def verifyNumberOfCompletedRefinements(self,
multiModelRefinementRun=False):
"""
queries te database to determine how many iterations of individual refinements have been completed:
returns a list of completed iterations in a dictionary of completed refinements
"""
refine_complete = {}
if multiModelRefinementRun is False:
iterdata = appiondata.ApRefineIterData()
iterdata['refineRun'] = self.refinerunq
itercompletedata = iterdata.query()
iter_complete = []
for iter in itercompletedata:
iter_complete.append(iter['iteration'])
iter_complete.sort()
refine_complete[
self.refinerunq['reference_number']] = iter_complete
else:
refinedata = appiondata.ApRefineRunData()
refinedata['multiModelRefineRun'] = self.multimodelq
refinecompletedata = refinedata.query()
for i, refine in enumerate(refinecompletedata):
iterdata = appiondata.ApRefineIterData()
iterdata['refineRun'] = refine
itercompletedata = iterdata.query()
iter_complete = []
for iter in itercompletedata:
iter_complete.append(iter['iteration'])
iter_complete.sort()
refine_complete[refine['reference_number']] = iter_complete
return refine_complete
def getReconRunIdFromNamePath(runname, path):
reconrunq = appiondata.ApRefineRunData()
reconrunq['runname'] = runname
reconrunq['path'] = appiondata.ApPathData(path=os.path.abspath(path))
reconrundatas = reconrunq.query(results=1)
if not reconrundatas:
return None
return reconrundatas[0].dbid
def insertRefinementRunData(self, iteration, reference_number=1):
''' fills in database entry object for ApRefineRunData table '''
### fill in ApMultiModelRefineRunData object, if valid
if self.multiModelRefinementRun is True:
multimodelq = appiondata.ApMultiModelRefineRunData()
multimodelq['runname'] = self.params['runname']
multimodelq[
'REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(
self.runparams['stackid'])
multimodelq['session'] = apStack.getSessionDataFromStackId(
self.runparams['stackid'])
multimodelq['num_refinements'] = self.runparams[
'NumberOfReferences']
self.multimodelq = multimodelq
### fill in ApRefineRunData object
runq = appiondata.ApRefineRunData()
runq['runname'] = self.params['runname']
runq['stack'] = self.stackdata
runq['reference_number'] = reference_number
earlyresult = runq.query(results=1) # check unique run
if earlyresult:
apDisplay.printWarning(
"Run already exists in the database.\nIdentical data will not be reinserted"
)
paramdescription = self.params['description']
if not paramdescription:
paramdescription = None
runq['job'] = self.params['jobinfo']
if len(self.modeldata) > 1:
runq['initialModel'] = self.modeldata[reference_number - 1]
else:
runq['initialModel'] = self.modeldata[0]
runq['package'] = self.package
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.resultspath))
runq['description'] = paramdescription
runq['num_iter'] = self.runparams['numiter']
if self.multiModelRefinementRun is True:
runq['multiModelRefineRun'] = self.multimodelq
result = runq.query(results=1)
# save run entry in the parameters
if result:
self.refinerunq = result[0]
elif self.params['commit'] is True:
apDisplay.printMsg(
"Refinement Run was not found, setting to inserted values")
self.refinerunq = runq
else:
apDisplay.printWarning(
"Refinement Run was not found, setting to 'None'")
self.refinerunq = None
return
def getReconRunsIds():
reconrunids = []
reconrunq = appiondata.ApRefineRunData()
reconrundatas = reconrunq.query()
if not reconrundatas:
return reconrunids
for reconrundata in reconrundatas:
reconrunids.append(reconrundata.dbid)
return reconrunids
def getRunData(self): ### setup refinement run jobdata = apDatabase.getJobDataFromPathAndType(self.params['rundir'], "runfrealign") runq = appiondata.ApRefineRunData() runq['runname'] = self.params['runname'] runq['package'] = "Frealign" runq['description'] = self.params['description'] runq['hidden'] = False runq['num_iter'] = self.numiter runq['stack'] = apStack.getOnlyStackData(self.params['stackid']) runq['initialModel'] = apModel.getModelFromId(self.params['modelid']) runq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) runq['job'] = jobdata return runq
def insertRefinementRun(self):
runq = appiondata.ApRefineRunData()
#first two must be unique
runq['runname'] = self.params['runname']
runq['stack'] = self.params['stack']
#Recon upload can be continued
earlyresult = runq.query(results=1)
if earlyresult:
apDisplay.printWarning(
"Run already exists in the database.\nIdentical data will not be reinserted"
)
# empty <> than None for Sinedon query
paramdescription = self.params['description']
if not paramdescription:
paramdescription = None
runq['job'] = self.params['jobinfo']
runq['initialModel'] = self.params['model']
runq['package'] = self.params['package']
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq['description'] = paramdescription
runq['initialModel'] = self.params['model']
runq['num_iter'] = len(self.iterationdatas)
result = runq.query(results=1)
if earlyresult and not result:
if self.params['commit'] is True:
apDisplay.printError("Refinement Run parameters have changed")
else:
apDisplay.printWarning(
"Refinement Run parameters have changed")
# get stack apix
self.params['apix'] = apStack.getStackPixelSizeFromStackId(
self.params['stack'].dbid)
apDisplay.printMsg("inserting Refinement Run into database")
if self.params['commit'] is True:
runq.insert()
else:
apDisplay.printWarning("not committing results to database")
#if we insert runq then this returns no results !!!
# this is a workaround (annoying & bad)
runq = appiondata.ApRefineRunData()
runq['runname'] = self.params['runname']
runq['stack'] = self.params['stack']
runq['job'] = self.params['jobinfo']
runq['initialModel'] = self.params['model']
runq['package'] = self.params['package']
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq['description'] = paramdescription
runq['package'] = self.params['package']
runq['initialModel'] = self.params['model']
result = runq.query(results=1)
# save run entry in the parameters
if result:
self.params['refineRun'] = result[0]
elif self.params['commit'] is True:
apDisplay.printWarning(
"Refinement Run was not found, setting to inserted values")
self.params['refineRun'] = runq
else:
apDisplay.printWarning(
"Refinement Run was not found, setting to 'None'")
self.params['refineRun'] = None
return True