2010 Appion Developer Workshop¶

Setting up a development enviroment¶

Subversion¶

svn checkout http://emg.nysbc.org/svn/myami/trunk/ myami/

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.

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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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:
  1. add feature to python code
     1. add command line input
     2. check flag to add to xmipp program
     3. insert value into database
  2. add feature to web page
     1. add radio button to web page
     2. add help message
     3. receive variable from $_POST
     4. check if value is valid
     5. add flag to command line

Add an output directory to hierarchical classification¶

• You cannot change the directory if the filesystem is full.

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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.

Most important python files:¶

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

Appion Script hierarchy¶

basicScript

• source:trunk/appion/appionlib/basicScript.py
  contains all the base functions:
• write a log file *

• source:trunk/appion/appionlib/appionScript.py
  • source:trunk/appion/appionlib/appionLoop2.py
    • source:trunk/appion/appionlib/filterLoop.py
      • source:trunk/appion/appionlib/particleLoop2.py
        

Organization of the PHP programs¶

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Create a program from scratch¶

• Problem statement: I have program X that I want to put into the pipeline:
  • EMAN 2d alignment, refine2d.py or classalign2
  • Bsoft program, nothing really any good

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

• 3D MSA?