function grplot
% grplot: multiple time series plots of ring width on a page
% grplot;
% Last revised 4-15-99
%
% grplot plots "groups" of ring-width series, several to a page. The plots
% are similar to what used to be produced by the mainframe "pageplot" program.
% Up to eight series can be plotted per page. Annotated at left of each plot
% is the range of ring widths in hundredths of mm (e.g., "2-300" means the smallest and
% largest ring widths are .02 mm and 3.00 mm. Annotated at right is the sequential
% number of the core ring-width series in the source .rwl file, and the core id.
% The user can control which series are plotted and in what order. The default is in
% order as the series are stored in the original .rwl file. A useful option is to select
% ordering by start year of the series. Before running grplot.m, the ring-width series
% must be stored in a .mat file. You can do this by running rwlinp.m on a .rwl file.<P>
%
% The intended use of grplot is as an aid in deciding on the form of the
% growth curve to use in ARSTAN or other standarization programs.
% Low-frequency ring-width fluctuations not shared by different trees can be spotted
% in the plots. If the chronology is supposed to track climate variations,
% it's usually a good idea to select detrending curves that remove such low-frequency
% fluctuations. <P>
%
% grplot can optionally be run in two modes: "single" or "batch". Single mode
% applies to a set of ring-width series from one site. Single mode is most
% interactive (with zoom options) and is the most likely mode. Batch mode applies to
% multiple files of ring-width series, perhaps from several sites. Batch mode is
% not interactive, but is useful if you have to plot series from many sites. In
% batch mode, .ps files, one per site, for later printing and viewing.<P>
%
%*** IN ******************************************************
%
% No input arguments
%
% User prompted for various options, and to point to files for input and
% output
%
%*** OUT *******
%
% No output args.
%
% File output is optional, and consists of one or more postscript (.ps) files, one for
% each input .mat ring-width file. The user can specify the filename in interactive
% mode. In batch mode, the .ps suffix is assigned to the same prefix as the input
% .mat file containing the ring-width file.
%
% In "single" mode you can view the figure windows as the program runs and afterwards.
% In "batch" mode, figure windows are not saved, but are overwritten from on
% ring-width file to ring-width file. But in batch mode, have the plots stored in
% .ps files for later plotting.
%
%*** REFERENCES -- none
%
%*** UW FUNCTIONS CALLED ******************************
%
% eightplt.m - utility function that plots up to 8 sets of axes on page
%
%*** TOOLBOXES NEEDED -- none
%
%*** NOTES *******************************************************8
%
% Modes:
%
% One mode is "single" for a single .mat ring-width file. In this mode, user
% points to the desired .mat file holding the ring-width series. This .mat
% file is created beforehand by running rwlinp.m on a .rwl file (see rwlinp.m).
% Series are plotted up-to-8 per figure window, with zoom capability.
%
% Other mode is "batch", in which the user points to a file that contains filenames
% of several .mat files of ring-width data (corresponding, say, to several sites).
% These files are processed in sequence, and postscript printer files of figure windows
% are produced, one postscript file for each .mat input file.
%
% In either mode, series can be plotted in order as they are stored in the .rwl or
% .mat file, or can be re-ordered in one of two ways:
% 1) from oldest to youngest
% 2) arbitrarily, as indicated by an optional pointer variable. The pointer variable
% is stored in a separate .mat file that the user is prompted to click on.
%
% Plots are annotated with core id and with minimum and maximum ring width
% (hundredths of mm) in the plot window. These values are useful because the y-axis
% is scaled differently from core-to-core to accomodate diffences in growth rates, and
% y-axis tick marks are not labeled.
%
% Requirements for input files:
% .mat ring-width file: contains nms, yrs, X, as created by rwlinp.m
%
% .mat pointer file <optional>: contains a row-cell variable Vselect. Each element
% of Vselect is an n x 8 matrix, where n is the number of figure windows
% to be produced. The integer elements of a row of any given matrix from Vselect
% are pointers to the series to be plotted on a single page. The pointers reference
% series by their order in the .mat storage matrix, as given by the character
% matrix of names (nms). The pointer tells which ring-width
% series to plot and in what order. The col-size of 8 corresponds to the max number
% of series that can be plotted in any figure window. For fewer than 8 plots,
% NaN-fill the rows of the pointer matrix. Example for "single" mode:
% V={[4 6 1 7 2 3 NaN NaN; 12 34 18 9 19 21 5 8]}
% specifies plotting 6 cores in figure on page1 and 8 on page 2. Series will be
% plotted from bottom to top on the page. So, the lowermost plot will be series
% #4, followed by #6, #1, etc.
%
% .txt file <batch mode only> with names of .mat files, one per line. Example:
% shr.mat
% dit.mat
% ketnew.mat
%
% Close any open figure window
close all;
% Get current directory path
pathcurr=[eval('cd') '\'];
%************* What is mode: 'batch' or 'single'? *********
btchmode=questdlg('Batch mode (requires a .txt filelist)?');
switch btchmode;
case 'No';
% no action needed
case 'Cancel';
% no action needed;
case 'Yes';
[file3,path3]=uigetfile('*.txt','Input .txt file with list of .mat filenames');
pf3=[path3 file3];
if ~(exist(pf3)==2);
error(['Claimed file ' pf2 ' with list of .mat filenames does not exist']);
end
% Prompt for directory you want the .ps files to go into
prompt={'Enter path:'};
def={pathcurr};
dlgTitle='Directory to store postcript (.ps) output files in';
lineNo=1;
answer=inputdlg(prompt,dlgTitle,lineNo,def);
pathps=answer{1};
end; % switch
% btchmode == 'Yes' means use batch mode
% pf3 would be the .txt filelist file if in batch mode
%*************** Compute number of ring-width files to treat in this run
if strcmp(btchmode,'No') | strcmp(btchmode,'Cancel'); % using 'single' mode
nfiles=1; % number of .mat ring-width files
filecell=[]; % row-cell holding names of the .mat files
else; % batch mode
filecell = textread(pf3,'%s','delimiter','\n','whitespace','');
nfiles=size(filecell,1); % number of .mat files to read
end; % strcmp(btchmode...)
% filecell is a row-cell with names of the .mat files
% nfiles is the number of .mat files
%****************** Plot all series in each file, or use a pointer to select files **
pointopt=questdlg('Use pointer to select ring-width series?');
switch pointopt;
case 'No'
% no action needed;
case 'Cancel';
% no action needed
case 'Yes';
% load file with pointer variable;
[file5,path5]=uigetfile('*.mat','Input file with selection pointer');
pf5=[path5 file5];
eval(['load ' pf5 ' Vselect;']); % pointer variable
if exist('Vselect')~=1; error(['File ' pf5 ' does not contain Vselect']);end
% Check size of Vselect
[mcheck,ncheck]=size(Vselect);
if (mcheck~=1 | ncheck~=nfiles);
error('Vselect must be cell-row with row-size nfiles');
end
clear mcheck ncheck ;
end; % switch
% pointopt is 'Yes' if using a pointer file
% If using a pointer file, Vselect is a rv or matrix of pointers to ring-width series
%------ Prompt for optional re-ordering of cores in .mat file from oldest to youngest for plotting
oldfirst= questdlg('Arrange cores in order of age in plots?');
% If pointopt=='yes', the ordering is within rows of Vmtx, which means
% that retain the restriction that a specified group of cores is plotted
% in each window
% If pointopt ~='yes', the ordering is over all cores in the .mat file
% Actual re-ordering is done within eightplt.m
%------ Loop over .mat files
for n = 1:nfiles;
%----- Get the .mat filename
if ~strcmp(btchmode,'Yes'); % single mode
[flmat,path1]=uigetfile('*.mat','.MAT filename ?');
pf1=[path1 flmat];
else; % batch mode -- use a .txt list of .mat filenames
pf1=filecell{n}; % file name, with or without drive\path
len1=length(pf1);
fslash=findstr(pf1,'\');
if isempty(fslash); % no path prefix in file name; set path1 to current dir
flmat=pf1; % filename (w/o path)
path1=[eval('cd') '\']; % path
else; % separate path and filename
flmat=pf1((max(fslash)+1):len1); % filename
path1=pf1(1:max(fslash)); % path
end
% If needed, put on the .mat suffix
if isempty(findstr(pf1,'.'));
pf1=[pf1 '.mat'];
flmat=[flmat '.mat'];
end
end
% pf1 now is complete path\filename, including .mat
% flmat is the filename, with .mat
% path1 is the path, with ending slash
%----- Load the .mat file containing the ring-width series, names, years, etc;
% Check that it holds the vital variables
eval(['load ',pf1]);
if ~all(exist('X')==1 & exist('nms')==1 & exist('yrs')==1);
error('.mat input ring-width file does not have required variables');
end
ncore=size(nms,1); % number of ring-width series (cores) in the file,
% and maybe number to be plotted (depending on pointeropt)
%-------- Make or pull matrix of selection pointers
if strcmp(pointopt,'Yes'); % use read-in pointer variable
Vmtx = Vselect{n}; % Matrix of pointers to core series
Ltemp = ~isnan(Vmtx);
ncore = sum(sum(Ltemp)); % total number of cores to be plotted
numfig = size(Vmtx,1); % number of figure windows
clear Ltemp;
else; % not using pointer option; build matrix of core pointers
numfig = ceil(ncore/8); % number of figure windows
i1=1:8;
I1=repmat(i1,numfig,1);
j1=(0:8:ncore-1)';
J1=repmat(j1,1,8);
Vmtx=I1+J1;
ntemp = 8 * numfig;
nquash = ntemp - ncore;
if nquash>0;
Vmtx(numfig,(8-nquash+1):8)=NaN;
end
end
%------ Order cores from oldest to youngest before plotting.
if strcmp(oldfirst,'No'); % No re-ordering wanted
else; % re-order
if strcmp(pointopt,'Yes'); % using pointer option to specify cores in plot windows
for ii=1:numfig; % loop over number of figure windows
i1 = Vmtx(ii,:); % core sequence no's for this window
L1 = isnan(i1); % any NaN's for this window
if any(L1);
nquash=sum(L1);
i1(L1)=[];
if length(i1)==1; % just one series to be plotted in window
Vmtx(ii,:)=[i1 repmat(NaN,1,7)];
else; % more than one series; need to sort
yrborn = yrs(i1,1); % start year of rw for selected series
[yrtemp,isort]=sort(yrborn);
i2=i1(isort);
Vmtx(ii,:)=[i2,repmat(NaN,1,nquash)];
end;
else; % no NaN -- have 8 series to be plotted
yrborn=yrs(i1,1); % start years
[yrtemp,isort]=sort(yrborn);
Vmtx(ii,:)=i1(isort);
end; % if any(L1)
end; % for ii=1:numfig
else; % not using pointer option; re-order all cores in the .mat file
i1=(1:ncore)'; % col vector of indices corresp to sequence of cores
yrborn = yrs(:,1); % col vector of first years of ringwidths
[yrtemp,isort]=sort(yrborn);
i2=i1(isort); % core seq rearranged in order of start year of series
if nquash>0; % need to make n of plot series multiple of 8
i2=[i2; repmat(NaN,nquash,1)];
end
Vmtx=(reshape(i2,8,numfig))';
end; % strcmp(pointopt,...);
end; % strcmp(oldfirst,...) That's it for re-ordering
% ---- Set datin{} contents that do not vary over figure windows
datin{2}=X; % sov of ring widths
datin{3}=nms; % core Ids
datin{4}=yrs; % start year, end year, start row index of ring widths
datin{7}=flmat; % (1 x ?)ch name of .mat file from which ring widths come
% (e.g., 'shr.mat')
%-------- Loop over figure windows
for nn = 1:numfig;
%------- Load up input args for call to eightplt.m
datin{1}=[nn numfig]; % window number & number of windows (not counting zoom)
datin{5}=Vmtx(nn,:); % (? x 1)i row-index to nms of series to be plotted on this page
datin{6}=[]; % (1 x 2)d specified first and last year for plot (as in zooming),
% or [], which means figure must cover
%--- Make the plots
eightplt(datin);
end; % for nn=1:numfig
%------- ZOOM CAPABILITY
if strcmp(btchmode,'Yes'); % zooming not implemented in batch mode
% no zooming
else; % 'single' mode
kzoom=1;
while kzoom==1;
kmen1=menu('Choose One',...
'Zoom a figure window',...
'Quit zooming');
if kmen1==1; % zoom a figure window
if exist('nzw')==1;
close(nzw);
end
nzw = numfig+1; % figure window in which to put zoomed plot
% close any existing zoom window
% Build menu of possible windows to zoom
figcell= cellstr(num2str((1:numfig)'));
% Prompt for choosing a figure window , then switch to that window
zwind=menu('Zoom on which window?',figcell);
figure(zwind);
% Prompt user to point to zoom region
hhlp1=helpdlg('Click L and R edge of desired zoom region');
pause(1.5);
xypnts=ginput(2); % Get the corner points of the region to be zoomed in
xmx=max(xypnts(:,1));
xmn=min(xypnts(:,1));
% Make zoomed plot
%------- Load up input args for call to eightplt.m
datin{1}=[nzw zwind]; % zoom window & source window
datin{5}=Vmtx(zwind,:); % (? x 1)i row-index to nms of series to be plotted on this page
datin{6}=[xmn xmx]; % (1 x 2)d specified first and last year for plot (as in zooming),
% or [], which means figure must cover
%--- Make the plots
eightplt(datin);
elseif kmen1==2; % quit zoom, but keep figures available
kzoom=0;
end; % if kmen1=1;
end; % while kzoom==1
end; % strcmp(btchmode,...)
%****************** OPTIONALLY MAKE POSTSCRIPT FILE OF THE FIGURE WINDOWS
if ~strcmp(btchmode,'Yes'); % not in batch mode; optional making of .ps file
psfile=questdlg('Make a postscript plot file?');
switch psfile;
case 'Yes'; %make a ps output file
txt3=[' Output ps file for ' pf1];
[file2,path2]=uiputfile('*.ps',txt3);
pf2=[path2 file2];
for npost = 1:numfig;
figure(npost);
eval(['print -dps -append pf2;']);
end;
case 'No';
case 'Cancel';
end; % switch psfile
else; % batch mode; assumed you want .ps files; these will go in current directory
pf4=[pathps strtok(flmat,'.') '.ps'];
for npost=1:numfig;
figure(npost);
eval(['print -dps -append ' pf4]);
end
close all
end; % strcmp(btchmode,...);
% IF IN 'SINGLE' MODE, OPTIONALLY CLOSE ALL FIGURE WINDOWS
if ~strcmp(btchmode,'Yes');
kclose=questdlg('Close the figure windows?');
switch kclose;
case 'Yes';
close all;
case 'No';
case 'Cancel';
end
end
end; % for n=1:nfiles
