Out of (host) memory at Data Pre-Processing step

[bobonannan]

numpy.core._exceptions._ArrayMemoryError: Unable to allocate 30.7 GiB for an array with shape (1417, 2260, 2573) and data type float32

how to set patch size?
and how to resolve the question of memory?

[qin-yu]

Hey @bobonannan I guess this error is from the very first step of plantseg, i.e. pre-processing? My guess is that your RAM is not big enough for keep this volume. This is, in turn, due to the rescaling of pre-processing, which makes your original volume huge. The first thing I would do is to see if the rescaling is really necessary. We provide networks trained by the same data with different resolution. You may choose a network of lower resolution so you don't have to rescale the data.

Please have a look at https://github.com/hci-unihd/plant-seg?tab=readme-ov-file#pre-trained-networks

[qin-yu]

We currently don't support pre-/post-processing by patch. Please confirm this @lorenzocerrone

[qin-yu]

Hey @bobonannan is this solved or do you still need more assistance?