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