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STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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GEF to cGEF file process died #169

Closed predictowner closed 11 months ago

predictowner commented 11 months ago

Hi,

I'm trying to convert GEF to cGEF file using tools:

**from stereo.tools.cell_cut import CellCut

cgef_out_dir = "./cell_cut_out" bgef_path = "../.raw.gef" mask_path = "../mask.tif"

cc = CellCut(cgef_out_dir=cgef_out_dir) out_path = cc.cell_cut(bgef_path=bgef_path, mask_path=mask_path)**

But it seems that notebook died always. GEF file is around 3.4GB. Is it due to the short of RAM or is there other solution that I can make the transfer.

Many thanks!

UglyRay7 commented 11 months ago

What is the equipment configuration of your computer or cluster server?

Ray

predictowner commented 11 months ago

Hi Ray,

I'm using cluster server with 40 core with 8G for each. Is that enough?

Thx

tanliwei-coder commented 11 months ago

because of a part of memory is occupied by system, the remaining memory can be used must be less than 8G, i note that the size of your data has reached almost half of the memory, I think it is not enough, you can try to increase the memory to 16G to try again.

predictowner commented 11 months ago

Hi tanliwei,

I try to use 40core with 16G for each, and run the code as below, but the kernel still dies, could you give me some suggestions? Do we have some code for generating this on each smaller Tiff file?:

%%writefile temp.py from stereo.tools.cell_correct import cell_correct

bgef_path = "/data/......" mask_path = "/data/......" out_dir = "/data/......"

data = cell_correct( out_dir=out_dir, bgef_path=bgef_path, mask_path=mask_path, process_count=40, only_save_result=True, fast='v2' ) %run temp.py

tanliwei-coder commented 11 months ago

Could you go into shell to run it? it may able to get more infomation about this problem.