Bug #3569
closedmakestack "pixlimit" feature adding black pixels.
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Description
When we use the "pixlimit=4" option in makestack, our particles have lots of black spots appearing on them, like high intensity pixels are being replaced with low intensity ones. I'm attaching images of a stack made with and without this option. Not sure it's capping the value properly.
Files
Updated by Scott Stagg about 9 years ago
I am also getting screwy results with this option. I say we should turn it off by default and only have it as an option. I added other interested parties as watchers. Any other thoughts about having pixlimit be off by default?
Updated by Gabriel Lander about 9 years ago
We need some sort mechanism for removing hot pixels, since RELION will crash if these pixels haven't been corrected somehow, and these hot pixels introduce severe ringing effects if you do CTF correction on the particles. The XMIPP method worked really well, and we need some way to do this. Should we go back to XMIPP as an option?
Updated by Neil Voss about 9 years ago
We have two options, set high pixels to a constant or figure out what is wrong. Sorry, I had a grant due this afternoon.
Updated by Neil Voss about 9 years ago
Should be fixed now in r19195, I was using a uniform distribution, instead of a normal proper normal one. Check if it works, if still broken switch to the original version where we replace values over pixlimit, with a constant value by setting "const=True"
Updated by Gabriel Lander about 9 years ago
- Status changed from New to Closed
appears to be working properly now, thanks Neil.