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¶

2010 ADW/Add a new option to a program

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Organization of the Python programs¶

2010 ADW/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: 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

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

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

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)

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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Organization of the PHP programs¶

2010 ADW/Organization of the PHP programs

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Create a program from scratch¶

2010 ADW/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?