All segmap images are black

[Sangwon91]

I just realized all the segmap images are black. Is this normal? When I load a segmap.jpg, all pixel values are 0.

[by256]

Hi,

If you try to view a segmap as an image, the particle instance class values will be interpreted as image pixel values. This means that particles with class 1 or 2 for example will be essentially invisible in the image since these are very low pixel values.

I would suggest visualizing the segmap with matplotlib using plt.imshow or plt.matshow with a discrete colormap so that the individual classes are visible. The colormap I usually use is tab20, but you can choose this to your taste.

Please let me know if this solves your problem so that I can close the issue. If not, let me know and we can discuss it further.

Batuhan

[by256]

I also just remembered that the segmaps are 32bit integer images as opposed to 8 bits. This is because some images contained greater than 256 particles, and 8 bits were not enough to encode these values in a segmap. This may explain why they appear as black.

[Sangwon91]

You are right. The problem was that cv.imread() automatically converts image type to np.uint8 .
All problems are resolved.

Thank you!

[by256]

Glad to help.