Bug #1376
closedGrab extrema pixel to correction plan does not handle Dead and hot pixel well enough
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Description
For detectors that have strong bias in dark image or many dead and hot pixels, it is too difficult to use this tool which only grab two pixels at a time.
Gabe Lander has reported that they always get 0 as min for corrected image because of the dead pixels that gave the same values for bright and dark acquisition. Leginon keeps norm from exploding but still will give zero in corrected image unless the dead pixel is removed.
We have the same problem with the new DD chip. It is too hard to get all of its larger number of dead pixels.
Updated by Anchi Cheng over 13 years ago
- Status changed from New to In Test
- Assignee changed from Anchi Cheng to Gabriel Lander
- Target version set to Appion/Leginon 2.2.0
Gabe,
From the images you sent me, I saw that a few pixels were dead in the sense that bright = dark. Since Leginon restrict the max of norm image value, these pixek end up with 0 / finite_number = 0 The best way to keep them from becoming zero, you should mark them as bad pixels.
What I committed for this issue (both in trunk and 2.1 branch) fixed a few bugs in makes the extreme pixel value searching and also more efficient and usable. Here is what you can try once updating your myami 2.1 svn checkout.
The "Add Extrem Points To Bad Pixel List" tool will add all pixels with maximum intensity to the bad pixel list, not just two pixels as before. It will also add minimum if it is <= 0.0
The "Display Normalization Image" tool actually displays whatever reference type you select as long as only one of the channel is selected. You will find one new type "Bright-Dark".
To use these to solve your problem, here is what you do:
1. acquire or display the dark image at one of the channel. Use "Add Extreme Points To Bad Pixel List" tool to add hot or dead-dead (always 0 count ones) to the bad pixel list. You can repeat the clicking of the tool to add the next extrema in line until it becomes reasonable.
2. repeat the same with bright image if there are hot pixels not picked by step 1.
3. repeat the same with "bright-dark" This will remove dead pixels that always give the same non-zero values.
These should give you a better corrected image. If it is still not enough, you can repeat the procedure on the acquired corrected image.
For unstable hot pixel, you will have to activate despike (in image plan)
Updated by Gabriel Lander over 12 years ago
- Status changed from In Test to Closed
This is working properly, thanks Anchi