Find large spots median hysth

ufo-kit / tofu

Helper scripts for tomographic reconstruction using the ufo-core framework

GNU Lesser General Public License v3.0

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Find large spots median hysth #136

Closed tfarago closed 5 months ago

tfarago commented 5 months ago

unifies the behavior of spot and grow thresholds amongst "grow" and "median" method
adds --averaging-mode
adds --max-spot-size
allows writing of the median-filtered image
holes removal happens after dilation

TODO: ~- [ ] do median calculations in UFO to speed things up~ later

tfarago commented 5 months ago

@sgasilov I put the sequence reader to util and updated all ez paths, please take a look, it should work.

sgasilov commented 5 months ago

Hello Tomas,

Everything is working well now! One Q: - did you investigate that very slow convergence in my example if I set threshold to a low value like 1000? I left it the other day to run for 30 minutes and it was still computing. I wonder if I shall leave it running overnight just to see if it returns something at all? With 2000 and larger threshold all is well.

tfarago commented 5 months ago

Good to hear. It is slow because the time complexity is O(n^3), which is harsh for a python-based program, even with numpy backend. i will rewrite it on GPUs before merging.

tfarago commented 5 months ago

Merging as other updates are waiting