Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_a.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_a.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_a.m	(revision 7893)
@@ -32,5 +32,5 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Documents and Settings\frankp\My Documents\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -102,5 +102,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex]  %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -127,5 +127,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -304,4 +304,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 21 13]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expa.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_b.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_b.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_b.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -94,5 +95,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = interp1(x, surfVel, newX);
@@ -119,5 +120,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
@@ -296,4 +297,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 21 13]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expb.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_c.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_c.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_c.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Documents and Settings\frankp\My Documents\work\ismip_all\ismip_mat\';
+%location = 'C:\Documents and Settings\frankp\My Documents\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -102,5 +103,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -127,5 +128,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -304,4 +305,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 21 13]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expc.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_d.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_d.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_d.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -94,5 +95,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = interp1(x, surfVel, newX);
@@ -119,5 +120,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
@@ -296,4 +297,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 21 13]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expd.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -93,5 +94,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = interp1(x, surfVel, newX);
@@ -118,5 +119,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
@@ -296,4 +297,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 11 17]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expe.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e_txz.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e_txz.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_e_txz.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -95,5 +96,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = interp1(x, surfVel, newX);
@@ -118,5 +119,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
@@ -294,3 +295,4 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 11 17]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expetxz.eps', 'psc2');
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_f.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_f.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_f.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -102,5 +103,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -127,5 +128,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -334,4 +335,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 11 17]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expf.eps', 'psc2');
 
Index: /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_fs.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_fs.m	(revision 7892)
+++ /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_exp_fs.m	(revision 7893)
@@ -32,5 +32,6 @@
 % sub dirs lie)
 % NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+%location = 'C:\Program Files\MATLAB\R2006a\work\ismip_all\ismip_mat\';
+location = '../ismip_mat/'; %ISSM->THIS LINE HAS BEEN CHANGED
 
 % The experiment we're interested in
@@ -102,5 +103,5 @@
             % If the current data is from a full stokes
             if (fullStokesMask(i) == 1)
-                [i j fsIndex]
+                %[i j fsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the full stokes structure
                 fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -127,5 +128,5 @@
             % Else its non-full stokes
             else
-                [i j nfsIndex]
+                %[i j nfsIndex] %ISSM->THIS LINE HAS BEEN CHANGED
                 % Store the data in the non-full stokes structure
                 nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
@@ -333,4 +334,5 @@
         'portrait','papertype','A4','paperunits', 'centimeters', ...
         'paperposition',[1 4 11 17]);
+return %ISSM->THIS LINE HAS BEEN CHANGED
 saveas(gcf, 'expfs.eps', 'psc2');
 
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_a.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_a.m	(revision 7892)
+++ 	(revision )
@@ -1,294 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'tpa1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = 'C:\Documents and Settings\frankp\My Documents\work\ismip_all\ismip_mat\';
-
-% The experiment we're interested in
-exp = 'a';
-
-% The file we're intersted in
-fileNames = {[exp '005.txt'], [exp '010.txt'], [exp '020.txt'], ...
-             [exp '040.txt'], [exp '080.txt'], [exp '160.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-newY = 1/4*ones(250,1)';
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '\' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f %f %f %f');
-
-            % Store the values 
-            x = data{1,1};
-            y = data{1,2};
-            xvel = data{1,3};
-            yvel = data{1,4};
-            zvel = data{1,5};
-            
-            % Make sure the data is normalized
-            x = x./max(x);
-            
-            % Make sure the data is normalized
-            y = y./max(y);
-            
-            x = inpaint_nans(x, 4);
-            y = inpaint_nans(y, 4);
-            xvel = inpaint_nans(xvel, 4);
-            yvel = inpaint_nans(yvel, 4);
-            zvel = inpaint_nans(zvel, 4);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2 + zvel.^2);
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                    
-                    % Increment the full stokes index
-                    fsIndex = fsIndex + 1;
-                
-                end
-                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                
-                    % Increment the non-full stokes index
-                    nfsIndex = fsIndex + 1;
-                
-                end
-            
-            end
-            
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'5km' '10km' '20km' '40km' '80km' '160km'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'normal';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 3, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                       fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                       nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_b.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_b.m	(revision 7892)
+++ 	(revision )
@@ -1,282 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'tpa1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = '/Applications/MATLAB_R2007b/work/ismip_all/';
-
-% The experiment we're interested in
-exp = 'b';
-
-% The file we're intersted in
-fileNames = {[exp '005.txt'], [exp '010.txt'], [exp '020.txt'], ...
-             [exp '040.txt'], [exp '080.txt'], [exp '160.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '/' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f');
-
-            % Store the values into the current spot in the cell arrays
-            x = data{1,1};
-            xvel = data{1,2};
-            yvel = data{1,3};
-            
-            % Make sure the data is normalized
-            x = x./max(x);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-            surfVel = sqrt(xvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = interp1(x, surfVel, newX);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                    
-                    % Increment the full stokes index
-                    fsIndex = fsIndex + 1;
-                
-                end
-                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                
-                    % Increment the non-full stokes index
-                    nfsIndex = fsIndex + 1;
-                
-                end
-            
-            end
-            
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'5km' '10km' '20km' '40km' '80km' '160km'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'times new roman';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 3, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                       fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                       nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_c.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_c.m	(revision 7892)
+++ 	(revision )
@@ -1,295 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'tpa1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = '/Applications/MATLAB_R2007b/work/ismip_all/';
-
-% The experiment we're interested in
-exp = 'c';
-
-% The file we're intersted in
-fileNames = {[exp '005.txt'], [exp '010.txt'], [exp '020.txt'], ...
-             [exp '040.txt'], [exp '080.txt'], [exp '160.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-newY = 1/4*ones(250,1)';
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '/' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f %f %f %f %f %f');
-
-            % Store the values 
-            x = data{1,1};
-            y = data{1,2};
-            xvel = data{1,3};
-            yvel = data{1,4};
-            zvel = data{1,5};
-            
-            % Make sure the data is normalized
-            x = x./max(x);
-            
-            % Make sure the data is normalized
-            y = y./max(y);
-            
-            % Make sure there are no nans in the data
-            x = inpaint_nans(x, 4);
-            y = inpaint_nans(y, 4);
-            xvel = inpaint_nans(xvel, 4);
-            yvel = inpaint_nans(yvel, 4);
-            zvel = inpaint_nans(zvel, 4);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2 + zvel.^2);
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = griddata(x, y, surfVel, newX, newY);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                    
-                    % Increment the full stokes index
-                    fsIndex = fsIndex + 1;
-                
-                end
-                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = griddata(x, y, surfVel, newX, newY);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                
-                    % Increment the non-full stokes index
-                    nfsIndex = fsIndex + 1;
-                
-                end
-            
-            end
-            
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'5km' '10km' '20km' '40km' '80km' '160km'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'times new roman';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 3, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                       fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                       nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_d.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_d.m	(revision 7892)
+++ 	(revision )
@@ -1,286 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'tpa1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION ON YOUR MACHINE
-location = '/Applications/MATLAB_R2007b/work/ismip_all/';
-
-% The experiment we're interested in
-exp = 'd';
-
-% The file we're intersted in
-fileNames = {[exp '005.txt'], [exp '010.txt'], [exp '020.txt'], ...
-             [exp '040.txt'], [exp '080.txt'], [exp '160.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '/' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f %f');
-
-            % Store the values into the current spot in the cell arrays
-            x = data{1,1};
-            xvel = data{1,2};
-            yvel = data{1,3};
-            
-            % Make sure the data is normalized
-            x = x./max(x);
-            
-            x = inpaint_nans(x, 4);
-            xvel = inpaint_nans(xvel, 4);
-            yvel = inpaint_nans(yvel, 4);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-            surfVel = sqrt(xvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = interp1(x, surfVel, newX);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                    
-                    % Increment the full stokes index
-                    fsIndex = fsIndex + 1;
-                
-                end
-                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                
-                    % Increment the non-full stokes index
-                    nfsIndex = fsIndex + 1;
-                
-                end
-            
-            end
-            
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'5km' '10km' '20km' '40km' '80km' '160km'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'times new roman';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 3, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                       fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                       nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_e
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_e	(revision 7892)
+++ 	(revision )
@@ -1,281 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'tpa1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = '/home/jfishbaugh/Desktop/frank/ismip_all/';
-
-% The experiment we're interested in
-exp = 'e';
-
-% The file we're intersted in
-fileNames = {[exp '000.txt'] [exp '001.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '/' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f');
-
-            % Store the values into the current spot in the cell arrays
-            x = data{1,1};
-            xvel = data{1,2};
-            yvel = data{1,3};
-            
-            x = inpaint_nans(x, 4);
-            xvel = inpaint_nans(xvel, 4);
-            yvel = inpaint_nans(yvel, 4);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = interp1(x, surfVel, newX);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                    
-                    % Increment the full stokes index
-                    fsIndex = fsIndex + 1;
-                
-                end
-                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                % If we are on the last file we can increment the index
-                if (j == (length(fileNames)-1))
-                
-                    % Increment the non-full stokes index
-                    nfsIndex = fsIndex + 1;
-                
-                end
-            
-            end
-            
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'5km' '10km' '20km' '40km' '80km' '160km'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'times new roman';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 1, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                       fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                       nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);
Index: sm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_e.m
===================================================================
--- /issm/trunk/test/IsmipHomResults/plotting_scripts/plot_ismip_exp_e.m	(revision 7892)
+++ 	(revision )
@@ -1,281 +1,0 @@
-%-----------------------------------------------------------------
-% Author:       James Fishbaugh
-% Date:         05/21/2008
-% Description:  Reads experiment data and generates a plot
-%               of a region of one standard deviation from the
-%               mean for the different types of models used.
-%----------------------------------------------------------------
-
-%--------------------------------------------------------
-% THIS IS THE FILE IO SECTION WHERE THE DATA FILES ARE
-% READ AND VALUES STORED 
-%--------------------------------------------------------
-
-% The names of the folders (also prefix for filenames)
-dirs = {'aas2' 'ahu1' 'ahu2' 'ahu2' 'bds1' 'cma1' 'cma2' 'dpo1' ...
-        'fpa1' 'fpa2' 'fsa1' 'jvj1' 'lpe1' 'mbr1' 'mmr1' 'mtk1' ...
-        'oga1' 'oso1' 'rhi1' 'rhi2' 'rhi3' 'rhi4' 'rhi5' 'spr1' ...
-        'ssu1' 'yuv1'};
-
-% The entries in this vector correspond to the vector of directory names
-% For example:  aas2 is full stokes, ahu1 is not, ahu2 is not, etc
-% NOTE: THIS NEEDS TO BE CHECKED FOR ACCURACY
-fullStokesMask = [0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1];
-
-% The location of the data (this is the path to the directory where all the
-% sub dirs lie)
-% NOTE:  CHANGE THIS TO THE LOCATION OF YOUR DATA
-location = '/home/jfishbaugh/Desktop/ismip_all/';
-
-% The experiment we're interested in
-exp = 'e';
-
-% The file we're intersted in
-fileNames = {[exp '000.txt'] [exp '001.txt']};
-
-% The desired vector for normalized x.  Used for interpolation so every
-% data set has the same number of points.
-newX = linspace(0.0,1.0,250);
-
-% Will hold all the full stokes surface velocities
-fsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 1)));
-% Will hold all the non-full stokes surface velocities
-nfsVels = cell(length(fileNames), length(fullStokesMask(fullStokesMask == 0)));
-
-% Keeps track of the index we are currently on (this is necessary because
-% some submittors didn't do all experiments so we can't rely on the loop
-% counter to keep track of where we are at)
-fsIndex = 1;
-nfsIndex = 1;
-
-% Keeps track of the number of submittors for each domain length (this will
-% help us later on in allocating the correct size of data structures)
-fsSizes = zeros(1, length(fileNames));
-nfsSizes = zeros(1, length(fileNames));
-
-% Loop over all folders
-for i=1:length(dirs)
-    
-    % Loop over all files
-    for j=1:length(fileNames)
-    
-        % Create the full file path from the base path and current directory
-        fullFilePath = [location dirs(i) '/' dirs(i) fileNames(j)];
-
-        % Open the current file for reading
-        file = fopen(cell2mat(fullFilePath),'r');
-
-        % If that file exists
-        if (file ~= -1)
-
-            % Creates a cell array from the file
-            data = textscan(file, '%f %f %f %f %f');
-
-            % Store the values into the current spot in the cell arrays
-            x = data{1,1};
-            
-            % Make sure the data is normalized
-            x = x./max(x);
-            
-            xvel = data{1,2};
-            yvel = data{1,3};
-            
-            x = inpaint_nans(x, 4);
-            xvel = inpaint_nans(xvel, 4);
-            yvel = inpaint_nans(yvel, 4);
-            
-            % Calculates the magnitude of the surface velocity
-            surfVel = sqrt(xvel.^2 + yvel.^2);
-
-            % If the current data is from a full stokes
-            if (fullStokesMask(i) == 1)
-                
-                % Store the data in the full stokes structure
-                fsVels{j, fsIndex} = interp1(x, surfVel, newX);
-                fsVels{j, fsIndex} = inpaint_nans(fsVels{j,fsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(fsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    fsSizes(j) = fsSizes(j) + 1;
-                    
-                end
-                
-                                
-            % Else its non-full stokes
-            else
-                
-                % Store the data in the non-full stokes structure
-                nfsVels{j, nfsIndex} = interp1(x, surfVel, newX);
-                nfsVels{j, nfsIndex} = inpaint_nans(nfsVels{j, nfsIndex}, 4);
-                
-                % Keep track of the number of entries in the array
-                if (length(nfsVels{j, fsIndex}) > 0)
-                   
-                    % Increment the number who performed this experiment
-                    nfsSizes(j) = nfsSizes(j) + 1;
-                
-                end
-                
-                      
-            end
-                            
-            % If we are on the last file we can increment the index
-            if (j == (length(fileNames)-1))
-                    
-                % Increment the full stokes index
-                fsIndex = fsIndex + 1;
-                % Increment the non-full stokes index
-                nfsIndex = fsIndex + 1;
-                
-            end
-
-            % We are done with this file, we can close it
-            fclose('all');
-            
-        end
-    
-    end
-    
-end 
-
-%--------------------------------------------------------
-% THIS IS THE PROCESSING AND DISPLAY SECTION WHERE THE 
-% MEAN AND STANDARD DEVIATION ARE CALCULATED AND PLOTTED
-%--------------------------------------------------------
-
-% The titles for the plots
-plotTitles = {'No-Slip Bed' 'Slip Bed'};
-% The label for the x-axis
-xLabel = 'Normalized x';
-% The label for the y-axis
-yLabel = 'Velocity (m/yr)';
-
-% The font to use for the axis labels
-axisLabelFont = 'times new roman';
-% The font size to use for the axis labels
-axisLabelSize = 14;
-% The font weight to use for the axis labels
-axisFontWeight = 'normal';
-
-% The font size to use for tick mark labels
-axisTickLabelSize = 11;
-% The font weight to use for tick mark labels
-axisTickFontWeight = 'normal';
-
-% The font size to use for the title
-titleFontSize = 12;
-% The font weight to use for the title
-titleFontWeight = 'bold';
-
-% Loop over each domain length
-for i=1:length(fileNames)
-   
-    % Allocate a matrix for full stokes surface velocities
-    fsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    fsIndex = 1;
-    
-    % Allocate a matrix for non-full stokes surface velocities
-    nfsCurDomainVels = zeros(250, fsSizes(i));
-    % Again we need a seperate index
-    nfsIndex = 1;
-    
-    % Loop over full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 1))
-        
-        % If there are data at this entry
-        if (length(fsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            fsCurDomainVels(:,fsIndex) = fsVels{i,j};
-            
-            % Increment the index
-            fsIndex = fsIndex + 1;
-            
-        end
-        
-    end
-    
-    % Loop over non-full stokes
-    for j=1:length(fullStokesMask(fullStokesMask == 0))
-        
-        % If there are data at this entry
-        if (length(nfsVels{i,j}) ~= 0)
-            
-            % Add it to the matrix
-            nfsCurDomainVels(:,nfsIndex) = nfsVels{i,j};
-            
-            % Increment the index
-            nfsIndex = nfsIndex + 1;
-        end
-        
-    end
-    
-    % Calcuate the mean for each domain length (full stokes)
-    fsMeanVel = mean(fsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (full stokes)
-    fsStdVel = std(fsCurDomainVels, 0, 2)';
-    
-    % Calcuate the mean for each domain length (non-full stokes)
-    nfsMeanVel = mean(nfsCurDomainVels, 2)';
-    % Calculate the std deviation for each domain length (non-full stokes)
-    nfsStdVel = std(nfsCurDomainVels, 0, 2)';
-    
-    % Tell MATLAB which subplot we are currently on
-    subplot(2, 1, i);    
-    
-    % The fill color (rgb) for full stokes
-    fsFillColor = [0.254 0.625 0.660];
-    % The fill color (rgb) for non-full stokes
-    nfsFillColor = [0.422 0.688 0.367];
-
-    % Plot full stokes
-    [fh1, msg1] = jbfill(newX, fsMeanVel+fsStdVel, fsMeanVel-fsStdVel, ...
-                         fsFillColor, fsFillColor, 1, 0.5);
-    
-    % Plot non-full stokes
-    [fh2, msg2] = jbfill(newX, nfsMeanVel+nfsStdVel, nfsMeanVel-nfsStdVel, ...
-                         nfsFillColor, nfsFillColor, 1, 0.35);               
-           
-    % Turn the grid on
-    grid on;
-        
-    % Set title properties
-    th = title(plotTitles(i));
-    set(th, 'FontSize', titleFontSize);
-    set(th, 'FontWeight', titleFontWeight);
-    
-    % Set x label properties
-    xlabel(xLabel);
-    xh = get(gca, 'xlabel');
-    set(xh, 'FontName', axisLabelFont);
-    set(xh, 'FontSize', axisLabelSize);
-    set(xh, 'FontWeight', axisFontWeight);
-
-    % Set y label properties
-    ylabel('Velocity (m/yr)');
-    yh = get(gca, 'ylabel');
-    set(yh, 'FontName', axisLabelFont);
-    set(yh, 'FontSize', axisLabelSize);
-    set(yh, 'FontWeight', axisFontWeight);
-
-    % Set tick mark properties
-    set(gca, 'FontSize', axisTickLabelSize);
-    set(gca, 'FontWeight', axisTickFontWeight);
-    
-    % This turns the box around the axis on
-    set(gca, 'Box', 'on' );
-    
-    % These lines plot the mean
-    hold on;
-    plot(newX, fsMeanVel, 'k');
-    set(findobj(gca,'Type','line','Color',[0 0 0]),'Color',fsFillColor,'LineWidth',2);
-    plot(newX, nfsMeanVel, 'b');
-    set(findobj(gca,'Type','line','Color',[0 0 1]),'Color',nfsFillColor,'LineWidth',2);
-    
-end
-
-% Add the legend to the final subplot (in upper left corner)
-legend('FS', 'NFS', 'FS Mean', 'NFS Mean', 2);