I am attempting to locate all green pixels in an image by converting vegetative indices using the scikit-image module in python. However, when I try to compute the Red-Green index, I get the following warning:
C:\Users\AppData\Local\Temp\ipykernel_1508\3901298948.py:3: RuntimeWarning: divide by zero encountered in divide
RG_ratio = R/G
C:\Users\AppData\Local\Temp\ipykernel_1508\3901298948.py:3: RuntimeWarning: invalid value encountered in divide
RG_ratio = R/G
The code below is what I have tried. Here is the image I am working with. It must be saved as a .jpg for this code to work:
Here is what I have done so far:
# Import modules
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
from skimage.color import rgb2gray, label2rgb
from skimage.filters import threshold_otsu
# Read example image
filename = 'wheat.jpg'
RGB = mpimg.imread(filename)
# Display image
plt.axis('off')
plt.imshow(RGB)
plt.show()
# Convert image from float in the range 0-1 to unsigned integer in the range 0-255
RGB = (RGB*255).astype('uint8')
RGB.dtype
# Separate RGB channels
R = RGB[:, :, 0] #All the rows and all the columns for the first band (R)
G = RGB[:, :, 1]
B = RGB[:, :, 2]
# Display bands and histograms for each band
plt.figure(figsize=(12,8))
plt.subplot(2, 3, 1)
plt.axis('off')
plt.imshow(R, cmap='gray')
plt.title('Red')
plt.subplot(2, 3, 2)
plt.axis('off')
plt.imshow(G, cmap='gray')
plt.title('Green')
plt.subplot(2, 3, 3)
plt.axis('off')
plt.imshow(B, cmap='gray')
plt.title('Blue')
plt.subplot(2, 3, 4)
plt.axis('off')
plt.hist(R.flatten())
plt.subplot(2, 3, 5)
plt.axis('off')
plt.hist(G.flatten())
plt.subplot(2, 3, 6)
plt.axis('off')
plt.hist(B.flatten())
plt.show()
# Compute Red-Green Ratio
RG_ratio = R/G
# Compute Excess Green Index
ExG = 2*G - R - B
The warning occurs after running the RG_Ratio code
C:\Users\AppData\Local\Temp\ipykernel_1508\3901298948.py:3: RuntimeWarning: divide by zero encountered in divide
RG_ratio = R/G
C:\Users\AppData\Local\Temp\ipykernel_1508\3901298948.py:3: RuntimeWarning: invalid value encountered in divide
RG_ratio = R/G
Now, to try to produce a histogram of the RG_Ratio index:
# Plot histogram of RG_ratio
plt.figure()
plt.hist(RG_ratio.flatten(), bins='scott')
plt.show()
The following error is thrown:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [37], in <cell line: 3>()
1 # Plot histogram of RG_ratio
2 plt.figure()
----> 3 plt.hist(RG_ratio.flatten(), bins='scott')
4 plt.show()
File ~\anaconda3\envs\agron893\lib\site-packages\matplotlib\pyplot.py:2600, in hist(x, bins, range, density, weights, cumulative, bottom, histtype, align, orientation, rwidth, log, color, label, stacked, data, **kwargs)
2594 @_copy_docstring_and_deprecators(Axes.hist)
2595 def hist(
2596 x, bins=None, range=None, density=False, weights=None,
2597 cumulative=False, bottom=None, histtype='bar', align='mid',
2598 orientation='vertical', rwidth=None, log=False, color=None,
2599 label=None, stacked=False, *, data=None, **kwargs):
-> 2600 return gca().hist(
2601 x, bins=bins, range=range, density=density, weights=weights,
2602 cumulative=cumulative, bottom=bottom, histtype=histtype,
2603 align=align, orientation=orientation, rwidth=rwidth, log=log,
2604 color=color, label=label, stacked=stacked,
2605 **({"data": data} if data is not None else {}), **kwargs)
File ~\anaconda3\envs\agron893\lib\site-packages\matplotlib\__init__.py:1414, in _preprocess_data.<locals>.inner(ax, data, *args, **kwargs)
1411 @functools.wraps(func)
1412 def inner(ax, *args, data=None, **kwargs):
1413 if data is None:
-> 1414 return func(ax, *map(sanitize_sequence, args), **kwargs)
1416 bound = new_sig.bind(ax, *args, **kwargs)
1417 auto_label = (bound.arguments.get(label_namer)
1418 or bound.kwargs.get(label_namer))
File ~\anaconda3\envs\agron893\lib\site-packages\matplotlib\axes\_axes.py:6641, in Axes.hist(self, x, bins, range, density, weights, cumulative, bottom, histtype, align, orientation, rwidth, log, color, label, stacked, **kwargs)
6637 # Loop through datasets
6638 for i in range(nx):
6639 # this will automatically overwrite bins,
6640 # so that each histogram uses the same bins
-> 6641 m, bins = np.histogram(x[i], bins, weights=w[i], **hist_kwargs)
6642 tops.append(m)
6643 tops = np.array(tops, float) # causes problems later if it's an int
File <__array_function__ internals>:180, in histogram(*args, **kwargs)
File ~\anaconda3\envs\agron893\lib\site-packages\numpy\lib\histograms.py:793, in histogram(a, bins, range, normed, weights, density)
681 r"""
682 Compute the histogram of a dataset.
683
(...)
789
790 """
791 a, weights = _ravel_and_check_weights(a, weights)
--> 793 bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights)
795 # Histogram is an integer or a float array depending on the weights.
796 if weights is None:
File ~\anaconda3\envs\agron893\lib\site-packages\numpy\lib\histograms.py:396, in _get_bin_edges(a, bins, range, weights)
392 if weights is not None:
393 raise TypeError("Automated estimation of the number of "
394 "bins is not supported for weighted data")
--> 396 first_edge, last_edge = _get_outer_edges(a, range)
398 # truncate the range if needed
399 if range is not None:
File ~\anaconda3\envs\agron893\lib\site-packages\numpy\lib\histograms.py:315, in _get_outer_edges(a, range)
312 raise ValueError(
313 'max must be larger than min in range parameter.')
314 if not (np.isfinite(first_edge) and np.isfinite(last_edge)):
--> 315 raise ValueError(
316 "supplied range of [{}, {}] is not finite".format(first_edge, last_edge))
317 elif a.size == 0:
318 # handle empty arrays. Can't determine range, so use 0-1.
319 first_edge, last_edge = 0, 1
ValueError: supplied range of [0.0, inf] is not finite
I do want to compute the RG_ratio index, but I'm not sure what is causing the "divide by zero" warning. How can I fix this issue?
Best Answer
This link contains the solution.
The problem occurs in Numpy and not in scikit-learn.
You can disable the warning with numpy.seterr. Put this before the possible division by zero:
That'll disable zero division warnings globally. If you just want to disable them for a little bit, you can use numpy.errstate in a with clause:
For a zero by zero division (undetermined, results in a NaN), the error behaviour has changed with numpy version 1.12.0: this is now considered "invalid", while previously it was "divide".
Thus, if there is a chance you your numerator could be zero as well, use
or