def filterStack(self, stackname, minx=600, maxx=1600, miny=82, maxy=150):
runnum = apStack.getNumStacksFromSession(self.sessionname)
filtstackname = "meanfilt%d-%s"%(runnum+1, self.timestamp)
stackid = apStack.getStackIdFromRunName(stackname, self.sessionname)
if not stackid:
apDisplay.printError("Failed to find stack %s for session %s"%(stackname, self.sessionname))
script = os.path.join(self.appiondir, "bin", "stackFilter.py ")
# params = ((" --runname=%s --projectid=%d --old-stack-id=%d --minx=%d --maxx=%d --miny=%d --maxy=%d --description='%s'")
# %(filtstackname, self.params['projectid'], stackid,
# 600, 1000, 82, 105,
# 'filtering junk with test suite application'))
params = ((" --runname=%s --projectid=%d --old-stack-id=%d --minx=%d --maxx=%d --miny=%d --maxy=%d --description='%s'")
%(filtstackname, self.params['projectid'], stackid,
minx, maxx, miny, maxy,
'filtering junk with test suite application'))
# Add appion flags
if self.params['commit'] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script+" "+params)
stackid = apStack.getStackIdFromSubStackName(filtstackname, self.sessionname)
if not stackid:
apDisplay.printError("Failed to create stack %s for session %s during stackFilter test."%(filtstackname, self.sessionname))
return filtstackname
def filterStack(self, stackname):
runnum = apStack.getNumStacksFromSession(self.sessionname)
filtstackname = "meanfilt%d-%s" % (runnum + 1, self.timestamp)
stackid = apStack.getStackIdFromRunName(stackname, self.sessionname)
if not stackid:
apDisplay.printError("Failed to find stack %s for session %s" % (stackname, self.sessionname))
script = os.path.join(self.appiondir, "bin", "stackFilter.py ")
params = (
" --runname=%s --projectid=%d --old-stack-id=%d --minx=%d --maxx=%d --miny=%d --maxy=%d --description='%s'"
) % (
filtstackname,
self.params["projectid"],
stackid,
600,
1000,
82,
105,
"filtering junk with test suite application",
)
if self.params["commit"] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script + " " + params)
return filtstackname
def makeStack(self):
runnum = apStack.getNumStacksFromSession(self.sessionname)
stackname = "stack%d-%s" % (runnum + 1, self.timestamp)
selectid = apParticle.getRecentSelectionIdFromSession(self.sessionname)
script = os.path.join(self.appiondir, "bin", "makestack2.py ")
params = (
" --runname=%s --projectid=%d --session=%s --no-wait --boxsize=%d --bin=%d --ctfcutoff=%.2f --invert --phaseflip --flip-type=ace2image --selectionid=%d --description='%s'"
) % (
stackname,
self.params["projectid"],
self.sessionname,
512,
2,
0.7,
selectid,
"running test suite application",
)
if self.params["commit"] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script + " " + params)
return stackname
def makeStack(self):
runnum = apStack.getNumStacksFromSession(self.sessionname)
stackname = "stack%d-%s"%(runnum+1, self.timestamp)
selectid = apParticle.getRecentSelectionIdFromSession(self.sessionname)
script = os.path.join(self.appiondir, "bin", "makestack2.py ")
params = ((" --runname=%s --projectid=%d --session=%s --no-wait --boxsize=%d --bin=%d --ctfcutoff=%.2f --invert --phaseflip --flip-type=ace2image --selectionid=%d --description='%s'")
%(stackname, self.params['projectid'], self.sessionname, 512, 2, 0.7, selectid, 'running test suite application'))
if self.params['commit'] is True:
params += " --commit "
else:
params += " --no-commit "
self.runCommand(script+" "+params)
return stackname
def makeStack(self, boxsize=512, bin=2, ctfcutoff=0.7):
runnum = apStack.getNumStacksFromSession(self.sessionname)
stackname = "stack%d-%s"%(runnum+1, self.timestamp)
selectid = apParticle.getRecentSelectionIdFromSession(self.sessionname)
script = os.path.join(self.appiondir, "bin", "makestack2.py ")
params = ((" --runname=%s --projectid=%d --session=%s --no-wait --boxsize=%d --bin=%d --ctfcutoff=%.2f --invert --phaseflip --flip-type=ace2image --selectionid=%d --description='%s'")
%(stackname, self.params['projectid'], self.sessionname, boxsize, bin, ctfcutoff, selectid, 'running test suite application'))
# Add appion flags
params += self.appionFlags
self.runCommand(script+" "+params)
return stackname