def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def commitToDatabase(self, imgdata):
"""
Uses the appionLoop commit
"""
imgassess = apDatabase.getImgCompleteStatus(imgdata)
tiltdata = apTiltPair.getTiltPair(imgdata)
msg = not self.params['background']
if tiltdata is None:
if imgassess is not False:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
self.reject+=1
return
if self.params['background'] is False:
apDisplay.printMsg("tiltpair: "+apDisplay.short(tiltdata['filename']))
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if imgassess is False or tiltassess is False:
if imgassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
if tiltassess is not False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(tiltdata['filename']), "magenta")
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runid'], False, msg=msg)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runid'], False, msg=msg)
self.reject+=2
if self.params['background'] is False:
print "Assessment:", imgassess, tiltassess
return
def loopCommitToDatabase(self, imgdata):
"""
Over-writes the particleLoop commit and uses the appionLoop commit
"""
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printWarning("Tilt data not found; not commiting data")
return False
### insert the runid
self.commitRunToDatabase(imgdata['session'], True)
if self.assess is not None:
#note runid is overrided to be 'run1'
apDatabase.insertImgAssessmentStatus(imgdata, self.params['runname'], self.assess)
apDatabase.insertImgAssessmentStatus(tiltdata, self.params['runname'], self.assess)
if len(self.peaktree1) < 3 or len(self.peaktree1) < 3:
apDisplay.printWarning("Not enough particle picks; not commiting transform or particle data")
return False
### insert the transform
transdata = apTiltPair.insertTiltTransform(imgdata, tiltdata, self.tiltparams, self.params)
### insert the particles
self.insertParticlePeakPairs(imgdata, tiltdata, transdata)
def rejectTiltPairs(self, imgdata):
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printColor("\nrejecting unpaired image: "+apDisplay.short(imgdata['filename']), "red")
return False
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if tiltassess is False:
apDisplay.printColor("\nrejecting bad tilt images: "+apDisplay.short(imgdata['filename']), "magenta")
return False
return True
def rejectTiltPairs(self, imgdata):
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printColor(
"\nrejecting unpaired image: " +
apDisplay.short(imgdata['filename']), "red")
return False
tiltassess = apDatabase.getImgCompleteStatus(tiltdata)
if tiltassess is False:
apDisplay.printColor(
"\nrejecting bad tilt images: " +
apDisplay.short(imgdata['filename']), "magenta")
return False
return True
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'])
def loopCommitToDatabase(self, imgdata):
"""
Over-writes the particleLoop commit and uses the appionLoop commit
"""
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
apDisplay.printWarning("Tilt data not found; not commiting data")
return False
### insert the runid
self.commitRunToDatabase(imgdata['session'], True)
if len(self.peaktree1) < 3 or len(self.peaktree2) < 3:
apDisplay.printWarning("Not enough particle picks; not commiting transform or particle data")
return False
### insert the transform
transdata = apTiltPair.insertTiltTransform(imgdata, tiltdata, self.data, self.params)
### insert the particles
self.insertParticlePeakPairs(imgdata, tiltdata, transdata)
def processAndSaveAllImages(self):
print "Pre-processing images before picking\nNow is a good time to go get a candy bar"
count = 0
total = len(self.imgtree)
for imgdata in self.imgtree:
count += 1
tiltdata = apTiltPair.getTiltPair(imgdata)
if tiltdata is None:
#reject it
apDatabase.insertImgAssessmentStatus(imgdata, "notiltpair", False)
continue
#First the image
imgpath = os.path.join(self.params['rundir'], imgdata['filename']+'.dwn.mrc')
if os.path.isfile(imgpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(imgdata['filename'])
else:
sys.stderr.write("#")
#print "processing: ",apDisplay.short(imgdata['filename'])
apFindEM.processAndSaveImage(imgdata, params=self.params)
#Now for its tilt pair
tiltpath = os.path.join(self.params['rundir'], tiltdata['filename']+'.dwn.mrc')
if os.path.isfile(tiltpath):
sys.stderr.write(".")
#print "already processed: ",apDisplay.short(tiltdata['filename'])
else:
sys.stderr.write("#")
#print "processing: ",apDisplay.short(tiltdata['filename'])
apFindEM.processAndSaveImage(tiltdata, params=self.params)
if count % 30 == 0:
sys.stderr.write(" %d left\n" % (total-count))
### check if automation was already run
outname1 = os.path.basename(imgdata['filename'])+"."+self.getExtension()
outname2 = os.path.basename(tiltdata['filename'])+"."+self.getExtension()
outfile1 = os.path.join(self.params['pickdatadir'], outname1)
outfile2 = os.path.join(self.params['pickdatadir'], outname2)
if os.path.isfile(outfile1):
sys.stderr.write(",")
else:
### set important parameters
picks1 = self.getParticlePicks(imgdata, False)
picks2 = self.getParticlePicks(tiltdata, False)
pixdiam = self.params['diam']/self.params['apix']/self.params['bin']
tilt1 = apDatabase.getTiltAngleDeg(imgdata)
tilt2 = apDatabase.getTiltAngleDeg(tiltdata)
tiltdiff = abs(tilt2) - abs(tilt1)
tiltaxis = self.params['inittiltaxis']
### run tilt automation
if self.params['autopick'] is True and self.params['importalign'] is False:
if len(picks1) > 0 and len(picks2) > 0:
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgpath, tiltpath, picks1, picks2,
tiltdiff, outfile1, pixdiam, tiltaxis, msg=False)
if os.path.isfile(outfile1):
if os.path.exists(outfile2):
os.remove(outfile2)
os.symlink(os.path.basename(outfile1), outfile2)
sys.stderr.write("%")
apDisplay.printMsg("done")
return
