def getEMGrid(self, gridname):
if self.projectid is not None:
emgridq = leginondata.EMGridData(project=self.projectid,
name=gridname)
else:
emgridq = leginondata.EMGridData(name=gridname)
results = emgridq.query(results=1)
if results:
return results[0]
else:
return None
def getGridNames(self):
gridnames = []
if self.projectid is not None:
emgridq = leginondata.EMGridData(project=self.projectid)
else:
emgridq = leginondata.EMGridData()
results = emgridq.query()
if results:
for result in results:
newname = result['name']
if newname not in gridnames:
gridnames.append(newname)
else:
self.logger.warning(
'Duplicated grid name "%s" not included' % newname)
return gridnames
def publishImageData(self, imagedata, save):
acquisitionimagedata = leginondata.AcquisitionImageData(
initializer=imagedata)
if save:
griddata = leginondata.GridData()
if self.grid is not None:
gridinfo = self.gridmapping[self.grid]
griddata['grid ID'] = gridinfo['gridId']
emgriddata = leginondata.EMGridData(
name=gridinfo['label'], project=gridinfo['projectId'])
griddata['emgrid'] = emgriddata
griddata['insertion'] = self.insertion
acquisitionimagedata['grid'] = griddata
self.gridlabel = gridlabeler.getGridLabel(griddata)
elif self.emgrid is not None:
# New style that uses emgridata only for grid entry
griddata['emgrid'] = self.emgrid
griddata['insertion'] = self.insertion
acquisitionimagedata['grid'] = griddata
else:
self.gridlabel = ''
acquisitionimagedata['label'] = self.settings['image label']
self.setImageFilename(acquisitionimagedata)
acquisitionimagedata.attachPixelSize()
try:
self.publish(imagedata['scope'], database=True)
self.publish(imagedata['camera'], database=True)
self.publish(acquisitionimagedata, database=True)
except RuntimeError:
raise node.PublishError
## publish event even if no save
self.publish(acquisitionimagedata, pubevent=True)
def getGridMakingPrintTrialNumber(self):
q = leginondata.EMGridData(project=self.projectid, plate=self.plate)
r = q.query()
if r:
trials = map((lambda x: x['print trial']), r)
return max(trials) + 1
else:
return 1
def publishNewEMGrid(self, newgrid):
emgridq = leginondata.EMGridData()
emgridq['name'] = newgrid
emgridq['project'] = self.projectid
try:
self.publish(emgridq, database=True)
except node.PublishError:
raise
self.settings['grid name'] = newgrid
self.logger.info('new grid inserted into the database')
def makeGrid(self, grid_index=0):
'''
make grid at given grid_index and print trial number.
Filenaming: p stands for print trial number. g is well group
in the database. known to users as grid number
'''
grid_number = int(grid_index) + 1
gridname = self.plate['name'] + 'p%dg%d' % (self.trial_number,
grid_number)
q = leginondata.EMGridData(project=self.projectid,
mapping=self.maptype,
plate=self.plate)
q['well group'] = grid_number
q['print trial'] = self.trial_number
q['name'] = gridname
q.insert()
return q
gridlocations = projectdata.getGridLocations()
gridboxidindex = gridlocations.Index(['gridboxId'])
gridlocations = gridboxidindex[gridboxid].fetchall()
for gridlocation in gridlocations:
if gridlocation['location'] == gridnumber:
return gridlocation['gridId']
return self.newGrid(gridboxid, gridnumber)
def publishEMGridData(self,gridid):
try:
projectdata = project.ProjectData()
except project.NotConnectedError, e:
self.logger.error('Failed to get grid labels: %s' % e)
return None
gridinfo = projectdata.getGridInfo(gridid)
emgriddata = leginondata.EMGridData()
emgriddata['name'] = gridinfo['label']
emgriddata['project'] = gridinfo['projectId']
self.publish(emgriddata, database=True)
return emgriddata
def makeGridData(self, gridnumber):
gridid = self.getGridID(self.gridtrayid, gridnumber)
if gridid is None:
return None
emgriddata = self.publishEMGridData(gridid)
initializer = {'grid ID': gridid}
querydata = leginondata.GridData(initializer=initializer)
griddatalist = self.research(querydata)
insertion = 0
for griddata in griddatalist:
