def pbr(I_path, Im_path):
# Load in images
I = plt.imread(I_path)
Im = plt.imread(Im_path)
# Set control points
X, Xm = util.my_cpselect(I_path, Im_path)
Xh = util.c2h(X)
Xmh = util.c2h(Xm)
# Find optimal affine transformation
T = ls_affine(Xh, Xmh)
# Transform Im
Im_t, X_t = image_transform(Im, T)
# Display images
fig = plt.figure(figsize=(12, 5))
ax1 = fig.add_subplot(131)
im11 = ax1.imshow(I)
ax2 = fig.add_subplot(132)
im21 = ax2.imshow(Im)
ax3 = fig.add_subplot(133)
im31 = ax3.imshow(I)
im32 = ax3.imshow(Im_t, alpha=0.7)
ax1.set_title('Original image (I)')
ax2.set_title('Warped image (Im)')
ax3.set_title('Overlay with I and transformed Im')
def pbr(I_path, Im_path):
I = plt.imread(I_path)
Im = plt.imread(Im_path)
X, Xm = util.my_cpselect(I_path, Im_path)
if len(X[1]) == 1:
print('x must be larger than 1')
return
X = util.c2h(X)
Xm = util.c2h(Xm)
T = reg.ls_affine(X, Xm)
It, Xt = reg.image_transform(Im, T)
fig = plt.figure(figsize=(30, 30))
ax1 = fig.add_subplot(121)
ax1.set_title('Overlay of original images', fontsize=35)
ax1.axis('off')
im11 = ax1.imshow(I)
im12 = ax1.imshow(Im, alpha=0.7)
ax2 = fig.add_subplot(122)
ax2.set_title('Overlay transformed image over the fixed image',
fontsize=35)
ax2.axis('off')
im21 = ax2.imshow(I)
im22 = ax2.imshow(It, alpha=0.7)
return I, Im, It
def point_based_registration(I_path, Im_path, X, Xm):
#read/load the images I and Im
imageI = plt.imread(I_path)
imageIm = plt.imread(Im_path)
#convert to homogenous coordinates using c2h
X_h = util.c2h(X)
Xm_h = util.c2h(Xm)
#compute affine transformation and make a homogenous transformation matrix
Th = reg.ls_affine(X_h, Xm_h)
#transfrom the moving image using the transformation matrix
It, Xt = reg.image_transform(imageIm, Th)
#plotting the results
fig = plt.figure(figsize=(20, 30))
ax1 = fig.add_subplot(131)
im1 = ax1.imshow(imageI) #plot first image (fixed or T1) image
ax2 = fig.add_subplot(132)
im2 = ax2.imshow(imageIm) #plot second image (moving or T2) image
ax3 = fig.add_subplot(133)
im3 = ax3.imshow(It) #plot (T1 moving or T2) transformed image
ax1.set_title('T1 (fixed)')
ax2.set_title('T1 moving or T2')
ax3.set_title('Transformed (T1 moving or T2) image')
return Th
def Evaluate_point_based_registration(Th, X_target, Xm_target):
X_target = util.c2h(X_target)
Xmh_target = util.c2h(Xm_target)
#transform the selected points
Xm_target_transformed = Th.dot(Xmh_target)
#average distance between points (= target registration error)
Error_avgdist = calculateAvg_Distance(X_target, Xm_target_transformed)
return Error_avgdist
def point_based_affine_registration(I, Im):
# let the user selecte points
X, Xm = util.my_cpselect(I, Im)
# find affine transformation matrix
T, reg_error = reg.ls_affine(util.c2h(X), util.c2h(Xm))
# transform the moving image according to T
Im = plt.imread(Im)
It, _ = reg.image_transform(Im, T)
return It, reg_error
def arbitrary_rotation():
X = util.test_object(1) # The object that is rotated
Xh = util.c2h(X) # Convert the object vectors to homogeneous coords
t = X[:, 0] # First vertex to rotate around
# Define separate transformations in homogeneous coords
T_ftrans = util.t2h(reg.identity(), -1 *
t) # Translate to ensure first vertex is in the origin
T_rot = util.t2h(reg.rotate(np.pi / 4), np.array([0,
0])) # Rotate 45 degrees
T_btrans = util.t2h(reg.identity(),
t) # Translate back to the original position
# Create the final transformation matrix
T = T_btrans.dot(T_rot.dot(T_ftrans))
#------------------------------------------------------------------#
# TODO: TODO: Perform rotation of the test shape around the first vertex
#------------------------------------------------------------------#
# Transform
X_rot = T.dot(Xh)
# Plot
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X) #the object in homogeneous form
#------------------------------------------------------------------#
Xt = np.array(X[:, 0])
T_rot = reg.rotate(np.pi / 4)
Xt_down = util.t2h(
reg.identity(),
-Xt) #with Xt being the translation vector set into homogeneous form
Xt_up = util.t2h(reg.identity(), Xt)
T_rot = util.t2h(T_rot, np.array(
[0, 0])) #with T being the rotational vector set into homogeneous form
T = Xt_up.dot(T_rot).dot(Xt_down)
X_fin = T.dot(Xh)
#------------------------------------------------------------------#
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_fin)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
#perform rotation around the first vertex
phi = 45
c = np.cos(phi)
s = np.sin(phi)
coord_1 = X[:, 0] #rotatie om dit punt
x_r = coord_1[0]
y_r = coord_1[1]
T_1 = np.array([[1, 0, x_r], [0, 1, y_r], [0, 0, 1]])
T_2 = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
T_3 = np.array([[1, 0, -x_r], [0, 1, -y_r], [0, 0, 1]])
T = T_1.dot(T_2).dot(T_3)
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: Perform rotation of the test shape around the first vertex
Xt = X[:, 0]
phi = (45 / 180) * np.pi
#matrix to move the figure to new origin
translate_matrix = util.t2h(reg.identity(), -Xt)
translate_matrix[2][
2] = 1 #add the 1 in de third row and column to get 'ones'on the diagonal
rotate_matrix = np.array([[np.cos(phi), -np.sin(phi), 0],
[np.sin(phi), np.cos(phi), 0], [0, 0, 1]])
#matrix to move the figure back to original origin
translate_matrix_2 = util.t2h(reg.identity(), Xt)
translate_matrix_2[2][
2] = 1 #add the 1 in de third row and column to get 'ones'on the diagonal
T = (rotate_matrix.dot(translate_matrix)) #rotate the moved figure
T = translate_matrix_2.dot(T) #move the figure back
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def image_transform(I, Th, output_shape=None):
# Image transformation by inverse mapping.
# Input:
# I - image to be transformed
# Th - homogeneous transformation matrix
# output_shape - size of the output image (default is same size as input)
# Output:
# It - transformed image
# we want double precision for the interpolation, but we want the
# output to have the same data type as the input - so, we will
# convert to double and remember the original input type
input_type = type(I);
# default output size is same as input
if output_shape is None:
output_shape = I.shape
# spatial coordinates of the transformed image
x = np.arange(0, output_shape[1])
y = np.arange(0, output_shape[0])
xx, yy = np.meshgrid(x, y)
# convert to a 2-by-p matrix (p is the number of pixels)
X = np.concatenate((xx.reshape((1, xx.size)), yy.reshape((1, yy.size))))
# convert to homogeneous coordinates
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: Perform inverse coordinates mapping.
#------------------------------------------------------------------#
It = ndimage.map_coordinates(I, [Xt[1,:], Xt[0,:]], order=1, mode='constant').reshape(I.shape)
return It, Xt
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# Perform rotation of the test shape around the first vertex
t = -X[:, 0]
Trot = reg.rotate(np.pi / 4)
Throt = util.t2h(Trot, np.zeros([1, np.size(Trot, axis=1)]))
th = util.t2h(reg.identity(), t)
thin = np.linalg.inv(th)
T = thin.dot(Throt.dot(th))
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#Define rotation angle 45degrees
phi = np.pi / 4
#Define seperate homogenous transformation matrices
T_1 = np.array([[1, 0, -X[0, 0]], [0, 1, -X[1, 0]], [0, 0, 1]])
T_rot = np.array([[cos(phi), -sin(phi), 0], [sin(phi),
cos(phi), 0], [0, 0, 1]])
T_2 = np.array([[1, 0, X[0, 0]], [0, 1, X[1, 0]], [0, 0, 1]])
#Combine them
T = T_2.dot(T_rot.dot(T_1))
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def ls_affine_test():
X = util.test_object(1)
# convert to homogeneous coordinates
Xh = util.c2h(X)
T_rot = reg.rotate(np.pi / 4)
T_scale = reg.scale(1.2, 0.9)
T_shear = reg.shear(0.2, 0.1)
T = util.t2h(T_rot.dot(T_scale).dot(T_shear), [10, 20])
Xm = T.dot(Xh)
Te = reg.ls_affine(Xh, Xm)
Xmt = Te.dot(Xm)
fig = plt.figure(figsize=(12, 5))
ax1 = fig.add_subplot(131)
ax2 = fig.add_subplot(132)
ax3 = fig.add_subplot(133)
util.plot_object(ax1, Xh)
util.plot_object(ax2, Xm)
util.plot_object(ax3, Xmt)
ax1.set_title('Test shape')
ax2.set_title('Arbitrary transformation')
ax3.set_title('Retrieved test shape')
ax1.grid()
ax2.grid()
ax3.grid()
def pbr(I_path, Im_path):
# Load in images
I = plt.imread(I_path)
Im = plt.imread(Im_path)
# Set control points
X, Xm = util.my_cpselect(I_path, Im_path)
Xh = util.c2h(X)
Xmh = util.c2h(Xm)
# Find optimal affine transformation
T = ls_affine(Xh, Xmh)
# Transform Im
Im_t, X_t = image_transform(Im, T)
return Im_t, X_t, X, Xm, T
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: Perform rotation of the test shape around the first vertex
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5,5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def t2h_test():
X = util.test_object(1)
Xh = util.c2h(X)
# translation vector
t = np.array([10, 20])
# rotation matrix
T_rot = reg.rotate(np.pi / 4)
Th = util.t2h(T_rot, t)
X_rot_tran = Th.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot_tran)
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
Xt= X[:0]
T_trans = util.t2h(reg.identity(), Xt)
T_rot = reg.rotate(0.25*np.pi)
T_trans_inv = np.linalg.inv(T_trans)
T = T_trans_inv.dot(T_rot.dot(T_trans))
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5,5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
p_rot = X[:, 0]
T_to_zero = util.t2h(reg.identity(), -p_rot)
T_return = util.t2h(reg.identity(), p_rot)
T_rot = util.t2h(reg.rotate(45))
T = T_return.dot(T_rot.dot(T_to_zero))
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
fig.show()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: Perform rotation of the test shape around the first vertex
Xt = X[:, 0]
T = util.t2h(reg.rotate(np.pi / 4), Xt).dot(util.t2h(reg.identity(), -Xt))
#------------------------------------------------------------------#
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
# ------------------------------------------------------------------#
Tlat = util.t2h(reg.identity(), np.array(X[:, 0]))
Tlat_down = util.t2h(reg.identity(), -np.array(X[:, 0]))
T_rot = reg.rotate(np.pi / 4)
T_rot_hom = util.t2h(T_rot, np.array([0, 0]))
T_tot = Tlat.dot(T_rot_hom).dot(Tlat_down)
X_fin = T_tot.dot(Xh)
# ------------------------------------------------------------------#
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_fin)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: TODO: Perform rotation of the test shape around the first vertex
a_point = X[:,0]
ax = a_point[0]
ay = a_point[1]
trans1 = np.array([[1,0,ax],[0,1,ay],[0,0,1]]) #translatiematrix 1 (zie slides)
trans2 = np.array([[1, 0, -ax], [0, 1, -ay], [0, 0, 1]]) #translatiematrix 2
phi = (np.pi/4)
c = np.cos(phi)
s = np.sin(phi)
extra = ([[0,0]])
extra_vertical = np.transpose(extra)
extra_horizontal = ([[0,0,1]])
r = np.array([[c, -s], [s, c]])
rot1 = np.concatenate((r, extra_vertical), 1)
rot2 = np.concatenate((rot1, extra_horizontal), 0) #rotatiematrix
Transformation = trans1.dot(rot2.dot(trans2))
X_rot = Transformation.dot(Xh)
#------------------------------------------------------------------#
#X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5,5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
def arbitrary_rotation():
X = util.test_object(1)
Xh = util.c2h(X)
#------------------------------------------------------------------#
# TODO: TODO: Perform rotation of the test shape around the first vertex
#------------------------------------------------------------------#
tdown = X[:, 0] * -1
tup = X[:, 0]
tdown = util.t2h(reg.identity(), tdown)
tup = util.t2h(reg.identity(), tup)
r = util.t2h(reg.rotate(45), [0, 0])
T = tup.dot(r.dot(tdown))
X_rot = T.dot(Xh)
fig = plt.figure(figsize=(5, 5))
ax1 = fig.add_subplot(111)
util.plot_object(ax1, X)
util.plot_object(ax1, X_rot)
ax1.set_xlim(ax1.get_ylim())
ax1.grid()
plt.show()
