Appion

h1. Organization of the PHP programs

* Location:

** /myami/myamiweb/processing

* Sub Folders:

** @inc@ — include directory, common libraries like @appionlib@

** @js@ — javascript directory, contains @help.js@ the help pop-up window text

** @img@ — image director, contains images like program logos (e.g., EMAN, Appion, Spider) and check, cross, and ext icons for image assessor

** @css@ — style sheets, custom look and feel of website, usually not modified

* The include (@inc@) folder

** @appionloop.inc@ — contains the common interface for all appionLoop programs (CTF estimators, Particle pickers, and Make Stack)

** -@euler.inc@- — depricated on the fly Euler plot generation script, was way too slow moved to python

** @menuprocessing.php@ — a single, giant function that generates the menu on the left side of all appion pages

** @particledata.inc@ — collection of all database queries, e.g., getStackIds(), getParticlesFromImageId(), getPixelSizeFromImgId(), or getStackIdFromReconId()

** @processing.inc@ — functions that are common to all Appion pages, e.g., processing_header(), referenceBox(), submitAppionJob(), getProjectId()

** @summarytables.inc@ — provides summary tables that are common on many pages, e.g., stacksummarytable(), alignstacksummarytable(), and modelsummarytable()

* Important base scripts:

** @checkAppionJob.php@ — follow the progress of the job (common to all scripts, except reconstructions, see @checkRefineJobs.php@)

** @index.php@ — provides the final report with methods section for any exemplar reconstructions

** @config.php@ — the customization file for the 

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** @viewstack.php@ — the famous stack viewer

* Ideal flow for a job process:

** _select program_ (e.g., @selectParticleAlignment.php@) — a selection page for each program that provides a detailed description to help user decide which on to use

** _run Appion script_ (e.g., @runDogPicker.php@) — setup parameters and run the program

** @checkAppionJob.php@ — follow the progress of the job (common to all scripts, except reconstructions, see @checkRefineJobs.php@)

** _process summary_ (e.g., @stackhierarchy.php@) — show all runs of that process type, e.g., stacks

** _process report_ (e.g., @stackreport.php@ — report on a particular run of that process type, e.g. stack id 12