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ChristophKirst / ClearMap

ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
http://christophkirst.github.io/ClearMap/build/html/index.html
GNU General Public License v3.0
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ClearMap hanging when running resampling in XY #3

Closed pforai closed 8 years ago

pforai commented 8 years ago

Hi,

I'm hitting an issue (probably with Python multiprocessing) within ClearMap in that when it starts to execute the Process 0: resampleData: resampling in XY step. I tried setting processes to 1 and also passing in "sequential" as the processMethod. Any ideas? The only syscalls being executed are wait4() and futex() within the processes of the pool. Which would be normal for the way multiprocessing works, I'm just surprised that no work happens within the workers of the pool ( 0% CPU usage) and hanging for hours.

[...]
resampleData: processing 0/549
resampleData: processing 25/549
resampleData: processing 50/549
resampleData: processing 75/549
resampleData: processing 100/549
resampleData: processing 125/549
resampleData: processing 150/549
resampleData: processing 175/549
resampleData: processing 200/549
resampleData: processing 225/549
resampleData: processing 250/549
resampleData: processing 275/549
resampleData: processing 300/549
resampleData: processing 325/549
resampleData: processing 350/549
resampleData: processing 375/549
resampleData: processing 400/549
resampleData: processing 425/549
resampleData: processing 450/549
resampleData: processing 475/549
resampleData: processing 500/549
resampleData: processing 525/549
resampleData: resampled data size: (549, 650, 287)
Process 0: resampleData: resampling in XY: image 0 / 1727
Process 0: resampleData: Imagesize: 2160, 2560 Resampled Imagesize: 549, 650
pforai commented 8 years ago

Just figured out that multiprocessing and the OpenCV functions ClearMap uses are not compatible with OpenCV 3.1.x, but work fine with OpenCV 2.4.x.