def upgradeAppionDB(self):
if self.appion_dbupgrade.columnExists('ApContourData', 'runname'):
if not self.appion_dbupgrade.columnExists(
'ApContourData', 'REF|ApSelectionRunData|selectionrun'):
self.appion_dbupgrade.addColumn(
'ApContourData',
'REF|ApSelectionRunData|selectionrun',
self.appion_dbupgrade.link,
index=True)
contourq = appiondata.ApContourData()
contours = contourq.query()
for contourdata in contours:
if not contourdata['runname']:
continue
selectionrundata = apParticle.getSelectionRunDataFromName(
contourdata['image'], contourdata['runname'])
contourid = contourdata.dbid
selectionid = selectionrundata.dbid
if contourid and selectionid:
updateq = (
"UPDATE ApContourData AS contour " + " SET " +
" contour.`REF|ApSelectionRunData|selectionrun` = "
+ " %d " % selectionid +
" WHERE contour.`DEF_id` = %d " % contourid)
self.appion_dbupgrade.executeCustomSQL(updateq)
def upgradeAppionDB(self):
if self.appion_dbupgrade.columnExists('ApContourData', 'runname'):
if not self.appion_dbupgrade.columnExists('ApContourData', 'REF|ApSelectionRunData|selectionrun'):
self.appion_dbupgrade.addColumn('ApContourData', 'REF|ApSelectionRunData|selectionrun', self.appion_dbupgrade.link, index=True)
contourq = appiondata.ApContourData()
contours = contourq.query()
for contourdata in contours:
if not contourdata['runname']:
continue
selectionrundata = apParticle.getSelectionRunDataFromName(contourdata['image'], contourdata['runname'])
contourid = contourdata.dbid
selectionid = selectionrundata.dbid
if contourid and selectionid:
updateq = ("UPDATE ApContourData AS contour "
+" SET "
+" contour.`REF|ApSelectionRunData|selectionrun` = "
+" %d " % selectionid
+" WHERE contour.`DEF_id` = %d " % contourid
)
self.appion_dbupgrade.executeCustomSQL(updateq)
def runManualPicker(self, imgdata):
# Contourpicker does not do assessment. Setting the current assessment to be
# the same as the old prevents committing it to the database
self.assessold = None
self.assess = self.assessold
#reset targets
self.targets = {}
for label in self.labels:
self.app.panel.setTargets(label, [])
self.targets[label] = []
#open new file
imgname = imgdata['filename']+'.dwn.mrc'
imgpath = os.path.join(self.params['rundir'],imgname)
self.app.panel.openImageFile(imgpath)
self.app.panel.originaltargets = {}
#set vital stats
self.app.vitalstats.SetLabel("Vital Stats: Image "+str(self.stats['count'])
+" of "+str(self.stats['imagecount'])
+" image name: "+imgdata['filename'])
#run the picker
self.loadOld(imgdata)
self.app.MainLoop()
#targets are copied to self.targets by app
#parse and return the targets in peaktree form
self.app.panel.openImageFile(None)
peaktree=[]
for label,targets in self.targets.items():
for target in targets:
peaktree.append(self.XY2particle(target.x, target.y, label=label))
targetsList = self.getPolyParticlePoints()
contourTargets = self.app.panel.getTargets('Auto Create Contours')
try:
rundata = apParticle.getSelectionRunDataFromName(imgdata,self.params['runname'])
except IndexError:
# the first image does not have rundata in the database, yet
rundata = self.commitRunToDatabase(imgdata['session'], True)
bin = rundata['manparams']['bin']
c = None
counter = 0
for i in range(len(targetsList)):
# safe-guard from 1 or 2 point target
if len(targetsList[i]) < 3:
apDisplay.printWarning('contour %d has only %d points....IGNORED' % (i,len(targetsList[i])))
counter += 1
continue
c=appiondata.ApContourData(name="contour"+str(int(self.startPoint)+i), image=imgdata, x=contourTargets[counter].x, y=contourTargets[counter].y,version=self.maxVersion+1, method='auto', particleType=self.app.particleTypeList[counter], selectionrun=rundata)
c.insert()
counter += 1
for point in targetsList[i]:
# save points in the scale of the original image, like particles
point1=appiondata.ApContourPointData(x=point[0]*bin, y=point[1]*bin, contour=c)
point1.insert()
return peaktree