Make DDD movie stack » History » Revision 14
Revision 13 (Anchi Cheng, 05/01/2015 12:41 AM) → Revision 14/17 (Sargis Dallakyan, 05/07/2015 01:29 PM)
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 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_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* attached here can do the same as well using the library of Leginon/Appion, but not the database.