def _isMaxLikeJobUploaded(maxjobdata): maxrunq = appiondata.ApMaxLikeRunData() maxrunq['job'] = maxjobdata maxrundatas = maxrunq.query(results=1) if maxrundatas: return True return False
def insertRunIntoDatabase(self, alignimagicfile, runparams):
apDisplay.printMsg("Inserting MaxLike Run into DB")
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = runparams['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '"+runparams['runname']+"' and path already exist in database")
### setup max like run
maxlikeq = appiondata.ApMaxLikeRunData()
maxlikeq['runname'] = runparams['runname']
maxlikeq['run_seconds'] = runparams['runtime']
#maxlikeq['mask_diam'] = 2.0*runparams['maskrad']
maxlikeq['fast'] = runparams['fast']
maxlikeq['fastmode'] = runparams['fastmode']
maxlikeq['mirror'] = runparams['mirror']
maxlikeq['student'] = bool(runparams['student'])
maxlikeq['init_method'] = "xmipp default"
maxlikeq['job'] = self.getMaxLikeJob(runparams)
### finish alignment run
alignrunq['maxlikerun'] = maxlikeq
alignrunq['hidden'] = False
alignrunq['runname'] = runparams['runname']
alignrunq['description'] = runparams['description']
alignrunq['lp_filt'] = runparams['lowpass']
alignrunq['hp_filt'] = runparams['highpass']
alignrunq['bin'] = runparams['bin']
### setup alignment stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['imagicfile'] = alignimagicfile
alignstackq['avgmrcfile'] = "average.mrc"
alignstackq['refstackfile'] = "part"+self.params['timestamp']+"_average.hed"
alignstackq['iteration'] = self.lastiter
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
alignstackq['alignrun'] = alignrunq
### check to make sure files exist
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(runparams['stackid'])
alignstackq['boxsize'] = apFile.getBoxSize(alignimagicfilepath)[0]
alignstackq['pixelsize'] = apStack.getStackPixelSizeFromStackId(runparams['stackid'])*runparams['bin']
alignstackq['description'] = runparams['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = runparams['numpart']
### insert
if self.params['commit'] is True:
alignstackq.insert()
self.alignstackdata = alignstackq
return