def loadOld(self,imgdata):
partq = appiondata.ApContourData()
partq['image'] = imgdata
partd = partq.query()
try:
name = partd[0]['name']
self.startPoint = name.lstrip('contour')
except IndexError:
self.startPoint = 0
points = appiondata.ApContourPointData()
oldPolyPoints = []
contourPoints = []
types = []
singleTypes = []
singleTargets = []
tubePoints = []
self.maxVersion = -1
bin = float(self.params['bin'])
for i in partd:
if not i['version']==None and int(i['version'])>self.maxVersion and i['runname']==self.params['runname']:
self.maxVersion = int(i['version'])
for i in partd:
if not i['version']==None and int(i['version'])==self.maxVersion and not i['method']=='single' and i['runname']==self.params['runname']:
contourPoints.append((i['x'],i['y']))
types.append(i['particleType'])
contour = i['name']
points['contour'] = i
point = points.query()
contourList = []
for j in point:
contourList.append((int(j['x']/bin), int(j['y'])/bin))
oldPolyPoints.append(contourList)
return self.app.loadOld((contourPoints,oldPolyPoints,types))
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 getImagePixelSizeFromContourId(contourid):
# This returns pixelsize in Angstrom
q = appiondata.ApSelectionRunData()
rundata = q.direct_query(contourid)
q = appiondata.ApContourData(selectionrun=rundata)
r = q.query(results=1)
lastimagedata = r[0]['image']
apix = apDatabase.getPixelSize(lastimagedata)
return apix
def start(self):
sessionname = self.params['sessionname']
runname = self.params['runname']
preset = self.params['preset']
sessionq = leginondata.SessionData(name=sessionname)
presetq = leginondata.PresetData(name=preset)
imgquery = leginondata.AcquisitionImageData()
imgquery['preset'] = presetq
imgquery['session'] = sessionq
imgtree = imgquery.query(readimages=False)
partq = appiondata.ApContourData()
sessiond = sessionq.query()
file = open('contourpickerTubeCircleData-' + sessionname + '.txt', 'w')
file.write('experiment_name ' + sessionname + '\n')
file.write('experiment_description ' + sessiond[0]['comment'] + '\n')
numimages = 0
for imgdata in imgtree:
partq['image'] = imgdata
partd = partq.query()
if len(partd) > 0:
numimages += 1
file.write('nimages ' + str(numimages) + '\n')
numparticles = 0.0
numcircles = 0.0
numtubes = 0.0
for imgdata in imgtree:
partq['image'] = imgdata
partd = partq.query()
maxversion = 0
for part in partd:
if int(part['version']
) > maxversion and part['runname'] == runname:
maxversion = int(part['version'])
for part in partd:
if int(part['version']
) == maxversion and part['runname'] == runname:
numparticles += 1
if part['particleType'] == 'Circle':
numcircles += 1
if part['particleType'] == 'Tube':
numtubes += 1
file.write('nparticles ' + str(numparticles) + '\n')
if numparticles == 0:
precenttubes = 0
file.write('%tubes ' + str(0.0))
else:
percenttubes = numtubes / numparticles
percent = percenttubes * 100
percent *= 100
percent = int(percent)
percent = percent / 100.0
file.write('%tubes ' + str(percent))
def upgradeAppionDB(self):
if self.appion_dbupgrade.columnExists('ApContourData', 'runname'):
if not self.appion_dbupgrade.columnExists('ApManualParamsData', 'trace'):
self.appion_dbupgrade.addColumn('ApManualParamsData', 'trace', self.appion_dbupgrade.bool)
contourq = appiondata.ApContourData()
contours = contourq.query()
for contourdata in contours:
paramid = contourdata['selectionrun']['manparams'].dbid
if paramid:
updateq = ("UPDATE ApManualParamsData AS mp "
+" SET "
+" mp.`trace` = 1 "
+" WHERE mp.`DEF_id` = %d " % paramid
)
self.appion_dbupgrade.executeCustomSQL(updateq)
def getContoursFromImageTraceRun(imagedata,tracerundata):
q = appiondata.ApContourData(image=imagedata,selectionrun=tracerundata)
r = q.query()
return r
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
def start(self):
sessionname = self.params['sessionname']
runname = self.params['runname']
preset = self.params['preset']
sessionq = leginondata.SessionData(name=sessionname)
presetq = leginondata.PresetData(name=preset)
imgquery = leginondata.AcquisitionImageData()
imgquery['preset'] = presetq
imgquery['session'] = sessionq
imgtree = imgquery.query(readimages=False)
partq = appiondata.ApContourData()
sessiond = sessionq.query()
selectionid = apParticle.getSelectionIdFromName(runname, sessionname)
if not selectionid:
apDisplay.printWarning(
'No Object Tracing Run found in database, Skipping.......')
return
selectionrundata = apParticle.getSelectionRunDataFromID(selectionid)
file = open('contourpickerData-' + sessionname + '.txt', 'w')
file.write('session_id ' + runname + '\n')
file.write('usr_id ' + os.getlogin() + '\n')
file.write('experiment_name ' + sessionname + '\n')
file.write('experiment_description ' + sessiond[0]['comment'].strip() +
'\n')
file.write('nimages ' + str(len(imgtree)) + '\n')
for imgdata in imgtree:
file.write('START_IMAGE' + '\n')
partq['image'] = imgdata
partq['selectionrun'] = selectionrundata
partd = partq.query()
if len(partd) > 0:
file.write('image_refID ' + str(partd[0]['image'].dbid) + '\n')
file.write('image_name ' + imgdata['filename'] + '\n')
if len(partd) > 0:
file.write('time_roi ' + str(partd[0].timestamp) + '\n')
#file.write('time_roi ' + partd[0]['DEF_timestamp'] + '\n')
file.write('dfac = 1\n')
maxversion = 0
numparticles = 0
for part in partd:
if int(part['version']) > maxversion:
maxversion = int(part['version'])
for part in partd:
if int(part['version']) == maxversion:
numparticles += 1
file.write('version_id ' + str(maxversion) + '\n')
file.write('ncontours ' + str(numparticles) + '\n')
pointq = appiondata.ApContourPointData()
for part in partd:
if int(part['version']) == maxversion:
# file.write('contour_number ' + )
file.write('method_used ' + part['method'] + ' ')
pointq['contour'] = part
pointd = pointq.query()
for point in pointd:
file.write(
str(point['x']) + ',' + str(point['y']) + ';')
file.write('\n')
file.write('END_IMAGE' + '\n')
