Calculating Just A Specific Property In Regionprops Python

Answer :

There seems to be a more direct way to do the same thing using regionprops with cache=False. I generated labels using skimage.segmentation.slic with n_segments=10000. Then:

rps = regionprops(labels, cache=False) [r.area for r in rps] 

My understanding of the regionprops documentation is that setting cache=False means that the attributes won't be calculated until they're called. According to %%time in Jupyter notebook, running the code above took 166ms with cache=False vs 247ms with cache=True, so it seems to work.

I tried an equivalent of the other answer and found it much slower.

%%time ard = np.empty(10000, dtype=int) for i in range(10000):    ard[i] = size(np.where(labels==0)[1]) 

That took 34.3 seconds.

Here's a full working example comparing the two methods using the skimage astronaut sample image and labels generated by slic segmentation:

import numpy as np import skimage from skimage.segmentation import slic from skimage.data import astronaut  img = astronaut() # `+ 1` is added to avoid a region with the label of `0` # zero is considered unlabeled so isn't counted by regionprops # but would be counted by the other method. segments = slic(img, n_segments=1000, compactness=10) + 1  # This is just to make it more like the original poster's  # question. labels, num = skimage.measure.label(segments, return_num=True) 

Calculate areas using the OP's suggested method with index values adjusted to avoid the having a zero label:

%%time area = {} for i in range(1,num + 1):     area[i + 1] = np.size(np.where(labels==i)[1]) 

CPU times: user 512 ms, sys: 0 ns, total: 512 ms Wall time: 506 ms

Same calculation using regionprops:

%%time rps = skimage.measure.regionprops(labels, cache=False) area2 = [r.area for r in rps] 

CPU times: user 16.6 ms, sys: 0 ns, total: 16.6 ms Wall time: 16.2 ms

Verify that the results are all equal element-wise:

np.equal(area.values(), area2).all() 

True

So, as long as zero labels and the difference in indexing is accounted for, both methods give the same result but regionprops without caching is faster.