def findShift(image, reference, scale, angle):
image = scipy.ndimage.zoom(image, scale)
image = scipy.ndimage.rotate(image, angle)
image = pad(image, reference.shape)
cor = correlator.phase_correlate(reference, image, zero=False)
results = peakfinder.findSubpixelPeak(cor, lpf=1.2)
shift = correlator.wrap_coord(results['subpixel peak'], cor.shape)
mrc_write(cor, 'finalcor.mrc')
mrc_write(image, 'finalimage.mrc')
mrc_write(reference, 'reference.mrc')
return shift
def findShift(image, reference, scale, angle):
image = scipy.ndimage.zoom(image, scale)
image = scipy.ndimage.rotate(image, angle)
image = pad(image, reference.shape)
cor = correlator.phase_correlate(reference, image, zero=False)
results = peakfinder.findSubpixelPeak(cor, lpf=1.2)
shift = correlator.wrap_coord(results['subpixel peak'], cor.shape)
mrc_write(cor, 'finalcor.mrc')
mrc_write(image, 'finalimage.mrc')
mrc_write(reference, 'reference.mrc')
return shift
def findBestTransformValue(image, reference, start, end, increment, transfunc, *args, **kwargs):
bestvalue = None
bestshift = None
bestsnr = 6.0
bestnewimage = None
for i, value in enumerate(numpy.arange(start, end, increment)):
newimage = transfunc(image, value, *args, **kwargs)
newimage = pad(newimage, reference.shape)
cor = correlator.phase_correlate(reference, newimage, zero=False)
mrc_write(cor, 'cor-%s-%03d.mrc' % (transfunc.__name__, i))
results = peakfinder.findSubpixelPeak(cor, lpf=1.2)
shift = correlator.wrap_coord(results['subpixel peak'], cor.shape)
snr = results['snr']
if debug:
print i, value, snr, shift
if snr > bestsnr:
bestsnr = snr
bestvalue = value
bestshift = shift
bestnewimage = newimage
return bestvalue, shift, cor, bestnewimage
def findBestTransformValue(image, reference, start, end, increment, transfunc,
*args, **kwargs):
bestvalue = None
bestshift = None
bestsnr = 6.0
bestnewimage = None
for i, value in enumerate(numpy.arange(start, end, increment)):
newimage = transfunc(image, value, *args, **kwargs)
newimage = pad(newimage, reference.shape)
cor = correlator.phase_correlate(reference, newimage, zero=False)
mrc_write(cor, 'cor-%s-%03d.mrc' % (transfunc.__name__, i))
results = peakfinder.findSubpixelPeak(cor, lpf=1.2)
shift = correlator.wrap_coord(results['subpixel peak'], cor.shape)
snr = results['snr']
if debug:
print i, value, snr, shift
if snr > bestsnr:
bestsnr = snr
bestvalue = value
bestshift = shift
bestnewimage = newimage
return bestvalue, shift, cor, bestnewimage
