def getBestCtfValue(self, imgdata, msg=False):
if self.params['ctfrunid'] is not None:
return ctfdb.getCtfValueForCtfRunId(imgdata,
self.params['ctfrunid'],
msg=msg)
return ctfdb.getBestCtfValue(imgdata,
sortType=self.params['ctfsorttype'],
method=self.params['ctfmethod'],
msg=msg)
def start(self):
### default parameters
starfile = self.params['starfile']
images = self.params['images']
dbnum = self.params['dbnum']
ctfrunid = self.params['ctfrunid']
stackid = self.params['stackid']
voltage = self.params['voltage']
cs = self.params['cs']
wgh = self.params['wgh']
### particles, angles
appiondata.sinedon.setConfig('appiondata', db="ap%d" % dbnum)
particledata = apStack.getStackParticlesFromId(stackid)
### write Relion starfile header
sf = open(starfile, "w")
sf.write("data_images\n")
sf.write("loop_\n")
sf.write("_rlnImageName\n")
sf.write("_rlnMicrographName\n")
sf.write("_rlnDefocusU\n")
sf.write("_rlnDefocusV\n")
sf.write("_rlnDefocusAngle\n")
sf.write("_rlnVoltage\n")
sf.write("_rlnSphericalAberration\n")
sf.write("_rlnAmplitudeContrast\n")
### write info to starfile
olddx = 0
micn = 0
oldimgid = None
for i in range(len(particledata)):
if i % 1000 == 0:
print "done with %d particles" % i
### CTF info
image = particledata[i]['particle']['image']
imgid = image.dbid
try:
ctf = ctfdb.getCtfValueForCtfRunId(image, ctfrunid, msg=False)
dx = ctf['defocus1'] * 10e9
dy = ctf['defocus2'] * 10e9
astig = ctf['angle_astigmatism']
except:
ctf = None
# print "didn't find CTF values for image ", image.dbid
if ctf is None:
if oldimgid != imgid:
print "particle %d: " % i, "getting best value for image: %d" % imgid
ctf = ctfdb.getBestCtfValueForImage(image,
msg=False,
method='ctffind')
dx = ctf[0]['defocus1'] * 10e9
dy = ctf[0]['defocus2'] * 10e9
astig = ctf[0]['angle_astigmatism']
oldctf = ctf
oldimgid = imgid
else:
try:
ctf = oldctf
dx = oldctf[0]['defocus1'] * 10e9
dy = oldctf[0]['defocus2'] * 10e9
astig = oldctf[0]['angle_astigmatism']
except:
apDisplay.printError("no CTF information for image")
if dx != olddx:
micn += 1
olddx = dx
### write input Relion parameters
sf.write("%06d@%s%10d%12.3f%12.3f%12.3f%8.3f%8.3f%8.3f\n" %
(i + 1, images, micn, dx, dy, astig, voltage, cs, wgh))
sf.close()
def start(self):
### default parameters
starfile = self.params['starfile']
images = self.params['images']
dbnum = self.params['dbnum']
ctfrunid = self.params['ctfrunid']
stackid = self.params['stackid']
voltage = self.params['voltage']
cs = self.params['cs']
wgh = self.params['wgh']
### particles, angles
appiondata.sinedon.setConfig('appiondata', db="ap%d" % dbnum)
particledata = apStack.getStackParticlesFromId(stackid)
### write Relion starfile header
sf = open(starfile, "w")
sf.write("data_images\n")
sf.write("loop_\n")
sf.write("_rlnImageName\n")
sf.write("_rlnMicrographName\n")
sf.write("_rlnDefocusU\n")
sf.write("_rlnDefocusV\n")
sf.write("_rlnDefocusAngle\n")
sf.write("_rlnVoltage\n")
sf.write("_rlnSphericalAberration\n")
sf.write("_rlnAmplitudeContrast\n")
### write info to starfile
olddx = 0
micn = 0
oldimgid = None
for i in range(len(particledata)):
if i % 1000 == 0:
print "done with %d particles" % i
### CTF info
image = particledata[i]['particle']['image']
imgid = image.dbid
try:
ctf = ctfdb.getCtfValueForCtfRunId(image, ctfrunid, msg=False)
dx = ctf['defocus1'] * 10e9
dy = ctf['defocus2'] * 10e9
astig = ctf['angle_astigmatism']
except:
ctf = None
# print "didn't find CTF values for image ", image.dbid
if ctf is None:
if oldimgid != imgid:
print "particle %d: " % i, "getting best value for image: %d" % imgid
ctf = ctfdb.getBestCtfValueForImage(image, msg=False, method='ctffind')
dx = ctf[0]['defocus1'] * 10e9
dy = ctf[0]['defocus2'] * 10e9
astig = ctf[0]['angle_astigmatism']
oldctf = ctf
oldimgid = imgid
else:
try:
ctf = oldctf
dx = oldctf[0]['defocus1'] * 10e9
dy = oldctf[0]['defocus2'] * 10e9
astig = oldctf[0]['angle_astigmatism']
except:
apDisplay.printError("no CTF information for image")
if dx != olddx:
micn += 1
olddx = dx
### write input Relion parameters
sf.write("%06d@%s%10d%12.3f%12.3f%12.3f%8.3f%8.3f%8.3f\n"
% (i+1, images, micn, dx, dy, astig, voltage, cs, wgh)
)
sf.close()
def getBestCtfValue(self, imgdata, msg=False): if self.params['ctfrunid'] is not None: return ctfdb.getCtfValueForCtfRunId(imgdata, self.params['ctfrunid'], msg=msg) return ctfdb.getBestCtfValue(imgdata, sortType=self.params['ctfsorttype'], method=self.params['ctfmethod'], msg=msg)