def runTiltAligner(self, imgdata, tiltdata):
### set tilt
tilt1 = apDatabase.getTiltAngleDeg(imgdata)
tilt2 = apDatabase.getTiltAngleDeg(tiltdata)
theta = abs(tilt2) - abs(tilt1)
### pre-load particle picks
picks1 = self.getParticlePicks(imgdata)
picks2 = self.getParticlePicks(tiltdata)
if len(picks1) < 10 or len(picks2) < 10:
apDisplay.printWarning(
"Not enough particles ot run program on image pair")
self.badprocess = True
return
### set image file 1
imgname = imgdata['filename'] + ".dwn.mrc"
imgpath = os.path.join(self.params['rundir'], imgname)
### set tilt file 2
tiltname = tiltdata['filename'] + ".dwn.mrc"
tiltpath = os.path.join(self.params['rundir'], tiltname)
### set out file
outname1 = os.path.basename(
imgdata['filename']) + "." + self.getExtension()
outfile1 = os.path.join(self.params['pickdatadir'], outname1)
outname2 = os.path.basename(
tiltdata['filename']) + "." + self.getExtension()
outfile2 = os.path.join(self.params['pickdatadir'], outname1)
pixdiam = self.params['diam'] / self.params['apix'] / self.params['bin']
tiltaxis = self.params['inittiltaxis']
### run tilt automation
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgpath, tiltpath, picks1, picks2,
theta, outfile1, pixdiam, tiltaxis)
if result is None:
apDisplay.printWarning("Image processing failed")
self.badprocess = True
return
if os.path.isfile(outfile1) and outfile1 != outfile2:
if os.path.exists(outfile2):
os.remove(outfile2)
os.symlink(os.path.basename(outfile1), outfile2)
### read alignment results
if not os.path.isfile(outfile1):
apDisplay.printWarning("Image processing failed")
self.badprocess = True
return
self.data = tiltfile.readData(outfile1)
self.currentpicks1 = numpy.asarray(self.data['picks1'])
self.currentpicks2 = numpy.asarray(self.data['picks2'])
#print self.data
# 1. tilt data are copied to self.tiltparams by app
# 2. particles picks are copied to self.peaks1 and self.peaks2 by app
# 3. particle errors are copied to self.peakerrors by app
# 4. assessment status is copied to self.assess
self.peaktree1 = apPeaks.convertListToPeaks(self.currentpicks1,
self.params)
self.peaktree2 = apPeaks.convertListToPeaks(self.currentpicks2,
self.params)
self.peakerrors = self.getRmsdArray()
self.getOverlap(imgpath, tiltpath)
def runTiltAligner(self, imgdata, tiltdata):
#reset targets
self.app.onResetParams(None, False)
self.tiltparams = {}
#set tilt
tilt1 = apDatabase.getTiltAngleDeg(imgdata)
tilt2 = apDatabase.getTiltAngleDeg(tiltdata)
self.theta = abs(tilt2) - abs(tilt1)
self.app.data['theta'] = self.theta
self.app.data['filetypeindex'] = self.params['outtypeindex']
outname = os.path.basename(imgdata['filename'])+"."+self.getExtension()
outfile = os.path.join(self.params['pickdatadir'], outname)
self.app.data['outfile'] = outfile
self.app.data['dirname'] = self.params['pickdatadir']
self.app.data['image1file'] = apDisplay.short(imgdata['filename'])
self.app.data['image2file'] = apDisplay.short(tiltdata['filename'])
self.app.data['pixdiam'] = self.params['diam']/self.params['apix']/self.params['bin']
#print "pixdiam=", self.app.data['pixdiam']
#print "theta=",self.app.data['theta']
#pre-load particle picks
self.app.picks1 = self.getParticlePicks(imgdata)
self.app.picks2 = self.getParticlePicks(tiltdata)
#set image assessment
self.assess = self.getTiltAssess(imgdata, tiltdata)
self.assessold = self.assess
self.app.setAssessStatus()
#open image file 1
imgname = imgdata['filename']+".dwn.mrc"
imgpath = os.path.join(self.params['rundir'],imgname)
self.app.panel1.openImageFile(imgpath)
#open tilt file 2
tiltname = tiltdata['filename']+".dwn.mrc"
tiltpath = os.path.join(self.params['rundir'],tiltname)
self.app.panel2.openImageFile(tiltpath)
#guess the shift
outfile = self.app.data['outfile']
if not os.path.exists(outfile):
if self.params['autopick'] is True and self.params['importalign'] is False:
if len(self.app.picks1) > 0 and len(self.app.picks2) > 0:
apDisplay.printMsg("Autopicking image")
self.app.onGuessShift(None)
elif self.params['importalign'] is True:
self.importPreviousTiltParams(imgdata)
else:
self.app.readData(outfile)
self.app.onAutoOptim(None)
time.sleep(0.1)
#run the picker
self.app.MainLoop()
#########################################
# RESULTS
#########################################
self.app.panel1.openImageFile(None)
self.app.panel2.openImageFile(None)
# 1. tilt data are copied to self.tiltparams by app
# 2. particles picks are copied to self.peaks1 and self.peaks2 by app
# 3. particle errors are copied to self.peakerrors by app
# 4. assessment status is copied to self.assess
self.appdata = self.app.data
self.peaktree1 = apPeaks.convertListToPeaks(self.peaks1, self.params)
self.peaktree2 = apPeaks.convertListToPeaks(self.peaks2, self.params)
def runTiltAligner(self, imgdata, tiltdata):
### set tilt
tilt1 = apDatabase.getTiltAngleDeg(imgdata)
tilt2 = apDatabase.getTiltAngleDeg(tiltdata)
theta = abs(tilt2) - abs(tilt1)
### pre-load particle picks
picks1 = self.getParticlePicks(imgdata)
picks2 = self.getParticlePicks(tiltdata)
if len(picks1) < 10 or len(picks2) < 10:
apDisplay.printWarning("Not enough particles ot run program on image pair")
self.badprocess = True
return
### set image file 1
imgname = imgdata['filename']+".dwn.mrc"
imgpath = os.path.join(self.params['rundir'], imgname)
### set tilt file 2
tiltname = tiltdata['filename']+".dwn.mrc"
tiltpath = os.path.join(self.params['rundir'], tiltname)
### set out file
outname1 = os.path.basename(imgdata['filename'])+"."+self.getExtension()
outfile1 = os.path.join(self.params['pickdatadir'], outname1)
outname2 = os.path.basename(tiltdata['filename'])+"."+self.getExtension()
outfile2 = os.path.join(self.params['pickdatadir'], outname1)
pixdiam = self.params['diam']/self.params['apix']/self.params['bin']
tiltaxis = self.params['inittiltaxis']
### run tilt automation
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgpath, tiltpath, picks1, picks2, theta, outfile1, pixdiam, tiltaxis)
if result is None:
apDisplay.printWarning("Image processing failed")
self.badprocess = True
return
if os.path.isfile(outfile1) and outfile1 != outfile2:
if os.path.exists(outfile2):
os.remove(outfile2)
os.symlink(os.path.basename(outfile1), outfile2)
### read alignment results
if not os.path.isfile(outfile1):
apDisplay.printWarning("Image processing failed")
self.badprocess = True
return
self.data = tiltfile.readData(outfile1)
self.currentpicks1 = numpy.asarray(self.data['picks1'])
self.currentpicks2 = numpy.asarray(self.data['picks2'])
#print self.data
# 1. tilt data are copied to self.tiltparams by app
# 2. particles picks are copied to self.peaks1 and self.peaks2 by app
# 3. particle errors are copied to self.peakerrors by app
# 4. assessment status is copied to self.assess
self.peaktree1 = apPeaks.convertListToPeaks(self.currentpicks1, self.params)
self.peaktree2 = apPeaks.convertListToPeaks(self.currentpicks2, self.params)
self.peakerrors = self.getRmsdArray()
self.getOverlap(imgpath, tiltpath)