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2010 Appion Developer Workshop » History » Version 6

Neil Voss, 06/08/2010 10:15 AM

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h1. 2010 Appion Developer Workshop
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h2. Setting up a development enviroment
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h4. Subversion
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<pre>
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svn checkout http://emg.nysbc.org/svn/myami/trunk/ myami/
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</pre>
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h4. Sinedon.cfg
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At AMI, you do not normally need a sinedon.cfg file, but if you have your own testing environment you will need one.
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h4. Web page
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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/
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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
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* Problem statement: Add student's T distribution to maxlike alignment, see #552
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* Goal: allow user to use the @-student@ option for maxlike alignment using a radio button
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* Steps to implement:
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*# add feature to python code
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*## add command line input
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*## check flag to add to xmipp program
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*## insert value into database
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*# add feature to web page
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*## add radio button to web page
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*## add help message
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*## receive variable from $_POST
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*## check if value is valid
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*## add flag to command line
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h2. Add an output directory to hierarchical classification
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* You cannot change the directory if the filesystem is full.
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h2. Organization of the Python programs
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We have two major folders in the appion folder:
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* appionlib: contains libraries, a collection of common functions that are needed by more than one python program, e.g., ssnrResolution, averageStack, and lowPassFilter.
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* bin: contains the programs that take command line input, e.g., makestack2.py, templateCorrelator.py, maxlikeAlignment.py
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Other useful directories:
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* pyami: a collection of common functions to both appion and leginon, save MRC file, save SPIDER file, etc.
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h2. Most important python files:
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h3. Database mapping file
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* source:trunk/appion/appionlib/appiondata.py: describes how the database is put together, if you need to add a new column go here
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.bq see also source:trunk/leginon/leginondata.py and source:trunk/leginon/projectdata.py
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h3. Appion Script hierarchy
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h4. basicScript
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* source:trunk/appion/appionlib/basicScript.py
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* contains all the base functions: @setupParserOptions@, @checkConflicts@, @start@
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* used only for basic scripts outside of the pipeline, e.g., _source:trunk/appion/bin/makeSnapshots.py_, _source:trunk/appion/bin/ApDogPicker.py_
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* write a log file
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* running statistics
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h4. appionScript
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* source:trunk/appion/appionlib/appionScript.py
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* 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_
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* based on basicScript, but 
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** adds database connection to log information about run
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** adds default commandline options, such as --runname, --commit, --
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*** source:trunk/appion/appionlib/appionLoop2.py
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**** source:trunk/appion/appionlib/filterLoop.py
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***** source:trunk/appion/appionlib/particleLoop2.py
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h2. Organization of the PHP programs
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h2. Create a program from scratch
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* Problem statement: I have program X that I want to put into the pipeline:
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** 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
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** Bsoft program, nothing really any good
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h2. Create a program, database structure, and report pages from scratch (if time)
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* 3D MSA?