2010 ADWCreate an image uploader program from scratch » History » Version 7
Neil Voss, 06/11/2010 09:46 AM
1 | 1 | Neil Voss | h1. Create an image uploader program from scratch |
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5 | h2. Problem statement: |
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7 | We want to upload images, including defocal pairs into the database |
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9 | 4 | Neil Voss | * four types of data collection: tomogram, tiltseries (RCT/OTR), defocal pairs, and normal |
10 | * current version does tiltseries (maybe tomogram series) and normal, but not defocal pairs |
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12 | 4 | Neil Voss | h2. Background info for defocal pairs |
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14 | 4 | Neil Voss | images are linked using |
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16 | 4 | Neil Voss | h2. New python program: |
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18 | 1 | Neil Voss | h4. determine what the inputs are and what is required: |
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20 | 7 | Neil Voss | # folder with mrc images – only support mrc files |
21 | # pixel size, specified in meters |
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22 | # tiltseries/defocal information (# per set) – cannot have both<pre> |
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23 | --images-per-tilt-series=3 --images-per-defocal-group=3</pre> |
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24 | # two session modes, create new session or append to existing session |
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25 | #* appending to a session is a dangerous things, so I am not going to support it. |
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26 | #* single mode simplifies things dramatically |
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27 | # input defocus and tilt angle: |
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28 | #* optionally allow a batch file for individual defocus and angle information<pre> |
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29 | 4 | Neil Voss | imagename <tab> defocus <tab> angle</pre> |
30 | 7 | Neil Voss | #* have override commandline flags<pre> |
31 | 4 | Neil Voss | --anglelist=-45,0,45 --defocus=-2.0e-6</pre> |
32 | 7 | Neil Voss | # four data collection modes: |
33 | #* *tomogram*: we cannot support uploading tomograms, pipeline requires Leginon information |
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34 | #* *RCT/OTR*: requires a tiltseries connection |
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35 | #* *defocal pairs*: require a AcquisitionImageTargetData connection, source:trunk/appion/appionlib/apDefocalPairs.py#L28 |
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36 | #* *normal mode*: does not need any special treatment |
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47 | 1 | Neil Voss | ** run the program |
48 | ** uploading to the database |
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49 | * Create new php interface |