def createParamsFromGoodAligner(self,alignerid):
q = appiondata.ApTomoAlignerParamsData()
alignerdata = q.direct_query(alignerid)
self.params['goodcycle'] = alignerdata['refine_cycle']['cycle']
alignrundata = alignerdata['alignrun']
if self.params['runname'] is None:
self.params['runname'] = alignrundata['name']
else:
if self.params['runname'] != alignrundata['name']:
apDisplay.printError("Alignment run name can not be changed between cycles")
if self.params['description'] is None:
self.params['description'] = alignrundata['description']
q = appiondata.ApTiltsInAlignRunData(alignrun=alignrundata)
results = q.query()
if results:
if len(results) == 1:
tiltdata = results[0]['tiltseries']
self.params['tiltseries'] = tiltdata
self.params['tiltseriesnumber'] = tiltdata['number']
self.params['othertiltseries'] = None
else:
runpathdata = alignrundata['path']
for tiltdata in results:
pathdata = tiltdata['path']
if pathdata.dbid == runpathdata.dbid:
self.params['tiltseries'] = tiltdata
self.params['tiltseriesnumber'] = tiltdata['number']
else:
self.params['othertiltseries'] = tiltdata
self.params['othertilt'] = tiltdata['number']
def insertTiltsInAlignRun(alignrundata, tiltdata, settingsdata, primary=True):
q = appiondata.ApTiltsInAlignRunData()
q['alignrun'] = alignrundata
q['tiltseries'] = tiltdata
q['settings'] = settingsdata
q['primary_tiltseries'] = primary
return publish(q)
def getTiltListFromAligner(alignerid):
alignerdata = getAlignerdata(alignerid)
q = appiondata.ApTiltsInAlignRunData(alignrun=alignerdata['alignrun'])
results = q.query()
for i, result in enumerate(results):
if result['primary_tiltseries']:
primkey = i
break
tiltdatalist = [
results[primkey]['tiltseries'],
]
del results[primkey]
for r in results:
tiltdatalist.append(r['tiltseries'])
return tiltdatalist
def getAlignersFromTiltSeries(tiltseriesdata, alignrunname=''):
q = appiondata.ApTiltsInAlignRunData(tiltseries=tiltseriesdata)
if alignrunname:
runq = appiondata.ApTomoAlignmentRunData(name=alignrunname)
q['alignrun'] = runq
results = q.query()
if results:
allaligners = []
allalignerids = []
for tilt_in_run in results:
alignerq = appiondata.ApTomoAlignerParamsData(
alignrun=tilt_in_run['alignrun'])
aligners = alignerq.query()
for aligner in aligners:
if aligner.dbid not in allalignerids:
allaligners.append(aligner)
allalignerids.append(aligner.dbid)
return allaligners
return []
def commitToJensenDatabase(session_time, fulltomodata, stackdir, processdir,
stackname, description):
if not upload_to_Jensen_database:
return
raptordatabase = 0
apDisplay.printMsg("Uploding to Jensen tomography database")
alignrun = fulltomodata['alignrun']
tiltseries = fulltomodata['tiltseries']
nn = len(stackname)
mrcbase = processdir + '/align/' + stackname[0:-3]
mrcpath = mrcbase + '_full.rec'
if not os.path.exists(mrcpath):
mrcpath = mrcbase + '_part.rec'
if not os.path.exists(mrcpath):
mrcpath = ''
if mrcpath == '':
apDisplay.printWarning('No output full or part mrc found.')
raptordatabase = 1
else:
print '!!!0', ' mrcpath=', mrcpath
print '!!!1', ' stackdir=', stackdir, ' stackname=', stackname, ' processdir=', processdir, ' description=', description
imagelist = apTomo.getImageList([tiltseries])
defocus = imagelist[0]['preset']['defocus']
magnification = imagelist[0]['preset']['magnification']
q = appiondata.ApTiltsInAlignRunData(alignrun=alignrun)
r = q.query()
tomosettings = r[0]['settings']
tilt_min = tomosettings['tilt min']
tilt_max = tomosettings['tilt max']
tilt_step = tomosettings['tilt step']
dose = tomosettings['dose']
print '!!!2', ' defocus=', defocus, ' magnification=', magnification, ' tilt_min=', tilt_min, ' tilt_max=', tilt_max, ' tilt_step=', tilt_step, ' dose=', dose
#sessiondata = tiltdatalist[0]['session']
session_id = tiltseries.dbid
print '!!!3', ' session_id=', session_id, ' session_time=', session_time
return raptordatabase
def insertTiltsInAlign(alignrun):
q = appiondata.ApTiltsInAlignRunData()
q['alignrun'] = alignrun
q['tiltseries'] = alignrun['tiltseries']
q['primary_tiltseries'] = True
q.insert()