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Watershed uses only one CPU and runs very slow on large volumes #270

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qin-yu opened this issue Jun 4, 2024 · 2 comments
Open

Watershed uses only one CPU and runs very slow on large volumes #270

qin-yu opened this issue Jun 4, 2024 · 2 comments
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enhancement New feature or request

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@qin-yu
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qin-yu commented Jun 4, 2024

I'm running PlantSeg for FOR2581 but found watershed step uses only one CPU. I'll try to improve it but please stop me if it's not possible @lorenzocerrone

@qin-yu qin-yu added the enhancement New feature or request label Jun 4, 2024
@lorenzocerrone
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Parallelizing the distance transform might be possible in Vigra, but I think the watershed is single-core only

@qin-yu
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qin-yu commented Jun 4, 2024

Parallelizing the distance transform might be possible in Vigra, but I think the watershed is single-core only

Cry :' (

It took > 35 minutes to run watershed on a clear nuclear boundary pmap of size [473, 1712, 1712]! I have 63 cores idling

INFO:  PlantSeg Napari info - 15:15:55 04.06.2024 - Watershed Segmentation: Widget Watershed Segmentation computation started
Missing chrome or resource URL: resource://gre/modules/UpdateListener.jsm
Missing chrome or resource URL: resource://gre/modules/UpdateListener.sys.mjs
INFO:  PlantSeg Napari info - 15:51:27 04.06.2024 - Watershed Segmentation: Widget Watershed Segmentation computation complete in 2132.12s

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