K2 raw frame saving » History » Version 4
Anchi Cheng, 04/24/2015 09:00 AM
1 | 1 | Anchi Cheng | h1. K2 raw frame saving |
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3 | # Typical frame saving preset parameters for counted/super-resolution: 0.2 s frame exposure time, 4-5 s total exposure time at 8-10 e/physical pixel/s (Some argues that 5 e/physical pixel/s is better). You can use DM's reading of dose rate while it is in counted mode and *UNBINNed* to get a reasonable estimate. |
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5 | h2. Camera configuration for frame saving |
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7 | # "Exposure time" specifies the total time in which the frames are saved. |
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8 | 2 | Anchi Cheng | # "Frame time" defines the length of each frame. The minimal value is 50 ms for K2 Summit and the values must be multiple of 50 ms. |
9 | 1 | Anchi Cheng | # "Frames to use" is not used |
10 | # "Readout Delay" is not used |
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12 | !K2Saveframe.png! |
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13 | 3 | Anchi Cheng | |
14 | h2. File location: |
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16 | The raw frame files can be saved in one of the three locations: |
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18 | # K2 computer X:\\frames\\ Use this if you set up rawtransfer.py to transfer and remove files on the drive fast enough that there is no accumunation during data collection. K2 camera uses X drive for processing the frames. It is therefore important not to fill it up. |
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19 | # K2 computer D:\\frames\\ Use this if file transfer is slow and network drive mounting is not stable. This ensures that frames are saved and can handle some accumulation of data. |
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20 | # Network file server mounted on K2 computer. |
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22 | 4 | Anchi Cheng | The file location is determined in pyscope/dmsem.py constant RAW_FRAME_DIR. For example: |
23 | 3 | Anchi Cheng | <pre> |
24 | K2_FRAME_DIR = 'D:\\frames\\ |
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25 | </pre> |
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27 | You must create this parent directory manually before start saving the frames. |
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29 | Each set of raw frame is saved in mrc format as an image stack identified by the date and a unique number. This is set by Leginon in pyscope/dmsem.py. |
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30 | 1 | Anchi Cheng | Leginon retrieve this and saved in its database so that [[DDD_raw_frame_file_transfer|rawtransfer.py]] script can transfer it to the Leginon rawdata directory under the same session. |
31 | 4 | Anchi Cheng | |
32 | h2. Next: [[DDD_raw_frame_file_transfer|Transfer and/or rename the movie frames]] |