plotData.m

% plotData.m
% 
% uses 
%           Data - 2-D array of data for all channels
%       metaData - a structure that contains location

%  return full data set (no decimation);scale into 
%  physical units (but no other filter corrections applied)
decFac = 1; 
scale = 1; %if scale == 1 data are returned with units of nT and mV
           %   note: not divided by dipole length!
%   tUnits = time units for labeling time series plots
%     other choices are 'Seconds','Minutes','Days'
tUnits = 'Hours';
%   Number of Hours (more generally, tUnits) to plot on one pag3e
nTunits = 24;
%   Assumed sampling rate (used to calculate number of points in
%   the plotting window only ... should recompute after reading file)

% *******************************************************************
% [y,SysTF,dt,t0,ch,sta,error] = readTSnims(FileNames,decFac,scale);
%
% The code below now replaces readTSnims

%  these are now hard-coded for NIMS
nch = 5;
ch = ['Hx  ';'Hy  ';'Hz  ';'Ex  ';'Ey  '];
freq = [8,1e-5];

dt = metaData.dt;
STA = metaData.runID;
DateStart = istime(metaData.startDate,metaData.startTime);
if isempty(DateStart)
    disp('Unable to determine start time from the metaData');
end
DateZero = [DateStart(1) 1 1 0 0 0];
%  compute relative starting scan number
dt = dt*decFac;
%  here t0 is in samples, not seconds
t0 = round((datenum(DateStart)-datenum(DateZero))*24*3600/dt);
%   convert t0 to seconds
t0 = t0*dt;
[SysTF] = setUnitSysTF(nch,freq);

% create a temporary copy of the Data !!!!!
y = Data;

if isfield(metaData,'gainApplied') && isfield(metaData,'gain_char')
    if ~metaData.gainApplied
        % gain H(igh) or L(ow) or E(X) high or E(Y) high
        if strcmp(metaData.gain_char,'L')
            disp('Applied software gain of 10 to low gain Ex and Ey data');
            y(4,:) = 10 * y(4,:);
            y(5,:) = 10 * y(5,:);
        elseif strcmp(metaData.gain_char,'X') % E(X) high
            disp('Applied software gain of 10 to low gain Ey data');
            y(5,:) = 10 * y(5,:);
        elseif strcmp(metaData.gain_char,'Y') % E(Y) high
            disp('Applied software gain of 10 to low gain Ex data');
            y(4,:) = 10 * y(4,:);
        end
    end
end

% insert the missing data flags
if isfield(metaData,'gapsFilled') && isfield(metaData,'gaps')
    if ~metaData.gapsFilled && metaData.ngaps > 0
        len = metaData.gaps.len;
        ind = metaData.gaps.ind;
        missingdataflag = NaN;
        y = fillDataGaps(y,ind,len,missingdataflag);
    end
end

if decFac > 1
    %  decimate
    y = y(:,1:decFac:end);
end
if scale
    if isfield(metaData,'scaling')
        scaling = metaData.scaling;
        for k = 1:nch
            y(k,:) = y(k,:)*scaling(k);
        end
    else
        %  scale to nT, mV
        gain=200;
        Ecount=8.192*1e3/(256*256*256)/gain;
        y(1:3,:) = y(1:3,:)/100;
        y(4:5,:) = y(4:5,:)*Ecount;
    end
end

clear sta
for ic = 1:nch
    sta(ic,:) = char(STA);
end
% *******************************************************************

%   initialize structure "plotStart" using dt obtained from metaData
[plotStart] = plotSetup(tUnits,nTunits,dt);
   
%  reset nPw (# of points to plot initially on one page) now
%   that dt has been read from data file  (NOTE: dt returned
%   by readTSnims accounts for subsampling by a factor of decFac)
nPw = round(plotStart.tFac*plotStart.nTunits/dt);
plotStart.nPw = min(nPw,size(y,2));

%   Initialize cell arrays for data, time series metadata, 
%     window metadata, etc.
TSc = {};
TSp = {};
TSd = {};
TSw = {};
TSdata = {};
TSfigInd = zeros(100,1);

%   set up TSd
TSd1 = setTSd(y,t0,dt,ch,sta,SysTF);
TSd1.sta = char(TSd1.sta);
TSdata0 = (TSd1.range(:,1)+TSd1.range(:,2))/2;
rng = (TSd1.range(:,2)-TSd1.range(:,1))/2;
rng = plotStart.rangeScale*rng;
TSd1.range(:,1:2) = [ TSdata0-rng TSdata0+rng];

%   are these needed???
TSd1.DataDir = '';
TSd1.arrayID = '';

%   copy into cell arrays
iA = 1;
TSdata{iA} = y;
TSd{iA} = TSd1;

[hTSw,TSw1] = plotTSwin(TSd{1},plotStart);
TSfigInd(hTSw.Number) = 1;
i0 = TSw1.i0; i1 = TSw1.i1; di = TSw1.di;
yFac = TSw1.yFac;
ddt = TSd{1}.dt/TSw1.tFac;
t0 = (TSd{1}.t0)*(1-TSw1.t0Eq0)/TSw1.tFac;
I = (i0:di:i1);
[TSw1] = plotPage(ddt*I+t0,...
                yFac*TSdata{1}(:,I),...
                TSw1,TSd{1},1);
TSw{1} = TSw1;