def getDefocPairParticles(imgdata, selectionid, particlelabel=None):
### get defocal pair
if imgdata['preset'] is not None:
defimgdata = apDefocalPairs.getDefocusPair(imgdata)
else:
# For pairs from Leginon Manual Application
defimgdata = apDefocalPairs.getManualDefocusPair(imgdata)
if defimgdata is None:
apDisplay.printWarning(
"Could not find defocal pair for image %s (id %d)" %
(apDisplay.short(imgdata['filename']), imgdata.dbid))
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
apDisplay.printMsg(
"Found defocus pair %s (id %d) for image %s (id %d)" %
(apDisplay.short(defimgdata['filename']), defimgdata.dbid,
apDisplay.short(imgdata['filename']), imgdata.dbid))
### get particles
partq = appiondata.ApParticleData()
partq['image'] = defimgdata
partq['selectionrun'] = appiondata.ApSelectionRunData.direct_query(
selectionid)
if particlelabel is not None:
partq['label'] = particlelabel
partdatas = partq.query()
apDisplay.printMsg("Found %d particles for defocal pair %s (id %d)" % (
len(partdatas),
apDisplay.short(defimgdata['filename']),
defimgdata.dbid,
))
if len(partdatas) == 0:
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
### get shift information
has_tried = False
while True:
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = defimgdata
shiftdatas = shiftq.query()
if shiftdatas:
shiftdata = shiftdatas[0]
apDisplay.printMsg(
"Shifting particles by %.1f,%.1f (%d X)" %
(shiftdata['shiftx'], shiftdata['shifty'], shiftdata['scale']))
break
else:
if has_tried == True:
apDisplay.printError(
"No shift inserted to database after one try")
apDisplay.printMsg("Calculating shift....")
shiftpeak = apDefocalPairs.getShift(defimgdata, imgdata)
apDefocalPairs.insertShift(defimgdata, imgdata, shiftpeak)
has_tried = True
return (partdatas, shiftdata)
def getDefocPairParticles(imgdata, selectionid, particlelabel=None):
### get defocal pair
if imgdata['preset'] is not None:
defimgdata = apDefocalPairs.getDefocusPair(imgdata)
else:
# For pairs from Leginon Manual Application
defimgdata = apDefocalPairs.getManualDefocusPair(imgdata)
if defimgdata is None:
apDisplay.printWarning("Could not find defocal pair for image %s (id %d)"
%(apDisplay.short(imgdata['filename']), imgdata.dbid))
return ([], {'shiftx':0, 'shifty':0, 'scale':1})
apDisplay.printMsg("Found defocus pair %s (id %d) for image %s (id %d)"
%(apDisplay.short(defimgdata['filename']), defimgdata.dbid, apDisplay.short(imgdata['filename']), imgdata.dbid))
### get particles
partq = appiondata.ApParticleData()
partq['image'] = defimgdata
partq['selectionrun'] = appiondata.ApSelectionRunData.direct_query(selectionid)
if particlelabel is not None:
partq['label'] = particlelabel
partdatas = partq.query()
apDisplay.printMsg("Found %d particles for defocal pair %s (id %d)"
%(len(partdatas), apDisplay.short(defimgdata['filename']), defimgdata.dbid,))
if len(partdatas) == 0:
return ([], {'shiftx':0, 'shifty':0, 'scale':1})
### get shift information
has_tried = False
while True:
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = defimgdata
shiftdatas = shiftq.query()
if shiftdatas:
shiftdata = shiftdatas[0]
apDisplay.printMsg("Shifting particles by %.1f,%.1f (%d X)"
%(shiftdata['shiftx'], shiftdata['shifty'], shiftdata['scale']))
break
else:
if has_tried == True:
apDisplay.printError("No shift inserted to database after one try")
apDisplay.printMsg("Calculating shift....")
shiftpeak = apDefocalPairs.getShift(defimgdata, imgdata)
apDefocalPairs.insertShift(defimgdata, imgdata, shiftpeak)
has_tried = True
return (partdatas, shiftdata)
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 commitToDatabase(self, imgdata):
apDefocalPairs.insertShift(imgdata, self.sibling, self.shiftpeak)
def commitToDatabase(self, imgdata):
apDefocalPairs.insertShift(imgdata, self.sibling, self.shiftpeak)
