Appion

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. Background info for defocal pairs

images are linked using

h2. New python program:

h4. 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<pre>

imagename <tab> defocus <tab> angle</pre>

** have override commandline flags<pre>

--anglelist=-45,0,45 --defocus=-2.0e-6</pre>

* 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