Threshold segmentation in area defined by mask

Question

I am having a problem with segmentation. I have an image (74, 78, 75) and mask (512, 512, 97). I would like to threshold all intensity values in the image above 500, but confine it to the area defined by the mask (pixels with non-zero values).

newMask = np.zeros(image.shape)
newMask = np.where(image[np.any(mask != 0)] > 500)

The above logical operation returns a tuple, instead of an array. What i am i doing wrong? Cheers

Hopefully this will help: https://scikit-image.org/docs/dev/user_guide/numpy_images.html — Nick H, Jan 29 '20 at 11:50
Thanks. I managed to solve by cropping the mask to the same dimension as the image. :-) — Lamech, Jan 31 '20 at 10:12

score 0 · Accepted Answer · answered Sep 18 '20 at 10:56

0

mask[mask==0] = np.nan
maskedIm = np.ma.masked_where(mask == 0, mask)

answered Sep 18 '20 at 10:56

Lamech

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Threshold segmentation in area defined by mask

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