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@rougier
Last active August 13, 2024 10:35
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Fractal dimension computing
# -----------------------------------------------------------------------------
# From https://en.wikipedia.org/wiki/Minkowski–Bouligand_dimension:
#
# In fractal geometry, the Minkowski–Bouligand dimension, also known as
# Minkowski dimension or box-counting dimension, is a way of determining the
# fractal dimension of a set S in a Euclidean space Rn, or more generally in a
# metric space (X, d).
# -----------------------------------------------------------------------------
import scipy.misc
import numpy as np
def fractal_dimension(Z, threshold=0.9):
# Only for 2d image
assert(len(Z.shape) == 2)
# From https://github.com/rougier/numpy-100 (#87)
def boxcount(Z, k):
S = np.add.reduceat(
np.add.reduceat(Z, np.arange(0, Z.shape[0], k), axis=0),
np.arange(0, Z.shape[1], k), axis=1)
# We count non-empty (0) and non-full boxes (k*k)
return len(np.where((S > 0) & (S < k*k))[0])
# Transform Z into a binary array
Z = (Z < threshold)
# Minimal dimension of image
p = min(Z.shape)
# Greatest power of 2 less than or equal to p
n = 2**np.floor(np.log(p)/np.log(2))
# Extract the exponent
n = int(np.log(n)/np.log(2))
# Build successive box sizes (from 2**n down to 2**1)
sizes = 2**np.arange(n, 1, -1)
# Actual box counting with decreasing size
counts = []
for size in sizes:
counts.append(boxcount(Z, size))
# Fit the successive log(sizes) with log (counts)
coeffs = np.polyfit(np.log(sizes), np.log(counts), 1)
return -coeffs[0]
I = scipy.misc.imread("sierpinski.png")/256.0
print("Minkowski–Bouligand dimension (computed): ", fractal_dimension(I))
print("Haussdorf dimension (theoretical): ", (np.log(3)/np.log(2)))
@barbaroo
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Hi! I found this code very useful and I would like to cite it in my paper. Is there a correct way to cite this? Please help! I have to submit soon!

@rougier
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rougier commented Jan 31, 2022

Glad the code is useful but I'm afraid there there's no proper way to cite a it. Maybe as a misc bibitem with the relevant url/author.

@antoni27
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antoni27 commented Apr 9, 2022

hello

sorry, can anyone tell me how to change the data that I want to get from the link to my laptop data?
I want to try to extract features of an iris

@jankaWIS
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jankaWIS commented Apr 17, 2022

Hi @antoni27, I am not really sure what data you have and how you want to use it but simply changing the path in line 52 of the original code to link to another image should be enough.

@antoni27
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antoni27 commented May 9, 2022

thanks, @jankaWIS
and sorry if I ask again is the 52 line is
images = [
'https://upload.wikimedia.org/wikipedia/commons/thumb/7/7c/Peano_Sierpinski_carpet_4.svg/440px-Peano_Sierpinski_carpet_4.svg.png',
'https://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Sierpinski_carpet_3.svg/244px-Sierpinski_carpet_3.svg.png',
'https://upload.wikimedia.org/wikipedia/commons/f/f0/Flocke.PNG',
'https://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Quadratic_Koch_2.svg/2880px-Quadratic_Koch_2.svg.png',
'https://upload.wikimedia.org/wikipedia/commons/thumb/5/55/Quadratic_Koch.svg/300px-Quadratic_Koch.svg.png'
]
?

sorry I using the jupyter notebook so not to know about the number

@zyzhoux
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zyzhoux commented Jun 21, 2022

Why are boxes of 2x2 excluded?

@VaeKnt
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VaeKnt commented Aug 12, 2024

Hello, thank you very much for this function. I am finding it very useful in my study of fractals.

However, I drew a jagged line and tried to compute the fractal dimension

Using this code, I get a dimension of around 0.94 which is clearly wrong as it is < 1.

Why am I getting such a number?

Additionally, with other free fractal analysis software, I get a dimension of around 1.088

This is the line for reference
testcurve

@delton137
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FWIW the calculation is approximate.. also look at my comment above, there might still be a subtle issue with this code.

@VaeKnt
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VaeKnt commented Aug 13, 2024

Hi delton137!

I used another simple line that I generated, and then with altering the number of boxes, and then after iterating and computing the mean, I believe I got a better estimate. For this other curve, the box-count dimension was 1.06 ish. And it was well within the 95% CI range when I compared it to the FD from the one measured by the software.

I think I hopefully solved my own problem. I came across some papers re: optimal sizes of boxes. I will need to see how to implement that!

Also, I saw that you are also working in medical imaging. It is very inspiring to see interest in fractals and medical imaging. I am but a mere medical student currently, I hope to see a lot more fractals in the future, and a lot more collaboration!

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