def checkExistingFullTomoData(path, name):
pathq = appiondata.ApPath(path=path)
runq = appiondata.ApFullTomogramRunData(pathq)
tomoq = appiondata.ApFullTomogramData(name=name, reconrun=runq)
results = tomoq.query()
if not results:
return None
filepath = os.path.join(path, name + ".rec")
if not os.path.isfile(filepath):
return None
else:
return results[0]
def upgradeAppionDB(self):
if self.appion_dbupgrade.tableExists(
'ApFullTomogramRunData') and self.appion_dbupgrade.tableExists(
'ApFullTomogramData'):
if (not self.appion_dbupgrade.columnExists('ApFullTomogramRunData',
'SEQ|excluded')):
apDisplay.printWarning(
'No excluded image column available, not need for column move'
)
return
if (not self.appion_dbupgrade.columnExists('ApFullTomogramData',
'SEQ|excluded')):
self.appion_dbupgrade.addColumn('ApFullTomogramData',
'SEQ|excluded',
self.appion_dbupgrade.str)
q = appiondata.ApFullTomogramData()
results = q.query()
for qdata in results:
rundata = qdata['reconrun']
try:
runid = rundata.dbid
except:
apDisplay.printWarning(
'No associated ApFullTomgramRunData. Skip')
continue
tid = qdata.dbid
query = "Select `SEQ|excluded` from %s.`ApFullTomogramRunData` where `DEF_id`=%d;" % (
self.appion_dbupgrade.dbname, runid)
results = self.appion_dbupgrade.returnCustomSQL(query)
excludetext = results[0][0]
try:
existing_excludetext = results[0][0]
except IndexError:
apDisplay.printWarning(
'No excluded image info available, not need for column move'
)
continue
# only do the schema upgrade if ApFullTomogramData has no value in SEQ|excluded'
existing_excludetext = None
query = "Select `SEQ|excluded` from %s.`ApFullTomogramData` where `DEF_id`=%d;" % (
self.appion_dbupgrade.dbname, runid)
results = self.appion_dbupgrade.returnCustomSQL(query)
try:
existing_excludetext = results[0][0]
except IndexError:
pass
if (excludetext and not existing_excludetext):
query = "Update ApFullTomogramData set `SEQ|excluded`='%s' WHERE ApFullTomogramData.`DEF_id`=%d;" % (
excludetext, tid)
self.appion_dbupgrade.executeCustomSQL(query)
def isTomoInDB(md5sum, full=False, recfile=''):
abspath = os.path.abspath(recfile)
rundir = os.path.dirname(abspath)
basename = os.path.basename(abspath)
rootname = os.path.splitext(basename)
if not full:
tomoq = appiondata.ApTomogramData(name=rootname[0])
tomoq['md5sum'] = md5sum
else:
tomoq = appiondata.ApFullTomogramData(name=rootname[0])
tomod = tomoq.query(results=1)
if tomod:
tomodata = tomod[0]
# old style
if tomodata['path'] is not None and tomodata['path']['path'] == rundir:
return True
# new style
if tomodata['reconrun']['path']['path'] == rundir:
return True
return False
def getSubvolumeInfo(subtomorundata):
tomoq = appiondata.ApTomogramData(subtomorun=subtomorundata)
results = tomoq.query(results=1)
if results:
tomo = results[0]
subbin = subtomorundata['subbin']
fullq = appiondata.ApFullTomogramData()
fulltomogram = tomo['fulltomogram']
if fulltomogram['alignrun'] is None:
# new data has no alignrun
fullbin = tomo['fulltomogram']['aligner']['alignrun']['bin']
else:
# old data has no aligner
fullbin = tomo['fulltomogram']['alignrun']['bin']
totalbin = subbin * fullbin
shape = (tomo['dimension']['z'] / totalbin,
tomo['dimension']['y'] / totalbin,
tomo['dimension']['x'] / totalbin)
pixelsize = tomo['pixelsize']
return shape, totalbin, pixelsize
else:
return None, 1, None
def insertFullTomogram(sessiondata,
tiltdata,
aligner,
fullrundata,
name,
description,
projectimagedata,
thickness,
reconparamdata=None,
bin=1,
imageidlist=[]):
tomoq = appiondata.ApFullTomogramData()
tomoq['session'] = sessiondata
tomoq['tiltseries'] = tiltdata
tomoq['aligner'] = aligner
tomoq['reconrun'] = fullrundata
tomoq['name'] = name
tomoq['description'] = description
tomoq['zprojection'] = projectimagedata
tomoq['thickness'] = thickness
tomoq['bin'] = bin
tomoq['excluded'] = imageidlist
tomoq['reconparam'] = reconparamdata
return publish(tomoq)