Comments (3)
a quick hack to try this out https://github.com/VolkerH/Lattice_Lightsheet_Deskew_Deconv/blob/gputools_deconv/lls_dd/deconvolution_gputools.py
Worked surprisingly well.
Signficantly slower than flowdec, but also significantly faster than CPU and not limited to CUDA.
Does not seem to keep the FFT plan, so significant potential for speedup by keeping this.
Doesn't throw any memory allocation errors for datasets where flowdec competes with gputools.
Also has a spatial deconvolutoin option (without FFT). Might be worth a try for small PSFs if we can also find a seperable approximation.
Todo:
- create an abstract deconvolver class with an init and a process method.
- have concrete child classes for flowdec and gputools. Can also add cudaDeconv backend, but that requires different processing of PSFs so is slightly more complicated. Conversion of the PSF could be integrated into the init method of the deconvolver rather than modifying the current PSF handling.
from lattice_lightsheet_deskew_deconv.
closing this as this is implemented now. Not yet as a generic class that wraps all deconvolution backends but working.
from lattice_lightsheet_deskew_deconv.
Works reasonably fast with the changes in: https://github.com/VolkerH/Lattice_Lightsheet_Deskew_Deconv/blob/master/lls_dd/deconv_gputools_rewrite.py
Visually not quite the same quality as the flowdec result, but probably not too hard to include the additional tweaks. Low priority at the moment.
from lattice_lightsheet_deskew_deconv.
Related Issues (20)
- Think about deployment for end-users HOT 1
- Real-Time deskew visualization HOT 15
- Add scale to processed tiffs HOT 1
- fixed camera background subtraction - clip at 0, allow negative ? Also include for PSF. HOT 1
- openCL error HOT 6
- Assertion error in tensorflow
- PSF management - lattice pattern in file name
- Performance in batch mode HOT 5
- artefacts introduced by rotate to coverslip HOT 6
- Artefacts on RTX 2080 Ti HOT 1
- Architecture not well-suited for multiprocessing due to pickling limitations HOT 9
- Not enough GPU ram ... make a "slow" option HOT 12
- psf generation - change to two stage affine to avoid artefacts HOT 1
- reuse PSF
- Fail gracefully when out of GPU memory HOT 1
- bug: incompatible shapes HOT 4
- psf z_galvo step extraction fails for 20190802 dataset HOT 1
- CPU version — ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' HOT 6
- Allow deskewing when no PSF is present
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from lattice_lightsheet_deskew_deconv.