ArrayManagerNotes

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ArrayManager 
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function [] = ArrayManager(Survey,maxSites)

Usage: [] = ArrayManager(Survey,maxSites)

  Survey gives the path (relative to MTprocHome, which should be set
     as an environment variable before calling) of the specfic survey 
     being processed (e.g., "Yellowstone").  This is the directory 
     which contains subdirectories data, XML, original, MT, FC, tmp, etc.

  maxSites is an optional variable that is passed to dataTimes;
     this is used to control how many sites are

Array Manager calls these routines (all in ArrayManager): 

  [DataFiles,metaData] = listFromXML(XMLdir) to generate a list of available run files
     and a structure containing all associated metadata.
     This is generated from the *.xml files, which ArrayManager now 
     assumes are in a single directory, namely XMLdir = <Survey>/XML

  [NIMSinfo] = mkNIMSinfo(Survey,metaData);

  [plotStart] = plotSetup(tUnits,nTunits,decFac);

  [] = dataTimes(DataFiles,NIMSinfo,plotStart,maxSites);


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[DataFiles,metaData] = listFromXML(XMLdir);
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Generates a list of data files names (runs), and the
corresponding metadata from list of xml files in XMLdir

calls: xml_read (xml_io_tools), cleanMetaData (SS/NIMSread)

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[NIMSinfo] = mkNIMSinfo(Survey,metaData)
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This is a new version of makeNIMSinfo; only used for
display of what has been done (and bad record segments)
in ArrayManager.  Input metaData structure is used to generate
the list of runs to check for existence of *.bin, *.sp, *.f5, *.br
files.  If bad record (*.br) files exist for a run they are read, 
and the list of marked segments is returned in the corresponding
NIMSinfo cell.

calls: rdBadRec (TSplot)

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function dataTimes(DataFiles,NIMSinfo,plotStart,Tlims);
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dataTimes initializes arrayManager interface

  Inputs:
         DataFiles = cell array of all data file names
         NIMSinfo = cell array of information for each
                     data file, including metadata structure
         plotStart = structure used to initialize time series
                     plotting
         Tlims = optional argument used to allow plotting
             only a fraction of the available files:
             --> if Tlims is not present, display all files
             --> if Tlims is a single integer, display this
                   many sites, starting from the first in time
             --> if Tlims is a pair of real numbers,
                    use these as time limits (in days) for
                    choosing data files to display

calls: uniqueSites, sortSites, and creates callbacks to  dataTimesCB
      (all in ArrayManager)

if ZFILES = 1 (set inside dataTimes) a list of *.zrr files available
   in  ../MT is generated for each site.  Not clear how useful this
   now is, as clicking the site name button now opens a browse window
   in dataDir/MT, listing all *.zrr files available for the site
    (and easily enabling plotting)

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dataTimesCB
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Callback script for dataTimes interface

Calls: Routines in TSplot (readTSnims, setTSd, plotStart, plotPage,
            plotTSwin  (+ routines in plotTS called by these)

       Routines in EMTF/matlab : apresplt (+ routines in EMTF/matlab
            called by these)

       Other routines in ArrayManager: shiftPlotStart, 
              ComputeTF, EnableButtons, uniqueSites, dataTimes

Also uses "unix" to execute programs in binDir: dnff

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function [Sites] = uniqueSites(DataFiles);
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Parse data file list to get a cell array containing: 
  --> list of unique site names
  --> list of data file suffixes for each site+indices into
        DataFiles list for all files associated with the site

Usage:  [Sites] = uniqueSites(DataFiles);

calls: standard matlab only
   
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function [SitesOrdered,UseSite] = sortSites(Sites,DataFiles,Tlims)
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Sort sites by start time of first data file associated with that
site.

Usage: [SitesOrdered,UseSite] = sortSites(Sites,DataFiles,Tlims);
    If optional third argument Tlims is present, also returns
    an indicator array, with UseSite = 1 iff any segment for this
    site overlaps time limits given in Tlims.  If Tlims
    is not input, UseSite is identically 1 for all sites

calls: standard matlab only

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function [] = shiftPlotStart(data,LoadedDataFiles,options)
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Extract overlapping section of array data for channels ch1, ch2
(fields in input structure "options"); intialize ShiftInfo,
a structure containing the two data channels + other information

calls: shiftPlot to plot data (and attach ShiftInfo to plot as UserData)

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function [] = shiftPlot(ShiftInfo)
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Using two channels of time series + shifts in ShiftInfo structure,
shift and plot time series; all variables need to be put into
structure shiftInfo before calling

Usage: shiftPlot(ShiftInfo)

calls: nothing but standard matlab functions; creates callbacks to
shiftPlotCB.m

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shiftPlotCB
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Callback script for ShiftPlot.  

Calls: shiftRePlot.m, shiftPlotStart.m

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shiftRePlot
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Replots shifted data.

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function [] = ComputeTF(SelectedDataFiles,Task);
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Creates interface for RR, SS or MMT processing
  using selected data files to initialize list of files;
Control file names are now hard-coded (but can be
   edited in the interface).

       calls :  MakeTFoutFile

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ComputeTF_CB
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Callback script for ComputeTF.

Calls: Other routines in ArrayManager: ComputeTF

       calls :  rdBadRec, wrBadRec (in TSplot at present ...  
           should these be?)

Uses "unix" to execute programs in binDir: tranmtlr, multmtrn

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function [outName] = MakeTFoutFile(Files,Task);
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Makes output file names for transfer functions, using
list of input file names for local and remote sites.
Input argument Task defines SS, RR, MMT case

Usage : [outName] = MakeTFoutFile(Files,Task);

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function [] = updateSP(Survey,metaData)
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Goes through list of run files in input structure metaData,
and checks for presence of corresponding system parameter
file in directory <Survey>/SP.  If not, the *.sp file is generated.
If argument metaData is not provided when calling, the metaData
structure is generated using contents of <Survey>/XML.

Calls writeSp.m (SS/NIMSread) and listFromXML (ArrayManager)

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function [] = updateFC(Survey,metaData,DataFileSuffix)
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Runs dnff for all data files *.bin in Survey/data for which there are
binary data (*.bin) and system parameter files (*.sp) 
in Survey/daa and Survey/SP respectively.  Uses the list of available 
run files stored in cell array metaData.  Optional argument DataFileSuffix 
can be used to change data file names from default *.bin to some other
suffix (e.g., *.dbn, to run dnff on decimated files).  If second argument
(metaData) is missing this generates the file list (i.e., metaData)
by calling listFromXML

Calls: listFromXML (ArrayManager)

Executes binDir/dnff through system command