Appion

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/

______

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.

______

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_

______

h2. Organization of the PHP programs

______

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

______

h2. Create a program, database structure, and report pages from scratch (if time)

* 3D MSA?