2010 ADWCreate an image uploader program from scratch » History » Version 9
Neil Voss, 06/11/2010 09:50 AM
1 | 1 | Neil Voss | h1. Create an image uploader program from scratch |
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3 | 2 | Neil Voss | h2. Problem statement: |
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5 | We want to upload images, including defocal pairs into the database |
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7 | 4 | Neil Voss | * four types of data collection: tomogram, tiltseries (RCT/OTR), defocal pairs, and normal |
8 | 1 | Neil Voss | * current version does tiltseries (maybe tomogram series) and normal, but not defocal pairs |
9 | 4 | Neil Voss | |
10 | 9 | Neil Voss | h2. determine what the inputs are and what is required: |
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12 | 7 | Neil Voss | # folder with mrc images – only support mrc files |
13 | # pixel size, specified in meters |
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14 | # tiltseries/defocal information (# per set) – cannot have both<pre> |
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15 | --images-per-tilt-series=3 --images-per-defocal-group=3</pre> |
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16 | # two session modes, create new session or append to existing session |
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17 | #* appending to a session is a dangerous things, so I am not going to support it. |
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18 | #* single mode simplifies things dramatically |
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19 | # input defocus and tilt angle: |
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20 | #* optionally allow a batch file for individual defocus and angle information<pre> |
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21 | 4 | Neil Voss | imagename <tab> defocus <tab> angle</pre> |
22 | 7 | Neil Voss | #* have override commandline flags<pre> |
23 | 4 | Neil Voss | --anglelist=-45,0,45 --defocus=-2.0e-6</pre> |
24 | 1 | Neil Voss | #* not required to allow future uploading from the web |
25 | 8 | Neil Voss | # four data collection modes: |
26 | 7 | Neil Voss | #* *tomogram*: we cannot support uploading tomograms, pipeline requires Leginon information |
27 | #* *RCT/OTR*: requires a tiltseries connection |
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28 | #* *defocal pairs*: require a AcquisitionImageTargetData connection, source:trunk/appion/appionlib/apDefocalPairs.py#L28 |
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29 | #* *normal mode*: does not need any special treatment |
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30 | # override session name??? |
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31 | 1 | Neil Voss | # require a description |
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33 | 9 | Neil Voss | h2. Create the program file |
34 | 8 | Neil Voss | |
35 | 1 | Neil Voss | * Find the feature request in redmine or file a new one |
36 | 4 | Neil Voss | * Copy appionScript.py.template |
37 | 8 | Neil Voss | * Make executable |
38 | * Commit to subversion |
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40 | 9 | Neil Voss | h2. Preliminary setup |
41 | 4 | Neil Voss | |
42 | 8 | Neil Voss | * Input options |
43 | 3 | Neil Voss | * Check conflicts |
44 | 8 | Neil Voss | |
45 | 9 | Neil Voss | h2. Setup program to do the work |
46 | 3 | Neil Voss | |
47 | 1 | Neil Voss | * Create session |
48 | 8 | Neil Voss | * Obtain Scope/Camera information |
49 | * Uploading to the database |
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50 | 1 | Neil Voss | |
51 | 9 | Neil Voss | h2. Test the program |
52 | 1 | Neil Voss | |
53 | 9 | Neil Voss | h2. Create web interface |