirtualStackParticlesFromId(params["stackid"])
plist = [int(p["particleNumber"]) - 1 for p in vstackdata["particles"]]
a = proc2dLib.RunProc2d()
a.setValue("infile", vstackdata["filename"])
a.setValue("outfile", fname)
a.setValue("list", plist)
a.setValue("apix", apStack.getStackPixelSizeFromStackId(params["stackid"]))
apDisplay.printMsg("generating stack: '%s' with %i particles" % (fname, len(plist)))
a.run()
outavg = os.path.join(stackpath, "average.mrc")
if not os.path.isfile(outavg):
apStack.averageStack(stack=fname, outfile=outavg)
if __name__ == "__main__":
params = parseOptions()
apProject.setDBfromProjectId(params['projectid'])
stackdata = apStack.getOnlyStackData(params['stackid'])
stackpath = stackdata['path']['path']
# generate stack if it doesn't exist.
if not os.path.isdir(stackpath):
os.makedirs(stackpath)
fname = os.path.join(stackpath, stackdata['name'])
# check if stack file already exists
if os.path.isfile(fname):
apDisplay.printError("file: '%s' already exists" % fname)
vstackdata = apStack.getVirtualStackParticlesFromId(params['stackid'])
plist = [int(p['particleNumber']) - 1 for p in vstackdata['particles']]
a = proc2dLib.RunProc2d()
a.setValue('infile', vstackdata['filename'])
a.setValue('outfile', fname)
a.setValue('list', plist)
a.setValue('apix', apStack.getStackPixelSizeFromStackId(params['stackid']))
apDisplay.printMsg("generating stack: '%s' with %i particles" %
(fname, len(plist)))
a.run()
outavg = os.path.join(stackpath, "average.mrc")
if not os.path.isfile(outavg):
apStack.averageStack(stack=fname, outfile=outavg)
def makeStackMeanPlot(stackid, gridpoints=16):
if gridpoints > 30:
apDisplay.printError("Too large of a grid")
apDisplay.printMsg("creating Stack Mean Plot montage for stackid: "+str(stackid))
t0 = time.time()
### big stacks are too slow
boxsize = apStack.getStackBoxsize(stackid)
bin = 1
if boxsize is not None:
while boxsize/bin > 128:
bin+=1
apDisplay.printMsg("binning stack by "+str(bin))
stackdata = apStack.getOnlyStackData(stackid, msg=False)
stackpath = stackdata['path']['path']
stackfile = os.path.join(stackpath, stackdata['name'])
# if no stackfile, likely virtual stack
if not os.path.isfile(stackfile):
apDisplay.printMsg("possible virtual stack, searching for original stack")
vstackdata = apStack.getVirtualStackParticlesFromId(stackid)
partdatas = vstackdata['particles']
stackfile = vstackdata['filename']
stackdata = apStack.getOnlyStackData(vstackdata['stackid'], msg=False)
# otherwise get stack info
else:
# get stats from stack:
sqlcmd = "SELECT " + \
"particleNumber, mean, stdev " + \
"FROM ApStackParticleData " + \
"WHERE `REF|ApStackData|stack` = %i"%(stackid)
partdatas = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
#check only first 100 particles for now
#partdatas = partdatas[:500]
apFile.removeFile("montage"+str(stackid)+".png")
### find limits
limits = {'minmean': 1e12, 'maxmean': -1e12, 'minstdev': 1e12, 'maxstdev': -1e12,}
for partdata in partdatas:
if partdata['mean'] is None:
continue
mean = partdata['mean']
stdev = partdata['stdev']
if mean < limits['minmean']:
limits['minmean'] = mean
if mean > limits['maxmean']:
limits['maxmean'] = mean
if stdev < limits['minstdev']:
limits['minstdev'] = stdev
if stdev > limits['maxstdev']:
limits['maxstdev'] = stdev
if limits['minmean'] > 1e11:
apDisplay.printWarning("particles have no mean values in database")
return
apDisplay.printMsg(str(limits))
### create particle bins
partlists = {}
for i in range(gridpoints):
for j in range(gridpoints):
key = ("%02dx%02d"%(i,j))
partlists[key] = []
### sort particles into bins
for partdata in partdatas:
key = meanStdevToKey(partdata['mean'], partdata['stdev'], limits, gridpoints)
partnum = int(partdata['particleNumber'])
partlists[key].append(partnum)
printPlot(partlists, gridpoints)
### createStackAverages
keys = partlists.keys()
keys.sort()
count = 0
backs = "\b\b\b\b\b\b\b\b\b\b\b"
montagestack = os.path.join(stackpath,"montage"+str(stackid)+".hed")
apFile.removeStack(montagestack)
mystack = []
for key in keys:
count += 1
sys.stderr.write(backs+backs+backs+backs)
sys.stderr.write("% 3d of % 3d, %s: % 6d"%(count, len(keys), key, len(partlists[key])))
avgimg = averageSubStack(partlists[key], stackfile, bin)
if avgimg is not False:
avgimg = numpy.fliplr(avgimg)
mystack.append(avgimg)
apImagicFile.writeImagic(mystack, montagestack)
sys.stderr.write("\n")
assemblePngs(keys, str(stackid), montagestack)
apDisplay.printMsg("/bin/mv -v montage"+str(stackid)+".??? "+stackpath)
apDisplay.printMsg("finished in "+apDisplay.timeString(time.time()-t0))
def start(self):
### new stack path
stackdata = apStack.getOnlyStackData(self.params["stackid"])
oldstack = os.path.join(stackdata["path"]["path"], stackdata["name"])
newstack = os.path.join(self.params["rundir"], stackdata["name"])
apStack.checkForPreviousStack(newstack)
includelist = []
excludelist = []
### list of classes to be excluded
if self.params["dropclasslist"] is not None:
excludestrlist = self.params["dropclasslist"].split(",")
for excludeitem in excludestrlist:
excludelist.append(int(excludeitem.strip()))
apDisplay.printMsg("Exclude list: " + str(excludelist))
### list of classes to be included
if self.params["keepclasslist"] is not None:
includestrlist = self.params["keepclasslist"].split(",")
for includeitem in includestrlist:
includelist.append(int(includeitem.strip()))
### or read from keepfile
elif self.params["keepfile"] is not None:
keeplistfile = open(self.params["keepfile"])
for line in keeplistfile:
if self.params["excludefrom"] is True:
excludelist.append(int(line.strip()))
else:
includelist.append(int(line.strip()))
keeplistfile.close()
apDisplay.printMsg("Include list: " + str(includelist))
### get particles from align or cluster stack
apDisplay.printMsg("Querying database for particles")
q0 = time.time()
if self.params["alignid"] is not None:
# DIRECT SQL STUFF
sqlcmd = (
"SELECT "
+ "apd.partnum, "
+ "apd.xshift, apd.yshift, "
+ "apd.rotation, apd.mirror, "
+ "apd.spread, apd.correlation, "
+ "apd.score, apd.bad, "
+ "spd.particleNumber, "
+ "ard.refnum "
+ "FROM ApAlignParticleData apd "
+ "LEFT JOIN ApStackParticleData spd ON "
+ "(apd.`REF|ApStackParticleData|stackpart` = spd.DEF_id) "
+ "LEFT JOIN ApAlignReferenceData ard ON"
+ "(apd.`REF|ApAlignReferenceData|ref` = ard.DEF_id) "
+ "WHERE `REF|ApAlignStackData|alignstack` = %i" % (self.params["alignid"])
)
# These are AlignParticles
particles = sinedon.directq.complexMysqlQuery("appiondata", sqlcmd)
elif self.params["clusterid"] is not None:
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq["clusterstack"] = self.clusterstackdata
# These are ClusteringParticles
particles = clusterpartq.query()
apDisplay.printMsg("Completed in %s\n" % (apDisplay.timeString(time.time() - q0)))
### write included particles to text file
includeParticle = []
excludeParticle = 0
badscore = 0
badshift = 0
badspread = 0
f = open("test.log", "w")
count = 0
t0 = time.time()
apDisplay.printMsg("Parsing particle information")
# find out if there is alignparticle info:
is_cluster_p = False
# alignparticle is a key of any particle in particles if the latter is
# a CluateringParticle
if "alignparticle" in particles[0]:
is_cluster_p = True
for part in particles:
count += 1
if is_cluster_p:
# alignpart is an item of ClusteringParticle
alignpart = part["alignparticle"]
try:
classnum = int(part["refnum"]) - 1
except:
apDisplay.printWarning("particle %d was not put into any class" % (part["partnum"]))
emanstackpartnum = alignpart["stackpart"]["particleNumber"] - 1
else:
# particle has info from AlignedParticle as results of direct query
alignpart = part
try:
classnum = int(alignpart["refnum"]) - 1
except:
apDisplay.printWarning("particle %d was not put into any class" % (part["partnum"]))
classnum = None
emanstackpartnum = int(alignpart["particleNumber"]) - 1
### check shift
if self.params["maxshift"] is not None:
shift = math.hypot(alignpart["xshift"], alignpart["yshift"])
if shift > self.params["maxshift"]:
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n" % (count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n" % (count, emanstackpartnum))
badshift += 1
continue
if self.params["minscore"] is not None:
### check score
if alignpart["score"] is not None and alignpart["score"] < self.params["minscore"]:
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n" % (count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n" % (count, emanstackpartnum))
badscore += 1
continue
### check spread
if alignpart["spread"] is not None and alignpart["spread"] < self.params["minscore"]:
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n" % (count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n" % (count, emanstackpartnum))
badspread += 1
continue
if classnum is not None:
if includelist and (classnum in includelist):
includeParticle.append(emanstackpartnum)
f.write("%d\t%d\t%d\tinclude\n" % (count, emanstackpartnum, classnum))
elif excludelist and not (classnum in excludelist):
includeParticle.append(emanstackpartnum)
f.write("%d\t%d\t%d\tinclude\n" % (count, emanstackpartnum, classnum))
else:
excludeParticle += 1
f.write("%d\t%d\t%d\texclude\n" % (count, emanstackpartnum, classnum))
else:
excludeParticle += 1
f.write("%d\t%d\texclude\n" % (count, emanstackpartnum))
f.close()
includeParticle.sort()
if badshift > 0:
apDisplay.printMsg("%d paricles had a large shift" % (badshift))
if badscore > 0:
apDisplay.printMsg("%d paricles had a low score" % (badscore))
if badspread > 0:
apDisplay.printMsg("%d paricles had a low spread" % (badspread))
apDisplay.printMsg("Completed in %s\n" % (apDisplay.timeString(time.time() - t0)))
apDisplay.printMsg(
"Keeping " + str(len(includeParticle)) + " and excluding " + str(excludeParticle) + " particles"
)
### write kept particles to file
self.params["keepfile"] = os.path.join(self.params["rundir"], "keepfile-" + self.timestamp + ".list")
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()
### get number of particles
numparticles = len(includeParticle)
if excludelist:
self.params["description"] += " ... %d particle substack with %s classes excluded" % (
numparticles,
self.params["dropclasslist"],
)
elif includelist:
self.params["description"] += " ... %d particle substack with %s classes included" % (
numparticles,
self.params["keepclasslist"],
)
outavg = os.path.join(self.params["rundir"], "average.mrc")
### create the new sub stack
# first check if virtual stack
if not os.path.isfile(oldstack):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params["stackid"])
vparts = vstackdata["particles"]
oldstack = vstackdata["filename"]
# get subset of virtualstack
vpartlist = [int(vparts[p]["particleNumber"]) - 1 for p in includeParticle]
if self.params["writefile"] is True:
apStack.makeNewStack(oldstack, newstack, vpartlist, bad=self.params["savebad"])
apStack.averageStack(stack=oldstack, outfile=outavg, partlist=vpartlist)
else:
if self.params["writefile"] is True:
apStack.makeNewStack(oldstack, newstack, self.params["keepfile"], bad=self.params["savebad"])
apStack.averageStack(stack=oldstack, outfile=outavg, partlist=includeParticle)
if self.params["writefile"] is True and not os.path.isfile(newstack):
apDisplay.printError("No stack was created")
if self.params["commit"] is True:
apStack.commitSubStack(self.params, included=includeParticle)
newstackid = apStack.getStackIdFromPath(newstack)
apStackMeanPlot.makeStackMeanPlot(newstackid, gridpoints=4)
def start(self):
### new stack path
stackdata = apStack.getOnlyStackData(self.params['stackid'])
oldstack = os.path.join(stackdata['path']['path'], stackdata['name'])
newstack = os.path.join(self.params['rundir'], stackdata['name'])
apStack.checkForPreviousStack(newstack)
includelist = []
excludelist = []
### list of classes to be excluded
if self.params['dropclasslist'] is not None:
excludestrlist = self.params['dropclasslist'].split(",")
for excludeitem in excludestrlist:
excludelist.append(int(excludeitem.strip()))
apDisplay.printMsg("Exclude list: "+str(excludelist))
### list of classes to be included
if self.params['keepclasslist'] is not None:
includestrlist = self.params['keepclasslist'].split(",")
for includeitem in includestrlist:
includelist.append(int(includeitem.strip()))
### or read from keepfile
elif self.params['keepfile'] is not None:
keeplistfile = open(self.params['keepfile'])
for line in keeplistfile:
if self.params['excludefrom'] is True:
excludelist.append(int(line.strip()))
else:
includelist.append(int(line.strip()))
keeplistfile.close()
apDisplay.printMsg("Include list: "+str(includelist))
### get particles from align or cluster stack
apDisplay.printMsg("Querying database for particles")
q0 = time.time()
if self.params['alignid'] is not None:
# DIRECT SQL STUFF
sqlcmd = "SELECT " + \
"apd.partnum, " + \
"apd.xshift, apd.yshift, " + \
"apd.rotation, apd.mirror, " + \
"apd.spread, apd.correlation, " + \
"apd.score, apd.bad, " + \
"spd.particleNumber, " + \
"ard.refnum "+ \
"FROM ApAlignParticleData apd " + \
"LEFT JOIN ApStackParticleData spd ON " + \
"(apd.`REF|ApStackParticleData|stackpart` = spd.DEF_id) " + \
"LEFT JOIN ApAlignReferenceData ard ON" + \
"(apd.`REF|ApAlignReferenceData|ref` = ard.DEF_id) " + \
"WHERE `REF|ApAlignStackData|alignstack` = %i"%(self.params['alignid'])
# These are AlignParticles
particles = sinedon.directq.complexMysqlQuery('appiondata',sqlcmd)
elif self.params['clusterid'] is not None:
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = self.clusterstackdata
# These are ClusteringParticles
particles = clusterpartq.query()
apDisplay.printMsg("Completed in %s\n"%(apDisplay.timeString(time.time()-q0)))
### write included particles to text file
includeParticle = []
excludeParticle = 0
badscore = 0
badshift = 0
badspread = 0
f = open("test.log", "w")
count = 0
t0 = time.time()
apDisplay.printMsg("Parsing particle information")
# find out if there is alignparticle info:
is_cluster_p = False
# alignparticle is a key of any particle in particles if the latter is
# a CluateringParticle
if 'alignparticle' in particles[0]:
is_cluster_p = True
for part in particles:
count += 1
if is_cluster_p:
# alignpart is an item of ClusteringParticle
alignpart = part['alignparticle']
try:
classnum = int(part['refnum'])-1
except:
apDisplay.printWarning("particle %d was not put into any class" % (part['partnum']))
emanstackpartnum = alignpart['stackpart']['particleNumber']-1
else:
# particle has info from AlignedParticle as results of direct query
alignpart = part
try:
classnum = int(alignpart['refnum'])-1
except:
apDisplay.printWarning("particle %d was not put into any class" % (part['partnum']))
classnum = None
emanstackpartnum = int(alignpart['particleNumber'])-1
### check shift
if self.params['maxshift'] is not None:
shift = math.hypot(alignpart['xshift'], alignpart['yshift'])
if shift > self.params['maxshift']:
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n"%(count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n"%(count, emanstackpartnum))
badshift += 1
continue
if self.params['minscore'] is not None:
### check score
if ( alignpart['score'] is not None
and alignpart['score'] < self.params['minscore'] ):
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n"%(count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n"%(count, emanstackpartnum))
badscore += 1
continue
### check spread
if ( alignpart['spread'] is not None
and alignpart['spread'] < self.params['minscore'] ):
excludeParticle += 1
if classnum is not None:
f.write("%d\t%d\t%d\texclude\n"%(count, emanstackpartnum, classnum))
else:
f.write("%d\t%d\texclude\n"%(count, emanstackpartnum))
badspread += 1
continue
if classnum is not None:
if includelist and (classnum in includelist):
includeParticle.append(emanstackpartnum)
f.write("%d\t%d\t%d\tinclude\n"%(count, emanstackpartnum, classnum))
elif excludelist and not (classnum in excludelist):
includeParticle.append(emanstackpartnum)
f.write("%d\t%d\t%d\tinclude\n"%(count, emanstackpartnum, classnum))
else:
excludeParticle += 1
f.write("%d\t%d\t%d\texclude\n"%(count, emanstackpartnum, classnum))
else:
excludeParticle += 1
f.write("%d\t%d\texclude\n"%(count, emanstackpartnum))
f.close()
includeParticle.sort()
if badshift > 0:
apDisplay.printMsg("%d paricles had a large shift"%(badshift))
if badscore > 0:
apDisplay.printMsg("%d paricles had a low score"%(badscore))
if badspread > 0:
apDisplay.printMsg("%d paricles had a low spread"%(badspread))
apDisplay.printMsg("Completed in %s\n"%(apDisplay.timeString(time.time()-t0)))
apDisplay.printMsg("Keeping "+str(len(includeParticle))+" and excluding "+str(excludeParticle)+" particles")
### write kept particles to file
self.params['keepfile'] = os.path.join(self.params['rundir'], "keepfile-"+self.timestamp+".list")
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()
### get number of particles
numparticles = len(includeParticle)
if excludelist:
self.params['description'] += ( " ... %d particle substack with %s classes excluded"
% (numparticles, self.params['dropclasslist']))
elif includelist:
self.params['description'] += ( " ... %d particle substack with %s classes included"
% (numparticles, self.params['keepclasslist']))
outavg = os.path.join(self.params['rundir'],"average.mrc")
### create the new sub stack
# first check if virtual stack
if not os.path.isfile(oldstack):
vstackdata=apStack.getVirtualStackParticlesFromId(self.params['stackid'])
vparts = vstackdata['particles']
oldstack = vstackdata['filename']
# get subset of virtualstack
vpartlist = [int(vparts[p]['particleNumber'])-1 for p in includeParticle]
if self.params['writefile'] is True:
apStack.makeNewStack(oldstack, newstack, vpartlist, bad=self.params['savebad'])
apStack.averageStack(stack=oldstack,outfile=outavg,partlist=vpartlist)
else:
if self.params['writefile'] is True:
apStack.makeNewStack(oldstack, newstack, self.params['keepfile'], bad=self.params['savebad'])
apStack.averageStack(stack=oldstack,outfile=outavg,partlist=includeParticle)
if self.params['writefile'] is True and not os.path.isfile(newstack):
apDisplay.printError("No stack was created")
if self.params['commit'] is True:
apStack.commitSubStack(self.params,included=includeParticle)
newstackid = apStack.getStackIdFromPath(newstack)
apStackMeanPlot.makeStackMeanPlot(newstackid, gridpoints=4)
