2010 Appion Developer Workshop » History » Revision 10
Revision 9 (Neil Voss, 06/08/2010 10:37 AM) → Revision 10/18 (Neil Voss, 06/09/2010 08:17 AM)
h1. 2010 Appion Developer Workshop
h2. Setting up a development enviroment
h4. Subversion
<pre>
svn checkout http://emg.nysbc.org/svn/myami/trunk/ myami/
</pre>
h4. Sinedon.cfg
At AMI, you do not normally need a sinedon.cfg file, but if you have your own testing environment you will need one.
h4. Web page
At AMI, put myamiweb into your ami_html directory and it will be available on both cronus3 and fly as http://cronus3.scripps.edu/~username/myamiweb/
You will need to run Eric's web setup wizard to get it working: http://cronus3.scripps.edu/~username/myamiweb/setup/
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h2. Add a new option to a program
[[2010 ADW/Add a new option to a program]]
* Problem statement: Add student's T distribution to maxlike alignment, see #552
* Goal: allow user to use the @-student@ option for maxlike alignment using a radio button
* Steps to implement:
*# add feature to python code
*## add command line input
*## check flag to add to xmipp program
*## insert value into database
*# add feature to web page
*## add radio button to web page
*## add help message
*## receive variable from $_POST
*## check if value is valid
*## add flag to command line
h2. Add an output directory to hierarchical classification
* You cannot change the directory if the filesystem is full.
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h2. Organization of the Python programs
We have two major folders in the appion folder:
* appionlib: contains libraries, a collection of common functions that are needed by more than one python program, e.g., ssnrResolution, averageStack, and lowPassFilter.
* bin: contains the programs that take command line input, e.g., makestack2.py, templateCorrelator.py, maxlikeAlignment.py
Other useful directories:
* pyami: a collection of common functions to both appion and leginon, save MRC file, save SPIDER file, etc.
h2. Most important python files:
h3. Database mapping file
* source:trunk/appion/appionlib/appiondata.py: describes how the database is put together, if you need to add a new column go here
.bq see also source:trunk/leginon/leginondata.py and source:trunk/leginon/projectdata.py
h3. Appion Script hierarchy
h4. basicScript
* source:trunk/appion/appionlib/basicScript.py
* contains all the base functions: @setupParserOptions@, @checkConflicts@, @start@
* used only for basic scripts outside of the pipeline, e.g., _source:trunk/appion/bin/makeSnapshots.py_, _source:trunk/appion/bin/ApDogPicker.py_
* write a log file
* running statistics
h4. appionScript
* source:trunk/appion/appionlib/appionScript.py
* Most common function class used 68 programs in appion, e.g., _source:trunk/appion/bin/uploadStack.py_, _source:trunk/appion/bin/subStack.py_, and _source:trunk/appion/bin/maxlikeAlignment.py_
* based on basicScript, but
** adds database connection to log information about run
** adds default commandline options, such as @--runname@, @--commit/--no-commit@, @--rundir@, @--projectid@, and @--description@
h4. appionLoop2
* source:trunk/appion/appionlib/appionLoop2.py
* based on appionScript but loops over all images in a session
** adds default commandline options, such as @--sessionname@, @--preset@, @--limit@, @--continue@, @--shuffle@, and @--no-rejects@
** requires @--runname@ to be defined
* ideal when the same function needs to be run on all images, e.g. ACE
* used in 15 programs, e.g., _source:trunk/appion/bin/pyace.py_, _source:trunk/appion/bin/pyace2.py_, and _source:trunk/appion/bin/makestack2.py_
h4. filterLoop
* source:trunk/appion/appionlib/filterLoop.py
* based on appionLoop2 but add low pass, high pass, plane regression and other filters
* used in only two functions, manualmask.py and _source:trunk/appion/bin/jpgmaker.py_ (a program to make jpeg cache images of the session)
h4. particleLoop2
* source:trunk/appion/appionlib/particleLoop2.py
* based on filterLoop but adds particle picking capabilies
** creates the jpeg with the circles
** uploads particle picks to the database
* used in 7 different particle pickers, e.g., _source:trunk/appion/bin/manualpicker.py_, _source:trunk/appion/bin/tiltAutoAligner.py_ and _source:trunk/appion/bin/templateCorrelator.py_
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h2. Organization of the PHP programs
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h2. Create a program from scratch
* Problem statement: I have program X that I want to put into the pipeline:
** EMAN 2d alignment, "refine2d.py":http://blake.bcm.tmc.edu/eman/eman1/progs/refine2d.py.html or "classalign2":http://blake.bcm.tmc.edu/eman/eman1/progs/classalign2.html
** Bsoft program, nothing really any good
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h2. Create a program, database structure, and report pages from scratch (if time)
* 3D MSA?