def loopProcessImage(self, imgdata):
#creates self.peaktree and filterLoop sets self.filtarray
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
if self.params['background'] is False:
apDisplay.printMsg("Found " + str(len(self.peaktree)) +
" particles for " +
apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = len(self.peaktree)
if self.params['nojpegs'] is False:
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createPeakJpeg,
args=(imgdata, self.peaktree, self.params,
self.filtarray)).start()
else:
apPeaks.createPeakJpeg(imgdata, self.peaktree, self.params,
self.filtarray)
elif self.params['background'] is False:
apDisplay.printWarning("Skipping JPEG creation")
if self.params['defocpair'] is True:
self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(
imgdata, self.params['sessionname'])
return
def getParticlesFromStack(self, stackdata,imgdata,is_defocpair=False):
"""
For image (or defocal pair), imgdata get particles in corresponding stack
"""
if is_defocpair is True:
sibling, shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname'])
if shiftpeak is None:
return [],{'shiftx':0, 'shifty':0, 'scale':1}
shiftdata = {'shiftx':shiftpeak['shift'][0], 'shifty':shiftpeak['shift'][1], 'scale':shiftpeak['scalefactor']}
searchimgdata = sibling
else:
searchimgdata = imgdata
shiftdata = {'shiftx':0, 'shifty':0, 'scale':1}
partq = appiondata.ApParticleData()
partq['image'] = searchimgdata
stackpartq = appiondata.ApStackParticleData()
stackpartq['stack'] = stackdata
stackpartq['particle'] = partq
stackpartdatas = stackpartq.query()
partdatas = []
partorder = []
for stackpartdata in stackpartdatas:
if self.params['partlimit'] and self.params['partlimit'] < stackpartdata['particleNumber']:
continue
partdata = stackpartdata['particle']
partdatas.append(partdata)
partorder.append(stackpartdata['particleNumber'])
partdatas.reverse()
partorder.reverse()
self.writeStackParticleOrderFile(partorder)
return partdatas, shiftdata
def getParticlesFromStack(self, stackdata, imgdata, is_defocpair=False):
"""
For image (or defocal pair), imgdata get particles in corresponding stack
"""
if is_defocpair is True:
sibling, shiftpeak = apDefocalPairs.getShiftFromImage(
imgdata, self.params['sessionname'])
if shiftpeak is None:
return [], {'shiftx': 0, 'shifty': 0, 'scale': 1}
shiftdata = {
'shiftx': shiftpeak['shift'][0],
'shifty': shiftpeak['shift'][1],
'scale': shiftpeak['scalefactor']
}
searchimgdata = sibling
else:
searchimgdata = imgdata
shiftdata = {'shiftx': 0, 'shifty': 0, 'scale': 1}
partq = appiondata.ApParticleData()
partq['image'] = searchimgdata
stackpartq = appiondata.ApStackParticleData()
stackpartq['stack'] = stackdata
stackpartq['particle'] = partq
stackpartdatas = stackpartq.query()
partdatas = []
partorder = []
for stackpartdata in stackpartdatas:
if self.params['partlimit'] and self.params[
'partlimit'] < stackpartdata['particleNumber']:
continue
partdata = stackpartdata['particle']
partdatas.append(partdata)
partorder.append(stackpartdata['particleNumber'])
partdatas.reverse()
partorder.reverse()
self.writeStackParticleOrderFile(partorder)
return partdatas, shiftdata
def loopProcessImage(self, imgdata):
#creates self.peaktree and filterLoop sets self.filtarray
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
if self.params['background'] is False:
apDisplay.printMsg("Found "+str(len(self.peaktree))+" particles for "
+apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = len(self.peaktree)
if self.params['nojpegs'] is False:
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createPeakJpeg, args=(imgdata, self.peaktree, self.params, self.filtarray)).start()
else:
apPeaks.createPeakJpeg(imgdata, self.peaktree, self.params, self.filtarray)
elif self.params['background'] is False:
apDisplay.printWarning("Skipping JPEG creation")
if self.params['defocpair'] is True:
self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname'])
return
def processImage(self, imgdata):
self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(
imgdata, self.params['sessionname'])
def processImage(self, imgdata):
self.sibling, self.shiftpeak = apDefocalPairs.getShiftFromImage(imgdata, self.params['sessionname'])
