2010 ADWCreate an image uploader program from scratch » History » Revision 10
Revision 9 (Neil Voss, 06/11/2010 09:50 AM) → Revision 10/11 (Neil Voss, 06/11/2010 10:27 AM)
h1. Create an image uploader program from scratch h2. Problem statement: We want to upload images, including defocal pairs into the database * four types of data collection: tomogram, tiltseries (RCT/OTR), defocal pairs, and normal * current version does tiltseries (maybe tomogram series) and normal, but not defocal pairs h2. determine what the inputs are and what is required: # folder with mrc images – only support mrc files # pixel size, specified in meters # tiltseries/defocal information (# per set) – cannot have both<pre> --images-per-tilt-series=3 --images-per-defocal-group=3</pre> # two session modes, create new session or append to existing session #* appending to a session is a dangerous things, so I am not going to support it. #* single mode simplifies things dramatically # input defocus and tilt angle: #* optionally allow a batch file for individual defocus and angle information<pre> imagename <tab> defocus <tab> angle</pre> #* have override commandline flags<pre> --angle-list=-45,0,45 --defocus-list=-2.0e-6,-4.0e-6,-6.0e-6</pre> --anglelist=-45,0,45 --defocus=-2.0e-6</pre> #* not required to allow future uploading from the web # four data collection modes: #* *tomogram*: we cannot support uploading tomograms, pipeline requires Leginon information #* *RCT/OTR*: requires a tiltseries connection #* *defocal pairs*: require a AcquisitionImageTargetData connection, source:trunk/appion/appionlib/apDefocalPairs.py#L28 #* *normal mode*: does not need any special treatment # override session name??? # require a description h2. Create the program file * Find the feature request in redmine or file a new one * Copy appionScript.py.template * Make executable * Commit to subversion h2. Preliminary setup * Input options * Check conflicts h2. Setup program to do the work * Create session * Obtain Scope/Camera information * Uploading to the database h2. Test the program h2. Create web interface