Пример #1
0
	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
Пример #2
0
    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
Пример #3
0
    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
Пример #4
0
	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