def insertAlignStackRunIntoDatabase(self, alignimagicfile):
apDisplay.printMsg("Inserting CL2D Run into DB")
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.runparams['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
# if uniquerun:
# apDisplay.printError("Run name '"+self.runparams['runname']+"' and path already exist in database")
### setup cl2d run
cl2dq = appiondata.ApCL2DRunData()
cl2dq['runname'] = self.runparams['runname']
cl2dq['run_seconds'] = self.runparams['runtime']
cl2dq['fast'] = self.runparams['fast']
self.cl2dqdata=cl2dq
### finish alignment run
alignrunq['cl2drun'] = cl2dq
alignrunq['hidden'] = False
alignrunq['runname'] = self.runparams['runname']
alignrunq['description'] = self.runparams['description']
alignrunq['lp_filt'] = self.runparams['lowpass']
alignrunq['hp_filt'] = self.runparams['highpass']
alignrunq['bin'] = self.runparams['bin']
### setup alignment stack
alignstackq = appiondata.ApAlignStackData()
if self.runparams['align'] is True: ### option to create aligned stack
alignstackq['imagicfile'] = alignimagicfile
alignstackq['avgmrcfile'] = "average.mrc"
alignstackq['refstackfile'] = "part"+self.params['timestamp']+"_level_%02d_.hed"%(self.Nlevels-1)
alignstackq['iteration'] = self.runparams['maxiter']
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
alignstackq['alignrun'] = alignrunq
### check to make sure files exist
if self.runparams['align'] is True: ### option to create aligned stack
alignimagicfilepath = os.path.join(self.params['rundir'], alignstackq['imagicfile'])
if not os.path.isfile(alignimagicfilepath):
apDisplay.printError("could not find stack file: "+alignimagicfilepath)
avgmrcfile = os.path.join(self.params['rundir'], alignstackq['avgmrcfile'])
if not os.path.isfile(avgmrcfile):
apDisplay.printError("could not find average mrc file: "+avgmrcfile)
refstackfile = os.path.join(self.params['rundir'], alignstackq['refstackfile'])
if not os.path.isfile(refstackfile):
apDisplay.printError("could not find reference stack file: "+refstackfile)
alignstackq['stack'] = apStack.getOnlyStackData(self.runparams['stackid'])
alignstackq['boxsize'] = self.boxsize
alignstackq['pixelsize'] = apStack.getStackPixelSizeFromStackId(self.runparams['stackid'])*self.runparams['bin']
alignstackq['description'] = self.runparams['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.runparams['numpart']
### insert
if self.params['commit'] is True:
alignstackq.insert()
self.alignstackdata = alignstackq
return
def insertCL2DParamsIntoDatabase(self):
### setup cl2d run
cl2dq = appiondata.ApCL2DRunData()
cl2dq['runname'] = self.runparams['runname']
cl2dq['run_seconds'] = self.runparams['runtime']
cl2dq['fast'] = self.runparams['fast']
cl2dq[
'REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(
self.params['stackid'])
cl2dq['timestamp'] = self.params['timestamp']
cl2dq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
cl2dq['finished'] = True
cl2dq['max-iter'] = self.params['maxiter']
cl2dq['num-ref'] = self.params['numrefs']
if self.params['correlation'] is True:
cl2dq['correlation'] = True
cl2dq['correntropy'] = False
else:
cl2dq['correlation'] = False
cl2dq['correntropy'] = True
if self.params['classical'] is True:
cl2dq['classical_multiref'] = True
cl2dq['intracluster_multiref'] = False
else:
cl2dq['classical_multiref'] = False
cl2dq['intracluster_multiref'] = True
### insert if commit is true
if self.params['commit'] is True:
cl2dq.insert()
self.cl2dqdata = cl2dq
def getCL2DJob(self): cl2djobq = appiondata.ApCL2DRunData() cl2djobq['runname'] = self.runparams['runname'] cl2djobq['path'] = appiondata.ApPathData(path=os.path.abspath(self.runparams['rundir'])) cl2djobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.runparams['stackid']) cl2djobq['timestamp'] = self.params['timestamp'] cl2djobdata = cl2djobq.query(results=1) if not cl2djobdata: return None return cl2djobdata[0]