Make movie stack with darkbrightnormgain references yourself without LeginonAppion libraries » History » Revision 3
Revision 2 (Sargis Dallakyan, 05/07/2015 01:55 PM) → Revision 3/10 (Anchi Cheng, 06/12/2015 08:50 AM)
h2. Make movie stack with dark/bright/norm/gain references yourself without Leginon/Appion libraries If you want to do everything yourself, you can use the python script "getReferences.py":http://emg.nysbc.org/projects/leginon/repository/changes/branches/myami-3.1/leginon/getReferences.py to find the location and filenames of the bright, dark, norm (also known as gain) references and work on them yourself. The filenames are formatted to include various information. For example, *14aug12a_12221419_00_512x512_norm_0.mrc* *14aug12a_12221419_00_512x512_dark_0.mrc* is a norm dark reference image at dimension of 512x512. It was calculated from the dark and bright images shown by the script and was taken during session 14aug12a at 22:14:19 and is for correction channel 0. *Beware that the fames are often in different orientation from the reference images in Leginon* To apply the correction, you need to use the equations found in [[Corrector]] If there are no bad pixel/column/row on your camera that you included in your correction plan, you can feed the properly rotated/flipped references to the 2.0+ version of the drift correction program (motioncorr) by Xueming Li. *"simple_correctstack.py":/redmine/attachments/download/3791/simple_correctstack.py* can do the same as well using the library of Leginon/Appion, but not the database.