Index: /issm/trunk-jpl/src/m/Makefile.am =================================================================== --- /issm/trunk-jpl/src/m/Makefile.am (revision 13012) +++ /issm/trunk-jpl/src/m/Makefile.am (revision 13013) @@ -1,40 +1,51 @@ -bin_SCRIPTS=./classes/*.m \ - ./classes/model/*.m \ - ./classes/clusters/*.m \ - ./enum/*.m \ - ./kml/*.m \ - ./model/*.m \ - ./model/plot/*.m \ - ./model/mesh/*.m \ - ./model/display/*.m \ - ./model/parameterization/*.m \ - ./model/partition/*.m \ - ./model/solvers/*.m \ - ./qmu/*.m \ - ./utils/*.m \ - ./utils/Array/*.m \ - ./utils/BC/*.m \ - ./utils/Basins/*.m \ - ./utils/Cluster/*.m \ - ./utils/DataProcessing/*.m \ - ./utils/Ecco3/*.m \ - ./utils/Exp/*.m \ - ./utils/Exp/manipulation/*.m \ - ./utils/Exp/readwrite/*.m \ - ./utils/Geometry/*.m \ - ./utils/ImageProcessing/*.m \ - ./utils/Interp/*.m \ - ./utils/Kml/*.m \ - ./utils/LatLong/*.m \ - ./utils/Math/*.m \ - ./utils/Meca/*.m \ - ./utils/Mesh/*.m \ - ./utils/Miscellaneous/*.m \ - ./utils/Model/*.m \ - ./utils/Numerics/*.m \ - ./utils/OS/*.m \ - ./utils/Plot/*.m \ - ./utils/Shell/*.m \ - ./utils/String/*.m \ - ./utils/consistency/*.m \ - ./utils/qmu/*.m +#To generate list of directories +# +#find . -type d -exec ls -d {} \; + +bin_SCRIPTS= ./qmu/*.m \ + ./qmu/setupdesign/*.m \ + ./qmu/plot/*.m \ + ./qmu/examples/*.m \ + ./kml/*.m \ + ./enum/*.m \ + ./classes/*.m \ + ./classes/qmu/*.m \ + ./classes/qmu/@dakota_method/*.m \ + ./classes/clusters/*.m \ + ./classes/model/*.m \ + ./consistency/*.m \ + ./array/*.m \ + ./boundaryconditions/*.m \ + ./exp/*.m \ + ./exp/manipulation/*.m \ + ./geometry/*.m \ + ./interp/*.m \ + ./latlong/*.m \ + ./meca/*.m \ + ./mesh/*.m \ + ./mesh/planet/*.m \ + ./mesh/rifts/*.m \ + ./miscellaneous/*.m \ + ./os/*.m \ + ./plot/*.m \ + ./plot/colormaps/*.m \ + ./string/*.m \ + ./contrib/*.m \ + ./contrib/massbalance/*.m \ + ./contrib/ecco/*.m \ + ./contrib/hydrology/*.m \ + ./contrib/hack/*.m \ + ./contrib/gslib/*.m \ + ./contrib/uci/*.m \ + ./contrib/oasis/*.m \ + ./contrib/bamg/*.m \ + ./extrusion/*.m \ + ./inversions/*.m \ + ./io/*.m \ + ./parameterization/*.m \ + ./partition/*.m \ + ./print/*.m \ + ./regional/*.m \ + ./solve/*.m \ + ./solvers/*.m \ + ./materials/*.m Index: sm/trunk-jpl/src/m/os/ucisvn.m =================================================================== --- /issm/trunk-jpl/src/m/os/ucisvn.m (revision 13012) +++ (revision ) @@ -1,15 +1,0 @@ -function UCI_SVN=ucisvn() -%ISSMDIR - Get UCI_SVN environment variable -% -% Usage: -% UCI_SVN=ucisvn() - -if ~ispc, - UCI_SVN =getenv('UCI_SVN'); -else - UCI_SVN =getenv('UCI_SVN_WIN'); -end - -if (isempty(UCI_SVN)), - error('ucisvn error message: ''UCI_SVN'' environment variable is empty! You should define UCI_SVN in your .cshrc or .bashrc'); -end Index: sm/trunk-jpl/src/m/plot/imagescnan.m =================================================================== --- /issm/trunk-jpl/src/m/plot/imagescnan.m (revision 13012) +++ (revision ) @@ -1,303 +1,0 @@ -function [h,hcb] = imagescnan(x,y,U,varargin) -%IMAGESCNAN Scale data and display as image with uncolored NaNs. -% -% Syntax -% imagescnan(x,y,U) -% imagescnan(x,y,U,...,colormask) -% imagescnan(x,y,U,...,color) -% imagescnan(x,y,U,...,cbfit_opt) -% h = imagescnan(...); -% [h,hcb] = imagescnan(...,cbfit_opt); -% -% Input: -% x - X-axis vector data. Optional, i.e., can be empty. -% Default: 1:n (rows index). -% y - Y-axis vector data. Optional, i.e., can be empty. -% Default: 1:m (column index). -% U - Matrix [m x n] data or an RGB image [m x n x 3] (with/ -% without NaNs). -% colormask - Logical matrix indicating the U elements to be -% uncolored, if is empty then ISNAN(U) is used. Or it can -% be a single value which will be uncolored. -% Default: ~isfinite(U) (NaNs and Infs elements uncolored) -% color - A vector with 3 elements specifying the [R G B] color -% for the NaNs color. It can be specified by the known -% char colors: 'k', etcerera. Optional. -% Default: get(gca,'color') (axes background color) -% cbfit_opt - Cell array with the options to call COLORBARFIT. -% Default: COLORBARFIT function is not used by default. -% -% Output: -% h - Image handle. Optional -% hcb - Colorbar handle. Optional -% -% Description: -% This function draws a matrix data as an image with uncolored NaN's -% elements using IMAGESC. The difference between IMAGESC and the -% PCOLOR, MESH or SURF function is that EVERY element is colored and -% no one is interpolated, besides, the pixels are centered with the -% axis value, although it is a flat image. -% -% The color mask is added because IMAGESC do not work with NaN's, in -% fact it colors them with the lower value of the current colormap. -% -% The cbfit_opt is include in order to be able to define a diferent -% color map with the COLORBARFIT function which can be found at: -% http://www.mathworks.com/matlabcentral/fileexchange/. -% If this function is not found, a normal COLORBAR is generated. -% -% The data and the colorbar are scaled with the current colormap, so, -% the use of COLORMAP after this function doesn't affects the -% generated image and colorbar! Therefore, COLORMAP and CAXIS should -% be used before this function. -% -% Notes: * The inputs arguments for the COLORBARFIT function are 3 -% plus the normal COLORBAR function options, for this reason, -% if the former is not found, the latter is used ignoring -% these first 3 options. Anyway, to generate a colorbar, at -% least an empty cell is needed for cbfit_opt = {[]}. -% -% Examples: -% -% % Compares with normal IMAGESC: -% N = 100; -% PNaNs = 0.10; -% X = peaks(N); -% X(round(1 + (N^2-1).*rand(N^2*PNaNs,1))) = NaN; -% subplot(221), imagesc(X) -% title('With IMAGESC: ugly NaNs') -% subplot(222), imagescnan([],[],X) -% title('With IMAGESCNAN: uncolored NaNs') -% -% % Compares with SPY: -% subplot(223), spy(isnan(X)) -% title('SPY NaNs') -% subplot(224), imagescnan([],[],isnan(X),0), axis equal tight -% title('No-NaNs with IMAGESCNAN') -% -% See also IMAGE, IMAGESC, COLORBAR, IMREAD, IMWRITE and COLORBARFIT by -% Carlos Vargas. - -% Copyright 2008 Carlos Adrian Vargas Aguilera -% $Revision: 1.1 $ $Date: 2009/04/03 22:56:05 $ - -% Written by -% M.S. Carlos Adrian Vargas Aguilera -% Physical Oceanography PhD candidate -% CICESE -% Mexico, 2008 -% nubeobscura@hotmail.com -% -% Download from: -% http://www.mathworks.com/matlabcentral/fileexchange/loadAuthor.do?objec -% tType=author&objectId=1093874 - -% 1.0 Released (30/06/2008) -% 1.1 Fixed bug when CAXIS used. -% 1.2 Colorbar freezed colormap. -% 1.3 Fixed bug in color vector input (Found by Greg King) and now -% accets RGB image as input. - -%% INPUTS: - -% Error checking: -% Note: At least 3 inputs and no more than 6: -if nargin<3 || nargin>6 - error('Imagescnan:IncorrectInputNumber',... - 'Input arguments must be at least 3 and less than 7.') -end - -% Check the x,y,U: -% Note: x,y should be the axes data. -m = size(U); -if numel(m)>3 - error('Imagescnan:IncorrectInputSize',... - 'Input image must be a matrix or an RGB image.') -else - if isempty(x) || numel(x)~=m(2) - %warning('Imagescnan:IncorrectInputSize',... - % 'Index column axis has been used.') - x = 1:m(2); - end - if isempty(y) || numel(y)~=m(1) - %warning('Imagescnan:IncorrectInputSize',... - % 'Index row axis has been used.') - y = 1:m(1); - end -end - -% Get color limits: -% Note: If you would like to use specific color limits, use CAXIS before -% this function. -switch get(gca,'CLimMode') - case 'manual' - clim = caxis; - otherwise - clim = [min(U(:)) max(U(:))]; -end - -% Parse inputs and defaults: -% Note: * Mask color will be the not-finite elements plus the elements -% indicated by the user. -% * Default colormask is the current axes background. -% * Default currentmap is current figure colormap (probably JET). -colormask = ~isfinite(U); -color_nan = get(gca,'color'); -color_map = get(gcf,'colormap'); -cbfit_opt = []; -ycolorbarfit = (exist('colorbarfit','file')==2); -if nargin>3 - while ~isempty(varargin) - if iscell(varargin{1}) - if length(varargin{1})<3 - error('Imagescnan:IncorrectInputType',... - 'Options for COLORBARFIT must be at least 3, although empty.') - end - caxis(clim) - cbfit_opt = varargin{1}; - if ycolorbarfit - colorbarfit(cbfit_opt{:}) - color_map = get(gcf,'colormap'); - else - % warning('Imagescnan:ColorBarFitNotFound',... - % 'COLORBARFIT function not found, used default COLORBAR.') - end - varargin(1) = []; - elseif ischar(varargin{1}) - switch varargin{1} - case 'y', color_nan = [1 1 0]; - case 'm', color_nan = [1 0 0]; - case 'c', color_nan = [0 1 1]; - case 'r', color_nan = [1 0 0]; - case 'g', color_nan = [0 1 0]; - case 'b', color_nan = [0 0 1]; - case 'w', color_nan = [1 1 1]; - case 'k', color_nan = [0 0 0]; - otherwise - error('Imagescnan:InvalidColor',... - 'Color char must be one of: ''ymcrgbwk''.') - end - varargin(1) = []; - elseif islogical(varargin{1}) - if numel(varargin{1})~=numel(U) - error('Imagescnan:InvalidMask',... - 'The logical mask must have the same elements as the matrix.') - end - colormask = varargin{1} | colormask; - varargin(1) = []; - elseif length(varargin{1})==3 - if (max(varargin{1})>1) || (min(varargin{1})<0) % Fixed BUG 2008/07/11 - error('Imagescnan:InvalidColor',... - 'The color must be on the range of [0 1].') - end - color_nan = varargin{1}; - varargin(1) = []; - elseif length(varargin{1})==1 - colormask = (U==varargin{1}) | colormask; - varargin(1) = []; - else - error('Imagescnan:IncorrectInputType',... - 'Incorrect optional(s) argument(s).') - end - end -end - - -%% MAIN: - -% Matrix data to RGB: -if numel(m)==2 - - % Sets to double data: - if ~isfloat(U) - U = double(U); - end - - % Normalizes and rounds data to range [0 N]: - N = size(color_map,1); - U = (U - clim(1))/diff(clim); % Fixed bug when CAXIS used - U = U*N; - if N<=256 - U = uint8(U); - else - U = uint16(U); - end - - % Scales data with colormap: - U = ind2rgb(U,color_map); % 2D to 3D RGB values [0 1] -else - % Already is an RGB image, so do nothing. -end - - % Set mask color to color_nan: - mn = prod(m(1:2)); - ind = find(colormask); - U(ind) = color_nan(1); % Red color - U(ind+mn) = color_nan(2); % Green color - U(ind+mn*2) = color_nan(3); % Blue color - - % Draws the RGB image: - h = imagesc(x,y,U,clim); - -%% OUTPUTS: - -% Calls to colorbarfit and freezes his colormap: -if ~isempty(cbfit_opt) - % Creates a temporary colorbar: - if ycolorbarfit - hcb = colorbarfit(cbfit_opt{:}); - else - Nopt = min([3 length(cbfit_opt)]); - cbfit_opt(1:Nopt) = []; - hcb = colorbar(cbfit_opt{:}); - end - % Save image position: - ha = gca; position = get(ha,'Position'); - % Gets colorbar axes properties: - ghcb = get(hcb); - CData = ind2rgb(get(ghcb.Children,'CData'),color_map); - XData = get(ghcb.Children,'XData'); - YData = get(ghcb.Children,'YData'); - % Move ticks because IMAGESC draws them like centered pixels: - XTick = ghcb.XTick; - YTick = ghcb.YTick; - if ~isempty(XTick) - XTick = XTick(1:end-1) + diff(XTick(1:2))/2; - end - if ~isempty(YTick) - YTick = YTick(1:end-1) + diff(YTick(1:2))/2; - end - % Deletes the colorbar: - delete(hcb) - % Generates other colorbar: - hcb = axes('Position',ghcb.Position); - hcbim = imagesc(XTick,YTick,CData,'Parent',hcb); axis tight - set(hcbim,... - 'HitTest','off',... - 'Interruptible','off',... - 'SelectionHighlight','off',... - 'Tag','TMW_COLORBAR',... - 'XData',XData,... - 'YData',YData) - set(hcb,... - 'XAxisLocation',ghcb.XAxisLocation,... - 'YAxisLocation',ghcb.YAxisLocation,... - 'XLim',ghcb.XLim,... - 'YLim',ghcb.YLim,... - 'XDir',ghcb.XDir,... - 'YDir',ghcb.YDir,... - 'XTick',ghcb.XTick,... - 'YTick',ghcb.YTick,... - 'XTickLabel',ghcb.XTickLabel,... - 'YTickLabel',ghcb.YTickLabel,... - 'ButtonDownFcn',@resetCurrentAxes,... - 'Interruptible','off',... - 'Tag','Colorbar') - % Returns the image position: - axes(ha), set(ha,'Position',position) -end - -% Sets output: -if ~nargout - clear h -end Index: sm/trunk-jpl/src/m/plot/plot2patch.m =================================================================== --- /issm/trunk-jpl/src/m/plot/plot2patch.m (revision 13012) +++ (revision ) @@ -1,16 +1,0 @@ -function [px py]=plot2patch(x,y,miny) -%PLOT2PATCH: build patch out of x,y plot. -% -% Usage: [px,py]=plot2patch(x,y,miny) -% -% where px and py are a list of point defining a closed polygon. -% x,y are the values of the plot -% miny is the y-value used to close the plot into a closed polygon. -% -% See also patch, plot - -px=x; -py=y; - -px=[px; flipud(x)]; -py=[py; ; miny*ones(length(x),1)]; Index: sm/trunk-jpl/src/m/string/ddeblank.m =================================================================== --- /issm/trunk-jpl/src/m/string/ddeblank.m (revision 13012) +++ (revision ) @@ -1,29 +1,0 @@ -function sout = ddeblank(s) -%DDEBLANK Double deblank. Strip both leading and trailing blanks. -% -% DDEBLANK(S) removes leading and trailing blanks and null characters from -% the string S. A null character is one that has a value of 0. -% -% See also DEBLANK, DEWHITE, DDEWHITE. - -% Author: Peter J. Acklam -% Time-stamp: 2003-10-13 11:13:07 +0200 -% E-mail: pjacklam@online.no -% URL: http://home.online.no/~pjacklam - - error(nargchk(1, 1, nargin)); - if ~ischar(s) - warning('Input must be a string (char array).'); - end - - if isempty(s) - sout = s; - return; - end - - [r, c] = find( (s ~= ' ') & (s ~= 0) ); - if size(s, 1) == 1 - sout = s(min(c) : max(c)); - else - sout = s(:, min(c) : max(c)); - end Index: sm/trunk-jpl/src/m/string/logoutput.m =================================================================== --- /issm/trunk-jpl/src/m/string/logoutput.m (revision 13012) +++ (revision ) @@ -1,7 +1,0 @@ -function logoutput(logstring,message) -%LOGOUTPUT - embed a log string into an error message, used in the nightly runs. -% -% Usage: -% logoutput(logstring,message) - -disp(sprintf('%s%s',logstring,message));