def check_gauss(self):
# Function to check if gaussian algorithm was used to pick and is so
# ask user if she wants to perform an automatic picking for the remaining micrographs
gaussJsonFile = join("e2boxercache", "gauss_box_DB.json")
# Check if gauss json file exists and load it
if os.path.exists(gaussJsonFile):
jsonGaussDict = loadJson(gaussJsonFile)
gaussParsDict = None
micList = [os.path.relpath(mic.getFileName(), self.workingDir.get()) for mic in self.inputMics]
# Go over the list of input micrographs and see if gaussian was used to pick any of them
for mic in micList:
if mic in jsonGaussDict:
gaussParsDict = jsonGaussDict[mic]
break
if gaussParsDict is not None:
# If found ask user if she wats to perform an automatic gaussian picking for the rest of mics
# if askYesNo(Message.TITLE_PICK_GAUSS, Message.LABEL_PICK_GAUSS, None):
self._params['boxSize'] = gaussParsDict['boxsize']
# Run sxprocess.py to store parameters
program = eman2.getEmanProgram("sxprocess.py")
argsList = ["'%s'=%s:" %(key, val) for (key, val) in gaussParsDict.iteritems()]
args = 'demoparms --makedb ' + "".join(argsList)
# Remove last ":" to avoid error
args = args[:-1]
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + args)
self.runJob(program, args)
# Now run e2boxer.py with stored parameters
#arguments = "--gauss_autoboxer=demoparms --write_ptcl --boxsize=%(boxSize)s --norm=normalize.ramp.normvar" + arguments
arguments = "--gauss_autoboxer=demoparms --write_dbbox --boxsize=%(boxSize)s " + "%(inputMics)s"
program = eman2.getEmanProgram("e2boxer.py")
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
def createInitialModelStep(self, args):
""" Run the EMAN program to create the initial model. """
cleanPattern(self._getExtraPath('initial_models'))
if self._isHighSym():
program = eman2.getEmanProgram('e2initialmodel_hisym.py')
else:
program = eman2.getEmanProgram('e2initialmodel.py')
self.runJob(program, args, cwd=self._getExtraPath())
def launchBoxingGUIStep(self):
# Print the eman version, useful to report bugs
self.runJob(eman2.getEmanProgram('e2version.py'), '')
# Program to execute and it arguments
program = eman2.getEmanProgram("e2boxer.py")
arguments = "%(inputMics)s"
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, None):
self.check_gauss()
self._leaveDir()# going back to project dir
self._createOutput(self.getWorkingDir())
def launchBoxingGUIStep(self):
# First we go to runs directory (we create if it does not exist)
#path.makePath("runs")
# Program to execute and it arguments
program = eman2.getEmanProgram("e2boxer.py")
arguments = "%(inputMics)s"
# Run the command with formatted parameters
self._log.info('Launching: ' + program + ' ' + arguments % self._params)
self.runJob(program, arguments % self._params)
# Open dialog to request confirmation to create output
if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, None):
self.check_gauss()
self._leaveDir()# going back to project dir
self._createOutput(self.getWorkingDir())
def createInitialModelStep(self, args):
""" Run the EMAN program to create the initial model. """
cleanPattern(self._getExtraPath('initial_models'))
program = eman2.getEmanProgram('e2initialmodel.py')
self.runJob(program, args, cwd=self._getExtraPath())
