def checkDuplicateRefBasedRun(self):
### setup ref based run
refrunq = appiondata.ApRefBasedRunData()
refrunq['name'] = self.params['runname']
refrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = refrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '"+self.params['runname']+"' and path already exist in database")
return
def insertRefBasedRun(self, partlist, imagicstack, insert=False):
apDisplay.printMsg("committing results to DB")
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['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 ref based run
refrunq = appiondata.ApRefBasedRunData()
refrunq['runname'] = self.params['runname']
refrunq['xysearch'] = self.params['xysearch']
refrunq['xystep'] = self.params['xystep']
refrunq['first_ring'] = self.params['firstring']
refrunq['last_ring'] = self.params['lastring']
refrunq['num_iter'] = self.params['numiter']
refrunq['invert_templs'] = self.params['inverttemplates']
refrunq['num_templs'] = self.params['numtemplate']
#refrunq['csym', int),
refrunq['run_seconds'] = self.params['runtime']
### finish alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['refbasedrun'] = refrunq
alignrunq['hidden'] = False
alignrunq['bin'] = self.params['bin']
alignrunq['hp_filt'] = self.params['highpass']
alignrunq['lp_filt'] = self.params['lowpass']
alignrunq['runname'] = self.params['runname']
alignrunq['description'] = self.params['description']
### setup alignment stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['alignrun'] = alignrunq
alignstackq['imagicfile'] = imagicstack
alignstackq['avgmrcfile'] = "average.mrc"
emancmd = "proc2d templatestack%02d.spi templatestack%02d.hed"%(self.params['numiter'],self.params['numiter'])
apEMAN.executeEmanCmd(emancmd)
alignstackq['refstackfile'] = ("templatestack%02d.hed"%(self.params['numiter']))
alignstackq['alignrun'] = alignrunq
alignstackq['iteration'] = self.params['numiter']
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### check to make sure files exist
imagicfile = os.path.join(self.params['rundir'], alignstackq['imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find stack file: "+imagicfile)
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'] = self.stack['data']
alignstackq['boxsize'] = self.boxsize
alignstackq['pixelsize'] = self.stack['apix']*self.params['bin']
alignstackq['description'] = self.params['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.params['numpart']
if insert is True:
alignstackq.insert()
### insert reference data
reflist = []
for j in range(self.params['numiter']):
iternum = j+1
for i in range(len(self.templatelist)):
refnum = i+1
templateid = self.templatelist[i]
refq = appiondata.ApAlignReferenceData()
refq['refnum'] = refnum
refq['iteration'] = iternum
refq['template'] = apTemplate.getTemplateFromId(templateid)
refq['mrcfile'] = ("templateavg%02d-%02d.mrc"%(iternum,refnum))
refpath = os.path.join(self.params['rundir'], "templates")
refq['path'] = appiondata.ApPathData(path=os.path.abspath(refpath))
refq['alignrun'] = alignrunq
if refnum in self.resdict:
refq['ssnr_resolution'] = self.resdict[refnum]
if insert is True:
refq.insert()
if iternum == self.params['numiter']:
reflist.append(refq)
#refq['varmrcfile', str),
#refq['frc_resolution', float),
### insert particle data
apDisplay.printColor("Inserting particle alignment data, please wait", "cyan")
for partdict in partlist:
### see apSpider.alignment.alignStack() for more info
"""
partdict.keys()
'num': int(data[0]), #SPIDER NUMBERING: 1,2,3,...
'template': int(abs(templatenum)), #SPIDER NUMBERING: 1,2,3,...
'mirror': checkMirror(templatenum),
'score': float(data[3]),
'rot': float(data[4]),
'xshift': float(data[5]),
'yshift': float(data[6]),
"""
alignpartq = appiondata.ApAlignParticleData()
alignpartq['ref'] = reflist[partdict['template']-1]
alignpartq['partnum'] = partdict['num']
alignpartq['alignstack'] = alignstackq
stackpartdata = apStack.getStackParticle(self.params['stackid'], partdict['num'])
alignpartq['stackpart'] = stackpartdata
alignpartq['xshift'] = partdict['xshift']
alignpartq['yshift'] = partdict['yshift']
alignpartq['rotation'] = partdict['rot']
alignpartq['score'] = partdict['score']
alignpartq['mirror'] = partdict['mirror']
if insert is True:
alignpartq.insert()
return