Project

General

Profile

2010 ADWCreate an image uploader program from scratch » History » Version 9

Neil Voss, 06/11/2010 09:50 AM

1 1 Neil Voss
h1. Create an image uploader program from scratch
2
3 2 Neil Voss
h2. Problem statement: 
4
5
We want to upload images, including defocal pairs into the database
6
7 4 Neil Voss
* four types of data collection: tomogram, tiltseries (RCT/OTR), defocal pairs, and normal
8 1 Neil Voss
* current version does tiltseries (maybe tomogram series) and normal, but not defocal pairs
9 4 Neil Voss
10 9 Neil Voss
h2. determine what the inputs are and what is required:
11 1 Neil Voss
12 7 Neil Voss
# folder with mrc images – only support mrc files
13
# pixel size, specified in meters
14
# tiltseries/defocal information (# per set) &ndash; cannot have both<pre>
15
--images-per-tilt-series=3 --images-per-defocal-group=3</pre>
16
# two session modes, create new session or append to existing session
17
#* appending to a session is a dangerous things, so I am not going to support it.
18
#* single mode simplifies things dramatically
19
# input defocus and tilt angle:
20
#*  optionally allow a batch file for individual defocus and angle information<pre>
21 4 Neil Voss
imagename <tab> defocus <tab> angle</pre>
22 7 Neil Voss
#* have override commandline flags<pre>
23 4 Neil Voss
--anglelist=-45,0,45 --defocus=-2.0e-6</pre>
24 1 Neil Voss
#* not required to allow future uploading from the web
25 8 Neil Voss
# four data collection modes:
26 7 Neil Voss
#* *tomogram*: we cannot support uploading tomograms, pipeline requires Leginon information
27
#* *RCT/OTR*: requires a tiltseries connection
28
#* *defocal pairs*: require a AcquisitionImageTargetData connection, source:trunk/appion/appionlib/apDefocalPairs.py#L28
29
#* *normal mode*: does not need any special treatment
30
# override session name???
31 1 Neil Voss
# require a description
32 8 Neil Voss
33 9 Neil Voss
h2. Create the program file
34 8 Neil Voss
35 1 Neil Voss
* Find the feature request in redmine or file a new one
36 4 Neil Voss
* Copy appionScript.py.template
37 8 Neil Voss
* Make executable
38
* Commit to subversion
39
40 9 Neil Voss
h2. Preliminary setup
41 4 Neil Voss
42 8 Neil Voss
* Input options
43 3 Neil Voss
* Check conflicts
44 8 Neil Voss
45 9 Neil Voss
h2. Setup program to do the work
46 3 Neil Voss
47 1 Neil Voss
* Create session
48 8 Neil Voss
* Obtain Scope/Camera information
49
* Uploading to the database
50 1 Neil Voss
51 9 Neil Voss
h2. Test the program
52 1 Neil Voss
53 9 Neil Voss
h2. Create web interface