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