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:¶

• folder with images
• pixel size
• tiltseries/defocal information (# per set)
• 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

    imagename <tab> defocus <tab> angle

  • have override commandline flags

    --anglelist=-45,0,45 --defocus=-2.0e-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 does not need these

• run the program
• uploading to the database

• Create new php interface