[PYTHON] I tried fractal dimension analysis by the box count method in 3D

Introduction

Let's quantitatively evaluate the ** beauty ** of the structure. I am doing research. As a quantification method, ** fractal dimension ** is used as one index.

And, in order to find the fractal dimension, we use a method called ** box counting method **. I did not find an example of dealing with this in 3D, so I wrote an article.

What is fractal dimension?

[Fractal dimension](https://ja.wikipedia.org/wiki/%E3%83%95%E3%83%A9%E3%82%AF%E3%82%BF%E3%83%AB%E6% AC% A1% E5% 85% 83) Wikipedia has it like this. To put it simply, the dimensions between 1D and 2D, and between 2D and 3D can be represented by ** non-integer values **. You can express ** complexity **. Quantitative evaluation of landscapes and paintings is performed using this.

Fractal dimension analysis

This time, as an example, we will use a * 200 × 200 × 200 * cube. Let's experiment as a 3D * numpy * array initialized with * 1 *.

Actually read * STL * file numpy-stlArrange using. (Details will be written in the future)

Box counting method

Regarding the box counting method, I think this article is easy to understand, so I will link to it. Fractal analysis of surface roughness curve

Think of this three-dimensionally.

1. Divide the cube into a grid
2. Count if there are objects in the grid
3. Let grid_size be the length of the grid side and n be the count.
4. Plot log (grid_size) and log (n)
5. Perform linear regression by least squares method
6. Let the regression coefficient be the fractal dimension

We will change the size of this grid one by one.

A function that counts the elements contained in a box

Scan the 3D array in the order of x direction → y direction → z direction

• 1 * is judged by np.any.

3d_fractal.py

def count(arr, x, y, z, b):
    i = j = k = 0
    b_tmp  = b
    b_tmp2 = b
    ct = 0

    j_tmp = b
    k_tmp = b
    while k < z:
        while j < y:
            while i < x:
                if (np.any(arr[i:b, j:j_tmp, k:k_tmp] == 1)):
                    ct += 1
                i += b_tmp
                b += b_tmp
            #Wrap back
            j += b_tmp2
            j_tmp += b_tmp2
            b = b_tmp2
            i = 0
        #Wrap back
        k += b_tmp2
        k_tmp += b_tmp2
        b = b_tmp2
        j = b_tmp2

        i = 0
        j = 0

main function

Repeat the process of count () until the grid size changes from * 200 * to * 1/2 * by 100, 50, ... and * 1 *. When the grid size is * 1 *, the count should be * 200 x 200 x 200 = 80,00,000 *.

3d_fractal.py

def main():

    x = y = z = 200

    graph_x = []
    graph_y = []

    array3d = np.ones((x, y, z))
    ct_1 = np.count_nonzero(array3d == 1)

    grid_size = max(x, y, z)

    while grid_size >= 1:
        n = count(array3d, x, y, z, grid_size)
        graph_x.append(math.log(grid_size))
        graph_y.append(math.log(n))
        print(grid_size, n)
        print (math.log(grid_size), math.log(n))
        grid_size = int(grid_size / 2)

Linear regression

Perform linear regression from the counted result. Scikit-learn class for regression processing Use sklearn.linear_model.LinearRegression.

3d_fractal.py

    graph_x = np.array(graph_x).reshape((len(graph_x), 1)) #Make one row
    graph_y = np.array(graph_y).reshape((len(graph_y), 1))

    model_lr = LinearRegression()

    #Predictive model creation
    model_lr.fit(graph_x, graph_y)

    plt.xlabel("log(grid_size)")
    plt.ylabel("log(n)")

    plt.plot(graph_x, graph_y, 'o')
    plt.plot(graph_x, model_lr.predict(graph_x), linestyle="solid")

    plt.grid()
    plt.show()

    #Fractal dimension=Regression coefficient
    fractal = model_lr.coef_[0][0] * -1 

    print("Fractal : ", fractal)

result

Here is the logarithmic graph of the result. Grid size * log * on the horizontal axis

• Log * of logarithm on the vertical axis The regression coefficient of this is the fractal dimension.

200 1
5.298317366548036 0.0
100 8
4.605170185988092 2.0794415416798357
50 64
3.912023005428146 4.1588830833596715
25 512
3.2188758248682006 6.238324625039508
12 4913
2.4849066497880004 8.499640032168648
6 39304
1.791759469228055 10.579081573848484
3 300763
1.0986122886681098 12.614077858172898
1 8000000
0.0 15.89495209964411
Fractal :  3.004579190748091

The result looks like this. The fractal dimension is * 3.004579190748091 * So it's almost a theoretical value. When repeating from * 200 *, there was a case where it was not divisible by * 25/2 = 12 *, so there was a slight deviation.

Summary

--We were able to verify the three-dimensional fractal dimension analysis by the box count method. -Next time, I would like to write a method to calculate the fractal dimension directly from the * STL * file.

References

"Fractal analysis of surface roughness curve", Takeo Kono, (2010), Nagano Prefectural Institute of Technology Research Bulletin, No.5, p.P52-P55.