def start(self):
apDisplay.printMsg("Getting box files")
boxfiles = self.getBoxFiles()
apDisplay.printMsg("Getting image data from database")
imgtree = apDatabase.getSpecificImagesFromDB(boxfiles)
if imgtree[0]['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match " +
imgtree[0]['filename'])
### insert params for manual picking
rundata = self.insertManualParams()
# upload Particles
for imgdata in imgtree:
### check session
if imgdata['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match " +
imgdata['filename'])
peaktree = self.boxFileToPeakTree(imgdata)
apParticle.insertParticlePeaks(peaktree,
imgdata,
self.params['runname'],
msg=True)
def start(self):
imgfilename2peaklist = self.readFileToPeakTree()
imglist = imgfilename2peaklist.keys()
apDisplay.printMsg("Getting image data from database")
imgtree = apDatabase.getSpecificImagesFromDB(imglist, self.sessiondata)
if imgtree[0]['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match " +
imgtree[0]['filename'])
### insert params for manual picking
rundata = self.insertManualParams()
# upload Particles
for imgdata in imgtree:
### check session
if imgdata['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match " +
imgdata['filename'])
peaktree = imgfilename2peaklist[imgdata['filename']]
apDisplay.printMsg(
"%d particles for image %s" %
(len(peaktree), apDisplay.short(imgdata['filename'])))
if self.params['commit'] is True:
apParticle.insertParticlePeaks(peaktree,
imgdata,
self.params['runname'],
msg=True)
def getParticles(self, zprojimagedata):
'''
start Etomo
insert particles
'''
os.chdir(self.params['fulltomodir'])
proc = subprocess.Popen("etomo --fg %s.edf" % (self.seriesname),
shell=True)
proc.wait()
xrange = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'x')
if not len(xrange):
apDisplay.printError(
'Subtomogram coordinate not generated, can not commit to database.'
)
# get subtomogram center from edf log
xmin, xmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'x')
ymin, ymax = apImod.getSubTomoBoundary(self.params['fulltomodir'],
self.seriesname, 'y')
xcenter = self.fullbin * (xmin + xmax) / 2
ycenter = self.fullbin * (ymin + ymax) / 2
peaktree = [{'xcoord': xcenter, 'ycoord': ycenter, 'peakarea': 1}]
# Use the same selection run name for all subtomogram centers
selectionrunname = zprojimagedata['session']['name'] + '_subtomo'
self.insertCenterSelectionRunData(zprojimagedata['session'],
selectionrunname)
apParticle.insertParticlePeaks(peaktree, zprojimagedata,
selectionrunname)
particles = apParticle.getParticlesForImageFromRunName(
zprojimagedata, selectionrunname)
return [particles[0]]
def makeParticleFromContour(imagedata,tracerundata,label='_trace'):
contours = getContoursFromImageTraceRun(imagedata,tracerundata)
peaktree = []
for contourdata in contours:
points = getContourPointsFromContour(contourdata)
center = polygon.getPolygonCenter(points)
peakdict = {'xcoord':center[0],'ycoord':center[1],'label':label,'peakarea':1}
peaktree.append(peakdict)
apParticle.insertParticlePeaks(peaktree, imagedata, tracerundata['name'], False)
def loopCommitToDatabase(self, imgdata):
### commit the run
sessiondata = imgdata['session']
rundata = self.commitRunToDatabase(sessiondata, True)
### commit custom picker specific params
value = self.commitToDatabase(imgdata, rundata)
### commit the particles
apParticle.insertParticlePeaks(self.peaktree, imgdata,
runname=self.params['runname'], msg=(not self.params['background']))
### commit defocal pairs
if self.params['defocpair'] is True:
apDefocalPairs.insertShift(imgdata, self.sibling, self.shiftpeak)
return value
def loopCommitToDatabase(self, imgdata): ### commit the run sessiondata = imgdata['session'] rundata = self.commitRunToDatabase(sessiondata, True) ### commit custom picker specific params value = self.commitToDatabase(imgdata, rundata) ### commit the particles apParticle.insertParticlePeaks(self.peaktree, imgdata, runname=self.params['runname'], msg=(not self.params['background'])) ### commit defocal pairs if self.params['defocpair'] is True: apDefocalPairs.insertShift(imgdata, self.sibling, self.shiftpeak) return value
def start(self):
apDisplay.printMsg("Getting box files")
boxfiles = self.getBoxFiles()
apDisplay.printMsg("Getting image data from database")
imgtree = apDatabase.getSpecificImagesFromDB(boxfiles)
if imgtree[0]['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match "+imgtree[0]['filename'])
### insert params for manual picking
rundata = self.insertManualParams()
# upload Particles
for imgdata in imgtree:
### check session
if imgdata['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match "+imgdata['filename'])
peaktree = self.boxFileToPeakTree(imgdata)
apParticle.insertParticlePeaks(peaktree, imgdata, self.params['runname'], msg=True)
def start(self):
imgfilename2peaklist = self.readFileToPeakTree()
imglist = imgfilename2peaklist.keys()
apDisplay.printMsg("Getting image data from database")
imgtree = apDatabase.getSpecificImagesFromDB(imglist, self.sessiondata)
if imgtree[0]['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match "+imgtree[0]['filename'])
### insert params for manual picking
rundata = self.insertManualParams()
# upload Particles
for imgdata in imgtree:
### check session
if imgdata['session']['name'] != self.sessiondata['name']:
apDisplay.printError("Session and Image do not match "+imgdata['filename'])
peaktree = imgfilename2peaklist[imgdata['filename']]
apDisplay.printMsg("%d particles for image %s"
%(len(peaktree), apDisplay.short(imgdata['filename'])))
if self.params['commit'] is True:
apParticle.insertParticlePeaks(peaktree, imgdata, self.params['runname'], msg=True)
def getParticles(self,zprojimagedata):
'''
start Etomo
insert particles
'''
os.chdir(self.params['fulltomodir'])
proc = subprocess.Popen("etomo --fg %s.edf" % (self.seriesname), shell=True)
proc.wait()
xrange = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'x')
if not len(xrange):
apDisplay.printError('Subtomogram coordinate not generated, can not commit to database.')
# get subtomogram center from edf log
xmin,xmax = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'x')
ymin,ymax = apImod.getSubTomoBoundary(self.params['fulltomodir'],self.seriesname,'y')
xcenter = self.fullbin * (xmin+xmax) / 2
ycenter = self.fullbin * (ymin+ymax) / 2
peaktree = [{'xcoord':xcenter,'ycoord':ycenter,'peakarea':1}]
# Use the same selection run name for all subtomogram centers
selectionrunname = zprojimagedata['session']['name']+'_subtomo'
self.insertCenterSelectionRunData(zprojimagedata['session'],selectionrunname)
apParticle.insertParticlePeaks(peaktree, zprojimagedata, selectionrunname)
particles = apParticle.getParticlesForImageFromRunName(zprojimagedata,selectionrunname)
return [particles[0]]