def find_axis_rotate(im0, im1, angmin, angmax, da):
"""
Find axis rotation position by 2 images in range of rotation [angmin, angmax, da]
:param im0:
:param im1:
:param angmin:
:param angmax:
:param da:
:return:
"""
if angmin==angmax:
return 1.0, angmin
mean_im0=numpy.mean(im0)
mean_im1=numpy.mean(im1)
coeff_corr=((im0-mean_im0)**2).sum()*((im1-mean_im1)**2).sum()
corr_rot = []
for ang in numpy.arange(angmin, angmax, da):
tmp_im0=rotate(im0, ang)
tmp_im1=rotate(im1, -ang)
tmp_corr = (tmp_im0 - mean_im0)*(tmp_im1 - mean_im1)
corr_rot.append(numpy.sqrt(tmp_corr * tmp_corr).sum()/numpy.sqrt(coeff_corr))
max_ind = numpy.array(corr_rot).argmax()
rot_val = numpy.arange(angmin, angmax, da)[max_ind]
logging.info(str.format('Found rotation angle {0:.5} with corr_factor={1:.3}',rot_val,corr_rot[max_ind]))
return corr_rot,rot_val
def fix_axis_position(angle_val, shift_val, normalized_data, pixel_size):
"""
Inplace fix axis position for list of frames.
:param angle_val:
:param shift_val:
:param normalized_data:
:param pixel_size:
"""
for i in range(len(normalized_data)):
normalized_data[i]['data'] = roll_zeropad(normalized_data[i]['data'], shift=shift_val, axis=1)
normalized_data[i]['data'] = rotate(normalized_data[i]['data'], angle_val)
normalized_data[i]['data'] = normalized_data[i]['data'] / pixel_size*1000 #absorption in mm^-1
def find_shift_and_rotation(data0, data1, image_process_config, res_folder=None):
"""
Find axis rotation and shift
:param data0:
:param data1:
:param image_process_config:
:param res_folder: folder to save diagnostic image
:return:
"""
ipc = image_process_config['axis_serch']
x0 = ipc['horizontal'][0]
x1 = ipc['horizontal'][1]
a0 = ipc['rotation'][0]
a1 = ipc['rotation'][1]
x0_start=x0
x1_start=x1
a0_start=a0
a1_start=a1
delta_x = int(x1 - x0) / 2
xc = int(x0 + x1) / 2
delta_a = float(a1 - a0) / 2.0
ac = (a0 + a1) / 2
angle_step = 0.01
tmp_data0 = data0
tmp_data1 = data1
corr=None
corr_rot=None
for i in range(10):
corr, shift_val = find_axis_hor_shift(tmp_data0, tmp_data1, xc - delta_x, xc + delta_x)
if shift_val<x0_start:
shift_val=x0_start
elif shift_val>x1_start:
shift_val=x1_start
tmp_data0 = roll_zeropad(data0, shift=shift_val, axis=1)
tmp_data1 = roll_zeropad(data1, shift=-shift_val, axis=1)
corr_rot, rot_ang = find_axis_rotate(tmp_data0, tmp_data1, ac - delta_a, ac + delta_a, angle_step)
if rot_ang<a0_start:
rot_ang=a0_start
elif rot_ang>a1_start:
rot_ang=a1_start
if not delta_a==0:
delta_a = max(0.1, 0.8 * delta_a)
angle_step = max(0.001, angle_step * 0.8)
if not delta_x==0:
delta_x = max(10, int(delta_x * 0.5))
tmp_data0 = rotate(data0, rot_ang)
tmp_data1 = rotate(data1, -rot_ang)
if xc == shift_val and ac == rot_ang:
break
xc = shift_val
ac = rot_ang
logging.info(str.format('x={0} delta_x={1} ac={2:.3} delta_a={3:.3} angle_step={4:.3}',
xc, delta_x, ac, delta_a, angle_step))
data0 = roll_zeropad(data0, shift=xc, axis=1)
data1 = roll_zeropad(data1, shift=-xc, axis=1)
data0 = rotate(data0, ac)
data1 = rotate(data1, -ac)
if not res_folder is None:
save_shifted_image(corr, corr_rot, data0, data1,os.path.join(res_folder,'shifting_pic.png'))
return {'angle':ac, 'shift':xc}