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
parser.add_option("-o", "--outfile", dest="outfile",
help="Particle picks and tilt parameters output file", metavar="FILE")
parser.add_option("-d", "--diam", "--pixdiam", dest="pixdiam", type="float",
help="Approximate diameter of particle in pixels", metavar="#")
parser.add_option("-x", "--tiltaxis", dest="tiltaxis", type="float",
help="Approximate tilt axis angle", metavar="#")
params = apParam.convertParserToParams(parser)
checkConflicts(params)
### set important parameters
imgfile1 = params['imgfile1']
imgfile2 = params['imgfile2']
picks1 = readPickFile(params['pickfile1'])
picks2 = readPickFile(params['pickfile2'])
theta = params['tiltangle']
outfile = params['outfile']
pixdiam = params['pixdiam']
tiltaxis = params['tiltaxis']
### run tilt automation
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgfile1, imgfile2, picks1, picks2, theta, outfile, pixdiam, tiltaxis)
if result is None:
apDisplay.printWarning("Image processing failed")
dest="pixdiam",
type="float",
help="Approximate diameter of particle in pixels",
metavar="#")
parser.add_option("-x",
"--tiltaxis",
dest="tiltaxis",
type="float",
help="Approximate tilt axis angle",
metavar="#")
params = apParam.convertParserToParams(parser)
checkConflicts(params)
### set important parameters
imgfile1 = params['imgfile1']
imgfile2 = params['imgfile2']
picks1 = readPickFile(params['pickfile1'])
picks2 = readPickFile(params['pickfile2'])
theta = params['tiltangle']
outfile = params['outfile']
pixdiam = params['pixdiam']
tiltaxis = params['tiltaxis']
### run tilt automation
autotilter = autotilt.autoTilt()
result = autotilter.processTiltPair(imgfile1, imgfile2, picks1, picks2,
theta, outfile, pixdiam, tiltaxis)
if result is None:
apDisplay.printWarning("Image processing failed")
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):
### 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)