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Make DDD movie stack » History » Version 14

Sargis Dallakyan, 05/07/2015 01:29 PM

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h2. Make DDD movie stack
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The following section comes from Appion Manual
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{{include(appion:Direct_Detector_Frame_Processing)}}
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h2. Making Gain/Dark correction one image at a time without saving results to databases
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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.
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*correctframes.py* let you correct a range of raw frames in an image and output as mrc file.
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*correctstack.py* let you correct each frame in the specified summed image and output at 2D image stack in mrc format.
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type:
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<pre>
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python correctframes.py
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</pre>
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for the options
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h2. Do it yourself
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If you want to do everything yourself, you can use the python script
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"getReferences.py":http://emg.nysbc.org/projects/leginon/repository/changes/branches/myami-3.1/leginon/getReferences.py
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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,
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*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.
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*Beware that the fames are often in different orientation from the reference images in Leginon*
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To apply the correction, you need to use the equations found in [[Corrector]]
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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.
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*simple_correctstack.py* attached here can do the same as well using the library of Leginon/Appion, but not the database.