def correct_drift(img1, img2, display_cc=False):
''' Returns two ImagePlus objects that are drift corrected to each other.
The first image is not changed.
The second image is a new image that is shifted using ImageJ's Translate.
:param img1: The reference image.
:param img2: The image to be shifted.
:param display_cc: Activate displaying the CrossCorrelation image (default False).
'''
img1_cc, img2_cc = cc.scale_to_power_of_two([img1, img2])
result = cc.perform_correlation(img1_cc, img2_cc)
x_off, y_off = cc.get_shift(result)
# style after maximum detection
if not display_cc:
result.hide()
else:
result.copyScale(img1)
cc.style_cc(result)
if x_off == 0 and y_off == 0:
print('No drift has been detected.')
return img1, img2
title = img2.getTitle()
img2_dk = Duplicator().run(img2)
img2_dk.setTitle('DK-' + title)
IJ.run(img2_dk, 'Translate...', 'x=%d y=%d interpolation=None' % (-x_off, -y_off))
img2_dk.copyScale(img2)
img2_dk.show()
return img1, img2_dk
def get_drift(i, j, _images):
'''Returns the drift of imagej compared to image i'''
cc_img = cc.perform_correlation(_images[i], _images[j])
offset = cc.get_drift(cc_img)
''' DEBUG
print 'Reference: %s at index %i' % (images[i],i)
print 'Drifted image: %s at index %i' % (images[j],j)
print 'Offset: %d,%d\n' % offset
'''
return offset
