def getParticleInPlaneRotation(self, tiltstackpartdata):
partid = tiltstackpartdata.dbid
if partid in self.rotmirrorcache:
### use cached value
return self.rotmirrorcache[partid]
partnum = tiltstackpartdata['particleNumber']
notstackpartdata = apTiltPair.getStackParticleTiltPair(
self.params['tiltstackid'], partnum, self.params['notstackid'])
alignpartq = appiondata.ApAlignParticleData()
alignpartq['stackpart'] = notstackpartdata
alignpartq['alignstack'] = self.alignstackdata
alignpartdatas = alignpartq.query()
if not alignpartdatas or len(alignpartdatas) != 1:
apDisplay.printError(
"could not get inplane rotation for particle %d" %
(tiltstackpartdata['particleNumber']))
inplane = alignpartdatas[0]['rotation']
mirror = alignpartdatas[0]['mirror']
if alignpartdatas[0]['alignstack']['alignrun'][
'maxlikerun'] is not None:
# maxlike does mirror then rotation, and its rotation is negative relative to spider
# April 6, 2009: rotation is negative independent of mirror
inplane = -1.0 * inplane
self.rotmirrorcache[partid] = (inplane, mirror)
return inplane, mirror
def getGoodParticles(self, classpartdatas, norefclassnum):
includeParticle = []
tiltParticlesData = []
nopairParticle = 0
excludeParticle = 0
apDisplay.printMsg("sorting particles")
for classpart in classpartdatas:
#write to text file
classnum = classpart['classNumber']-1
if classnum == norefclassnum:
notstackpartnum = classpart['noref_particle']['particle']['particleNumber']
tiltstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['notstackid'],
notstackpartnum, self.params['tiltstackid'])
if tiltstackpartdata is None:
nopairParticle += 1
else:
emantiltstackpartnum = tiltstackpartdata['particleNumber']-1
includeParticle.append(emantiltstackpartnum)
tiltParticlesData.append(tiltstackpartdata)
else:
excludeParticle += 1
includeParticle.sort()
apDisplay.printMsg("Keeping "+str(len(includeParticle))+" and excluding \n\t"
+str(excludeParticle)+" particles with "+str(nopairParticle)+" unpaired particles")
if len(includeParticle) < 1:
apDisplay.printError("No particles were kept")
return includeParticle, tiltParticlesData
def getParticleNoRefInPlaneRotation(self, stackpartdata):
notstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['tiltstackid'],
stackpartdata['particleNumber'], self.params['notstackid'])
classpartq = appiondata.ApNoRefClassParticlesData()
classpartq['classRun'] = self.norefclassdata
norefpartq = appiondata.ApNoRefAlignParticlesData()
norefpartq['particle'] = notstackpartdata
classpartq['noref_particle'] = norefpartq
classpartdatas = classpartq.query(results=1)
if not classpartdatas or len(classpartdatas) != 1:
apDisplay.printError("could not get inplane rotation")
inplane = classpartdatas[0]['noref_particle']['rotation']
return inplane
def getParticleInPlaneRotation(self, tiltstackpartdata):
partid = tiltstackpartdata.dbid
if partid in self.rotmirrorcache:
### use cached value
return self.rotmirrorcache[partid]
partnum = tiltstackpartdata['particleNumber']
notstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['tiltstackid'],
partnum, self.params['notstackid'])
alignpartq = appiondata.ApAlignParticleData()
alignpartq['stackpart'] = notstackpartdata
alignpartq['alignstack'] = self.alignstackdata
alignpartdatas = alignpartq.query()
if not alignpartdatas or len(alignpartdatas) != 1:
apDisplay.printError("could not get inplane rotation for particle %d"%(tiltstackpartdata['particleNumber']))
inplane = alignpartdatas[0]['rotation']
mirror = alignpartdatas[0]['mirror']
self.rotmirrorcache[partid] = (inplane, mirror)
return inplane, mirror
def getParticleInPlaneRotation(self, tiltstackpartdata):
partid = tiltstackpartdata.dbid
if partid in self.rotmirrorcache:
### use cached value
return self.rotmirrorcache[partid]
partnum = tiltstackpartdata['particleNumber']
notstackpartdata = apTiltPair.getStackParticleTiltPair(self.params['tiltstackid'],
partnum, self.params['notstackid'])
alignpartq = appiondata.ApAlignParticleData()
alignpartq['stackpart'] = notstackpartdata
alignpartq['alignstack'] = self.alignstackdata
alignpartdatas = alignpartq.query()
if not alignpartdatas or len(alignpartdatas) != 1:
apDisplay.printError("could not get inplane rotation for particle %d"%(tiltstackpartdata['particleNumber']))
inplane = alignpartdatas[0]['rotation']
mirror = alignpartdatas[0]['mirror']
if alignpartdatas[0]['alignstack']['alignrun']['maxlikerun'] is not None:
# maxlike does mirror then rotation, and its rotation is negative relative to spider
# April 6, 2009: rotation is negative independent of mirror
inplane = -1.0*inplane
self.rotmirrorcache[partid] = (inplane, mirror)
return inplane, mirror
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
