Make DDD movie stack » History » Version 11
Anchi Cheng, 03/19/2015 06:48 PM
1 | 3 | Anchi Cheng | h2. Make DDD movie stack |
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3 | The following section comes from Appion Manual |
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5 | {{include(appion:Direct_Detector_Frame_Processing)}} |
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7 | 5 | Anchi Cheng | h2. Making Gain/Dark correction one image at a time without saving results to databases |
8 | 4 | Anchi Cheng | |
9 | 7 | Anchi Cheng | 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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11 | *correctframes.py* let you correct a range of raw frames in an image and output as mrc file. |
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12 | *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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14 | type: |
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15 | <pre> |
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16 | python correctframes.py |
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17 | </pre> |
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18 | for the options |
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19 | 4 | Anchi Cheng | |
20 | h2. Do it yourself |
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22 | If you want to do everything yourself, you can use the python script |
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24 | "getReferences.py":http://emg.nysbc.org/projects/leginon/repository/changes/branches/myami-3.1/leginon/getReferences.py |
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26 | 11 | Anchi Cheng | to find the location and filenames of the references and work on them yourself. The filenames are formatted to include various information. For example, |
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28 | *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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29 | 6 | Anchi Cheng | |
30 | *Beware that the fames are often in different orientation from the reference images in Leginon* |
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32 | 9 | Anchi Cheng | To apply the correction, you need to use the equations found in [[Corrector]] |
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34 | 10 | Anchi Cheng | 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. |