def loopProcessImage(self, imgdata):
"""
Over-writes the particleLoop processImage and uses the appionLoop processImage
"""
#GET THE TILT PAIR
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
return
### process images
procimgpath = os.path.join(self.params['rundir'],
imgdata['filename'] + '.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for first image")
apFindEM.processAndSaveImage(imgdata, params=self.params)
procimg1 = apImage.mrcToArray(procimgpath, msg=False)
procimgpath = os.path.join(self.params['rundir'],
tiltdata['filename'] + '.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for second image")
apFindEM.processAndSaveImage(tiltdata, params=self.params)
procimg2 = apImage.mrcToArray(procimgpath, msg=False)
#RUN THE ALIGNER GUI
result = self.runTiltAligner(imgdata, tiltdata)
if self.badprocess is True:
return
numpeaks = len(self.peaktree1)
#apDisplay.printMsg("Found "+str(numpeaks)+" particles for "+apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = numpeaks
### mask the images
procimg1, procimg2 = apTiltTransform.maskOverlapRegion(
procimg1, procimg2, self.data)
#CREATE PEAK JPEG
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createTiltedPeakJpeg,
args=(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1,
procimg2)).start()
else:
apPeaks.createTiltedPeakJpeg(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1,
procimg2)
#EXTRA DONE DICT CALL
self._writeDoneDict(tiltdata['filename'])
def loopProcessImage(self, imgdata):
"""
Over-writes the particleLoop processImage and uses the appionLoop processImage
"""
#GET THE TILT PAIR
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
return
### process images
procimgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for first image")
apFindEM.processAndSaveImage(imgdata, params=self.params)
procimg1 = apImage.mrcToArray(procimgpath, msg=False)
procimgpath = os.path.join(self.params['rundir'], tiltdata['filename']+'.dwn.mrc')
if not os.path.isfile(procimgpath):
apDisplay.printMsg("processing mrc for second image")
apFindEM.processAndSaveImage(tiltdata, params=self.params)
procimg2 = apImage.mrcToArray(procimgpath, msg=False)
#RUN THE ALIGNER GUI
result = self.runTiltAligner(imgdata, tiltdata)
if self.badprocess is True:
return
numpeaks = len(self.peaktree1)
#apDisplay.printMsg("Found "+str(numpeaks)+" particles for "+apDisplay.shortenImageName(imgdata['filename']))
self.stats['lastpeaks'] = numpeaks
### mask the images
procimg1, procimg2 = apTiltTransform.maskOverlapRegion(procimg1, procimg2, self.data)
#CREATE PEAK JPEG
if self.threadJpeg is True:
threading.Thread(target=apPeaks.createTiltedPeakJpeg, args=(imgdata, tiltdata, self.peaktree1,
self.peaktree2, self.params, procimg1, procimg2)).start()
else:
apPeaks.createTiltedPeakJpeg(imgdata, tiltdata, self.peaktree1, self.peaktree2, self.params,
procimg1, procimg2)
#EXTRA DONE DICT CALL
self._writeDoneDict(tiltdata['filename'])