def insertJumpIntoDB(self,
stackpartid,
jumpdata,
reconrunid=None,
multimodelrunid=None):
if reconrunid is None and multimodelrunid is None:
return None
else:
if multimodelrunid is None:
#refinerundata=appiondata.ApRefineRunData.direct_query(reconid)
ejumpq = appiondata.ApEulerJumpData()
ejumpq[
'particle'] = appiondata.ApStackParticleData.direct_query(
stackpartid)
ejumpq['refineRun'] = appiondata.ApRefineRunData.direct_query(
reconrunid)
for key in ('median', 'mean', 'stdev', 'min', 'max'):
ejumpq[key] = jumpdata[key]
ejumpq.insert()
else:
ejumpq = appiondata.ApEulerJumpData()
ejumpq[
'particle'] = appiondata.ApStackParticleData.direct_query(
stackpartid)
ejumpq[
'multiModelRefineRun'] = appiondata.ApMultiModelRefineRunData.direct_query(
multimodelrunid)
for key in ('median', 'mean', 'stdev', 'min', 'max'):
ejumpq[key] = jumpdata[key]
ejumpq.insert()
def getJumpDataFromDB(self,
stackpartid,
reconrunid=None,
multimodelrunid=None):
if reconrunid is None and multimodelrunid is None:
return None
elif reconrunid is not None and multimodelrunid is None:
jumpq = appiondata.ApEulerJumpData()
jumpq['particle'] = appiondata.ApStackParticleData.direct_query(
stackpartid)
jumpq['refineRun'] = appiondata.ApRefineRunData.direct_query(
reconrunid)
jumpdatas = jumpq.query(results=1)
if not jumpdatas:
return None
return jumpdatas[0]
elif reconrunid is None and multimodelrunid is not None:
jumpq = appiondata.ApEulerJumpData()
jumpq['particle'] = appiondata.ApStackParticleData.direct_query(
stackpartid)
jumpq[
'multiModelRefineRun'] = appiondata.ApMultiModelRefineRunData.direct_query(
multimodelrunid)
jumpdatas = jumpq.query(results=1)
if not jumpdatas:
return None
return jumpdatas[0]
else:
return None
def start(self):
### new stack path
oldstack = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
newstack = os.path.join(self.params['rundir'], self.stackdata['name'])
apStack.checkForPreviousStack(newstack)
### get particles from stack
apDisplay.printMsg("Querying stack particles")
t0 = time.time()
stackpartq = appiondata.ApStackParticleData()
stackpartq['stack'] = self.stackdata
particles = stackpartq.query()
apDisplay.printMsg("Finished in " +
apDisplay.timeString(time.time() - t0))
### write included particles to text file
includeParticle = []
excludeParticle = 0
f = open("test.log", "w")
count = 0
apDisplay.printMsg("Processing stack particles")
t0 = time.time()
for part in particles:
count += 1
if count % 500 == 0:
sys.stderr.write(".")
emanstackpartnum = part['particleNumber'] - 1
### get euler jump data
jumpq = appiondata.ApEulerJumpData()
jumpq['particle'] = part
jumpq['refineRun'] = self.recondata
jumpdatas = jumpq.query(results=1)
if not jumpdatas or len(jumpdatas) < 1:
### no data
continue
jumpdata = jumpdatas[0]
if jumpdata['median'] is None or jumpdata['median'] > self.params[
'maxjump']:
### bad particle
excludeParticle += 1
f.write("%d\t%d\t%.1f\texclude\n" %
(count, emanstackpartnum, jumpdata['median']))
else:
### good particle
includeParticle.append(emanstackpartnum)
f.write("%d\t%d\t%.1f\tinclude\n" %
(count, emanstackpartnum, jumpdata['median']))
sys.stderr.write("\n")
apDisplay.printMsg("Finished in " +
apDisplay.timeString(time.time() - t0))
f.close()
includeParticle.sort()
apDisplay.printMsg("Keeping " + str(len(includeParticle)) +
" and excluding " + str(excludeParticle) +
" particles")
#print includeParticle
### 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)
self.params['description'] += (" ... %d no jumpers substack" %
(numparticles, ))
### create the new sub stack
apStack.makeNewStack(oldstack,
newstack,
self.params['keepfile'],
bad=True)
if not os.path.isfile(newstack):
apDisplay.printError("No stack was created")
apStack.averageStack(stack=newstack)
if self.params['commit'] is True:
apStack.commitSubStack(self.params)
newstackid = apStack.getStackIdFromPath(newstack)
apStackMeanPlot.makeStackMeanPlot(newstackid, gridpoints=6)