import Visualization
from scipy import ndimage
volume000 = sio.loadmat(
'F:\For JC\practice run/volume000.mat') # read the file
im1 = volume000['par1'] #[280:500,90:350,:] #[350:450,150:250,:]
volume125 = sio.loadmat('F:\For JC\practice run/volume125_regi.mat'
) # big region three point alignment
im2 = volume125['par1'] #[280:500,90:350,:]
fig = plt.figure()
plt.imshow(im1[:, :, 70], cmap='Greys_r')
ax = fig.add_subplot(111)
ax.set_title('click to build line segments')
line, = ax.plot([0], [0]) # empty line
linebuilder = ImageProcessing.LineBuilder(line)
plt.show()
x_cor = linebuilder.xs
y_cor = linebuilder.ys
points = np.array([x_cor, y_cor]).T
points = np.delete(points, (0), axis=0)
imx, imy = im1[:, :, 60].shape
mx, my = np.meshgrid(np.linspace(0, imx - 1, imx),
np.linspace(0, imy - 1, imy))
# meshgrid change the orientation of x,y: x becomes the horizontal axis, y becomes the vertical
# this change would affect the return statement of reshape.
Cord_xy = np.vstack([mx.flatten(), my.flatten()]).T # column major vector
