You have to define your arrays in terms of weights and coordinates. If you have two arrays a = [1,1,0,0,1] and b = [0,1,0,1] that represent one dimensional histograms, then the numpy arrays should look like this:
a = [[1 1]
[1 2]
[0 3]
[0 4]
[1 5]]
b = [[0 1]
[1 2]
[0 3]
[1 4]]
Notice that the number of rows can be different. The number of columns should be the dimensions + 1. The first column contains the weights, and the second column contains the coordinates.
The next step is to convert your arrays to a CV_32FC1 Mat before you input the numpy array as a signature to the CalcEMD2 function. The code would look like this:
from cv2 import *
import numpy as np
# Initialize a and b numpy arrays with coordinates and weights
a = np.zeros((5,2))
for i in range(0,5):
a[i][1] = i+1
a[0][0] = 1
a[1][0] = 1
a[2][0] = 0
a[3][0] = 0
a[4][0] = 1
b = np.zeros((4,2))
for i in range(0,4):
b[i][1] = i+1
b[0][0] = 0
b[1][0] = 1
b[2][0] = 0
b[3][0] = 1
# Convert from numpy array to CV_32FC1 Mat
a64 = cv.fromarray(a)
a32 = cv.CreateMat(a64.rows, a64.cols, cv.CV_32FC1)
cv.Convert(a64, a32)
b64 = cv.fromarray(b)
b32 = cv.CreateMat(b64.rows, b64.cols, cv.CV_32FC1)
cv.Convert(b64, b32)
# Calculate Earth Mover's
print cv.CalcEMD2(a32,b32,cv.CV_DIST_L2)
# Wait for key
cv.WaitKey(0)
Notice that the third parameter of CalcEMD2 is the Euclidean Distance CV_DIST_L2. Another option for the third parameter is the Manhattan Distance CV_DIST_L1.
I would also like to mention that I wrote the code to calculate the Earth Mover's distance of two 2D histograms in Python. You can find this code here.
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