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. 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) &ndash; 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>

#* 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