Create an image uploader program from scratch¶

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

Background info for defocal pairs¶

images are linked using

New python program:¶

determine what the inputs are and what is required:¶

1. folder with mrc images – only support mrc files
2. pixel size, specified in meters
3. tiltseries/defocal information (# per set) – cannot have both

   --images-per-tilt-series=3 --images-per-defocal-group=3

4. 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
5. input defocus and tilt angle:
   • optionally allow a batch file for individual defocus and angle information

     imagename <tab> defocus <tab> angle

   • have override commandline flags

     --anglelist=-45,0,45 --defocus=-2.0e-6

   • not required to allow future uploading from the web
6. 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
7. override session name???
8. require a description

Create the program file¶

• Find the feature request in redmine or file a new one
• Copy appionScript.py.template
• Make executable
• Commit to subversion

Preliminary setup¶

• Input options
• Check conflicts

Setup program to do the work¶

• Create session
• Obtain Scope/Camera information
• Uploading to the database

Test the program¶

Create web interface¶