Make DDD movie stack » History » Revision 12
Revision 11 (Anchi Cheng, 03/19/2015 06:48 PM) → Revision 12/17 (Anchi Cheng, 05/01/2015 12:40 AM)
h2. Make DDD movie stack The following section comes from Appion Manual {{include(appion:Direct_Detector_Frame_Processing)}} h2. Making Gain/Dark correction one image at a time without saving results to databases Two scripts are attached here. They use Leginon infrastructure to locate references and do gain/dark correction and bad pixel/column/row correction. It, however, does not involve saving results to the leginon/appion databases. These are good for testing of add your own idea to it. *correctframes.py* let you correct a range of raw frames in an image and output as mrc file. *correctstack.py* let you correct each frame in the specified summed image and output at 2D image stack in mrc format. type: <pre> python correctframes.py </pre> for the options h2. Do it yourself 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 references and work on them yourself. The filenames are formatted to include various information. For example, *14aug12a_12221419_00_512x512_dark_0.mrc* is a dark reference image at dimension of 512x512. It 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 can do the same as well using the library of Leginon/Appion, but not the database.