tfile

PURPOSE ^

tfile reads the data from an RDI ASCII output file and puts the

SYNOPSIS ^

function [A]=tfile(fullName,screenData,ignoreBS);

DESCRIPTION ^

 tfile reads the data from an RDI ASCII output file and puts the
 data in a Matlab data structure with major groups of:
 Sup - supporing data
 Wat - water data
 Nav - navigation data including GPS.
 Sensor - Sensor data
 Q - discharge related data

 The data can be screened (screenData=1) so that invalid data are set to
 nan or data reflect strictly the ASCII output file (screenData=0). If
 screenData=0 then the data reflect the ASCII file and -32768 and other
 RDI defined values are left in the data structure. If screenData=1 the
 RDI defined values are trapped and set to nan for many variables.

 WinRiver II will sometimes put a $ instead of the correct values for
 intensity of backscatter. Setting ignoreBS=1 will skip decoding the
 intensity of backscatter data to compensate for this bug in WR2.

 David S. Mueller, USGS, Office of Surface Water
 Frank L. Engel, USGS, Illinois Water Science Center

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [A]=tfile(fullName,screenData,ignoreBS);
0002 % tfile reads the data from an RDI ASCII output file and puts the
0003 % data in a Matlab data structure with major groups of:
0004 % Sup - supporing data
0005 % Wat - water data
0006 % Nav - navigation data including GPS.
0007 % Sensor - Sensor data
0008 % Q - discharge related data
0009 %
0010 % The data can be screened (screenData=1) so that invalid data are set to
0011 % nan or data reflect strictly the ASCII output file (screenData=0). If
0012 % screenData=0 then the data reflect the ASCII file and -32768 and other
0013 % RDI defined values are left in the data structure. If screenData=1 the
0014 % RDI defined values are trapped and set to nan for many variables.
0015 %
0016 % WinRiver II will sometimes put a $ instead of the correct values for
0017 % intensity of backscatter. Setting ignoreBS=1 will skip decoding the
0018 % intensity of backscatter data to compensate for this bug in WR2.
0019 %
0020 % David S. Mueller, USGS, Office of Surface Water
0021 % Frank L. Engel, USGS, Illinois Water Science Center
0022 
0023 %% Initial Scan of File
0024 %  Initial scan required to preallocate arrays. All ensembles must be
0025 %  scanned because RiverRay has variable number of bins.
0026 
0027 % Turn off LaTex interpreter to avoid subscripts in filenames containing _
0028 set(0, 'DefaulttextInterpreter', 'none');
0029 fid=fopen(fullName);
0030 % clc
0031 % disp(['Scanning Data File: ' fullName]);
0032 idx=find(fullName=='\',1,'last');
0033 fileName=fullName(idx:end);
0034 
0035 % Display waitbar
0036 waitmessage=['Reading ' fileName];
0037 hwait=waitbar(0,waitmessage);
0038 
0039 % Scan Fixed Leader.
0040 lineIn=fgetl(fid);
0041 lineIn=fgetl(fid);
0042 lineIn=fgetl(fid);
0043 
0044 % Count lines in file.
0045 k=1;
0046 fileEnd=0;
0047 
0048 % Loop required to determine number of variable leader lines due to bug
0049 % in ASCII output from WinRiver II for reference set to NONE.
0050 check=0;
0051 linecount=0;
0052 while check==0
0053     lineIn=fgetl(fid);
0054     idxBT=strfind(lineIn,'BT');
0055     idxGGA=strfind(lineIn,'GGA');
0056     idxVTG=strfind(lineIn,'VTG');
0057     idxNone=strfind(lineIn,'NONE');
0058     check=nansum([idxBT idxGGA idxVTG idxNone]);
0059     linecount=linecount+1;
0060 end
0061 
0062 % Read number of bins in 1st ensemble
0063 [bins(k),~,~,~,~,~]=strread(lineIn,'%f %s %s %s %f %f',1);
0064 
0065 % Skip bin data
0066 dummy=textscan(fid, '%s %*[^\n]',bins(k));
0067 
0068 % Set number of leader lines to get to number of bins in variable
0069 % leader
0070 leaderlines=linecount-1;
0071 
0072 % Begin loop to determin number of ensembles and maximum number of bins
0073 % for preallocating arrays. Looping through the entire file is required
0074 % because RiverRay data have variable numbers of bins in each ensemble.
0075 while fileEnd==0
0076     dummy=textscan(fid, '%s %*[^\n]',leaderlines);
0077     if length(dummy{1})>1
0078         k=k+1;
0079         bins(k)=cell2mat(textscan(fid, '%f %*[^\n]',1));
0080         dummy=textscan(fid, '%s %*[^\n]',bins(k));
0081     end
0082     fileEnd=feof(fid);
0083 end
0084 
0085 % Update waitbar
0086 waitbar(0.1);
0087 %% Complete scan of input file.
0088 % Close input file and report that the initial scan is completed.
0089 fclose(fid);
0090 % disp('Scan Complete');
0091 
0092 %% Initialize Data Structure
0093 % Preallocates arrays based on information from initial scan.
0094 
0095 % This is the number of ensembles actually contained in the input file.
0096 noe=k;
0097 bins=max(bins);
0098 
0099 % Initialize Data Structure.
0100 Sup=struct( 'absorption_dbpm',nan(noe,1),...
0101     'bins',nan(noe,1),...
0102     'binSize_cm',nan(1),...
0103     'nBins',nan(1),...
0104     'blank_cm',nan(1),...
0105     'draft_cm',nan(1),...
0106     'ensNo',nan(noe,1),...
0107     'nPings',nan(1),...
0108     'noEnsInSeg',nan(noe,1),...
0109     'noe',nan(1),...
0110     'note1',blanks(80),...
0111     'note2',blanks(80),...
0112     'intScaleFact_dbpcnt',nan(noe,1),...
0113     'intUnits',repmat(blanks(5),noe,1),...
0114     'vRef',repmat(blanks(4),noe,1),...
0115     'wm',nan(1),...
0116     'units',repmat(blanks(2),noe,1),...
0117     'year',nan(noe,1),...
0118     'month',nan(noe,1),...
0119     'day',nan(noe,1),...
0120     'hour',nan(noe,1),...
0121     'minute',nan(noe,1),...
0122     'second',nan(noe,1),...
0123     'sec100',nan(noe,1),...
0124     'timeElapsed_sec',nan(noe,1),...
0125     'timeDelta_sec100',nan(1));
0126 
0127 Wat=struct( 'binDepth',nan(bins,noe),...
0128     'backscatter',nan(bins,noe,4),...
0129     'vDir',nan(bins,noe),...
0130     'vMag',nan(bins,noe),...
0131     'vEast',nan(bins,noe),...
0132     'vError',nan(bins,noe),...
0133     'vNorth',nan(bins,noe),...
0134     'vVert',nan(bins,noe),...
0135     'percentGood',nan(bins,noe));
0136 
0137 Nav=struct( 'bvEast',nan(noe,1),...
0138     'bvError',nan(noe,1),...
0139     'bvNorth',nan(noe,1),...
0140     'bvVert',nan(noe,1),...
0141     'depth',nan(noe,4),...
0142     'dsDepth',nan(noe,1),...
0143     'dmg',nan(noe,1),...
0144     'length',nan(noe,1),...
0145     'totDistEast',nan(noe,1),...
0146     'totDistNorth',nan(noe,1),...
0147     'altitude',nan(noe,1),...
0148     'altitudeChng',nan(noe,1),...
0149     'gpsTotDist',nan(noe,1),...
0150     'gpsVariable',nan(noe,1),...
0151     'gpsVeast',nan(noe,1),...
0152     'gpsVnorth',nan(noe,1),...
0153     'lat_deg',nan(noe,1),...
0154     'long_deg',nan(noe,1),...
0155     'nSats',nan(noe,1),...
0156     'hdop',nan(noe,1));
0157 
0158 Sensor=struct(  'pitch_deg',nan(noe,1),...
0159     'roll_deg',nan(noe,1),...
0160     'heading_deg',nan(noe,1),...
0161     'temp_degC',nan(noe,1));
0162 
0163 Q=struct(   'endDepth',nan(noe,1),...
0164     'endDist',nan(noe,1),...
0165     'bot',nan(noe,1),...
0166     'end',nan(noe,1),...
0167     'meas',nan(noe,1),...
0168     'start',nan(noe,1),...
0169     'top',nan(noe,1),...
0170     'unit',nan(bins,noe),...
0171     'startDepth',nan(noe,1),...
0172     'startDist',nan(noe,1));
0173 
0174 Sup.noe=noe;
0175 
0176 %% Read File and Store Data
0177 % All data are read and stored in preallocated data structures
0178 
0179 % Reopen File for Reading
0180 fid=fopen(fullName);
0181 % disp('Reading Data File');
0182 
0183 % Read Fixed Leader
0184 Sup.note1=fgetl(fid);
0185 Sup.note2=fgetl(fid);
0186 C = textscan(fid,'%u %u %u %u %u %u %u',1);
0187 [...
0188     Sup.binSize_cm,...
0189     Sup.blank_cm,...
0190     Sup.draft_cm,...
0191     Sup.nBins,...
0192     Sup.nPings,...
0193     Sup.timeDelta_sec100,...
0194     Sup.wm] = deal(C{:});
0195 
0196 % Read Variable Leader
0197 waitstep = floor(noe/100);
0198 for n = 1:noe;
0199     % Update the waitbar only on whole percents
0200     if ~mod(n, waitstep) || n==noe
0201         waitbar(0.1+n/noe);
0202     end
0203     C = textscan(fid,'%u %u %u %u %u %f %f %u %u %f %f %f %f',1);
0204     [...
0205         Sup.year(n),...
0206         Sup.month(n),...
0207         Sup.day(n),...
0208         Sup.hour(n),...
0209         Sup.minute(n),...
0210         Sup.second(n),...
0211         Sup.sec100(n),...
0212         Sup.ensNo(n),...
0213         Sup.noEnsInSeg(n),...
0214         Sensor.pitch_deg(n),...
0215         Sensor.roll_deg(n),...
0216         Sensor.heading_deg(n),...
0217         Sensor.temp_degC(n)] = deal(C{:});
0218     
0219     % Required logic to account for bug in ASCII output when the
0220     % reference is set to NONE.
0221     C = textscan(fid,'%f %f %f %f %f %f %f %f %f %f %f %f',1);
0222     if sum(isnan([C{:}]))==0
0223         [...
0224             Nav.bvEast(n),...
0225             Nav.bvNorth(n),...
0226             Nav.bvVert(n),...
0227             Nav.bvError(n),...
0228             Nav.dsDepth(n),...
0229             Nav.altitude(n),...
0230             Nav.altitudeChng(n),...
0231             Nav.gpsVariable(n),...
0232             Nav.depth(n,1),...
0233             Nav.depth(n,2),...
0234             Nav.depth(n,3),...
0235             Nav.depth(n,4)] = deal(C{:});
0236         
0237         C = textscan(fid,'%f %f %f %f %f',1);
0238         [...
0239             Nav.length(n),...
0240             Sup.timeElapsed_sec(n),...
0241             Nav.totDistNorth(n),...
0242             Nav.totDistEast(n),...
0243             Nav.dmg(n)] = deal(C{:});
0244         
0245         C = textscan(fid,'%f %f %f %f %f',1);
0246         [...
0247             Nav.lat_deg(n),...
0248             Nav.long_deg(n),...
0249             Nav.gpsVeast(n),...
0250             Nav.gpsVnorth(n),...
0251             Nav.gpsTotDist(n)] = deal(C{:});
0252     else
0253         [...
0254             Nav.dsDepth(n),...
0255             Nav.altitude(n),...
0256             Nav.altitudeChng(n),...
0257             Nav.gpsVariable(n),...
0258             Nav.depth(n,1),...
0259             Nav.depth(n,2),...
0260             Nav.depth(n,3),...
0261             Nav.depth(n,4)]=deal(C{1:8});
0262         
0263         C = textscan(fid,'%f %f %f %f %f %f',1);
0264         [...
0265             dummy,...
0266             Nav.lat_deg(n),...
0267             Nav.long_deg(n),...
0268             Nav.gpsVeast(n),...
0269             Nav.gpsVnorth(n),...
0270             Nav.gpsTotDist(n)] = deal(C{:});
0271     end
0272     
0273     % Extract HDOP and number of satellites from gpsVariable
0274     if Nav.gpsVariable(n)>0
0275         Nav.hdop(n)=floor(Nav.gpsVariable(n))./10;  %/10 added 3-12-10 by PRJ (according to TRDI WRII manual)
0276         Nav.nSats(n)=(Nav.gpsVariable(n)-Nav.hdop(n).*10).*100;
0277     end;
0278     
0279     C = textscan(fid,'%f %f %f %f %f %f %f %f %f',1);
0280     [...
0281         Q.meas(n),...
0282         Q.top(n),...
0283         Q.bot(n),...
0284         Q.start(n),...
0285         Q.startDist(n),...
0286         Q.end(n),...
0287         Q.endDist(n),...
0288         Q.startDepth(n),...
0289         Q.endDepth(n)] = deal(C{:});
0290     
0291     C = textscan(fid,'%f %s %s %s %f %f',1);
0292     [...
0293         Sup.bins(n),...
0294         Sup.units,...
0295         Sup.vRef,...
0296         Sup.intUnits,...
0297         Sup.intScaleFact_dbpcnt(n),...
0298         Sup.absorption_dbpm(n)]= deal(C{:});
0299     
0300     % Read Profile Data.
0301     
0302     
0303     % Logic to account for WR2 bug that puts $ in for intensity or
0304     % backscatter.
0305     if ignoreBS==0
0306         C = textscan(fid,'%f %f %f %f %f %f %f %f %f %f %f %f %f',Sup.bins(n));
0307         [...
0308             Wat.binDepth(1:Sup.bins(n),n),...
0309             Wat.vMag(1:Sup.bins(n),n),...
0310             Wat.vDir(1:Sup.bins(n),n),...
0311             Wat.vEast(1:Sup.bins(n),n),...
0312             Wat.vNorth(1:Sup.bins(n),n),...
0313             Wat.vVert(1:Sup.bins(n),n),...
0314             Wat.vError(1:Sup.bins(n),n),...
0315             Wat.backscatter(1:Sup.bins(n),n,1),...
0316             Wat.backscatter(1:Sup.bins(n),n,2),...
0317             Wat.backscatter(1:Sup.bins(n),n,3),...
0318             Wat.backscatter(1:Sup.bins(n),n,4),...
0319             Wat.percentGood(1:Sup.bins(n),n),...
0320             Q.unit(1:Sup.bins(n),n)] = deal(C{:});
0321     else
0322         C = textscan(fid,'%f %f %f %f %f %f %f %s %s %s %s %f %f',Sup.bins(n));
0323         [...
0324             Wat.binDepth(1:Sup.bins(n),n),...
0325             Wat.vMag(1:Sup.bins(n),n),...
0326             Wat.vDir(1:Sup.bins(n),n),...
0327             Wat.vEast(1:Sup.bins(n),n),...
0328             Wat.vNorth(1:Sup.bins(n),n),...
0329             Wat.vVert(1:Sup.bins(n),n),...
0330             Wat.vError(1:Sup.bins(n),n),...
0331             dummy,...
0332             dummy,...
0333             dummy,...
0334             dummy,...
0335             Wat.percentGood(1:Sup.bins(n),n),...
0336             Q.unit(1:Sup.bins(n),n)] = deal(C{:});
0337     end
0338     
0339 end % for loop through ensembles
0340 
0341 % Close File
0342 fclose(fid);
0343 % disp('Data Input Complete');
0344 
0345 %% Screen Data
0346 % Screens invalid data replacing them with nan
0347 
0348 % Apply data screening if requested.
0349 if screenData==1
0350     
0351     Wat.vNorth(Wat.vNorth==-32768)=nan;
0352     Wat.vEast(Wat.vEast==-32768)=nan;
0353     Wat.vError(Wat.vError==-32768)=nan;
0354     Wat.vVert(Wat.vVert==-32768)=nan;
0355     Wat.vMag(Wat.vMag==-32768)=nan;
0356     Wat.vDir(Wat.vDir==-32768)=nan;
0357     Wat.percentGood(Wat.percentGood==-32768)=nan;
0358     Wat.backscatter(Wat.backscatter==-32768)=nan;
0359     
0360     
0361     Nav.bvNorth(Nav.bvNorth==-32768)=nan;
0362     Nav.bvEast(Nav.bvEast==-32768)=nan;
0363     Nav.bvError(Wat.vError==-32768)=nan;
0364     Nav.bvVert(Nav.bvVert==-32768)=nan;
0365     Nav.depth(Nav.depth==0)=nan;
0366     Nav.lat_deg(Nav.lat_deg==30000)=nan;
0367     Nav.long_deg(Nav.long_deg==30000)=nan;
0368     Nav.gpsVnorth(Nav.gpsVnorth==-32768)=nan;
0369     Nav.gpsVeast(Nav.gpsVeast==-32768)=nan;
0370     Q.unit(Q.unit==2147483647)=nan;
0371 end;
0372 
0373 % Assign Data to One Structure
0374 A.Sup=Sup;
0375 A.Wat=Wat;
0376 A.Nav=Nav;
0377 A.Sensor=Sensor;
0378 A.Q=Q;
0379 
0380 % Close waitbar
0381 close(hwait);
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