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
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
--images-per-tilt-series=3 --images-per-defocal-group=3
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
--angle-list=-45,0,45 --defocus-list=-2.0e-6,-4.0e-6,-6.0e-6
* not required to allow future uploading from the web
- four data collection modes: # tomographic tilt series: we cannot support uploading tomographic tilt series, 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
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