8000 Feature request: points to labels · Issue #5087 · scikit-image/scikit-image · GitHub
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Feature request: points to labels #5087

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jni opened this issue Nov 29, 2020 · 5 comments
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Feature request: points to labels #5087

jni opened this issue Nov 29, 2020 · 5 comments
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🔰 Good first issue A good task for those new to the library 🙏 Feature request

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@jni
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jni commented Nov 29, 2020

Description

I find myself repeating the following lines very often:

coords = ... # something that gives me an (npoints, ndim) array
indices = tuple(np.transpose(np.round(coords).astype(int)))
labels = np.zeros_like(image, dtype=np.uint32)
labels[indices] = np.arange(1, len(coords) + 1)

This is required for example to take a set of centroids and turn them into markers for watershed.

I think it would be great for skimage to provide a utility function to do this.
@jni jni added 🔰 Good first issue A good task for those new to the library type: new feature labels Nov 29, 2020
@emmanuelle
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Good idea. Should it be in segmentation or in utils?

@jni
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jni commented Dec 2, 2020

A great question. I don't have a strong preference. Maybe we reopen #1608? =P

@grlee77 grlee77 mentioned this issue Dec 7, 2020
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@harish-vnkt
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Hi, @jni. First timer in open source and would like to work on this issue. :)
Would it be enough to have a function that takes centroid coordinates and the image as arguments and uses ndi.label to assign labels to the centroids? Also, any idea on which module this function belongs to?

@jni jni mentioned this issue Dec 23, 2020
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@jni
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jni commented Dec 23, 2020

@harish-vnkt Hello! I think that approach will be slower than using the direct assignment in the above code snippet.

Regarding module, I'm not sure, nor do I know what the best name is. skimage.util.points_to_labels? skimage.segmentation.points_to_label_image? Some combination of the above? But, might as well open the PR and get the ball rolling! 😊

@harish-vnkt harish-vnkt mentioned this issue Jan 11, 2021
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@jni
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jni commented Feb 1, 2021

Closed by #5180

@jni jni closed this as completed Feb 1, 2021
@grlee77 grlee77 mentioned this issue Feb 15, 2021
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