def insertTomoAlignmentRun(sessiondata,
leginontomosettingsdata,
imodxcorrparamsdata,
protomorunparamsdata,
raptorparamsdata,
bin,
name,
path,
description=None,
bad_alignment=False):
pathq = appiondata.ApPathData(path=os.path.abspath(path))
qalign = appiondata.ApTomoAlignmentRunData(session=sessiondata,
bin=bin,
name=name,
path=pathq)
if leginontomosettingsdata:
qalign['coarseLeginonParams'] = leginontomosettingsdata
if imodxcorrparamsdata:
qalign['coarseImodParams'] = imodxcorrparamsdata
if protomorunparamsdata:
qalign['fineProtomoParams'] = protomorunparamsdata
if raptorparamsdata:
qalign['raptorParams'] = raptorparamsdata
results = qalign.query()
if not results:
qalign['badAlign'] = bad_alignment
qalign['description'] = description
qalign.insert()
return qalign
return results[0]
def getTomoAlignmentRuns():
alignrunids = []
alignrunq = appiondata.ApTomoAlignmentRunData()
alignrundatas = alignrunq.query()
if not alignrundatas:
return []
return alignrundatas
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 []