def insertACErunParams(self):
# first create an aceparam object
aceparamq = appiondata.ApAceParamsData()
for key in aceparamq.keys():
if key in self.params:
aceparamq[key] = self.params[key]
# if nominal df is set, save override df to database, else don't set
if self.params['nominal']:
dfnom = abs(self.params['nominal'])
aceparamq['df_override'] = dfnom
# create an acerun object
self.acerunq = appiondata.ApAceRunData()
self.acerunq['name'] = self.params['runname']
self.acerunq['session'] = self.getSessionData()
# see if acerun already exists in the database
acerundatas = self.acerunq.query(results=1)
if (acerundatas):
if not (acerundatas[0]['aceparams'] == aceparamq):
for i in acerundatas[0]['aceparams']:
if acerundatas[0]['aceparams'][i] != aceparamq[i]:
apDisplay.printWarning("the value for parameter '"+str(i)+"' is different from before")
apDisplay.printError("All parameters for a single ACE run must be identical! \n"+\
"please check your parameter settings.")
#create path
self.acerunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
self.acerunq['hidden'] = False
self.acerunq['aceparams'] = aceparamq
# if no run entry exists, insert new run entry into db
self.acerunq.insert()
def insertXmippCtfRun(self, imgdata):
if isinstance(self.ctfrun, appiondata.ApAceRunData):
return False
# first create an aceparam object
paramq = appiondata.ApXmippCtfParamsData()
paramq['fieldsize'] = self.params['fieldsize']
# create an acerun object
runq = appiondata.ApAceRunData()
runq['name'] = self.params['runname']
runq['session'] = imgdata['session'];
# see if acerun already exists in the database
runnames = runq.query(results=1)
if (runnames):
if not (runnames[0]['xmipp_ctf_params'] == paramq):
for i in runnames[0]['xmipp_ctf_params']:
if runnames[0]['xmipp_ctf_params'][i] != paramq[i]:
apDisplay.printWarning("the value for parameter '"+str(i)+"' is different from before")
apDisplay.printError("All parameters for a single CTF estimation run must be identical! \n"+\
"please check your parameter settings.")
self.ctfrun = runnames[0]
return False
#create path
runq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
runq['hidden'] = False
# if no run entry exists, insert new run entry into db
runq['xmipp_ctf_params'] = paramq
runq.insert()
self.ctfrun = runq
return True
def getNumCtfRunsFromSession(sessionname):
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
ctfrunq = appiondata.ApAceRunData()
ctfrunq['session'] = sessiondata
ctfrundatas = ctfrunq.query()
if not ctfrundatas:
return 0
return len(ctfrundatas)
def insertRunData(self):
runq = appiondata.ApAceRunData()
runq['name'] = self.params['runname']
runq['session'] = self.getSessionData()
runq['hidden'] = False
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq.insert()
self.ctfrundata = runq
def insertCtfRun(self, imgdata):
if isinstance(self.ctfrun, appiondata.ApAceRunData):
return False
# first create an aceparam object
paramq = appiondata.ApCtfFind4ParamsData()
copyparamlist = (
'ampcontrast',
'fieldsize',
'cs',
'bestdb',
'resmin',
'defstep',
)
for p in copyparamlist:
if p in self.params:
paramq[p] = self.params[p]
# create an acerun object
runq = appiondata.ApAceRunData()
runq['name'] = self.params['runname']
runq['session'] = imgdata['session']
# see if acerun already exists in the database
runnames = runq.query(results=1)
if (runnames):
prevrun = runnames[0]
if not (prevrun['ctffind4_params'] == paramq):
for i in prevrun['ctffind4_params']:
if prevrun['ctffind4_params'][i] != paramq[i]:
# float value such as cs of 4.1 is not quite equal
if type(paramq[i]) == type(
1.0) and abs(prevrun['ctffind4_params'][i] -
paramq[i]) < 0.00001:
continue
apDisplay.printWarning("the value for parameter '" +
str(i) +
"' is different from before")
apDisplay.printError("All parameters for a single CTF estimation run must be identical! \n"+\
"please check your parameter settings.")
self.ctfrun = prevrun
return False
#create path
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq['hidden'] = False
# if no run entry exists, insert new run entry into db
runq['ctffind4_params'] = paramq
runq.insert()
self.ctfrun = runq
return True
def insertCtfTiltRun(self, imgdata):
if isinstance(self.ctfrun, appiondata.ApAceRunData):
return False
# first create an aceparam object
paramq = appiondata.ApCtfTiltParamsData()
copyparamlist = ('medium', 'ampcarbon', 'ampice', 'fieldsize', 'cs',
'bin', 'resmin', 'resmax', 'defstep', 'dast')
for p in copyparamlist:
if p in self.params:
paramq[p] = self.params[p]
# create an acerun object
runq = appiondata.ApAceRunData()
runq['name'] = self.params['runname']
runq['session'] = imgdata['session']
# see if acerun already exists in the database
runnames = runq.query(results=1)
if (runnames):
if not (runnames[0]['ctftilt_params'] == paramq):
for i in runnames[0]['ctftilt_params']:
if runnames[0]['ctftilt_params'][i] != paramq[i]:
apDisplay.printWarning("the value for parameter '" +
str(i) +
"' is different from before")
apDisplay.printError("All parameters for a single CTF estimation run must be identical! \n"+\
"please check your parameter settings.")
self.ctfrun = runnames[0]
return False
#create path
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq['hidden'] = False
# if no run entry exists, insert new run entry into db
runq['ctftilt_params'] = paramq
runq.insert()
self.ctfrun = runq
return True
def insertRunData(self):
paramq = appiondata.ApAce2ParamsData()
paramq['bin'] = self.params['bin']
paramq['reprocess'] = self.params['reprocess']
paramq['cs'] = self.params['cs']
paramq['stig'] = True
paramq['min_defocus'] = self.params['mindefocus']
paramq['max_defocus'] = self.params['maxdefocus']
paramq['edge_thresh'] = self.params['edge_t']
paramq['edge_blur'] = self.params['edge_b']
paramq['rot_blur'] = self.params['rotblur']
paramq['refine2d'] = self.params['refine2d']
paramq['onepass'] = self.params['onepass']
paramq['zeropass'] = self.params['zeropass']
runq = appiondata.ApAceRunData()
runq['name'] = self.params['runname']
runq['session'] = self.getSessionData()
runq['hidden'] = False
runq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
runq['ace2_params'] = paramq
runq.insert()
self.ctfrundata = runq