Contents

 Database and batch processing functions for FMAToolbox.

 These functions can be used to perform batch data processing and store data
 and figures into one or more databases.

 Batch Processing

 Batch processing is useful if you need to repeatedly perform a given analysis
 on different data sets. This can be achieved using <a href="StartBatch">StartBatch</a>, which will
 repeatedly run a given 'batch' function on each data set. <a href="StartBatch">StartBatch</a> provides
 a number of advanced features such as error resilience, error logging, delayed
 processing, etc. The 'batch' function typically performs computations and
 stores the results in a database using <a href="DBAddVariable">DBAddVariable</a> and/or <a href="DBAddFigure">DBAddFigure</a>. Once
 the batch is completed, the results can be retrieved from the database using
 <a href="DBGetValues">DBGetValues</a>. Different sets of results can be combined using <a href="DBMatchValues">DBMatchValues</a>.

 Database Management

 Databases can be private and run on the local machine, or central databases
 running on a remote server and shared between many different users. Data and
 figures can be tagged (experiment ID, name, comments) so you can later search
 specific data subsets. Programs and parameters used to generate the data can
 also be stored for reference. Figures can be stored as matlab fig files
 and/or PNG images, and be later exported as HTML galleries which are easy to
 share with other investigators.

 Because variables can hold large amounts of data, one needs to set an upper
 limit to the size that can be stored in the actual database. Beyond this limit,
 the data must be stored to disk, and the database will contain a reference to
 its location. This will be transparently handled by the database functions.
 You must however indicate the directory where matlab files should be stored,
 and make sure it is shared across the network and writable by all users who
 are expected to use the database. This can typically be done by adding a line
 in the startup.m file, for instance:

   global SETTINGS;
   SETTINGS.dbExternalStoragePath = '/mnt/matlab_databases';

 Optionally, the size limit for external storage (64KiB by default) can also
 be customized:

   SETTINGS.DBAddVariable.maxSize = 10*1024*1024;  % limit of 10MiB

 Notes

  The database backend is MySQL and the interface is provided by the <a href="http://sourceforge.net/projects/mym/">mYm</a>
  toolbox by Y. Maret (EPFL, Lausanne, Switzerland).

  Although not required, installing <a href="http://sites.google.com/site/oliverwoodford/software/export_fig">export_fig</a> by O. Woodford (Oxford
  University, England) will yield better PNG images.

 Batch processing

   StartBatch            - Start a new batch job.
   ShowBatch             - Show data sets in a batch job.
   GetBatch              - Get batch job output.
   BatchInfo             - Get batch job information.
   CancelBatch           - Cancel batch job.
   CleanBatches          - Delete completed batch jobs from memory.
   DebugBatch            - Assign variables to help debug a batch job.
   Store                 - Store variable in memory to avoid redundant computations.
   Recall                - Recall variable from memory to avoid redundant computations.

 Database management.

   DBCreate              - Create a new database (requires admin rights)
   DBCreateTables        - Create tables for variables and figures
   DBConnect             - Connect to the database server
   DBExternalStoragePath - Get path for database external storage space
   DBUse                 - Set (or determine) current database
   DBList                - List existing databases
   DBDuplicate           - Duplicate database.
   DBMerge               - Merge databases.
   DBRemove              - Remove database.

 Storing data/figures.

   DBAddFigure           - Store a figure (+ tags, programs, etc.)
   DBAddVariable         - Store a variable (+ tags, programs, etc.)
   DBRemoveFigures       - Remove all figures that match given criteria.
   DBRemoveVariables     - Remove all variables that match given criteria.

 Searching data/figures.

   DBGetFigures          - Get all figures that match given criteria
   DBGetValues           - Group values for all variables that match given criteria
   DBMatchValues         - Match values for two different sets of variables
   DBGetVariables        - Get all variables that match given criteria
   DBListFigures         - List figures matching certain criteria.
   DBListVariables       - List variables matching certain criteria.

 Exporting figures.

   DBExportGallery       - Create an HTML gallery from a set of figures