def subStackCmd(self):
keepfile = os.path.join(self.params['rundir'],
"keeplist-tot" + self.datastr + ".lst")
stackdata = apStack.getRunsInStack(self.params['stackid'])
cmd = ("subStack.py " + " --projectid=" +
str(self.params['projectid']) + " --old-stack-id=" +
str(self.params['stackid']) + " --commit" +
" \\\n --keep-file=" + keepfile +
" \\\n --new-stack-name=sub-" +
stackdata[0]['stackRun']['stackRunName'] +
" \\\n --description='sat from recon " +
str(self.params['reconid']) + " iter " + str(self.iternum) +
" with angle " + str(self.params['angle']) + " +/- " +
str(self.params['cutrange']) + "' \n")
print "New subStack.py Command:"
apDisplay.printColor(cmd, "purple")
def subStackCmd(self): keepfile = os.path.join(self.params['rundir'], "keeplist-tot"+self.datastr+".lst") stackdata = apStack.getRunsInStack(self.params['stackid']) cmd = ( "subStack.py " +" --projectid="+str(self.params['projectid']) +" --old-stack-id="+str(self.params['stackid']) +" --commit" +" \\\n --keep-file="+keepfile +" \\\n --new-stack-name=sub-"+stackdata[0]['stackRun']['stackRunName'] +" \\\n --description='sat from recon "+str(self.params['reconid']) +" iter "+str(self.iternum) +" with angle "+str(self.params['angle']) +" +/- "+str(self.params['cutrange']) +"' \n" ) print "New subStack.py Command:" apDisplay.printColor(cmd, "purple")
def commitStack(self, stackid):
startpart = self.partnum
stackq = appiondata.ApStackData()
oldstackdata = apStack.getOnlyStackData(stackid)
stackq['name'] = self.params['stackfilename']
stackq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
stackq['description'] = self.params[
'description'] + " ... combined stack ids " + str(
self.params['stacks'])
stackq['substackname'] = self.params['runname']
stackq['hidden'] = False
stackq['pixelsize'] = self.newpixelsize * 1e-10
stackq['boxsize'] = self.newboxsize
rinstackdata = apStack.getRunsInStack(stackid)
for run in rinstackdata:
rinstackq = appiondata.ApRunsInStackData()
rinstackq['stack'] = stackq
rinstackq['stackRun'] = run['stackRun']
rinstackq.insert()
stpartsdata = apStack.getStackParticlesFromId(stackid)
apDisplay.printMsg("inserting " + str(len(stpartsdata)) +
" particles into DB")
for particle in stpartsdata:
stpartq = appiondata.ApStackParticleData()
stpartq['particleNumber'] = self.partnum
stpartq['stack'] = stackq
stpartq['stackRun'] = particle['stackRun']
stpartq['particle'] = particle['particle']
stpartq.insert()
self.partnum += 1
if self.partnum % 1000 == 0:
sys.stderr.write(".")
sys.stderr.write("\n")
apDisplay.printMsg("commited particles " + str(startpart) + "-" +
str(self.partnum))
return
def commitStack(self, stackid):
startpart = self.partnum
stackq = appiondata.ApStackData()
oldstackdata = apStack.getOnlyStackData(stackid)
stackq['name'] = self.params['stackfilename']
stackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
stackq['description'] = self.params['description']+" ... combined stack ids "+str(self.params['stacks'])
stackq['substackname'] = self.params['runname']
stackq['hidden'] = False
stackq['pixelsize'] = self.newpixelsize*1e-10
stackq['boxsize'] = self.newboxsize
rinstackdata = apStack.getRunsInStack(stackid)
for run in rinstackdata:
rinstackq = appiondata.ApRunsInStackData()
rinstackq['stack'] = stackq
rinstackq['stackRun'] = run['stackRun']
rinstackq.insert()
stpartsdata = apStack.getStackParticlesFromId(stackid)
apDisplay.printMsg("inserting "+str(len(stpartsdata))+" particles into DB")
for particle in stpartsdata:
stpartq = appiondata.ApStackParticleData()
stpartq['particleNumber'] = self.partnum
stpartq['stack'] = stackq
stpartq['stackRun'] = particle['stackRun']
stpartq['particle'] = particle['particle']
stpartq.insert()
self.partnum += 1
if self.partnum % 1000 == 0:
sys.stderr.write(".")
sys.stderr.write("\n")
apDisplay.printMsg("commited particles "+str(startpart)+"-"+str(self.partnum))
return
def uploadResults(self):
if self.params['commit'] is False:
return
# Produce new stacks
oldstack = apStack.getOnlyStackData(self.params['notstackid'], msg=False)
notstack = appiondata.ApStackData()
notstack['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
notstack['name'] = self.notstackdata['name']
if notstack.query(results=1):
apDisplay.printError("A stack with these parameters already exists")
tiltstack = appiondata.ApStackData()
tiltstack['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
tiltstack['name'] = self.tiltstackdata['name']
if tiltstack.query(results=1):
apDisplay.printError("A stack with these parameters already exists")
# Fill in data and submit
notstack['oldstack'] = oldstack
notstack['hidden'] = False
notstack['substackname'] = self.params['runname']
notstack['description'] = self.params['description']+" ... tilt stack sorted"
notstack['pixelsize'] = oldstack['pixelsize']
notstack.insert()
tiltstack['oldstack'] = oldstack
tiltstack['hidden'] = False
tiltstack['substackname'] = self.params['runname']
tiltstack['description'] = self.params['description']+" ... tilt stack sorted"
tiltstack['pixelsize'] = oldstack['pixelsize']
tiltstack.insert()
# Insert stack images
apDisplay.printMsg("Inserting stack particles")
count=0
for partdict in parttree:
count += 1
if count % 100 == 0:
sys.stderr.write("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b")
sys.stderr.write(str(count)+" of "+(str(total))+" complete")
# Get particles from the old stacks
oldnotparticle = apStack.getStackParticle(self.params['notstackid'], partdict['not'])
oldtiltparticle = apStack.getStackParticle(self.params['tiltstackid'], partdict['tilt'])
# Insert particle
notparticle = appiondata.ApStackParticleData()
notparticle.update(oldnotparticle)
notparticle['particleNumber'] = count
notparticle['stack'] = notstack
notparticle.insert()
tiltparticle = appiondata.ApStackParticleData()
tiltparticle.update(oldtiltparticle)
tiltparticle['particleNumber'] = count
tiltparticle['stack'] = tiltstack
tiltparticle.insert()
apDisplay.printMsg("\n%d particles have been inserted into the tilt synchronized stacks"%(count))
# Insert runs in stack
apDisplay.printMsg("Inserting Runs in Stack")
runsinstack = apStack.getRunsInStack(self.params['notstackid'])
for run in runsinstack:
newrunsq = appiondata.ApRunsInStackData()
newrunsq['stack'] = notstack
newrunsq['stackRun'] = run['stackRun']
newrunsq.insert()
runsinstack = apStack.getRunsInStack(self.params['tiltstackid'])
for run in runsinstack:
newrunsq = appiondata.ApRunsInStackData()
newrunsq['stack'] = tiltstack
newrunsq['stackRun'] = run['stackRun']
newrunsq.insert()
apDisplay.printMsg("finished")
return
def uploadResults(self):
if self.params['commit'] is False:
return
# Get the new file order
fh = open("sort_junk.sel", 'r')
lines = fh.readlines()
i = 0
fileorder = {}
for line in lines:
args = line.split()
if (len(args) > 1):
match = re.match('[A-Za-z]+([0-9]+)\.[A-Za-z]+',
(args[0].split('/'))[-1])
if (match):
filenumber = int(match.groups()[0])
fileorder[i] = filenumber
i += 1
fh.close()
# Produce a new stack
oldstack = apStack.getOnlyStackData(self.params['stackid'], msg=False)
newstack = appiondata.ApStackData()
newstack['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
newstack['name'] = "sorted.hed"
if newstack.query(results=1):
apDisplay.printError(
"A stack with these parameters already exists")
# Fill in data and submit
newstack['oldstack'] = oldstack
newstack['hidden'] = False
newstack['substackname'] = self.params['runname']
newstack['description'] = self.params['description']
newstack['pixelsize'] = oldstack['pixelsize']
newstack['boxsize'] = oldstack['boxsize']
newstack['junksorted'] = True
newstack.insert()
# Insert stack images
apDisplay.printMsg("Inserting stack particles")
count = 0
total = len(fileorder.keys())
if total == 0:
apDisplay.printError(
"No particles can be inserted in the sorted stack")
for i in fileorder.keys():
count += 1
if count % 100 == 0:
sys.stderr.write(
"\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b")
sys.stderr.write(
str(count) + " of " + (str(total)) + " complete")
# Get particle from the old stack
oldparticle = apStack.getStackParticle(self.params['stackid'],
fileorder[i] + 1)
# Insert particle
newparticle = appiondata.ApStackParticleData()
newparticle['particleNumber'] = i + 1
newparticle['stack'] = newstack
newparticle['stackRun'] = oldparticle['stackRun']
newparticle['particle'] = oldparticle['particle']
newparticle['mean'] = oldparticle['mean']
newparticle['stdev'] = oldparticle['stdev']
newparticle.insert()
apDisplay.printMsg(
"\n" + str(total) +
" particles have been inserted into the sorted stack")
# Insert runs in stack
apDisplay.printMsg("Inserting Runs in Stack")
runsinstack = apStack.getRunsInStack(self.params['stackid'])
for run in runsinstack:
newrunsq = appiondata.ApRunsInStackData()
newrunsq['stack'] = newstack
newrunsq['stackRun'] = run['stackRun']
newrunsq.insert()
apDisplay.printMsg("finished")
return
def uploadResults(self):
if self.params['commit'] is False:
return
# Get the new file order
fh=open("sort_junk.sel",'r')
lines=fh.readlines()
i=0;
fileorder={};
for line in lines:
args=line.split()
if (len(args)>1):
match=re.match('[A-Za-z]+([0-9]+)\.[A-Za-z]+',
(args[0].split('/'))[-1])
if (match):
filenumber=int(match.groups()[0])
fileorder[i]=filenumber
i+=1
fh.close()
# Produce a new stack
oldstack = apStack.getOnlyStackData(self.params['stackid'],msg=False)
newstack = appiondata.ApStackData()
newstack['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
newstack['name'] = "sorted.hed"
if newstack.query(results=1):
apDisplay.printError("A stack with these parameters already exists")
# Fill in data and submit
newstack['oldstack'] = oldstack
newstack['hidden'] = False
newstack['substackname'] = self.params['runname']
newstack['description'] = self.params['description']
newstack['pixelsize'] = oldstack['pixelsize']
newstack['boxsize'] = oldstack['boxsize']
newstack['junksorted'] = True
newstack.insert()
# Insert stack images
apDisplay.printMsg("Inserting stack particles")
count=0
total=len(fileorder.keys())
if total==0:
apDisplay.printError("No particles can be inserted in the sorted stack")
for i in fileorder.keys():
count += 1
if count % 100 == 0:
sys.stderr.write("\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b")
sys.stderr.write(str(count)+" of "+(str(total))+" complete")
# Get particle from the old stack
oldparticle = apStack.getStackParticle(self.params['stackid'], fileorder[i]+1)
# Insert particle
newparticle = appiondata.ApStackParticleData()
newparticle['particleNumber'] = i+1
newparticle['stack'] = newstack
newparticle['stackRun'] = oldparticle['stackRun']
newparticle['particle'] = oldparticle['particle']
newparticle['mean'] = oldparticle['mean']
newparticle['stdev'] = oldparticle['stdev']
newparticle.insert()
apDisplay.printMsg("\n"+str(total)+" particles have been inserted into the sorted stack")
# Insert runs in stack
apDisplay.printMsg("Inserting Runs in Stack")
runsinstack = apStack.getRunsInStack(self.params['stackid'])
for run in runsinstack:
newrunsq = appiondata.ApRunsInStackData()
newrunsq['stack'] = newstack
newrunsq['stackRun'] = run['stackRun']
newrunsq.insert()
apDisplay.printMsg("finished")
return
appion database and output a new binned stack to the current
directory. The new stack will be commited to the database
"""
sys.exit()
#parse params
params = {}
params['stackid'] = int(sys.argv[1])
params['newstackname'] = sys.argv[2]
params['bin'] = int(sys.argv[3])
params['newstackpath'] = os.getcwd()
params['description'] = "stackid %d was scaled by a factor of %d" % (
params['stackid'], params['bin'])
#check for multiple runs in stack
runs_in_stack = apStack.getRunsInStack(params['stackid'])
if len(runs_in_stack) > 1:
print "scalestack.py can't scale this stack because it is a combination of multiple makestack runs."
print "Instead, use makestack to create a new single scaled stack"
sys.exit()
#get stackdata
stackdata = apStack.getStackParticlesFromId(params['stackid'])
#do operations on stack
print "Scaling stack"
scaleStack(stackdata, params)
#commit new stack to db
print "Commiting new stack to db"
commitScaledStack(stackdata, params)
scalestack.py will take a stack that has been uploaded to the
appion database and output a new binned stack to the current
directory. The new stack will be commited to the database
"""
sys.exit()
#parse params
params={}
params['stackid']=int(sys.argv[1])
params['newstackname']=sys.argv[2]
params['bin']=int(sys.argv[3])
params['newstackpath']=os.getcwd()
params['description']="stackid %d was scaled by a factor of %d" % (params['stackid'],params['bin'])
#check for multiple runs in stack
runs_in_stack=apStack.getRunsInStack(params['stackid'])
if len(runs_in_stack) > 1:
print "scalestack.py can't scale this stack because it is a combination of multiple makestack runs."
print "Instead, use makestack to create a new single scaled stack"
sys.exit()
#get stackdata
stackdata=apStack.getStackParticlesFromId(params['stackid'])
#do operations on stack
print "Scaling stack"
scaleStack(stackdata,params)
#commit new stack to db
print "Commiting new stack to db"
commitScaledStack(stackdata,params)
