Make DDD movie stack » History » Version 8
Anchi Cheng, 08/26/2014 05:58 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 |
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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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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 | 6 | Anchi Cheng | to find the location and filenames of the references and work on them yourself. |
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28 | *Beware that the fames are often in different orientation from the reference images in Leginon* |
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30 | 8 | 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 by Xueming Li. |