I intend to alter the contrast/brightness of my images in my pytorch Dataset pipeline using the
sitk.AdaptiveHistogramEqualization method to make my neural network more robust against such differences. However, I found that it decreases my step rate from 5 it/s to just 1 it/s, which in turn increases my training time from a few days to weeks which I can’t afford. Am I perhaps misusing the method or is there a different, faster alternative?
The dataset looks like this
def __init__(self, dataset: Dataset):
self.data = dataset
def __getitem__(self, idx):
im, label = self.data[idx]
rndAlpha = uniform(0,1)
rndBeta = uniform(0,1)
new_im = sitk.AdaptiveHistogramEqualization(im, alpha=rndAlpha, beta=rndBeta)
return new_im, label
You are re-doing the equalization each time an image is fetched. Of course it is slow. All fancy augmentations are slow. You might consider doing this augmentation with some probability, e.g. 10%. That should allow your NN to learn it and be resistant to it, but would not be overly computationally expensive.
Deterministic, computationally complex augmentations are best done using a caching mechanism so that they are only performed once during training. For example, see the MONAI implementations for
For the size of images used for deep learning it should not be that time consuming. How long does just the AdaptiveHistogramEqualizationFilter take the filter to run? 4 seconds seems way too long.
What is your image size, pixel type and version of SimpleITK/ITK?
The current implementation using a moving histogram which should be fairly efficient.
Thanks for your replies. Simply not doing it in every step is totally reasonable.
@zivy thank you, I will take a look at those. I’ll do a big part of my data preparation before training already, but maybe this could improve it too - gotta hope my machine can handle it.
@blowekamp My images are 35x35x35 floats and I’m using SITK version 2.1.1. One call takes in the order of 0.33-0.40 seconds. I’m sorry if I didn’t say it clearly, but the numbers I gave are the iterations/steps per second that decrease. One step loads 4 images.
Not sure if that timing is just the Eq step, but this is what I am getting locally:
In : img = sitk.Image([35,35,35], sitk.sitkFloat32)
In : img = sitk.Noise(img)
In : %timeit -n 1 out = sitk.AdaptiveHistogramEqualization(img, alpha=1, beta=1, radius=(3,3,3))
4.78 ms ± 693 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)
I couldn’t quite manage to reprodue that timeit in visual studio I timed it only around the AdaptiveHistogramEqualization call, but I noticed I get float64 from a previous normalization step. I doubt that it would make that much of a difference, but I’ll change it anyways. Thank you!
For now I’ll wait and see whether I get satisfying results just not doing it every time.