def binAndAddCTFlabel(self, image, ht, rpixelsize, binning=1, defocus=None):
pow = imagefun.power(image)
binned = imagefun.bin(pow, binning)
# No ctf estimation until it works better so that this node does not
# depend on coma beam-tilt calibration
s = None
ctfdata = None
'''
try:
ctfdata = fftfun.fitFirstCTFNode(pow,rpixelsize['x'], defocus, ht)
except Exception, e:
self.logger.error("ctf fitting failed: %s" % e)
ctfdata = None
if ctfdata:
self.logger.info('z0 %.3f um, zast %.3f um (%.0f ), angle= %.1f deg' % (ctfdata[0]*1e6,ctfdata[1]*1e6,ctfdata[2]*100, ctfdata[3]*180.0/math.pi))
s = '%d' % int(ctfdata[0]*1e9)
#elif self.ace2exe:
elif False:
ctfdata = self.estimateCTF(imagedata)
z0 = (ctfdata['defocus1'] + ctfdata['defocus2']) / 2
s = '%d' % (int(z0*1e9),)
'''
if s:
t = numpil.textArray(s)
t = ndimage.zoom(t, (min(binned.shape)-40.0)*0.08/(t.shape)[0])
minvalue = arraystats.min(binned)
maxvalue = arraystats.max(binned)
t = minvalue + t * (maxvalue-minvalue)
imagefun.pasteInto(t, binned, (20,20))
return binned, ctfdata
def binAndAddCTFlabel(self,
image,
ht,
cs,
rpixelsize,
binning=1,
defocus=None):
pow = imagefun.power(image)
binned = imagefun.bin(pow, binning)
# No ctf estimation until it works better so that this node does not
# depend on coma beam-tilt calibration
s = None
ctfdata = None
'''
try:
ctfdata = fftfun.fitFirstCTFNode(pow,rpixelsize['x'], defocus, ht, cs)
except Exception, e:
self.logger.error("ctf fitting failed: %s" % e)
ctfdata = None
if ctfdata:
self.logger.info('z0 %.3f um, zast %.3f um (%.0f ), angle= %.1f deg' % (ctfdata[0]*1e6,ctfdata[1]*1e6,ctfdata[2]*100, ctfdata[3]*180.0/math.pi))
s = '%d' % int(ctfdata[0]*1e9)
#elif self.ace2exe:
elif False:
ctfdata = self.estimateCTF(imagedata)
z0 = (ctfdata['defocus1'] + ctfdata['defocus2']) / 2
s = '%d' % (int(z0*1e9),)
'''
if s:
t = numpil.textArray(s)
t = ndimage.zoom(t,
(min(binned.shape) - 40.0) * 0.08 / (t.shape)[0])
minvalue = arraystats.min(binned)
maxvalue = arraystats.max(binned)
t = minvalue + t * (maxvalue - minvalue)
imagefun.pasteInto(t, binned, (20, 20))
return binned, ctfdata
s = None
try:
ctfdata = fftfun.fitFirstCTFNode(pow,rpixelsize['x'], defocus, ht)
except Exception, e:
self.logger.error("ctf fitting failed: %s" % e)
ctfdata = None
if ctfdata:
self.logger.info('z0 %.3f um, zast %.3f um (%.0f ), angle= %.1f deg' % (ctfdata[0]*1e6,ctfdata[1]*1e6,ctfdata[2]*100, ctfdata[3]*180.0/math.pi))
s = '%d' % int(ctfdata[0]*1e9)
#elif self.ace2exe:
elif False:
ctfdata = self.estimateCTF(imagedata)
z0 = (ctfdata['defocus1'] + ctfdata['defocus2']) / 2
s = '%d' % (int(z0*1e9),)
if s:
t = numpil.textArray(s)
t = ndimage.zoom(t, (min(binned.shape)-40.0)*0.08/(t.shape)[0])
minvalue = arraystats.min(binned)
maxvalue = arraystats.max(binned)
t = minvalue + t * (maxvalue-minvalue)
imagefun.pasteInto(t, binned, (20,20))
return binned, ctfdata
def estimateCTF(self, imagedata):
mag = imagedata['scope']['magnification']
tem = imagedata['scope']['tem']
cam = imagedata['camera']['ccdcamera']
pixelsize = self.btcalclient.getPixelSize(mag, tem, cam)
inputparams = {
'input': os.path.join(imagedata['session']['image path'],imagedata['filename']+".mrc"),
'cs': 2.0,
