def uploadTemplateStack(self, insert=False):
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
uploadq = appiondata.ApTemplateStackData()
uploadq['REF|projectdata|projects|project'] = self.params['projectid']
if self.params['clusterId'] is not None:
uploadq[
'clusterstack'] = appiondata.ApClusteringStackData.direct_query(
self.params['clusterId'])
elif self.params['alignId'] is not None:
uploadq['alignstack'] = appiondata.ApAlignStackData.direct_query(
self.params['alignId'])
elif self.params['templatestack'] is not None:
uploadq['origfile'] = self.params['templatestack'] + ".hed"
uploadq['templatename'] = self.params['runname'] + ".hed"
if self.params['templatetype'] == "clsavg":
uploadq['cls_avgs'] = True
if self.params['templatetype'] == "forward_proj":
uploadq['forward_proj'] = True
uploadq['description'] = self.params['description']
uploadq['session'] = sessiondata
uploadq['apix'] = self.params['apix']
uploadq['boxsize'] = self.params['boxsize']
uploadq['numimages'] = self.numimages
uploadq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
if insert is True:
uploadq.insert()
def checkConflicts(self):
### make sure the necessary parameters are set
if self.params['description'] is None:
apDisplay.printError("enter a template description")
if self.params['templatestack'] is None and self.params['clusterId'] is None and self.params['alignId'] is None:
apDisplay.printError("enter a template stack file or a clusterId or an alignId")
if self.params['templatetype'] is None and self.params['templatetype'] is not "clsavg" and self.params['templatetype'] is not "forward_proj":
apDisplay.printError("enter the template type (i.e. class averages / forward projections)")
if self.params['runname'] is None:
templatestacksq = appiondata.ApTemplateStackData()
templatestacks = templatestacksq.query()
num_templatestacks = len(templatestacks)
new_num = num_templatestacks + 1
self.params['runname'] = "templatestack"+str(new_num)+"_"+str(self.params['sessionname'])
### get apix value
if (self.params['apix'] is None and self.params['clusterId'] is None and self.params['alignId'] is None):
apDisplay.printError("Enter value for angstroms per pixel")
elif (self.params['apix'] is None and self.params['clusterId'] is not None or self.params['alignId'] is not None):
if self.params['clusterId'] is not None:
clusterdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterId'])
self.params['apix'] = clusterdata['clusterrun']['pixelsize']
else:
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignId'])
self.params['apix'] = aligndata['pixelsize']
### get boxsize if not specified
if self.params['boxsize'] is None and self.params['templatestack'] is not None:
emancmd = "iminfo "+self.params['templatestack']
proc = subprocess.Popen(emancmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
results = proc.stdout
proc.wait()
for line in results:
res = re.search("([0-9]+)x([0-9]+)x([0-9])", line)
if res:
num1 = int(res.groups()[0])
num2 = int(res.groups()[1])
if num1 == num2:
self.params['boxsize'] = num1
elif self.params['boxsize'] is None and self.params['clusterId'] is not None or self.params['alignId'] is not None:
if self.params['clusterId'] is not None:
clusterdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterId'])
self.params['boxsize'] = clusterdata['clusterrun']['boxsize']
else:
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignId'])
self.params['boxsize'] = aligndata['boxsize']
### check for session
if self.params['sessionname'] is None:
if self.params['clusterId'] is not None:
clusterdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterId'])
stackid = clusterdata['clusterrun']['alignstack']['stack'].dbid
sessiondata = apStack.getSessionDataFromStackId(stackid)
self.params['sessionname'] = sessiondata['name']
elif self.params['alignId'] is not None:
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignId'])
stackid = aligndata['stack'].dbid
sessiondata = apStack.getSessionDataFromStackId(stackid)
self.params['sessionname'] = sessiondata['name']
else:
apDisplay.printError("Could not find session")
if self.params['templatestack'] is not None:
self.params['templatestack'] = os.path.abspath(self.params['templatestack'])
### exclusions and inclusions, if modifying previous stack
if self.params['clusterId'] is not None or self.params['alignId'] is not None:
if self.params['first'] is None and self.params['last'] is None:
if self.params['keepfile'] is None and self.params['exclude'] is None and self.params['include'] is None:
apDisplay.printError("Please define either keepfile, exclude or include")
elif self.params['keepfile']:
self.params['keepfile'] = os.path.abspath(self.params['keepfile'])
if not os.path.isfile(self.params['keepfile']):
apDisplay.printError("Could not find keep file: "+self.params['keepfile'])
if self.params['keepfile'] and (self.params['exclude'] is not None or self.params['include'] is not None):
apDisplay.printError("Please define only either keepfile, exclude or include")
if self.params['exclude'] and (self.params['keepfile'] is not None or self.params['include'] is not None):
apDisplay.printError("Please define only either keepfile, exclude or include")
if self.params['include'] and (self.params['exclude'] is not None or self.params['keepfile'] is not None):
apDisplay.printError("Please define only either keepfile, exclude or include")