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 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 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 makeEulerDoc(self, tiltParticlesData):
count = 0
eulerfile = os.path.join(self.params['rundir'],
"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.getParticleTiltRotationAngles(
stackpartdata)
if tiltrot is None:
apDisplay.printError("BAD particle " + str(stackpartdata))
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 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):
count = 0
eulerfile = os.path.join(self.params['rundir'], "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.getParticleTiltRotationAngles(stackpartdata)
if tiltrot is None:
apDisplay.printError("BAD particle "+str(stackpartdata))
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 getGoodAlignParticles(self):
includeParticle = []
tiltParticlesData = []
nopairParticle = 0
excludeParticle = 0
badmirror = 0
badscore = 0
apDisplay.printMsg("Sorting particles from classes at " +
time.asctime())
count = 0
startmem = mem.active()
t0 = time.time()
if self.params['clusterid'] is not None:
### method 1: get particles from clustering data
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq[
'clusterstack'] = appiondata.ApClusteringStackData.direct_query(
self.params['clusterid'])
clusterpartdatas = clusterpartq.query()
apDisplay.printMsg("Sorting " + str(len(clusterpartdatas)) +
" clustered particles")
for clustpart in clusterpartdatas:
count += 1
if count % 50 == 0:
sys.stderr.write(".")
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 3:
apDisplay.printColor(
"Memory increase: %d MB/part" % (memdiff), "red")
#write to text file
clustnum = clustpart['refnum'] - 1
if self.params['minscore'] is not None:
if (clustpart['alignparticle']['score'] is not None
and clustpart['alignparticle']['score'] <
self.params['minscore']):
badscore += 1
continue
elif (clustpart['alignparticle']['spread'] is not None
and clustpart['alignparticle']['spread'] <
self.params['minscore']):
badscore += 1
continue
if clustnum in self.classlist:
notstackpartnum = clustpart['alignparticle']['stackpart'][
'particleNumber']
tiltstackpartdata = apTiltPair.getStackParticleTiltPair(
self.params['notstackid'], notstackpartnum,
self.params['tiltstackid'])
if tiltstackpartdata is None:
nopairParticle += 1
continue
tiltrot, theta, notrot, tiltangle = apTiltPair.getParticleTiltRotationAngles(
tiltstackpartdata)
if tiltrot is None:
apDisplay.printWarning("BAD particle " +
str(tiltstackpartdata))
nopairParticle += 1
continue
else:
inplane, mirror = self.getParticleInPlaneRotation(
tiltstackpartdata)
if (self.params['mirror'] == "all" or
(self.params['mirror'] == "no" and mirror is False)
or (self.params['mirror'] == "yes"
and mirror is True)):
emantiltstackpartnum = tiltstackpartdata[
'particleNumber'] - 1
includeParticle.append(emantiltstackpartnum)
tiltParticlesData.append(tiltstackpartdata)
if self.params['numpart'] is not None and len(
includeParticle) > self.params['numpart']:
break
else:
badmirror += 1
else:
excludeParticle += 1
else:
### method 2: get particles from alignment data
alignpartq = appiondata.ApAlignParticleData()
alignpartq['alignstack'] = self.alignstackdata
alignpartdatas = alignpartq.query()
apDisplay.printMsg("Sorting " + str(len(alignpartdatas)) +
" aligned particles")
for alignpart in alignpartdatas:
count += 1
if count % 50 == 0:
sys.stderr.write(".")
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 3:
apDisplay.printColor(
"Memory increase: %d MB/part" % (memdiff), "red")
#write to text file
alignnum = alignpart['ref']['refnum'] - 1
if (self.params['minscore'] is not None
and alignpart['score'] is not None
and alignpart['score'] < self.params['minscore']):
badscore += 1
continue
if alignnum in self.classlist:
notstackpartnum = alignpart['stackpart']['particleNumber']
tiltstackpartdata = apTiltPair.getStackParticleTiltPair(
self.params['notstackid'], notstackpartnum,
self.params['tiltstackid'])
if tiltstackpartdata is None:
nopairParticle += 1
else:
inplane, mirror = self.getParticleInPlaneRotation(
tiltstackpartdata)
if (self.params['mirror'] == "all" or
(self.params['mirror'] == "no" and mirror is False)
or (self.params['mirror'] == "yes"
and mirror is True)):
emantiltstackpartnum = tiltstackpartdata[
'particleNumber'] - 1
includeParticle.append(emantiltstackpartnum)
tiltParticlesData.append(tiltstackpartdata)
if self.params['numpart'] is not None and len(
includeParticle) > self.params['numpart']:
break
else:
badmirror += 1
else:
excludeParticle += 1
### end methods
includeParticle.sort()
### messages
if time.time() - t0 > 1.0:
apDisplay.printMsg("\nSorting time: " +
apDisplay.timeString(time.time() - t0))
apDisplay.printMsg("Keeping " + str(len(includeParticle)) +
" and excluding \n\t" + str(excludeParticle) +
" particles with " + str(nopairParticle) +
" unpaired particles")
if badmirror > 0:
apDisplay.printMsg("Particles with bad mirrors: %d" % (badmirror))
if badscore > 0:
apDisplay.printColor("Particles with bad scores: %d" % (badscore),
"cyan")
if len(includeParticle) < 1:
apDisplay.printError("No particles were kept")
memdiff = (mem.active() - startmem) / count / 1024.0
if memdiff > 0.1:
apDisplay.printColor("Memory increase: %.2f MB/part" % (memdiff),
"red")
return includeParticle, tiltParticlesData
def getGoodAlignParticles(self):
includeParticle = []
tiltParticlesData = []
nopairParticle = 0
excludeParticle = 0
badmirror = 0
badscore = 0
apDisplay.printMsg("Sorting particles from classes at "+time.asctime())
count = 0
startmem = mem.active()
t0 = time.time()
if self.params['clusterid'] is not None:
### method 1: get particles from clustering data
clusterpartq = appiondata.ApClusteringParticleData()
clusterpartq['clusterstack'] = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
clusterpartdatas = clusterpartq.query()
apDisplay.printMsg("Sorting "+str(len(clusterpartdatas))+" clustered particles")
for clustpart in clusterpartdatas:
count += 1
if count%50 == 0:
sys.stderr.write(".")
memdiff = (mem.active()-startmem)/count/1024.0
if memdiff > 3:
apDisplay.printColor("Memory increase: %d MB/part"%(memdiff), "red")
#write to text file
clustnum = clustpart['refnum']-1
if self.params['minscore'] is not None:
if ( clustpart['alignparticle']['score'] is not None
and clustpart['alignparticle']['score'] < self.params['minscore'] ):
badscore += 1
continue
elif ( clustpart['alignparticle']['spread'] is not None
and clustpart['alignparticle']['spread'] < self.params['minscore'] ):
badscore += 1
continue
if clustnum in self.classlist:
notstackpartnum = clustpart['alignparticle']['stackpart']['particleNumber']
tiltstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['notstackid'],
notstackpartnum, self.params['tiltstackid'])
if tiltstackpartdata is None:
nopairParticle += 1
continue
tiltrot, theta, notrot, tiltangle = apTiltPair.getParticleTiltRotationAngles(tiltstackpartdata)
if tiltrot is None:
apDisplay.printWarning("BAD particle "+str(tiltstackpartdata))
nopairParticle += 1
continue
else:
inplane, mirror = self.getParticleInPlaneRotation(tiltstackpartdata)
if ( self.params['mirror'] == "all"
or (self.params['mirror'] == "no" and mirror is False)
or (self.params['mirror'] == "yes" and mirror is True) ):
emantiltstackpartnum = tiltstackpartdata['particleNumber']-1
includeParticle.append(emantiltstackpartnum)
tiltParticlesData.append(tiltstackpartdata)
if self.params['numpart'] is not None and len(includeParticle) > self.params['numpart']:
break
else:
badmirror += 1
else:
excludeParticle += 1
else:
### method 2: get particles from alignment data
alignpartq = appiondata.ApAlignParticleData()
alignpartq['alignstack'] = self.alignstackdata
alignpartdatas = alignpartq.query()
apDisplay.printMsg("Sorting "+str(len(alignpartdatas))+" aligned particles")
for alignpart in alignpartdatas:
count += 1
if count%50 == 0:
sys.stderr.write(".")
memdiff = (mem.active()-startmem)/count/1024.0
if memdiff > 3:
apDisplay.printColor("Memory increase: %d MB/part"%(memdiff), "red")
#write to text file
alignnum = alignpart['ref']['refnum']-1
if ( self.params['minscore'] is not None
and alignpart['score'] is not None
and alignpart['score'] < self.params['minscore'] ):
badscore += 1
continue
if alignnum in self.classlist:
notstackpartnum = alignpart['stackpart']['particleNumber']
tiltstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['notstackid'],
notstackpartnum, self.params['tiltstackid'])
if tiltstackpartdata is None:
nopairParticle += 1
else:
inplane, mirror = self.getParticleInPlaneRotation(tiltstackpartdata)
if ( self.params['mirror'] == "all"
or (self.params['mirror'] == "no" and mirror is False)
or (self.params['mirror'] == "yes" and mirror is True) ):
emantiltstackpartnum = tiltstackpartdata['particleNumber']-1
includeParticle.append(emantiltstackpartnum)
tiltParticlesData.append(tiltstackpartdata)
if self.params['numpart'] is not None and len(includeParticle) > self.params['numpart']:
break
else:
badmirror += 1
else:
excludeParticle += 1
### end methods
includeParticle.sort()
### messages
if time.time()-t0 > 1.0:
apDisplay.printMsg("\nSorting time: "+apDisplay.timeString(time.time()-t0))
apDisplay.printMsg("Keeping "+str(len(includeParticle))+" and excluding \n\t"
+str(excludeParticle)+" particles with "+str(nopairParticle)+" unpaired particles")
if badmirror > 0:
apDisplay.printMsg("Particles with bad mirrors: %d"%(badmirror))
if badscore > 0:
apDisplay.printColor("Particles with bad scores: %d"%(badscore), "cyan")
if len(includeParticle) < 1:
apDisplay.printError("No particles were kept")
memdiff = (mem.active()-startmem)/count/1024.0
if memdiff > 0.1:
apDisplay.printColor("Memory increase: %.2f MB/part"%(memdiff), "red")
return includeParticle, tiltParticlesData
