def insertCL2DParamsIntoDatabase(self): ### setup cl2d run cl2dq = appiondata.ApXMIPP3CL2DRunData() cl2dq['runname'] = self.runparams['runname'] cl2dq['run_seconds'] = self.runparams['runtime'] cl2dq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid']) cl2dq['timestamp'] = self.params['timestamp'] cl2dq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) cl2dq['finished'] = True cl2dq['max-iter'] = self.params['maxiter'] cl2dq['num-ref'] = self.params['numrefs'] if self.params['correlation'] is True: cl2dq['correlation'] = True cl2dq['correntropy'] = False else: cl2dq['correlation'] = False cl2dq['correntropy'] = True if self.params['classical'] is True: cl2dq['classical_multiref'] = True cl2dq['intracluster_multiref'] = False else: cl2dq['classical_multiref'] = False cl2dq['intracluster_multiref'] = True ### insert if commit is true if self.params['commit'] is True: cl2dq.insert() self.cl2dqdata=cl2dq
def insertSIMPLEAlignParamsIntoDatabase(self):
### setup simple run
simpleq = appiondata.ApSIMPLEClusterRunData()
simpleq['runname'] = self.runparams['runname']
simpleq['run_seconds'] = self.runparams['runtime']
simpleq[
'REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(
self.params['stackid'])
simpleq['timestamp'] = self.params['timestamp']
simpleq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
simpleq['finished'] = True
simpleq['num-ref'] = self.params['ncls']
if self.params['no_kmeans'] is False:
simpleq['kmeans'] = True
else:
simpleq['kmeans'] = False
if self.params['no_center'] is False:
simpleq['center'] = True
else:
simpleq['center'] = False
### insert if commit is true
if self.params['commit'] is True:
simpleq.insert()
self.simpleqdata = simpleq
def insertCL2DParamsIntoDatabase(self): ### setup cl2d run cl2dq = appiondata.ApCL2DRunData() cl2dq['runname'] = self.runparams['runname'] cl2dq['run_seconds'] = self.runparams['runtime'] cl2dq['fast'] = self.runparams['fast'] cl2dq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid']) cl2dq['timestamp'] = self.params['timestamp'] cl2dq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) cl2dq['finished'] = True cl2dq['max-iter'] = self.params['maxiter'] cl2dq['num-ref'] = self.params['numrefs'] if self.params['correlation'] is True: cl2dq['correlation'] = True cl2dq['correntropy'] = False else: cl2dq['correlation'] = False cl2dq['correntropy'] = True if self.params['classical'] is True: cl2dq['classical_multiref'] = True cl2dq['intracluster_multiref'] = False else: cl2dq['classical_multiref'] = False cl2dq['intracluster_multiref'] = True ### insert if commit is true if self.params['commit'] is True: cl2dq.insert() self.cl2dqdata=cl2dq
def insertMaxLikeJob(self):
maxjobq = appiondata.ApMaxLikeJobData()
maxjobq['runname'] = self.params['runname']
maxjobq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
maxjobdatas = maxjobq.query(results=1)
if maxjobdatas:
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
alignrundata = alignrunq.query(results=1)
if maxjobdatas[0]['finished'] is True or alignrundata:
apDisplay.printError(
"This run name already exists as finished in the database, please change the runname"
)
maxjobq[
'REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(
self.params['stackid'])
maxjobq['timestamp'] = self.timestamp
maxjobq['finished'] = False
maxjobq['hidden'] = False
if self.params['commit'] is True:
maxjobq.insert()
self.params['maxlikejobid'] = maxjobq.dbid
print "self.params['maxlikejobid']", self.params['maxlikejobid']
return
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 getCL2DJob(self): cl2djobq = appiondata.ApCL2DRunData() cl2djobq['runname'] = self.runparams['runname'] cl2djobq['path'] = appiondata.ApPathData(path=os.path.abspath(self.runparams['rundir'])) cl2djobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.runparams['stackid']) cl2djobq['timestamp'] = self.params['timestamp'] cl2djobdata = cl2djobq.query(results=1) if not cl2djobdata: return None return cl2djobdata[0]
def getCL2DJob(self): cl2djobq = appiondata.ApCL2DRunData() cl2djobq['runname'] = self.runparams['runname'] cl2djobq['path'] = appiondata.ApPathData(path=os.path.abspath(self.runparams['rundir'])) cl2djobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.runparams['stackid']) cl2djobq['timestamp'] = self.params['timestamp'] cl2djobdata = cl2djobq.query(results=1) if not cl2djobdata: return None return cl2djobdata[0]
def getMaxLikeJob(self, runparams): maxjobq = appiondata.ApMaxLikeJobData() maxjobq['runname'] = runparams['runname'] maxjobq['path'] = appiondata.ApPathData(path=os.path.abspath(runparams['rundir'])) maxjobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(runparams['stackid']) maxjobq['timestamp'] = self.params['timestamp'] maxjobdata = maxjobq.query(results=1) if not maxjobdata: return None return maxjobdata[0]
def getHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun["runname"] = self.params["runname"]
HipRun["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
HipRun["description"] = self.params["description"]
HipRun["REF|projectdata|projects|project"] = apProject.getProjectIdFromStackId(self.params["stackid"])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
HipRun["session"] = sessiondata
HipRun["apix"] = self.params["step"]
self.stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
HipRun["stack"] = self.stackdata
return HipRun
def getHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun['runname'] = self.params['runname']
HipRun['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
HipRun['description'] = self.params['description']
HipRun['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
HipRun['session'] = sessiondata
HipRun['apix'] = self.params['step']
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
HipRun['stack'] = self.stackdata
return HipRun
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 insertHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun["runname"] = self.params["runname"]
HipRun["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
HipRun["description"] = self.params["description"]
HipRun["REF|projectdata|projects|project"] = apProject.getProjectIdFromStackId(self.params["stackid"])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
HipRun["session"] = sessiondata
HipRun["apix"] = self.params["step"]
self.stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
HipRun["stack"] = self.stackdata
if self.params["commit"] is True:
HipRun.insert()
else:
print HipRun
self.params["HipRunID"] = HipRun.dbid
print "self.params['HipRunID']", self.params["HipRunID"]
self.params["HipRun"] = HipRun
return HipRun
def insertHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun['runname'] = self.params['runname']
HipRun['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
HipRun['description'] = self.params['description']
HipRun['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
HipRun['session'] = sessiondata
HipRun['apix'] = self.params['step']
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
HipRun['stack'] = self.stackdata
if self.params['commit'] is True:
HipRun.insert()
else:
print HipRun
self.params['HipRunID'] = HipRun.dbid
print "self.params['HipRunID']",self.params['HipRunID']
self.params['HipRun'] = HipRun
return HipRun
def insertTopolRepJob(self):
topoljobq = appiondata.ApTopolRepJobData()
topoljobq['runname'] = self.params['runname']
topoljobq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
topoljobdatas = topoljobq.query(results=1)
if topoljobdatas:
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
alignrundata = alignrunq.query(results=1)
if topoljobdatas[0]['finished'] is True or alignrundata:
apDisplay.printError("This run name already exists as finished in the database, please change the runname")
topoljobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
topoljobq['timestamp'] = self.timestamp
topoljobq['finished'] = False
topoljobq['hidden'] = False
if self.params['commit'] is True:
topoljobq.insert()
self.params['topoljob'] = topoljobq
return
def insertMaxLikeJob(self):
maxjobq = appiondata.ApMaxLikeJobData()
maxjobq['runname'] = self.params['runname']
maxjobq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
maxjobdatas = maxjobq.query(results=1)
if maxjobdatas:
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
alignrundata = alignrunq.query(results=1)
if maxjobdatas[0]['finished'] is True or alignrundata:
apDisplay.printError("This run name already exists as finished in the database, please change the runname")
maxjobq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
maxjobq['timestamp'] = self.timestamp
maxjobq['finished'] = False
maxjobq['hidden'] = False
if self.params['commit'] is True:
maxjobq.insert()
self.params['maxlikejobid'] = maxjobq.dbid
print "self.params['maxlikejobid']",self.params['maxlikejobid']
return
def insertSIMPLEOrigamiParamsIntoDatabase(self):
### setup simple run
simpleq = appiondata.ApSIMPLEOrigamiRunData()
simpleq['runname'] = self.runparams['runname']
simpleq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
# ### check unique run
# uniquerun = simpleq.query(results=1)
# if uniquerun:
# apDisplay.printError("runname already exists in the database")
paramsq = appiondata.ApSIMPLEOrigamiParamsData()
paramsq['lp'] = self.params['lp']
paramsq['hp'] = self.params['hp']
paramsq['froms'] = self.params['froms']
paramsq['tos'] = self.params['tos']
paramsq['maxits'] = self.params['maxits']
paramsq['msk'] = self.params['mask']
paramsq['mw'] = self.params['mw']
paramsq['amsklp'] = self.params['amsklp']
paramsq['edge'] = self.params['edge']
paramsq['trs'] = self.params['trs']
paramsq['pgrp'] = self.params['pgrp']
simpleq['description'] = self.params['description']
simpleq['box'] = self.boxsize
simpleq['apix'] = self.apix
simpleq['simple_params'] = paramsq
simpleq[
'REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(
self.params['stackid'])
simpleq['timestamp'] = self.params['timestamp']
simpleq['stack'] = apStack.getOnlyStackData(self.runparams['stackid'])
simpleq['alignstack'] = self.alignstackdata
simpleq['clusteringstack'] = self.clusterstackq
if self.params['commit'] is True:
simpleq.insert()
return
def insertSIMPLEAlignParamsIntoDatabase(self):
### setup simple run
simpleq = appiondata.ApSIMPLEClusterRunData()
simpleq["runname"] = self.runparams["runname"]
simpleq["run_seconds"] = self.runparams["runtime"]
simpleq["REF|projectdata|projects|project"] = apProject.getProjectIdFromStackId(self.params["stackid"])
simpleq["timestamp"] = self.params["timestamp"]
simpleq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
simpleq["finished"] = True
simpleq["num-ref"] = self.params["ncls"]
if self.params["no_kmeans"] is False:
simpleq["kmeans"] = True
else:
simpleq["kmeans"] = False
if self.params["no_center"] is False:
simpleq["center"] = True
else:
simpleq["center"] = False
### insert if commit is true
if self.params["commit"] is True:
simpleq.insert()
self.simpleqdata = simpleq
def insertSIMPLEAlignParamsIntoDatabase(self): ### setup simple run simpleq = appiondata.ApSIMPLEClusterRunData() simpleq['runname'] = self.runparams['runname'] simpleq['run_seconds'] = self.runparams['runtime'] simpleq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid']) simpleq['timestamp'] = self.params['timestamp'] simpleq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) simpleq['finished'] = True simpleq['num-ref'] = self.params['ncls'] if self.params['no_kmeans'] is False: simpleq['kmeans'] = True else: simpleq['kmeans'] = False if self.params['no_center'] is False: simpleq['center'] = True else: simpleq['center'] = False ### insert if commit is true if self.params['commit'] is True: simpleq.insert() self.simpleqdata=simpleq
def insertSIMPLEOrigamiParamsIntoDatabase(self):
### setup simple run
simpleq = appiondata.ApSIMPLEOrigamiRunData()
simpleq["runname"] = self.runparams["runname"]
simpleq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
# ### check unique run
# uniquerun = simpleq.query(results=1)
# if uniquerun:
# apDisplay.printError("runname already exists in the database")
paramsq = appiondata.ApSIMPLEOrigamiParamsData()
paramsq["lp"] = self.params["lp"]
paramsq["hp"] = self.params["hp"]
paramsq["froms"] = self.params["froms"]
paramsq["tos"] = self.params["tos"]
paramsq["maxits"] = self.params["maxits"]
paramsq["msk"] = self.params["mask"]
paramsq["mw"] = self.params["mw"]
paramsq["amsklp"] = self.params["amsklp"]
paramsq["edge"] = self.params["edge"]
paramsq["trs"] = self.params["trs"]
paramsq["pgrp"] = self.params["pgrp"]
simpleq["description"] = self.params["description"]
simpleq["box"] = self.boxsize
simpleq["apix"] = self.apix
simpleq["simple_params"] = paramsq
simpleq["REF|projectdata|projects|project"] = apProject.getProjectIdFromStackId(self.params["stackid"])
simpleq["timestamp"] = self.params["timestamp"]
simpleq["stack"] = apStack.getOnlyStackData(self.runparams["stackid"])
simpleq["alignstack"] = self.alignstackdata
simpleq["clusteringstack"] = self.clusterstackq
if self.params["commit"] is True:
simpleq.insert()
return
def insertSIMPLEOrigamiParamsIntoDatabase(self):
### setup simple run
simpleq = appiondata.ApSIMPLEOrigamiRunData()
simpleq['runname'] = self.runparams['runname']
simpleq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
# ### check unique run
# uniquerun = simpleq.query(results=1)
# if uniquerun:
# apDisplay.printError("runname already exists in the database")
paramsq = appiondata.ApSIMPLEOrigamiParamsData()
paramsq['lp'] = self.params['lp']
paramsq['hp'] = self.params['hp']
paramsq['froms'] = self.params['froms']
paramsq['tos'] = self.params['tos']
paramsq['maxits'] = self.params['maxits']
paramsq['msk'] = self.params['mask']
paramsq['mw'] = self.params['mw']
paramsq['amsklp'] = self.params['amsklp']
paramsq['edge'] = self.params['edge']
paramsq['trs'] = self.params['trs']
paramsq['pgrp'] = self.params['pgrp']
simpleq['description'] = self.params['description']
simpleq['box'] = self.boxsize
simpleq['apix'] = self.apix
simpleq['simple_params'] = paramsq
simpleq['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
simpleq['timestamp'] = self.params['timestamp']
simpleq['stack'] = apStack.getOnlyStackData(self.runparams['stackid'])
simpleq['alignstack'] = self.alignstackdata
simpleq['clusteringstack'] = self.clusterstackq
if self.params['commit'] is True:
simpleq.insert()
return