Index: /issm/trunk-jpl/src/m/Array/allempty.m =================================================================== --- /issm/trunk-jpl/src/m/Array/allempty.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/allempty.m (revision 12996) @@ -0,0 +1,22 @@ +% +% function to return an empty cell array if all array elements are empty +% +% function [cout]=allempty(cin) +% +function [cout]=allempty(cin) + +if ~nargin + help allempty + return +end + +for j=1:numel(cin) + if ~isempty(cin{j}) + cout=cin; + return + end +end +cout={}; + +end + Index: /issm/trunk-jpl/src/m/Array/allequal.m =================================================================== --- /issm/trunk-jpl/src/m/Array/allequal.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/allequal.m (revision 12996) @@ -0,0 +1,70 @@ +% +% function to return an empty array if all array elements are +% equal to the given value, which may also be empty but not nan. +% +% (note that by definition, nan is not equal to nan. this could +% be changed by using isequalwithequalnans.) +% +% function [aout]=allequal(ain,aval) +% +function [aout]=allequal(ain,aval) + +if ~nargin + help allequal + return +end + +aout=ain; + +if islogical(ain) && islogical(aval) + for i=1:numel(ain) + if ~isequal(ain(i),aval) + return + end + end + aout=logical([]); + +elseif isnumeric(ain) && isnumeric(aval) + for i=1:numel(ain) + if ~isequal(ain(i),aval) + return + end + end + aout=[]; + +elseif ischar(ain) && ischar(aval) + for i=1:size(ain,1) + if ~strcmp(ain(i,:),aval) + return + end + end + aout=''; + +elseif iscell(ain) + if islogical(aval) + for i=1:numel(ain) + if ~islogical(ain{i}) || ~isequal(ain{i},aval) + return + end + end + aout={}; + + elseif isnumeric(aval) + for i=1:numel(ain) + if ~isnumeric(ain{i}) || ~isequal(ain{i},aval) + return + end + end + aout={}; + + elseif ischar(aval) + for i=1:size(ain,1) + if ~ischar(ain{i}) || ~strcmp(ain{i},aval) + return + end + end + aout={}; + end +end + +end Index: /issm/trunk-jpl/src/m/Array/allnan.m =================================================================== --- /issm/trunk-jpl/src/m/Array/allnan.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/allnan.m (revision 12996) @@ -0,0 +1,22 @@ +% +% function to return an empty double array if all array elements are NaN +% +% function [dout]=allnan(din) +% +function [dout]=allnan(din) + +if ~nargin + help allnan + return +end + +for i=1:numel(din) + if ~isnan(din(i)) + dout=din; + return + end +end +dout=[]; + +end + Index: /issm/trunk-jpl/src/m/Array/any2str.m =================================================================== --- /issm/trunk-jpl/src/m/Array/any2str.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/any2str.m (revision 12996) @@ -0,0 +1,22 @@ +% +% function to convert anything to a string +% +% function [svec]=any2str(a,alim) +% +function [svec]=any2str(a,alim) + +if ~exist('alim','var') || (numel(a) <= alim) + if iscell(a) + svec=string_cell(a); + else + if (numel(a) > 1) && ~ischar(a) + svec=string_vec(a); + else + svec=item2str(a); + end + end +else + svec=[string_size(a) ' ''' class(a) '''']; +end + +end Index: /issm/trunk-jpl/src/m/Array/array_numel.m =================================================================== --- /issm/trunk-jpl/src/m/Array/array_numel.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/array_numel.m (revision 12996) @@ -0,0 +1,35 @@ +% +% function to find a number of elements from a list of arrays. +% +% [asize]=array_numel(varargin) +% +% see array_size to check the number and shape of elements, if +% multiple indices will be used. +% +function [anum]=array_numel(varargin) + +anum=1; + +for iarg=1:nargin + if ischar(varargin{iarg}) + inum=numel(cellstr(varargin{iarg})); + else + inum=numel(varargin{iarg}); + end + + if ~isequal(inum,1) + if isequal(anum,1) + anum=inum; + else + if ~isequal(inum,anum) + if ~isempty(inputname(iarg)) + error('Array ''%s'' has inconsistent number of elements.',inputname(iarg)); + else + error('Array %d has inconsistent number of elements.',iarg); + end + end + end + end +end + +end Index: /issm/trunk-jpl/src/m/Array/array_size.m =================================================================== --- /issm/trunk-jpl/src/m/Array/array_size.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/array_size.m (revision 12996) @@ -0,0 +1,35 @@ +% +% function to find an array size from a list of arrays. +% +% [asize]=array_size(varargin) +% +% see array_numel to check only the number of elements, if +% single indices will be used. +% +function [asize]=array_size(varargin) + +asize=[1 1]; + +for iarg=1:nargin + if ischar(varargin{iarg}) + isize=size(cellstr(varargin{iarg})); + else + isize=size(varargin{iarg}); + end + + if ~isequal(isize,[1 1]) + if isequal(asize,[1 1]) + asize=isize; + else + if ~isequal(isize,asize) + if ~isempty(inputname(iarg)) + error('Array ''%s'' has inconsistent size.',inputname(iarg)); + else + error('Array %d has inconsistent size.',iarg); + end + end + end + end +end + +end Index: /issm/trunk-jpl/src/m/Array/find_string.m =================================================================== --- /issm/trunk-jpl/src/m/Array/find_string.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/find_string.m (revision 12996) @@ -0,0 +1,18 @@ +% +% function to find a string in a cell array +% (could probably be replaced by matlab strmatch) +% +% [ifound]=find_string(cells,str) +% +function [ifound]=find_string(cells,str) + +ifound=false; + +for i=1:numel(cells) + if ischar(cells{i}) && strcmp(cells{i},str) + ifound=i; + return + end +end + +end Index: /issm/trunk-jpl/src/m/Array/item2str.m =================================================================== --- /issm/trunk-jpl/src/m/Array/item2str.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/item2str.m (revision 12996) @@ -0,0 +1,31 @@ +% +% function to convert an item to a string +% +% function [svec]=item2str(a) +% +function [svec]=item2str(a) + +if islogical(a) + if a + svec='true'; + else + svec='false'; + end +elseif ischar(a) + svec=['''' a '''']; +elseif isnumeric(a) + svec=num2str(a); +else + if ~isempty(inputname(1)) + warning('item2str:item_unrecog',... + 'Item ''%s'' is of unrecognized type ''%s''.',... + inputname(1),class(a)); + else + warning('item2str:item_unrecog',... + 'Item %d is of unrecognized type ''%s''.',... + 1,class(a)); + end + return +end + +end Index: /issm/trunk-jpl/src/m/Array/rotateticklabel.m =================================================================== --- /issm/trunk-jpl/src/m/Array/rotateticklabel.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/rotateticklabel.m (revision 12996) @@ -0,0 +1,69 @@ +function th=rotateticklabel(h,rot,demo) +%ROTATETICKLABEL rotates tick labels +% TH=ROTATETICKLABEL(H,ROT) is the calling form where H is a handle to +% the axis that contains the XTickLabels that are to be rotated. ROT is +% an optional parameter that specifies the angle of rotation. The default +% angle is 90. TH is a handle to the text objects created. For long +% strings such as those produced by datetick, you may have to adjust the +% position of the axes so the labels don't get cut off. +% +% Of course, GCA can be substituted for H if desired. +% +% TH=ROTATETICKLABEL([],[],'demo') shows a demo figure. +% +% Known deficiencies: if tick labels are raised to a power, the power +% will be lost after rotation. +% +% See also datetick. + +% Written Oct 14, 2005 by Andy Bliss +% Copyright 2005 by Andy Bliss + +%DEMO: +if nargin==3 + x=[now-.7 now-.3 now]; + y=[20 35 15]; + figure + plot(x,y,'.-') + datetick('x',0,'keepticks') + h=gca; + set(h,'position',[0.13 0.35 0.775 0.55]) + rot=90; +end + +%set the default rotation if user doesn't specify +if nargin==1 + rot=90; +end +%make sure the rotation is in the range 0:360 (brute force method) +while rot>360 + rot=rot-360; +end +while rot<0 + rot=rot+360; +end +%get current tick labels +a=get(h,'XTickLabel'); +%erase current tick labels from figure +set(h,'XTickLabel',[]); +%get tick label positions +b=get(h,'XTick'); +c=get(h,'YTick'); +%make new tick labels +% must consider yscale (jes, 9/14/10) +switch lower(get(h,'YScale')) + case 'linear' + if rot<180 + th=text(b,repmat(c(1)-.1*(c(2)-c(1)),length(b),1),a,'HorizontalAlignment','right','rotation',rot,'Interpreter','none'); + else + th=text(b,repmat(c(1)-.1*(c(2)-c(1)),length(b),1),a,'HorizontalAlignment','left','rotation',rot,'Interpreter','none'); + end + case 'log' + if rot<180 + th=text(b,repmat(10^(log10(c(1))-.1*(log10(c(2))-log10(c(1)))),length(b),1),a,'HorizontalAlignment','right','rotation',rot,'Interpreter','none'); + else + th=text(b,repmat(10^(log10(c(1))-.1*(log10(c(2))-log10(c(1)))),length(b),1),a,'HorizontalAlignment','left','rotation',rot,'Interpreter','none'); + end + otherwise + set(h,'XTickLabel',a); +end Index: /issm/trunk-jpl/src/m/Array/str2int.m =================================================================== --- /issm/trunk-jpl/src/m/Array/str2int.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/str2int.m (revision 12996) @@ -0,0 +1,46 @@ +% +% function to find and read the first or last positive integer +% in a character string. +% +% function [aint]=str2int(astr,cfl) +% +function [aint]=str2int(astr,cfl); + +aint=[]; + +if ~exist('cfl','var') || strncmpi(cfl,'f',1) + i=1; + + while (i <= length(astr)) + if (astr(i) >= '0' && astr(i) <= '9') + aint=sscanf(astr(i:length(astr)),'%d',[1,1]); + return + else + i=i+1; + end + end + +elseif strncmpi(cfl,'l',1) + i=length(astr); + ifound=false; + + while (i >= 1) + if (astr(i) >= '0' && astr(i) <= '9') + ifound=true; + i=i-1; + elseif ~ifound + i=i-1; + else + aint=sscanf(astr(i+1:length(astr)),'%d',[1,1]); + return + end + end + + if ifound + aint=sscanf(astr,'%d',[1,1]); + return + end +end + +end + Index: /issm/trunk-jpl/src/m/Array/string_cell.m =================================================================== --- /issm/trunk-jpl/src/m/Array/string_cell.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/string_cell.m (revision 12996) @@ -0,0 +1,26 @@ +% +% function to return the string of a cell array +% +% function [svec]=string_cell(a) +% +function [svec]=string_cell(a) + +if ~nargin + help string_cell + return +end + +if (numel(a) == 0) + svec='{}'; + return +end + +% assemble string for output + +svec ='{'; +for i=1:numel(a)-1; + svec=[svec item2str(a{i}) ' ']; +end +svec=[svec item2str(a{end}) '}']; + +end Index: /issm/trunk-jpl/src/m/Array/string_dim.m =================================================================== --- /issm/trunk-jpl/src/m/Array/string_dim.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/string_dim.m (revision 12996) @@ -0,0 +1,72 @@ +% +% function to return the string dimension of an array element +% +% function [sdim]=string_dim(a,idim,varargin) +% +function [sdim]=string_dim(a,idim,varargin) + +if ~nargin + help string_dim + return +end + +% check for scalar + +if (numel(a) == 1) && (idim == 1) + sdim=''; + return +end + +% check for overflow + +if (idim > numel(a)) + if ~isempty(inputname(1)) + error('Index %d exceeds number of elements in array ''%s''.',... + idim,inputname(1)); + else + error('Index %d exceeds number of elements in array %d.',... + idim,1); + end +end + +% check for column or row vector (Matlab uses a minimum of two +% dimensions, so this won't match Matlab standard output) + +for iarg=1:nargin-2 + if strcmpi(varargin{iarg},'vector') + if (ndims(a) == 2) && ((size(a,1) == 1) || (size(a,2) == 1)) + sdim =['(' num2str(idim) ')']; + return + end + end +end + +% do the general case + +asize=size(a); +index=zeros(size(asize)); +aprod=prod(asize); +idim =idim-1; + +% calculate indices base 0 and convert to base 1 + +% note that ind2sub might be useful, except that it requires a list +% of scalars rather than a vector for output. + +for i=length(asize):-1:1 + aprod=aprod/asize(i); + index(i)=floor(idim/aprod); + idim=idim-index(i)*aprod; +end +index=index+1; + +% assemble string for output + +sdim ='('; +for i=1:length(asize)-1; + sdim =[sdim num2str(index(i)) ',']; +end +sdim =[sdim num2str(index(end)) ')']; + +end + Index: /issm/trunk-jpl/src/m/Array/string_size.m =================================================================== --- /issm/trunk-jpl/src/m/Array/string_size.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/string_size.m (revision 12996) @@ -0,0 +1,38 @@ +% +% function to return the string size of an array +% +% function [ssize]=string_size(a,varargin) +% +function [ssize]=string_size(a,varargin) + +if ~nargin + help string_size + return +end + +% check for column or row vector (Matlab uses a minimum of two +% dimensions, so this won't match Matlab standard output) + +for iarg=1:nargin-1 + if strcmpi(varargin{iarg},'vector') + if (ndims(a) == 2) && ((size(a,1) == 1) || (size(a,2) == 1)) + ssize =['(' num2str(numel(a)) ')']; + return + end + end +end + +% do the general case + +asize=size(a); + +% assemble string for output + +ssize ='('; +for i=1:length(asize)-1; + ssize =[ssize num2str(asize(i)) 'x']; +end +ssize =[ssize num2str(asize(end)) ')']; + +end + Index: /issm/trunk-jpl/src/m/Array/string_vec.m =================================================================== --- /issm/trunk-jpl/src/m/Array/string_vec.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/string_vec.m (revision 12996) @@ -0,0 +1,26 @@ +% +% function to return the string of an vector +% +% function [svec]=string_vec(a) +% +function [svec]=string_vec(a) + +if ~nargin + help string_vec + return +end + +if (numel(a) == 0) + svec='[]'; + return +end + +% assemble string for output + +svec ='['; +for i=1:numel(a)-1; + svec=[svec item2str(a(i)) ' ']; +end +svec=[svec item2str(a(end)) ']']; + +end Index: /issm/trunk-jpl/src/m/Array/struc_class.m =================================================================== --- /issm/trunk-jpl/src/m/Array/struc_class.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/struc_class.m (revision 12996) @@ -0,0 +1,30 @@ +% +% function to find the structural fields of a specified class +% +% [sclasso]=struc_class(sclass,cstr) +% +function [sclasso]=struc_class(sclass,cstr) + +% collect only the objects of the appropriate class + +if isa(sclass,cstr) + if ~isempty(inputname(1)) + sclasso.(inputname(1))=sclass; + else + sclasso.(cstr) =sclass; + end + +elseif isstruct(sclass) + fnames=fieldnames(sclass); + for i=1:numel(fnames) + if isa(sclass.(fnames{i}),cstr) + sclasso.(fnames{i})=sclass.(fnames{i}); + end + end +end + +if ~exist('sclasso','var') + sclasso=struct([]); +end + +end Index: /issm/trunk-jpl/src/m/Array/struc_desc.m =================================================================== --- /issm/trunk-jpl/src/m/Array/struc_desc.m (revision 12996) +++ /issm/trunk-jpl/src/m/Array/struc_desc.m (revision 12996) @@ -0,0 +1,61 @@ +% +% function to find the structures with the specified descriptors +% +% [sarrayo]=struc_desc(sarray,varargin) +% +function [sarrayo]=struc_desc(sarray,varargin) + +if ~isfield(sarray,'descriptor') + if ~isempty(inputname(1)) + error('Field ''descriptor'' not found in array ''%s''.',inputname(1)); + else + error('Field ''descriptor'' not found in array %d.',1); + end +end + +sarrayo=struct([]); + +for iarg=1:nargin-1 + if iscell(varargin{iarg}) + desc= varargin{iarg}; + elseif ischar(varargin{iarg}) + desc=cellstr(varargin{iarg}); + end + + for i=1:length(desc) + sarrayoi=struc_desci(sarray,desc{i}); + if ~isempty(sarrayoi) + if isempty(sarrayo) + sarrayo =sarrayoi; + else + sarrayo(end+1)=sarrayoi; + end + end + end +end + +% if nothing found, return whole array + +if isempty(sarrayo) + sarrayo=sarray; +end + +end + +% +% function to find the structure with the specified descriptor +% +function [sarrayo]=struc_desci(sarray,str) + +sarrayo=struct([]); + +for i=1:numel(sarray) + if strcmp(sarray(i).descriptor,str) + sarrayo=sarray(i); + return + end +end + +warning(['String ''' str ''' not found in array ''' inputname(1) '''.']); + +end Index: /issm/trunk-jpl/src/m/BC/SetIceSheetBC.m =================================================================== --- /issm/trunk-jpl/src/m/BC/SetIceSheetBC.m (revision 12996) +++ /issm/trunk-jpl/src/m/BC/SetIceSheetBC.m (revision 12996) @@ -0,0 +1,64 @@ +function md=SetIceSheetBC(md) +%SETICESHEETBC - Create the boundary conditions for diagnostic and thermal models for an IceSheet with no Ice Front +% +% Usage: +% md=SetIceSheetBC(md) +% +% See also: SETICESHELFBC, SETMARINEICESHEETBC + +%node on Dirichlet +pos=find(md.mesh.vertexonboundary); +md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvx(pos)=0; +md.diagnostic.spcvy(pos)=0; +md.diagnostic.spcvz(pos)=0; +md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6); + +%Dirichlet Values +if (length(md.inversion.vx_obs)==md.mesh.numberofvertices & length(md.inversion.vy_obs)==md.mesh.numberofvertices) + disp(' boundary conditions for diagnostic model: spc set as observed velocities'); + md.diagnostic.spcvx(pos)=md.inversion.vx_obs(pos); + md.diagnostic.spcvy(pos)=md.inversion.vy_obs(pos); +else + disp(' boundary conditions for diagnostic model: spc set as zero'); +end + +%segment on neumann (Ice Front) -> none +if (md.mesh.dimension==2) + md.diagnostic.icefront=zeros(0,4); +else + md.diagnostic.icefront=zeros(0,6); +end + +%Create zeros basal melting rate and surface mass balance if not specified +if (isnan(md.surfaceforcings.precipitation) & (md.surfaceforcings.ispdd==1) & (md.surfaceforcings.ispdd==0)), + md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.precipitation specified: values set as zero'); +end +if isnan(md.surfaceforcings.mass_balance) & (md.surfaceforcings.ispdd==0), + md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.mass_balance specified: values set as zero'); +end +if isnan(md.basalforcings.melting_rate), + md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); + disp(' no basalforcings.melting_rate specified: values set as zero'); +end +if isnan(md.balancethickness.thickening_rate), + md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices,1); + disp(' no balancethickness.thickening_rate specified: values set as zero'); +end + +md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); +md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); + +if (length(md.initialization.temperature)==md.mesh.numberofvertices), + md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); + pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), + md.basalforcings.geothermalflux=50*10^-3*ones(md.mesh.numberofvertices,1); %50 mW/m^2 + end +else + disp(' no thermal boundary conditions created: no observed temperature found'); +end Index: /issm/trunk-jpl/src/m/BC/SetIceShelfBC.m =================================================================== --- /issm/trunk-jpl/src/m/BC/SetIceShelfBC.m (revision 12996) +++ /issm/trunk-jpl/src/m/BC/SetIceShelfBC.m (revision 12996) @@ -0,0 +1,95 @@ +function md=SetIceShelfBC(md,varargin) +%SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front +% +% Neumann BC are used on the ice front (an ANRGUS contour around the ice front +% must be given in input) +% Dirichlet BC are used elsewhere for diagnostic +% +% Usage: +% md=SetIceShelfBC(md,varargin) +% +% Example: +% md=SetIceShelfBC(md); +% md=SetIceShelfBC(md,'Front.exp'); +% +% See also: SETICESHEETBC, SETMARINEICESHEETBC + +%node on Dirichlet (boundary and ~icefront) +if nargin==2, + icefrontfile=varargin{1}; + if ~exist(icefrontfile), error(['SetIceShelfBC error message: ice front file ' icefrontfile ' not found']); end + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2); + nodeonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); +elseif nargin==1, + nodeonicefront=zeros(md.mesh.numberofvertices,1); +else + help SetIceShelfBC + error('bad usage'); +end +pos=find(md.mesh.vertexonboundary & ~nodeonicefront); +md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvx(pos)=0; +md.diagnostic.spcvy(pos)=0; +md.diagnostic.spcvz(pos)=0; +md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6); + +%Dirichlet Values +if (length(md.inversion.vx_obs)==md.mesh.numberofvertices & length(md.inversion.vy_obs)==md.mesh.numberofvertices) + disp(' boundary conditions for diagnostic model: spc set as observed velocities'); + md.diagnostic.spcvx(pos)=md.inversion.vx_obs(pos); + md.diagnostic.spcvy(pos)=md.inversion.vy_obs(pos); +else + disp(' boundary conditions for diagnostic model: spc set as zero'); +end + +%segment on Ice Front +%segment on Neumann (Ice Front) +pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); +if (md.mesh.dimension==2) + pressureload=md.mesh.segments(pos,:); +elseif md.mesh.dimension==3 + pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; + pressureload=[]; + for i=1:md.mesh.numberoflayers-1, + pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; + end +end + +%Add water or air enum depending on the element +pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; + +%plug onto model +md.diagnostic.icefront=pressureload; + +%Create zeros basalforcings and surfaceforcings +if (isnan(md.surfaceforcings.precipitation) & (md.surfaceforcings.ispdd==1) & (md.surfaceforcings.ispdd==0)), + md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.precipitation specified: values set as zero'); +end +if isnan(md.surfaceforcings.mass_balance) & (md.surfaceforcings.ispdd==0), + md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.mass_balance specified: values set as zero'); +end +if isnan(md.basalforcings.melting_rate), + md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); + disp(' no basalforcings.melting_rate specified: values set as zero'); +end +if isnan(md.balancethickness.thickening_rate), + md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices,1); + disp(' no balancethickness.thickening_rate specified: values set as zero'); +end + +md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); +md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); + +if (length(md.initialization.temperature)==md.mesh.numberofvertices), + md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); + pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), + md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); + end +else + disp(' no thermal boundary conditions created: no observed temperature found'); +end Index: /issm/trunk-jpl/src/m/BC/SetIceShelfBC.py =================================================================== --- /issm/trunk-jpl/src/m/BC/SetIceShelfBC.py (revision 12996) +++ /issm/trunk-jpl/src/m/BC/SetIceShelfBC.py (revision 12996) @@ -0,0 +1,98 @@ +import os +import numpy + +def SetIceShelfBC(md,icefrontfile=''): + """ + SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front + + Neumann BC are used on the ice front (an ANRGUS contour around the ice front + must be given in input) + Dirichlet BC are used elsewhere for diagnostic + + Usage: + md=SetIceShelfBC(md,varargin) + + Example: + md=SetIceShelfBC(md); + md=SetIceShelfBC(md,'Front.exp'); + + See also: SETICESHEETBC, SETMARINEICESHEETBC + """ + + #node on Dirichlet (boundary and ~icefront) + if icefrontfile: + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) + nodeonicefront=double(md.mesh.vertexonboundary and nodeinsideicefront) + else: + nodeonicefront=numpy.zeros(md.mesh.numberofvertices) + +# pos=find(md.mesh.vertexonboundary & ~nodeonicefront); + pos=[i for i,(vob,noif) in enumerate(zip(md.mesh.vertexonboundary,nodeonicefront)) if vob and not noif] + md.diagnostic.spcvx=float('NaN')*numpy.ones(md.mesh.numberofvertices) + md.diagnostic.spcvy=float('NaN')*numpy.ones(md.mesh.numberofvertices) + md.diagnostic.spcvz=float('NaN')*numpy.ones(md.mesh.numberofvertices) + md.diagnostic.spcvx[pos]=0 + md.diagnostic.spcvy[pos]=0 + md.diagnostic.spcvz[pos]=0 + md.diagnostic.referential=float('NaN')*numpy.ones((md.mesh.numberofvertices,6)) + + #Dirichlet Values + if numpy.size(md.inversion.vx_obs)==md.mesh.numberofvertices and numpy.size(md.inversion.vy_obs)==md.mesh.numberofvertices: + print ' boundary conditions for diagnostic model: spc set as observed velocities' + md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] + md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] + else: + print ' boundary conditions for diagnostic model: spc set as zero' + + #segment on Ice Front + #segment on Neumann (Ice Front) +# pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); + pos=[i for i,(noif1,noif2) in enumerate(zip(nodeonicefront[md.mesh.segments[:,0].astype('int')-1],nodeonicefront[md.mesh.segments[:,1].astype('int')-1])) if noif1 or noif2] + if md.mesh.dimension==2: + pressureload=md.mesh.segments[pos,:] + elif md.mesh.dimension==3: +# pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; + pressureload_layer1=numpy.concatenate((md.mesh.segments[pos,0:2],md.mesh.segments[pos,1]+md.mesh.numberofvertices2d,md.mesh.segments[pos,0]+md.mesh.numberofvertices2d,md.mesh.segments[pos,2]),axis=1) + pressureload=numpy.zeros((0,5)) + for i in xrange(1,md.mesh.numberoflayers): +# pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; + pressureload=numpy.concatenate((pressureload,numpy.concatenate((pressureload_layer1[:,0:3]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d),axis=1)),axis=0) + + #Add water or air enum depending on the element +# pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; + pressureload=numpy.concatenate((pressureload,1*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape((-1,1))),axis=1) + + #plug onto model + md.diagnostic.icefront=pressureload + + #Create zeros basalforcings and surfaceforcings + if numpy.isnan(md.surfaceforcings.precipitation).all(): + md.surfaceforcings.precipitation=numpy.zeros(md.mesh.numberofvertices) + print ' no surfaceforcings.precipitation specified: values set as zero' + if numpy.isnan(md.surfaceforcings.mass_balance).all(): + md.surfaceforcings.mass_balance=numpy.zeros(md.mesh.numberofvertices) + print ' no surfaceforcings.mass_balance specified: values set as zero' + if numpy.isnan(md.basalforcings.melting_rate).all(): + md.basalforcings.melting_rate=numpy.zeros(md.mesh.numberofvertices) + print ' no basalforcings.melting_rate specified: values set as zero' + if numpy.isnan(md.balancethickness.thickening_rate).all(): + md.balancethickness.thickening_rate=numpy.zeros(md.mesh.numberofvertices) + print ' no balancethickness.thickening_rate specified: values set as zero' + + md.prognostic.spcthickness=float('NaN')*numpy.ones(md.mesh.numberofvertices) + md.balancethickness.spcthickness=float('NaN')*numpy.ones(md.mesh.numberofvertices) + + if numpy.size(md.initialization.temperature)==md.mesh.numberofvertices: + md.thermal.spctemperature=float('NaN')*numpy.ones(md.mesh.numberofvertices) +# pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + pos=[i for i,vos in enumerate(md.mesh.vertexonsurface) if vos] + md.thermal.spctemperature[pos]=md.initialization.temperature[pos] # impose observed temperature on surface + if not numpy.size(md.basalforcings.geothermalflux)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=numpy.zeros(md.mesh.numberofvertices) + else: + print ' no thermal boundary conditions created: no observed temperature found' + + return md + Index: /issm/trunk-jpl/src/m/BC/SetMarineIceSheetBC.m =================================================================== --- /issm/trunk-jpl/src/m/BC/SetMarineIceSheetBC.m (revision 12996) +++ /issm/trunk-jpl/src/m/BC/SetMarineIceSheetBC.m (revision 12996) @@ -0,0 +1,107 @@ +function md=SetMarineIceSheetBC(md,varargin) +%SETICEMARINESHEETBC - Create the boundary conditions for diagnostic and thermal models for a Marine Ice Sheet with Ice Front +% +% Neumann BC are used on the ice front (an ARGUS contour around the ice front +% can be given in input, or it will be deduced as onfloatingice & onboundary) +% Dirichlet BC are used elsewhere for diagnostic +% +% Usage: +% md=SetMarineIceSheetBC(md,icefrontfile) +% md=SetMarineIceSheetBC(md) +% +% Example: +% md=SetMarineIceSheetBC(md,'Front.exp') +% md=SetMarineIceSheetBC(md) +% +% See also: SETICESHELFBC, SETMARINEICESHEETBC + +%node on Dirichlet (boundary and ~icefront) +if nargin==2, + %User provided Front.exp, use it + icefrontfile=varargin{1}; + if ~exist(icefrontfile) + error(['SetMarineIceSheetBC error message: ice front file ' icefrontfile ' not found']); + end + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2); + vertexonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront); +else + %Guess where the ice front is + vertexonfloatingice=zeros(md.mesh.numberofvertices,1); + vertexonfloatingice(md.mesh.elements(find(md.mask.elementonfloatingice),:))=1; + vertexonicefront=double(md.mesh.vertexonboundary & vertexonfloatingice); +end +pos=find(md.mesh.vertexonboundary & ~vertexonicefront); +if isempty(pos), + warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually') +end +md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1); +md.diagnostic.spcvx(pos)=0; +md.diagnostic.spcvy(pos)=0; +md.diagnostic.spcvz(pos)=0; +md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6); + +%Dirichlet Values +if (length(md.inversion.vx_obs)==md.mesh.numberofvertices & length(md.inversion.vy_obs)==md.mesh.numberofvertices) + disp(' boundary conditions for diagnostic model: spc set as observed velocities'); + md.diagnostic.spcvx(pos)=md.inversion.vx_obs(pos); + md.diagnostic.spcvy(pos)=md.inversion.vy_obs(pos); +else + disp(' boundary conditions for diagnostic model: spc set as zero'); +end + +md.hydrology.spcwatercolumn=zeros(md.mesh.numberofvertices,2); +pos=find(md.mesh.vertexonboundary); +md.hydrology.spcwatercolumn(pos,1)=1; + +%segment on Neumann (Ice Front) +pos=find(vertexonicefront(md.mesh.segments(:,1)) | vertexonicefront(md.mesh.segments(:,2))); +if (md.mesh.dimension==2) + pressureload=md.mesh.segments(pos,:); +elseif md.mesh.dimension==3 + pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; + pressureload=[]; + for i=1:md.mesh.numberoflayers-1, + pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; + end +end + +%Add water or air enum depending on the element +pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))+ 0*md.mask.elementongroundedice(pressureload(:,end))]; + +%plug onto model +md.diagnostic.icefront=pressureload; + + +%Create zeros basalforcings and surfaceforcings +if (isnan(md.surfaceforcings.precipitation)& (md.surfaceforcings.ispdd==1) & (md.surfaceforcings.ispdd==0)), + md.surfaceforcings.precipitation=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.precipitation specified: values set as zero'); +end +if isnan(md.surfaceforcings.mass_balance) & (md.surfaceforcings.ispdd==0), + md.surfaceforcings.mass_balance=zeros(md.mesh.numberofvertices,1); + disp(' no surfaceforcings.mass_balance specified: values set as zero'); +end +if isnan(md.basalforcings.melting_rate), + md.basalforcings.melting_rate=zeros(md.mesh.numberofvertices,1); + disp(' no basalforcings.melting_rate specified: values set as zero'); +end +if isnan(md.balancethickness.thickening_rate), + md.balancethickness.thickening_rate=zeros(md.mesh.numberofvertices,1); + disp(' no balancethickness.thickening_rate specified: values set as zero'); +end + +md.prognostic.spcthickness=NaN*ones(md.mesh.numberofvertices,1); +md.balancethickness.spcthickness=NaN*ones(md.mesh.numberofvertices,1); + +if (length(md.initialization.temperature)==md.mesh.numberofvertices), + md.thermal.spctemperature=NaN*ones(md.mesh.numberofvertices,1); + pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), + md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); + md.basalforcings.geothermalflux(find(md.mask.vertexongroundedice))=50*10^-3; %50mW/m2 + end +else + disp(' no thermal boundary conditions created: no observed temperature found'); +end Index: /issm/trunk-jpl/src/m/Basins/basinzoom.m =================================================================== --- /issm/trunk-jpl/src/m/Basins/basinzoom.m (revision 12996) +++ /issm/trunk-jpl/src/m/Basins/basinzoom.m (revision 12996) @@ -0,0 +1,94 @@ +function varargout=basinzoom(varargin) +%ANTZOOM - zoom on a basin in Antarctica or Greenland. +% +% This function zooms on an existing figure describing Antarctica or Greenland +% The zooming depends on the region name provided as input. +% +% Usage: +% varargout=basinzoom(options) + +%recover some options, and set defaults + +%is varargin an options database already? +if nargin==0, + options=pairoptions(varargin{:}); +elseif (isa(varargin{1},'plotoptions') | isa(varargin{1},'pairoptions')), + %do nothing to the varargin: + options=varargin{1}; +else + %process varargin for options: + options=pairoptions(varargin{:}); +end + +unitmultiplier=getfieldvalue(options,'unit',NaN); +basin=getfieldvalue(options,'basin'); + +if exist(options,'basindelta'), + + basindeltax=getfieldvalue(options,'basindelta',300); + basindeltay=getfieldvalue(options,'basindelta',300); +else + basindeltax=getfieldvalue(options,'basindeltax',300); + basindeltay=getfieldvalue(options,'basindeltay',300); +end + +%multiply by 1000 to get kms +basindeltax=basindeltax*1000; +basindeltay=basindeltay*1000; + +%Ok, find basin we are talking about: +load([jplsvn() '/projects/ModelData/Names/Names.mat']); + +%Go through names: +found=0; +for i=1:size(names,1), + if strcmpi(names{i,1},basin), + %ok, we've got the region. Get lat and long: + long=names{i,2}; + lat=names{i,3}; + hemisphere=names{i,4}; + found=1; + break; + end +end + +if ~found, + error(['basinzoom error message: cannot find basin ' basin '. Use isbasin to determine a basin name.']); +end + +if hemisphere==+1, + central_meridian=getfieldvalue(options,'central_meridian',45); + standard_parallel=getfieldvalue(options,'standard_parallel',70); +else + central_meridian=getfieldvalue(options,'central_meridian',0); + standard_parallel=getfieldvalue(options,'standard_parallel',71); +end + +%Transform lat long into x,y: +[xc,yc]=ll2xy(lat,long,hemisphere,central_meridian,standard_parallel); + +%compute x0,x1 and y0,y1 using basindeltax and basindeltay +x0=xc-basindeltax/2; +x1=xc+basindeltax/2; +y0=yc-basindeltay/2; +y1=yc+basindeltay/2; + +if ~isnan(unitmultiplier) + x0=x0*unitmultiplier; + x1=x1*unitmultiplier; + y0=y0*unitmultiplier; + y1=y1*unitmultiplier; +end + +%if output arguments are present, return the limits, +%otherwise, set them on the current graphic. +if nargout==2, + found=1; + varargout{1}=[x0 x1]; + varargout{2}=[y0 y1]; +else + xlim([x0 x1]); + ylim([y0 y1]); + found=1; + daspect([1;1;1]); +end Index: /issm/trunk-jpl/src/m/Basins/isbasin.m =================================================================== --- /issm/trunk-jpl/src/m/Basins/isbasin.m (revision 12996) +++ /issm/trunk-jpl/src/m/Basins/isbasin.m (revision 12996) @@ -0,0 +1,19 @@ +function isbasin(name) +%ISBASIN: figure out if a basin name exists. +% +% +% Usage: index=isbasin('jks'); +% +% + + +%First, load basin names: +load([jplsvn '/projects/ModelData/Names/Names.mat']); + + +%go through names: +for i=1:length(names), + if ~isempty(strfind(names{i,1},name)), + disp(['''' names{i,1} ''' Long:' num2str(names{i,2}) ' Lat:' num2str(names{i,3}) ]); + end +end Index: /issm/trunk-jpl/src/m/Basins/plotbasins.m =================================================================== --- /issm/trunk-jpl/src/m/Basins/plotbasins.m (revision 12996) +++ /issm/trunk-jpl/src/m/Basins/plotbasins.m (revision 12996) @@ -0,0 +1,18 @@ +%display all the domain outlines in a directory + +basins=listfiles; + +hold on +for i=1:length(basins), + %check whether this is a .exp file + basin=basins{i}; + if strcmpi(basin(end-3:end),'.exp'), + + contour=expread(basin,0); + x=contour(1).x; + y=contour(1).y; + x0=mean(x); y0=mean(y); + text(x0,y0,basin(1:end-4),'Fontsize',14); + expdisp(basin); + end +end Index: /issm/trunk-jpl/src/m/Basins/showbasins.m =================================================================== --- /issm/trunk-jpl/src/m/Basins/showbasins.m (revision 12996) +++ /issm/trunk-jpl/src/m/Basins/showbasins.m (revision 12996) @@ -0,0 +1,69 @@ +function showbasins(varargin) +%SHOWBASINS - return basins that are within the xlim and ylim +% +% Usage: +% names=showbasins(options); +% Options: +% 'unit' default 1 +% 'hemisphere': default +1; +% 'central_meridian: 45 for Greenland and 0 for Antarctica +% 'standard_parallel: 70 for Greenland and 71 for Antarctica +% + +%is varargin an options database already? +if nargin==0, + options=pairoptions(varargin{:}); +elseif (isa(varargin{1},'plotoptions') | isa(varargin{1},'pairoptions')), + %do nothing to the varargin: + options=varargin{1}; +else + %process varargin for options: + options=pairoptions(varargin{:}); +end + + +%recover some options, and set defaults +unitmultiplier=getfieldvalue(options,'unit',1); +fontsize=getfieldvalue(options,'fontsize',12); +hemisphere=getfieldvalue(options,'hemisphere'); + +if strcmpi(hemisphere,'s'), + hemisphere=-1; +elseif strcmpi(hemisphere,'n'), + hemisphere=+1; +else + error('showbasins error message: hemispehre should be either ''n'' or ''s'''); + end + +if hemisphere==+1, + central_meridian=getfieldvalue(options,'central_meridian',45); + standard_parallel=getfieldvalue(options,'standard_parallel',70); +else + central_meridian=getfieldvalue(options,'central_meridian',0); + standard_parallel=getfieldvalue(options,'standard_parallel',71); +end + +%Ok, find basin we are talking about: +load([jplsvn '/projects/ModelData/Names/Names.mat']); + +%Get xlim and ylim, and convert into lat,long: +xlimits=xlim; x0=xlimits(1); x1=xlimits(2); +ylimits=ylim; y0=ylimits(1); y1=ylimits(2); + +%Convert names lat and long into x,y: +lat=cell2mat(names(:,3)); +long=cell2mat(names(:,2)); + +%Now, convert lat,long into x,y: +[x,y]=ll2xy(lat,long,hemisphere,central_meridian,standard_parallel); + +%Find x,y within xlimits and ylimits: +locations=find(x>x0 & xy0 & yrtime, + error(['QueueRequirements: time should be < ' num2str(rtime) ' for queue: ' queue]); +end + +%check on np requirements +if np<=0, + error('QueueRequirements: np should be a positive number'); +end Index: /issm/trunk-jpl/src/m/Cluster/parallelrange.m =================================================================== --- /issm/trunk-jpl/src/m/Cluster/parallelrange.m (revision 12996) +++ /issm/trunk-jpl/src/m/Cluster/parallelrange.m (revision 12996) @@ -0,0 +1,23 @@ +function [i1,i2]=parallelrange(rank,numprocs,globalsize) +%PARALLELRANGE - from a rank, and a number of processors, figure out a range, for parallel tasks. +% +% Usage: +% [i1,i1]=parallelrange(rank,numprocs,globalsize) + +num_local_rows=zeros(numprocs,1); + +for i=1:numprocs, + %we use floor. we under distribute rows. The rows left are then redistributed, therefore resulting in a more even distribution. + num_local_rows(i)=floor(globalsize/numprocs); +end + + +%There may be some rows left. Distribute evenly. +row_rest=globalsize - numprocs*floor(globalsize/numprocs); + +for i=1:row_rest, + num_local_rows(i)=num_local_rows(i)+1; +end + +i1=sum(num_local_rows(1:rank-1))+1; +i2=i1+num_local_rows(rank)-1; Index: /issm/trunk-jpl/src/m/Cluster/parallelrange.py =================================================================== --- /issm/trunk-jpl/src/m/Cluster/parallelrange.py (revision 12996) +++ /issm/trunk-jpl/src/m/Cluster/parallelrange.py (revision 12996) @@ -0,0 +1,25 @@ +#! /usr/bin/env python +def parallelrange(rank,numprocs,globalsize): + """ + PARALLELRANGE - from a rank, and a number of processors, figure out a range, for parallel tasks. + + Usage: + i1,i2=parallelrange(rank,numprocs,globalsize) + """ + + #We use floor. we under distribute rows. The rows left are then redistributed, therefore resulting in a more even distribution. + num_local_rows=[int(globalsize/numprocs) for i in xrange(numprocs)] + + #There may be some rows left. Distribute evenly. + row_rest=globalsize - numprocs*int(globalsize/numprocs) + + for i in xrange(row_rest): + num_local_rows[i]=num_local_rows[i]+1 + + i1=0 + for i in xrange(rank-1): + i1+=num_local_rows[i] + i2=i1+num_local_rows[rank-1]-1 + + return i1,i2 + Index: /issm/trunk-jpl/src/m/DataProcessing/CreateDataBoundaries.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/CreateDataBoundaries.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/CreateDataBoundaries.m (revision 12996) @@ -0,0 +1,43 @@ +function [Xedge,Yedge,EdgeValues]=CreateDataBoundaries(x_m,y_m,x_matrix,y_matrix,datamatrix); +%CREATEDATABOUNDARIES - Create values on the edge of the matrix +% +% This function create vectors with coordinates and values to constrain a matrix +% on its edge from a given matrix tiwh data everywhere. +% x_m and y_m belongs to the matrix to be constrained +% x_matrix, y_matrix belongs to the matrix to be constrained with +% datamatrix is the matrix with values for the constraint +% +% Usage: +% [Xedge,Yedge,EdgeValues]=CreateDataBoundaries(x_m,y_m,x_matrix,y_matrix,datamatrix); +% +% See also: TRACKSTOMATRIX, CREATEDATAMATRIX + +%Check the consistency of the data matrix +if(length(x_matrix)~=(size(datamatrix,2)+1) | length(y_matrix)~=(size(datamatrix,1)+1)), + error('CreateDataBoundaries error message: size of matrix and vectors to constrained not consistent') +end + +nxglobal=length(x_m); +nyglobal=length(y_m); + +%Create the edgevalues and coordinates +xedge1=x_m(1)*ones(nyglobal,1); +xedge2=x_m(2:end-1); +xedge3=x_m(end)*ones(nyglobal,1); +xedge4=x_m(2:end-1); +xedge5=x_m(2)*ones(nyglobal-2,1); +xedge6=x_m(3:end-2); +xedge7=x_m(end-1)*ones(nyglobal-2,1); +xedge8=x_m(3:end-2); +yedge1=y_m; +yedge2=y_m(1)*ones(nxglobal-2,1); +yedge3=y_m; +yedge4=y_m(end)*ones(nxglobal-2,1); +yedge5=y_m(2:end-1); +yedge6=y_m(2)*ones(nxglobal-4,1); +yedge7=y_m(2:end-1); +yedge8=y_m(end-1)*ones(nxglobal-4,1); + +Xedge=[xedge1;xedge2;xedge3;xedge4;xedge5;xedge6;xedge7;xedge8]; +Yedge=[yedge1;yedge2;yedge3;yedge4;yedge5;yedge6;yedge7;yedge8]; +EdgeValues=DataInterp(x_matrix,y_matrix,datamatrix,Xedge,Yedge); Index: /issm/trunk-jpl/src/m/DataProcessing/CreateDataMatrix.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/CreateDataMatrix.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/CreateDataMatrix.m (revision 12996) @@ -0,0 +1,94 @@ +function [Mvalue Mx My]=CreateDataMatrix(x_m,y_m,track_coord,track_values), +%CREATEDATAMATRIX - Create a map with average values of map +% +% This routine creates a map with average values of tracks. +% x_m1 and y_m1 are two vectors containing the coordinates of the matrix +% trac_coord is an exp file containing the coordinates of the tracks (x and y) +% trav_values is a vector with the values along the track coordinates +% +% Usage: +% [Mvalue Mx My]=CreateDataMatrix(x_m,y_m,track_coord,track_values), +% +% Example: +% [Mvalue Mx My]=CreateDataMatrix(x_m,y_m,'trackcoord.exp',thickness_track) +% +% See also: CREATEDATABOUNDARIES, TRACKSTOMATRIX + +%Read the points of the tracks +stru=expread(track_coord,1); +nods=stru.nods; +xtracks=stru.x'; +ytracks=stru.y'; + +%First check that the parameters are ok: +if (size(track_values,1)~=nods) || (size(xtracks,2)~=nods) || (size(ytracks,2)~=nods), + error('CreateDataMatrix error message : track coordinates and track values must have the same size'); +end + +%Compute number of rows and columns +numrow=size(y_m,1)-1; +numcol=size(x_m,1)-1; + +%Remove useless points of the track +points=find(track_values==0); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; +points=find(isnan(track_values)); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; +points=find(track_values<0); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; + +points=find(xtracksx_m(end) | ytracksy_m(end)); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; + +%initialize some matrices +numpoints=zeros(numrow,numcol); +value=zeros(numrow,numcol); +coordx=zeros(numrow,numcol); +coordy=zeros(numrow,numcol); + +%Loop over the points of the track +nel=size(track_values,1); +fprintf('%s',' track processing progress: 0.00 %'); +for i=1:nel; + if mod(i,1000)==0, + fprintf('\b\b\b\b\b\b\b') + fprintf('%5.2f%s',i/nel*100,' %'); + end + + x=xtracks(i); + y=ytracks(i); + + %get indices for the matrix + indexx=max(find(x_m1000, + fprintf('\b\b\b\b\b\b\b\b') + fprintf('%4.2f%s\n',100,' %'); +end + +%Change the values of numoverlap to 1 if 0 since we are going to devide by this matrix +numpoints(find(~numpoints))=1; + +%Create the center of mass for coordiantes and values. +Mvalue=value./numpoints; +Mx=coordx./numpoints; +My=coordy./numpoints; Index: /issm/trunk-jpl/src/m/DataProcessing/MisfitDeinterlace.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/MisfitDeinterlace.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/MisfitDeinterlace.m (revision 12996) @@ -0,0 +1,21 @@ +function Jstruct=MisfitDeinterlace(misfit,type) +%MISFITDEINTERLACE - deinterlace misfits that are mixed together, using type. +% +% Usage: +% Jstruct=MisfitDeinterlace(misfit,type) +% +% Example: +% Jstruct=MisfitDeinterlace(md.results.diagnostic.J,md.fit) +% +% +Jstruct=struct(); + +count=1; +for i=0:max(type), + pos=find(type==i); + if length(pos), + Jstruct(count).type=i; + Jstruct(count).J=misfit(pos); + count=count+1; + end +end Index: /issm/trunk-jpl/src/m/DataProcessing/TracksToMatrix.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/TracksToMatrix.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/TracksToMatrix.m (revision 12996) @@ -0,0 +1,84 @@ +function [x_f y_f MatData]=TracksToMatrix(xmin,ymin,nx,ny,posting,track_coord,track_values,theta,varargin), +%TRACKSTOMATRIX - Create a map from tracks +% +% This routine creates a map from tracks using a Kriging algorithm given by the package DACE. +% - xmin and ymin are two scalars that are the extreme values of the data matrix one wants to create +% - posting is a scalar giving the posting of the matrix to be created in meters +% - trac_coord is an Argus file containing the coordinates of the tracks (x and y) +% - trav_values is a vector with the values along the track coordinates +% - theta is a parameter of the correlation function stricly positive +% varagin can contain a matrix of data to constrain the matrix to be created +% it shoud contain indices x and y and the matrix +% +% Usage: +% [x_ y_f MatData]=TracksToMatrix(xmin,ymin,nx,ny,posting,track_coord,track_values,theta), +% +% Example: +% [x_f y_f Thickness]=TracksToMatrix(-10^6,10^6,200,180,1000,'trackcoord.exp',thickness_values,theta), +% [x_f y_f Thickness]=TracksToMatrix(-10^6,10^6,200,180,1000,'trackcoord.exp',thickness_values,theta,x_m,y_m,globalthickness), +% +% See also: CREATEDATABOUNDARIES, CREATEDATAMATRIX + +%some checks +if nargin~=8 & nargin~=11, + error(' TracksToMatrix error message: wrong number of arguments') +end + +%Add path to dace +addpath([issmdir() '/externalpackages/dace/install']) + +%First create the x_m and y_m fot the matrix +x_f=[xmin:posting:xmin+posting*nx]'; +y_f=[ymin:posting:ymin+posting*ny]'; + +%Now create a bigger map we will then truncate +x_m=[xmin-posting*nx/2:posting:xmin+posting*nx*3/2]'; +y_m=[ymin-posting*ny/2:posting:ymin+posting*ny*3/2]'; + +%Create DataMatrix with local averaging of tracks +[Mvalue Mx My]=CreateDataMatrix(x_m,y_m,track_coord,track_values); + +%Create vector for these coordinates and values +Svalue=sparse(Mvalue); +Sx=sparse(Mx); +Sy=sparse(My); +[i,j,Values]=find(Svalue); +[i,j,X]=find(Sx); +[i,j,Y]=find(Sy); +Coord=[X,Y]; + +%Create boundaries for the track if specified +if nargin==11, + disp(' constain the border of matrix with global matrix'); + %Find out the elements to counstrain the border + x_matrix=varargin{1}; + y_matrix=varargin{2}; + datamatrix=varargin{3}; + + %Create values on the border of the smaller map + [Xedge,Yedge,EdgeValues]=CreateDataBoundaries(x_m,y_m,x_matrix,y_matrix,datamatrix); + + %Create values on the border of the larger map + [Xedge2,Yedge2,EdgeValues2]=CreateDataBoundaries(x_f,y_f,x_matrix,y_matrix,datamatrix); + + %Add these values to the track values + Values=[Values;EdgeValues;EdgeValues2]; + Coord=[X,Y;Xedge,Yedge;Xedge2,Yedge2]; +end + +%Create model for data +disp(' create the statiscal model of the data'); +[dmodel,perf]=dacefit(Coord,Values,@regpoly1,@corrgauss,theta); + +%Create design site(points where we are looking for the data) +Points=nodesamp([x_f(1)+posting/2,y_f(1)+posting/2;x_f(end)-posting/2,y_f(end)-posting/2],[length(x_f)-1;length(y_f)-1]); + +%Compute data on these points +disp(' predict the values'); +VecData=predictor(Points,dmodel); + +%Reshape to get a matrix +MatData=reshape(VecData,ny,nx); + +%remove DACE path +rmpath([issmdir() '/externalpackages/dace/install']); Index: /issm/trunk-jpl/src/m/DataProcessing/addtrack.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/addtrack.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/addtrack.m (revision 12996) @@ -0,0 +1,156 @@ +function [x_m2 y_m2 values2]=addtrack(x_m1,y_m1,values1,track_coord,track_values,distance,exponent,varargin), +%ADDTRACK - modify a map to take values of a track +% +% This routine modifies a map to improve it with values of tracks. +% This output map has more values than the input one so that the values +% of the tracks are relevant. +% x_m1 and y_m1 are two vectors containing the coordinates of the matrix +% the distance between two points must be the same everywhere +% values1 is a matrix of size (y_m1-1)*(x_m1-1) +% trac_coord is an exp file containing the coordinates of the tracks (x and y) +% trav_values is a vector with the values along the track coordinates +% distance indicates the distance from the tracks where points have to be modified +% exposant allows to chance the influence of the track and the map +% it must be positive and usually is superior to 1. +% +% Usage: +% [x_m2 y_m2 values1 values2]=addtrack(x_m1,y_m1,values1,track_coord,track_values,distance,exposant[,subdivision]) +% +% Example: +% [xnew ynew valuesnew]=addtrack(x_m,y_m,thickness,'trackcoord.exp',thickness_track,1000,2) +% [xnew ynew valuesnew]=addtrack(x_m,y_m,thickness,'trackcoord.exp',thickness_track,1000,2,3) + +%Create a new picture precise enough to be modified by the tracks +%Read the points of the tracks +stru=expread(track_coord,1); +nods=stru.nods; +xtracks=stru.x'; +ytracks=stru.y'; + +%First check that the parameters are ok: +if (size(track_values,1)~=nods) || (size(xtracks,2)~=nods) || (size(ytracks,2)~=nods), + error('addtrack error message : track coordinates and track values must have the same size'); +elseif distance<0, + error('addtrack error message : the distance must be a positive value'); +elseif exponent<0, + error('addtrack error message : the exponent must be a positive value'); +elseif (size(x_m1,1)~=(size(values1,2)+1)) || (size(y_m1,1)~=(size(values1,1)+1)), + error('addtrack error message : problem in the map, check the size of x_m1, y_m1 and values1'); +end + +%stru.nods=4; +%xtracks=[50 50 55 62]; % 2 3 4 5 6 7 8 9 1 ]'; +%ytracks=[40 40.5 41 41]; % 5 5 5 5 5 5 5 5 8 ]'; +%x_m1=[1:10:101]'; +%y_m1=[1:10:101]'; +%track_values=2*ones(4,1); +%values1=ones(10,10); + +%Find the average distance between two points of the tracks +av_x=sum(abs(diff(xtracks)))/(stru.nods-1); +av_y=sum(abs(diff(ytracks)))/(stru.nods-1); +dist_av=sqrt(av_x^2+av_y^2); + +%Calculate the multiplicate factor for the new values: +if nargin==7, + mult=round((x_m1(2)-x_m1(1))/(1*dist_av)); +else + mult=varargin{1}; +end + +%Plug the values in the new multiplied matrix +values=zeros(mult*size(values1,1),mult*size(values1,2)); + +for i=1:mult, + for j=1:mult, + values(i:mult:end,j:mult:end)=values1; + end +end + +%Create the new x and y addapted to the matrix +x_m2=linspace(x_m1(1),x_m1(end),mult*(size(x_m1,1)-1)+1)'; +y_m2=linspace(y_m1(1),y_m1(end),mult*(size(y_m1,1)-1)+1)'; + +%Create a new set of x and y correponding to the medium value on the matrix +x_med=(x_m2(1:end-1)+x_m2(2:end))/2; +y_med=(y_m2(1:end-1)+y_m2(2:end))/2; + +numrow=size(y_med,1); +numcol=size(x_med,1); + +%Create new x and y to have the hole matrix +x_mat=repmat(x_med',numrow,1); +y_mat=repmat(y_med,1,numcol); + +%Remove useless points of the track +points=find(track_values==0); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; +points=find(isnan(track_values)); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; + +%Remove points outside of the map +points=find(xtracksx_med(end) | ytracksy_med(end)); +track_values(points)=[]; +xtracks(points)=[]; +ytracks(points)=[]; + +%initialize some matrices +numoverlap=zeros(numrow,numcol); +weights=zeros(numrow,numcol); +weightsvalues=zeros(numrow,numcol); + +%Loop over the points of the track +nel=size(track_values,1); +fprintf('%s',' track processing progress: 0.00 %'); +for i=1:nel; + if mod(i,1000)==0, + fprintf('\b\b\b\b\b\b\b') + fprintf('%5.2f%s',i/nel*100,' %'); + end + + x=xtracks(i); + y=ytracks(i); + + %get indices that are modified + indexx1=max(find(x_medx+distance)); + if isempty( indexx2), indexx2=numrow; end + indexy1=max(find(y_medy+distance)); + if isempty( indexy2), indexy2=numcol; end + + + %get weighing coefficient + val=track_values(i); + distances=sqrt((x-x_mat(indexy1:indexy2,indexx1:indexx2)).^2+(y-y_mat(indexy1:indexy2,indexx1:indexx2)).^2); + coeff=min(1,(distances/distance)).^(1/exponent); + + %update numoverlap and weights + numoverlap(indexy1:indexy2,indexx1:indexx2)=numoverlap(indexy1:indexy2,indexx1:indexx2)+1; + weights(indexy1:indexy2,indexx1:indexx2)=weights(indexy1:indexy2,indexx1:indexx2)+coeff; + weightsvalues(indexy1:indexy2,indexx1:indexx2)=weightsvalues(indexy1:indexy2,indexx1:indexx2)+(1-coeff)*val; + +end +if nel>1000, + fprintf('\b\b\b\b\b\b\b\b') + fprintf('%4.2f%s\n',100,' %'); +end + + +%Change the values of numoverlap to 1 if 0 since we are going to devide by this matrix +numoverlap(find(~numoverlap))=1; + +%Same thing for weights since values far from the tracks don't change +weights(find(~weights))=1; + +%Create the final matrix depending on the previous matrix +values=(values.*weights+weightsvalues)./numoverlap; + +%Plug the values of the track in the new matrix +values2=values; Index: /issm/trunk-jpl/src/m/DataProcessing/data_processing_tool.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/data_processing_tool.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/data_processing_tool.m (revision 12996) @@ -0,0 +1,467 @@ +function varargout = data_processing_tool(varargin) +%DATA_PROCESSING_TOOL - GUI to process binary data +% +% this routine is a GUI that helps the user to open +% a binary file (Little Endian, Big Endian, Float 32, +% double,...) and save a Matlab file (.mat) with the +% processed data and the coordinates +% +% Usage: +% data_processing_tool + + gui_Singleton = 1; + gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @data_processing_tool_OpeningFcn, ... + 'gui_OutputFcn', @data_processing_tool_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); + if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); + end + + if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); + else + gui_mainfcn(gui_State, varargin{:}); + end +end + +function data_processing_tool_OpeningFcn(hObject, eventdata, handles, varargin) + handles.output = hObject; + + %enable toolbar (useful for caxis...) + set(hObject,'toolbar','figure'); + + % Update handles structure + guidata(hObject, handles); + + %this variable used to prevent users from breaking the GUI + %the variable is set to 1 once the data has been processed + handles.processDataCompleted=0; + + %initialize other variables + handles.Msize=NaN; + handles.Nsize=NaN; + handles.numvectors=NaN; + handles.endian=NaN; + handles.datatype=NaN; + handles.dx=NaN; + handles.dy=NaN; + handles.xEast=NaN; + handles.yNorth=NaN; + + %two files permitted + set(handles.inputFile,'Max',1); + set(handles.inputFile,'Min',0); + + % Update handles structure + guidata(hObject, handles); +end + +% --- Outputs from this function are returned to the command line. +function varargout = data_processing_tool_OutputFcn(hObject, eventdata, handles) + + % Get default command line output from handles structure + varargout{1} = handles.output; +end + + +function inputFile_Callback(hObject, eventdata, handles) +%no code needed for this callback, the listbox is only used as a visual +end + +function addFiles_pushbutton_Callback(hObject, eventdata, handles) + %gets input file(s) from user. the sample data files have extension .s2p + [input_file,pathname] = uigetfile( ... + {'*.*', 'All Files (*.*)'}, ... + 'Select files', ... + 'MultiSelect', 'on'); + + %if file selection is cancelled, pathname should be zero + %and nothing should happen + if pathname==0 + return + end + + handles.processDataCompleted=1; + + %gets the current data file names inside the listbox + inputFileName=get(handles.inputFile,'String'); + + %if they only select one file, then the data will not be a cell + inputFileName= fullfile(pathname,input_file); + + %updates the gui to display all filenames in the listbox + set(handles.inputFile,'String',inputFileName); + + %make sure first file is always selected so it doesn't go out of range + %the GUI will break if this value is out of range + set(handles.inputFile,'Value',1); + + % Update handles structure + guidata(hObject, handles); +end + +function reset_pushbutton_Callback(hObject, eventdata, handles) + %resets the GUI by clearing all relevant fields + + handles.processDataCompleted = 0; + + %clears the axes + cla(handles.axes1,'reset'); + + %set the popupmenu to default value +% set(handles.plot_popupmenu,'Value',1); + + %clears the contents of the listbox + set(handles.inputFile,'String',''); + set(handles.inputFile,'Value',0); + + %updates the handles structure + guidata(hObject, handles); +end + +function plotdata_pushbutton_Callback(hObject, eventdata, handles) + + %get the list of input file names from the listbox + inputFileName=get(handles.inputFile,'String'); + + %checks to see if the user selected any input files + %if not, nothing happens + if isempty(inputFileName) + errordlg('Select a file first!') + return + end + + %disables the button while data is processing + disableButtons(handles); + refresh(data_processing_tool); + + %parse options + if ~isnan(handles.Msize) + M=handles.Msize; + else + errordlg('Number of lines (M) not valid') + return + end + if ~isnan(handles.Nsize) + N=handles.Nsize; + else + errordlg('Number of rows (N) not valid') + return + end + if ~isnan(handles.numvectors) + numvectors=handles.numvectors; + %change M + M=numvectors*M; + else + numvectors=1; + end + if ~isnan(handles.endian) + endian=handles.endian; + else + endian=1; + end + if ~isnan(handles.datatype) + datatype=handles.datatype; + else + datatype='float32'; + end + + %open file + if endian==1 + fid=fopen(inputFileName,'r','ieee-be'); + else + fid=fopen(inputFileName,'r','ieee-le'); + end + + %read file + [u, numpoints]=fread(fid, [M,N],datatype); + + %close file + fclose(fid); + + %Pair of vectors? + if numvectors==2, + vx=u(1:2:M,:);vx=flipud(vx'); + vy=u(2:2:M,:);vx=flipud(vx'); + + %keep track + handles.vx=vx; + handles.vy=vy; + + u=sqrt(vx.^2+vy.^2); + end + + cla(handles.axes1); %clear the axes + axes(handles.axes1); %set the axes to plot + grid on + imagesc(u) + colorbar + + %keep track + handles.u=u; + + %to see whether the data has been processed or not + handles.processDataCompleted=2; + + %data is done processing, so re-enable the buttons + enableButtons(handles); + guidata(hObject, handles); +end + +function plotcoord_Callback(hObject, eventdata, handles) + + %check + if handles.processDataCompleted<2 + errordlg('Process data first !') + return + end + + %parse options + if ~isnan(handles.dx) + dx=handles.dx; + else + errordlg('value of x-spacing not supported') + return + end + if ~isnan(handles.dy) + dy=handles.dy; + else + errordlg('value of y-spacing not supported') + return + end + if ~isnan(handles.xEast) + xEast=handles.xEast; + else + errordlg('value of xEast not supported') + return + end + if ~isnan(handles.yNorth) + yNorth=handles.yNorth; + else + errordlg('value of yNorth not supported') + return + end + + disableButtons(handles); + + %process coordinates + u=handles.u; + s=size(u); + M=s(1)+1; + N=s(2)+1; + + %correction North and East -> real + yNorth=yNorth-M*dy; % corner north + x_m=xEast+dx*(0:N-1)'; + y_m=yNorth+dy*(0:M-1)'; + + %plot new axes + cla(handles.axes1); %clear the axes + axes(handles.axes1); %set the axes to plot + grid on + imagesc(x_m,y_m,handles.u) + set(handles.axes1,'Ydir','Normal'); + colorbar + + %Keep track of x_m and y_m + handles.x_m=x_m; + handles.y_m=y_m; + + %to see whether the data has been processed or not + handles.processDataCompleted=3; + + %data is done processing, so re-enable the buttons + enableButtons(handles); + guidata(hObject, handles); + +end + + +function save_pushbutton_Callback(hObject, eventdata, handles) + %if the data hasn't been processed yet, + %nothing happens when this button is pressed + if (handles.processDataCompleted ~= 3) + return + end + + disableButtons(handles); + + if handles.numvectors==2, + + prompt={'Enter the name of the variable 1:','Enter the name of the variable 2:','Enter the name of the file:'}; + name='Save Matlab File'; + numlines=1; + defaultanswer={'vx','vy','ProcessedFile'}; + answer=inputdlg(prompt,name,numlines,defaultanswer); + variablename1=answer{1}; + variablename2=answer{2}; + filename=answer{3}; + + if ~isempty(variablename1) & ~isempty(variablename2) & ~isempty(filename) + %get the variables + x_m=handles.x_m; + y_m=handles.y_m; + eval([variablename1 ' = handles.vx;']); + eval([variablename2 ' = handles.vy;']); + x_m=handles.x_m; + eval(['save ' filename ' x_m y_m ' variablename1 ' ' variablename2 ]); + disp(['in the file ' filename ' have been saved the following variables: x_m, y_m, ' variablename1 ' and ' variablename2]) + end + else + prompt={'Enter the name of the variable:','Enter the name of the file:'}; + name='Save Matlab File'; + numlines=1; + defaultanswer={'thickness','ProcessedFile'}; + answer=inputdlg(prompt,name,numlines,defaultanswer); + variablename=answer{1}; + filename=answer{2}; + + if ~isempty(variablename) & ~isempty(filename) + %get the variables + x_m=handles.x_m; + y_m=handles.y_m; + eval([variablename ' = handles.u;']); + eval(['save ' filename ' x_m y_m ' variablename]); + disp(['in the file ' filename ' have been saved the following variables: x_m, y_m, and ' variablename]) + end + end + enableButtons(handles); + guidata(hObject, handles); +end + +function inputFile_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function disableButtons(handles) + set(handles.figure1,'Pointer','watch'); + set(handles.plotdata_pushbutton,'Enable','off'); + set(handles.plotcoord,'Enable','off'); + set(handles.save_pushbutton,'Enable','off'); + set(handles.addFiles_pushbutton,'Enable','off'); + set(handles.reset_pushbutton,'Enable','off'); +end + +function enableButtons(handles) + set(handles.figure1,'Pointer','arrow'); + set(handles.plotdata_pushbutton,'Enable','on'); + set(handles.plotcoord,'Enable','on'); + set(handles.save_pushbutton,'Enable','on'); + set(handles.addFiles_pushbutton,'Enable','on'); + set(handles.reset_pushbutton,'Enable','on'); +end + +function EndianType_Callback(hObject, eventdata, handles) + handles.endian=get(handles.EndianType,'Value'); + guidata(hObject, handles); +end + +function EndianType_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function DataType_Callback(hObject, eventdata, handles) + + datatype= get(handles.DataType,'Value'); + switch datatype + case 1 + string='float32'; + + case 2 + string='single'; + + case 3 + string='float64'; + + case 4 + string='double'; + end + handles.datatype=string; + guidata(hObject, handles); +end + +function DataType_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function PairOfVectors_Callback(hObject, eventdata, handles) + handles.numvectors = get(handles.PairOfVectors,'Value'); + guidata(hObject, handles); +end + +function PairOfVectors_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function Msize_Callback(hObject, eventdata, handles) + handles.Msize=eval(get(hObject,'String')); + guidata(hObject, handles); +end + +function Msize_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function Nsize_Callback(hObject, eventdata, handles) + handles.Nsize=eval(get(hObject,'String')); + guidata(hObject, handles); +end + +function Nsize_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function dx_Callback(hObject, eventdata, handles) + handles.dx=eval(get(hObject,'String')); + guidata(hObject, handles); +end +function dx_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function dy_Callback(hObject, eventdata, handles) + handles.dy=eval(get(hObject,'String')); + guidata(hObject, handles); +end +function dy_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function xEast_Callback(hObject, eventdata, handles) + handles.xEast=eval(get(hObject,'String')); + guidata(hObject, handles); +end +function xEast_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end + +function yNorth_Callback(hObject, eventdata, handles) + handles.yNorth=eval(get(hObject,'String')); + guidata(hObject, handles); +end +function yNorth_CreateFcn(hObject, eventdata, handles) + if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); + end +end Index: /issm/trunk-jpl/src/m/DataProcessing/gamv.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/gamv.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/gamv.m (revision 12996) @@ -0,0 +1,70 @@ +function output = gamv(x,y,data,varargin); +%GAMV - use gslib for Kriging +% +% Usage: +% output = gamv(x,y,data,varargin) + +options=pairoptions(varargin{:}); + +nlag = getfieldvalue(options,'nlag', 20); +dlag = getfieldvalue(options,'dlag', 1000); + +%Write data file +fid=fopen('cluster.dat','w'); +fprintf(fid,'%s\n','Data file'); +fprintf(fid,'%i\n',3); +fprintf(fid,'%s\n','Xlocation'); +fprintf(fid,'%s\n','Ylocation'); +fprintf(fid,'%s\n','Data'); +fprintf(fid,'%g %g %g\n',[x y data]'); +fclose(fid); + +%Write parameter file +fid=fopen('gamv.par','w'); +fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); +fprintf(fid,'\t\t\t\t%s\n','*******************'); +fprintf(fid,'\n'); +fprintf(fid,'%s\n','START OF PARAMETERS:'); +fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); +fprintf(fid,'%-30s %s\n','1 2 0' ,'\columns for X, Y, Z coordinates'); +fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); +fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); +fprintf(fid,'%-30s %s\n','gamv.out' ,'\file for variogram output'); +fprintf(fid,'%-30s %s\n',num2str(nlag,'%i') ,'\number of lags'); +fprintf(fid,'%-30s %s\n',num2str(dlag,'%g') ,'\lag separation distance'); +fprintf(fid,'%-30s %s\n',num2str(dlag/2,'%g') ,'\lag tolerance'); +fprintf(fid,'%-30s %s\n','3' ,'\number of directions'); +fprintf(fid,'%-30s %s\n','0.0 90.0 50.0 0.0 90.0 50.0','\azm, atol, bandh, dip, dtol, bandv'); +fprintf(fid,'%-30s %s\n','0.0 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); +fprintf(fid,'%-30s %s\n','90. 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); +fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); +fprintf(fid,'%-30s %s\n','2' ,'\number of variograms'); +fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail var., head vars., variogram type'); +fprintf(fid,'%-30s %s\n','1 1 3' ,'\tail var., head vars., variogram type'); +fclose(fid); + +%Call gamv +system([issmdir() '/externalpackages/gslib/install/gamv gamv.par']); +delete('gamv.par'); + +%Read output +output = struct('Semivariogram',[],'Covariance',[]); +counter1 = 1; +counter2 = 1; +fid=fopen('gamv.out','r'); +while (~feof(fid)), + A=fscanf(fid,'%s',1); + if strcmp(A,'Covariance'); + A=fscanf(fid,'%s',4); %Read tail:Data head:Data direction 2 + output(counter1).Covariance=fscanf(fid,'%i %g %g %i %g %g',[6 nlag+2])'; + counter1=counter1+1; + elseif strcmp(A,'Semivariogram'), + A=fscanf(fid,'%s',4); %Read tail:Data head:Data direction 2 + output(counter2).Semivariogram=fscanf(fid,'%i %g %g %i %g %g',[6 nlag+2])'; + counter2=counter2+1; + else + %do nothing + end +end +fclose(fid); +delete('gamv.out') Index: /issm/trunk-jpl/src/m/DataProcessing/gslib.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/gslib.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/gslib.m (revision 12996) @@ -0,0 +1,112 @@ +function output = gslib(x,y,data,varargin); +%GSLIB - use gslib for Kriging +% +% Usage: +% output = gslib(x,y,data,varargin) + +%Output Matrix +xmin = xl(1); +ymin = yl(1); +nx = 101; +ny = 101; +deltax = 5000; +deltay = 5000; + +%Variogram +nugget=10; +sill =164; +range =25763; + +%Kriging options +mindata = 1; +maxdata = 50; +maxsearchradius = 50000; + +%Some intermediaries (Convert to gslib's parameters); +c = (sill-nugget); +a = sqrt(3)*range; + +%Write data file +fid=fopen('cluster.dat','w'); +fprintf(fid,'%s\n','Data file'); +fprintf(fid,'%i\n',3); +fprintf(fid,'%s\n','Xlocation'); +fprintf(fid,'%s\n','Ylocation'); +fprintf(fid,'%s\n','Data'); +fprintf(fid,'%g %g %g\n',[x y data]'); +fclose(fid); + +if 0, %GAMV + %Write parameter file + fid=fopen('gamv.par','w'); + fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); + fprintf(fid,'\t\t\t\t%s\n','*******************'); + fprintf(fid,'\n'); + fprintf(fid,'%s\n','START OF PARAMETERS:'); + fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); + fprintf(fid,'%-30s %s\n','1 2 0' ,'\columns for X, Y, Z coordinates'); + fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); + fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); + fprintf(fid,'%-30s %s\n','gamv.out' ,'\file for variogram output'); + fprintf(fid,'%-30s %s\n','20' ,'\number of lags'); + fprintf(fid,'%-30s %s\n','5.0' ,'\lag separation distance'); + fprintf(fid,'%-30s %s\n','3.0' ,'\lag tolerance'); + fprintf(fid,'%-30s %s\n','3' ,'\number of directions'); + fprintf(fid,'%-30s %s\n','0.0 90.0 50.0 0.0 90.0 50.0','\azm, atol, bandh, dip, dtol, bandv'); + fprintf(fid,'%-30s %s\n','0.0 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); + fprintf(fid,'%-30s %s\n','90. 22.5 25.0 0.0 22.5 25.0','\azm, atol, bandh, dip, dtol, bandv'); + fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); + fprintf(fid,'%-30s %s\n','2' ,'\number of variograms'); + fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail var., head vars., variogram type'); + fprintf(fid,'%-30s %s\n','1 1 3' ,'\tail var., head vars., variogram type'); + fclose(fid); + + %Call gamv + system([issmdir() '/externalpackages/gslib/install/gamv gamv.par']); + +else, %Kriging KB2D + %Write parameter file + fid=fopen('kb2d.par','w'); + fprintf(fid,'\t\t\t\t%s\n','Parameters for KB2D'); + fprintf(fid,'\t\t\t\t%s\n','*******************'); + fprintf(fid,'\n'); + fprintf(fid,'%s\n','START OF PARAMETERS:'); + fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); + fprintf(fid,'%-30s %s\n','1 2 3' ,'\columns for X, Y and variable'); + fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); + fprintf(fid,'%-30s %s\n','0' ,'\debugging level: 0,1,2,3'); + fprintf(fid,'%-30s %s\n','kb2d.dbg' ,'\file for debuggging output'); + fprintf(fid,'%-30s %s\n','kb2d.out' ,'\file for kriged output'); + fprintf(fid,'%-30s %s\n',num2str([nx xmin deltax],'%i %10g %6g') ,'\nx, xmn, xsiz'); + fprintf(fid,'%-30s %s\n',num2str([ny ymin deltay],'%i %10g %6g') ,'\nx, xmn, xsiz'); + fprintf(fid,'%-30s %s\n','1 1' ,'\x and y block discretization'); + fprintf(fid,'%-30s %s\n',num2str([mindata maxdata],'%6g') ,'\min and max data for kriging'); + fprintf(fid,'%-30s %s\n',num2str(maxsearchradius,'%6g') ,'\max search radius'); + fprintf(fid,'%-30s %s\n','1 2.302' ,'\0=SK, 1=OK, (mean if SK)'); + fprintf(fid,'%-30s %s\n',['1 ' num2str(nugget)] ,'\nst, nugget effect'); + fprintf(fid,'%-30s %s\n',['3 ' num2str([c 0.0 a a],'%10g')],'\it, c, azm, a_max, a_min'); + fclose(fid); + + tic;system([issmdir() '/externalpackages/gslib/install/kb2d kb2d.par']);toc; + delete('kb2d.par'); + + %Read output + fid=fopen('kb2d.out','r'); + while (~feof(fid)), + A=fscanf(fid,'%s',1); + if strcmp(A,'KB2D'); + A=fscanf(fid,'%s',1); %Read output + params=fscanf(fid,'%i %i %i %i %g %g %g %g %g %g %1',[11 1]); + elseif strcmp(A,' Estimate'), + continue; + elseif strcmp(A,'Estimation'), + A=fscanf(fid,'%s',1); %Read Variance + A=fscanf(fid,'%g %g',[params(1) params(2)*params(3)]); + B=A(1,:); B=reshape(B,[params(3),params(2)])'; + E=A(2,:); E=reshape(E,[params(3),params(2)])'; + else + %do nothing + end + end + fclose(fid); +end Index: /issm/trunk-jpl/src/m/DataProcessing/pkriging.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/pkriging.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/pkriging.m (revision 12996) @@ -0,0 +1,55 @@ +function [B E]=pkriging(x,y,observations,x_interp,y_interp,varargin); +%PKRIGING - parallel Kriging +% +% Usage: +% [B E]=pkriging(x,y,observations,x_interp,y_interp,varargin); + +options=pairoptions(varargin{:}); +cluster=getfieldvalue(options,'cluster',generic('np',10)); +options=removefield(options,'cluster',0); +name = ['krig' num2str(feature('GetPid'))]; + +% ========================================= MARSHALL.m ================================================= +disp(['marshalling file ' name '.bin']); +fid=fopen([name '.bin'],'wb'); +if fid==-1, + error(['marshall error message: could not open ' name '.bin file for binary writing']); +end + +%First, write MaximumNumberOfEnum to make sure that the Enums are synchronized +WriteData(fid,'enum',MaximumNumberOfEnums(),'data',true,'format','Boolean'); + +%Write all data +WriteData(fid,'enum',0,'data',x,'format','DoubleMat'); +WriteData(fid,'enum',1,'data',y,'format','DoubleMat'); +WriteData(fid,'enum',2,'data',observations,'format','DoubleMat'); +WriteData(fid,'enum',3,'data',x_interp,'format','DoubleMat'); +WriteData(fid,'enum',4,'data',y_interp,'format','DoubleMat'); +options.marshall(fid,5); +st=fclose(fid); +if st==-1, + error(['marshall error message: could not close file ' name '.bin']); +end +% ========================================= MARSHALL.m ================================================= + +%Launch job on remote cluster +BuildKrigingQueueScript(cluster,name,'',1,0,0); %gather, valgrind, gprof +tic +LaunchQueueJob(cluster,name,name,{[name '.bin'] [name '.queue']}); +toc +choice=input('Is the job successfully completed? (y/n)','s'); +Download(cluster,name,{[name '.outbin']}); +structure=parseresultsfromdisk([name '.outbin'],0); +delete([name '.outlog']); +delete([name '.errlog']); +delete([name '.outbin']); +delete([name '.bin']); +if ~ispc, + delete([name '.tar.gz']); +end + +%Process results +B=structure.AutodiffForward; +B=reshape(B,size(x_interp,2),size(x_interp,1))'; +E=structure.AutodiffIsautodiff; +E=reshape(E,size(x_interp,2),size(x_interp,1))'; Index: /issm/trunk-jpl/src/m/DataProcessing/varmap.m =================================================================== --- /issm/trunk-jpl/src/m/DataProcessing/varmap.m (revision 12996) +++ /issm/trunk-jpl/src/m/DataProcessing/varmap.m (revision 12996) @@ -0,0 +1,55 @@ +function output = varmap(x,y,data,varargin); +%VARMAP - use gslib for Kriging +% +% Usage: +% output = varmap(x,y,data,varargin) + +options=pairoptions(varargin{:}); + +nxlag = getfieldvalue(options,'nxlag', 20); +nylag = getfieldvalue(options,'nylag', 20); +dxlag = getfieldvalue(options,'dxlag', 1000); +dylag = getfieldvalue(options,'dylag', 1000); + +%Write data file +fid=fopen('cluster.dat','w'); +fprintf(fid,'%s\n','Data file'); +fprintf(fid,'%i\n',3); +fprintf(fid,'%s\n','Xlocation'); +fprintf(fid,'%s\n','Ylocation'); +fprintf(fid,'%s\n','Data'); +fprintf(fid,'%g %g %g\n',[x y data]'); +fclose(fid); + +%Write parameter file +fid=fopen('varmap.par','w'); +fprintf(fid,'\t\t\t\t%s\n','Parameters for GAMV'); +fprintf(fid,'\t\t\t\t%s\n','*******************'); +fprintf(fid,'\n'); +fprintf(fid,'%s\n','START OF PARAMETERS:'); +fprintf(fid,'%-30s %s\n','./cluster.dat' ,'\file with data'); +fprintf(fid,'%-30s %s\n','1 3 ' ,'\number of variables, column number'); +fprintf(fid,'%-30s %s\n','-1.0e21 1.0e21' ,'\trimming limits'); +fprintf(fid,'%-30s %s\n','0 ' ,'\1=regular grid, 0=scattered values'); +fprintf(fid,'%-30s %s\n','50 50 1' ,'\if =1: nx, ny, nz'); +fprintf(fid,'%-30s %s\n','1.0 1.0 1.0' ,'\ xsiz, ysiz, zsiz if igrid=1'); +fprintf(fid,'%-30s %s\n','1 2 0' ,'\if =0: columns for x, y and z coordinates'); +fprintf(fid,'%-30s %s\n','varmap.out' ,'\file for variogram output'); +fprintf(fid,'%-30s %s\n',num2str([nxlag nylag 0],'%i '),'\nxlag, nylag, nzlag'); +fprintf(fid,'%-30s %s\n',num2str([dxlag dylag 1],'%g %g %i'),'\dxlag, dylag, dzlag'); +fprintf(fid,'%-30s %s\n','5' ,'\minimum number of pairs'); +fprintf(fid,'%-30s %s\n','0' ,'\standardize sill? (0=no, 1=yes)'); +fprintf(fid,'%-30s %s\n','1' ,'\number of variograms'); +fprintf(fid,'%-30s %s\n','1 1 1' ,'\tail, head, variogram type'); +fclose(fid); + +%Call varmap +system([issmdir() '/externalpackages/gslib/install/varmap varmap.par']); +delete('varmap.par'); + +%Read output +fid=fopen('varmap.out','r'); +A = textscan(fid,'%f %f %f %f %f %f','headerlines',8); +fclose(fid); +delete('varmap.out') +output = reshape(A{1},[2*nxlag+1 2*nylag+1]); Index: /issm/trunk-jpl/src/m/Ecco3/ecco32issm.m =================================================================== --- /issm/trunk-jpl/src/m/Ecco3/ecco32issm.m (revision 12996) +++ /issm/trunk-jpl/src/m/Ecco3/ecco32issm.m (revision 12996) @@ -0,0 +1,8 @@ +function nodefield=ecco32issm(field,transition,xecco3,yecco3) + + xecco3linear=xecco3(:); yecco3linear=yecco3(:); %linearize + nodefieldlinear=zeros(length(xecco3linear),1); + nodefieldlinear(transition(:,1))=field(transition(:,2)); + nodefield=xecco3; + nodefield(:)=nodefieldlinear; + %nodefield=nodefield'; %not sure we need that Index: /issm/trunk-jpl/src/m/Ecco3/issm2ecco3.m =================================================================== --- /issm/trunk-jpl/src/m/Ecco3/issm2ecco3.m (revision 12996) +++ /issm/trunk-jpl/src/m/Ecco3/issm2ecco3.m (revision 12996) @@ -0,0 +1,8 @@ +function nodefield=issm2ecco3(field,transition,xecco3,yecco3) + + xecco3linear=xecco3(:); yecco3linear=yecco3(:); %linearize + nodefieldlinear=zeros(length(xecco3linear),1); + nodefieldlinear(transition(:,1))=field(transition(:,2)); + nodefield=xecco3; + nodefield(:)=nodefieldlinear; + %nodefield=nodefield'; %not sure we need that Index: /issm/trunk-jpl/src/m/Exp/clicktoflowline.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/clicktoflowline.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/clicktoflowline.m (revision 12996) @@ -0,0 +1,24 @@ +function clicktoflowline(index,x,y,u,v,filename) +%CLICKTOFLOWLINE - create a flowline ARGUS file +% +% create a flowline contour file (named 'filename') by clicking +% on a velocity field once (velocity must be plotted first) +% +% Usage: +% clicktoflowline(index,x,y,u,v,x0,y0,filename) +% +% Example: +% clicktoflowline(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vx_obs,md.inversion.vy_obs,'flowline.exp') + +%Get click position +[x0,y0]=ginput(1); + +%Get flowline +line=flowlines(index,x,y,u,v,x0,y0,200); + +%plot +hold on +plot(line.x,line.y,'r-'); + +%Write argus file +expwrite(line,filename); Index: /issm/trunk-jpl/src/m/Exp/downstreamflowlines.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/downstreamflowlines.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/downstreamflowlines.m (revision 12996) @@ -0,0 +1,110 @@ +function flowpath=downstreamflowlines(index,x,y,u,v,x0,y0,varargin) +%DOWNSTREAMFLOWLINES - compute flowlines from a given set of seed points +% +% Usage: +% flowpath=downstreamflowlines(index,x,y,u,v,x0,y0) +% +% the velocity field is given by the couple (u,v) and the coordinates +% of the seed points are (x0,y0). One can use one or several seed +% points +% +% Example: +% flowpath=downstreamflowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0) + +%check input size +if nargin>9 | nargin<7, + help flowlines + error('flowlines error message: bad usage'); +end + +%check input +if (length(x)~=length(y) | length(x)~=length(u) | length(x)~=length(v)), + error('flowlines error message: x,y,u and v must have the same length'); +end +if length(x)<3, + error('flowlines error message: at least one element is required'); +end +if length(x0)~=length(y0), + error('flowlines error message: x0 and y0 do not have the same length'); +end + +%get maxiter and precision +if nargin==9 + maxiter=varargin{1};%maximum number of iterations + precision=varargin{2}; %division of each segment (higer precision increases number of segments) +else + maxiter=200; %maximum number of iterations + precision=1; %division of each segment (higer precision increases number of segments) +end + +%check seed points +tria=TriaSearch(index,x,y,x0,y0); +pos=find(isnan(tria)); +x0(pos)=[]; +y0(pos)=[]; + +%initialize other variables +N=length(x0); +X=x0; Y=y0; +flowpath=struct('x',cell(N,1),'y',cell(N,1),'name','','density',1); +for i=1:N, + flowpath(i).x=x0(i); + flowpath(i).y=y0(i); +end +done=zeros(N,1); + +%get avegared length of each element +length_tria=1/3*(sqrt( (x(index(:,1))-x(index(:,2))).^2+(y(index(:,1))-y(index(:,2))).^2 )+... + sqrt((x(index(:,1))-x(index(:,3))).^2+(y(index(:,1))-y(index(:,3))).^2 )+... + sqrt((x(index(:,2))-x(index(:,3))).^2+(y(index(:,2))-y(index(:,3))).^2 )); + +%take velocity for each element +u=u(index)*[1;1;1]/3; +v=v(index)*[1;1;1]/3; + +%initialization: +counter=1; + +while any(~done) + + %find current triangle + queue=find(~done); + tria=TriaSearch(index,x,y,X(queue),Y(queue)); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); + for i=1:length(listnan) + %remove the last point + flowpath(queue(listnan(i))).x(end)=[]; + flowpath(queue(listnan(i))).y(end)=[]; + done(queue(listnan(i)))=1; + end + tria(listnan)=[]; + queue(listnan)=[]; + + if isempty(tria), + break; + end + + %velocity of the current triangle and norm it + ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2); + ut=ut./normv;vt=vt./normv; + + %check counter + if counter>maxiter + disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward']) + break + end + counter=counter+1; + + %remove stagnant point + done(queue(find(ut==0 & vt==0)))=1; + + %build next point + for i=1:length(queue) + X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision; + Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision; + flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision]; + flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision]; + end +end Index: /issm/trunk-jpl/src/m/Exp/expbox.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expbox.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expbox.m (revision 12996) @@ -0,0 +1,41 @@ +function expbox(filename) +%EXPBOX - Create a ARGUS file using to clicks +% +% Two clicks on a plot are used to generate a rectangular box +% This box is written in EXP format on filename +% +% Usage: +% expbox(filename) + +%check +if exist(filename,'file'), + choice=input(['A file ' filename ' already exists, do you want to modify it? (y/n)'],'s'); + if ~strcmpi(choice,'y'), + disp('no modification done ... exiting'); + return + end +end + +%Get points +disp('Click twice to define a rectangular domain. First click for upper left corner, second for lower right corner'); +[x,y]=ginput(2); + +x1=x(1); +x2=x(2); +x3=x2; +x4=x1; + +y1=y(1); +y2=y1; +y3=y(2); +y4=y3; + +%Build Exp structure +A=struct(); +A.nods=5; +A.density=1; +A.x=[x1 x2 x3 x4 x1]'; +A.y=[y1 y2 y3 y4 y1]'; + +%Write structure +expwrite(A,filename); Index: /issm/trunk-jpl/src/m/Exp/expboxgen.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expboxgen.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expboxgen.m (revision 12996) @@ -0,0 +1,99 @@ +function expboxgen(x0,y0,nx,ny,parameter_filename,box_filename) +%EXPBOXGEN - creates a domain outline box for a tiff image +% +% This function creates a domain outline box for a .tif image for the +% mosaic tiff. +% x0,y0 and x1,y1 are the cropping coordinates (upper left and lower right +% corners in the larger tiff image). +% paramter_filename is the parameter file name for the mosaic tiff image. +% box_filename is self explanatory. +% +% Usage: +% expboxgen(x0,y0,nx,ny,parameter_filename,box_filename) +% +% See also EXPMASTER, EXPDOC + +%initialize +nrows=-1; +ncols=-1; +X0=-1; +Y0=-1; +posting=-1; + +%first recover necessary information from the paramter_filename. +fid=fopen(parameter_filename,'r'); +count=1; +while(1), +tline=fgetl(fid); +if ~isstr(tline), break; end; + +ind=findstr('ant125m',tline); +if ~isempty(ind), +a=strsplit(tline,' '); +a=a(2); a=char(a); a=a(1:length(a)-1); +posting=str2num(a); +end + + +ind=findstr('no. of rows :',tline); +if ~isempty(ind), +a=strsplit(tline,' '); +nrows=str2num(char(a(length(a)))); +end + +ind=findstr('no. of columns:',tline); +if ~isempty(ind), +a=strsplit(tline,' '); +ncols=str2num(char(a(length(a)))); +end + +ind=findstr('Upper Left X:',tline); +if ~isempty(ind), +a=strsplit(tline,' '); +X0=str2num(char(a(length(a)))); +end + +ind=findstr('Upper Left Y:',tline); +if ~isempty(ind), +a=strsplit(tline,' '); +Y0=str2num(char(a(length(a)))); +end + + +end %while(1), + + +fclose(fid); + +if (X0==-1 | Y0==-1 | nrows==-1 | ncols==-1 | posting==-1), +disp(' '); +disp(['Could not recover all parameters from ' parameter_filename]); +disp('Here are the paramters recovered thus far: '); +disp(['no. of rows: ' num2str(nrows)]); +disp(['no. of columns: ' num2str(ncols)]); +disp(['Upper Left X: ' num2str(X0)]); +disp(['Upper Left Y: ' num2str(Y0)]); +disp(['Posting: ' num2str(posting)]); +end + +disp(' '); +disp(['Recovered the following parameters from ' parameter_filename]); +disp(['no. of rows: ' num2str(nrows)]); +disp(['no. of columns: ' num2str(ncols)]); +disp(['Upper Left X: ' num2str(X0)]); +disp(['Upper Left Y: ' num2str(Y0)]); +disp(['Posting: ' num2str(posting)]); + +%Create X,Y, arrays of coordinates: +X(1)=X0+x0*posting +Y(1)=Y0-y0*posting +X(2)=X(1); +Y(2)=Y(1)-ny*posting; +X(3)=X(1)+nx*posting; +Y(3)=Y(2); +Y(4)=Y(1); +X(4)=X(3); +plot(X,Y,'r*'); + +%Create box exp file using X and Y. Loop it. +expgen(box_filename,X,Y,1); Index: /issm/trunk-jpl/src/m/Exp/expcoarsen.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expcoarsen.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expcoarsen.m (revision 12996) @@ -0,0 +1,74 @@ +function expcoarsen(newfile,oldfile,resolution); +%EXPCOARSEN - coarsen an exp contour +% +% This routine read an Argus file and remove points with respect to +% the resolution (in meters) given in input. +% +% Usage: +% expcoarsen(newfile,oldfile,resolution) +% +% Example: +% expcoarsen('DomainOutline.exp','Antarctica.exp',4000) + +%Some checks +if nargin~=3 | nargout + error('expcoarsen usage: expcoarsen(newfile,oldfile,resolution)') +elseif ~exist(oldfile) + error(['expcut error message: the file ' oldfile 'does not exist']) +elseif exist(newfile), + choice=input(['A file ' newfile ' already exists, do you want to modify it? (y/n)'],'s'); + if ~strcmpi(choice,'y'), + disp('no modification done ... exiting'); + return; + end +end + +%Get exp oldfile +[path root ext ver]=fileparts(oldfile); +A=expread(oldfile); +numprofiles=size(A,2); + +%Go through the profiles +count=1; +while count<=numprofiles, + + %get number of points and initialize j + numpoints=length(A(count).x); + j=1; + + %stop if we have reached end of profile (always keep the last point) + while j=2, + x=linspace(A(count).x(j),A(count).x(j+1),division)'; + y=linspace(A(count).y(j),A(count).y(j+1),division)'; + A(count).x=[A(count).x(1:j);x(2:end-1); A(count).x(j+1:end)]; + A(count).y=[A(count).y(1:j);y(2:end-1); A(count).y(j+1:end)]; + + %update current point + j=j+1+division-2; + numpoints=numpoints+division-2; + else + %update current point + j=j+1; + end + end + end + if length(A(count).x)<=1, + A(count)=[]; + numprofiles=numprofiles-1; + else + count=count+1; + end +end + +%write output +expwrite(A,newfile); Index: /issm/trunk-jpl/src/m/Exp/expcontract.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expcontract.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expcontract.m (revision 12996) @@ -0,0 +1,34 @@ +function normal_node=expcontract(newfile,oldfile,distance) +%EXPCONTRACT - contract or expand a profile, according to the normal. +% +% Usage: +% expcontract(newfile,oldfile,distance) +% +% See also EXPMASTER, EXPDOC + + +contour=expread(oldfile); +num=numel(contour.x); + +normal=zeros(num-1,2); +normal_node=zeros(num-1,2); + +for i=1:num-1, + normal(i,:)=[ contour.y(i)-contour.y(i+1) contour.x(i+1)-contour.x(i)]; + normal(i,:)=normal(i,:)/sqrt(normal(i,1)^2+normal(i,2)^2); +end + +normal_node(2:end,:)=[normal(1:end-1,:)+normal(2:end,:)]; +normal_node(1,:)=normal(1,:)+normal(end,:); + +normal_node_norm=sqrt(normal_node(:,1).^2+normal_node(:,2).^2); +normal_node(:,1)=normal_node(:,1)./normal_node_norm; +normal_node(:,2)=normal_node(:,2)./normal_node_norm; + +contour.x(1:end-1)=contour.x(1:end-1)+distance*normal_node(:,1); +contour.y(1:end-1)=contour.y(1:end-1)+distance*normal_node(:,2); + +contour.x(end)=contour.x(1); +contour.y(end)=contour.y(1); + +expwrite(contour,newfile); Index: /issm/trunk-jpl/src/m/Exp/expcreatecircle.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expcreatecircle.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expcreatecircle.m (revision 12996) @@ -0,0 +1,31 @@ +function expcreatecircle(filename,x0,y0,radius,numberofnodes) +%EXPCREATECIRCLE - create a circular contour corresponding to given parameters +% +% Creates a closed argus contour centered on x,y of radius size. +% The contour is made of numberofnodes +% +% Usage: +% expcreatecircle(filename,x0,y0,radius,numberofnodes) +% +% See also EXPMASTER, EXPDOC + +%Calculate the cartesians coordinates of the points +x_list=ones(numberofnodes+1,1); +y_list=ones(numberofnodes+1,1); + +theta=(0:2*pi/numberofnodes:2*pi*(1-1/numberofnodes))'; +theta=[theta;0]; + +x_list=radius*x_list.*cos(theta); +y_list=radius*y_list.*sin(theta); + +%offset x_list and y_list by x0 and y0: +x_list=x_list+x0; +y_list=y_list+y0; + +contour.x=x_list; +contour.y=y_list; +contour.density=1; +contour.name='circle'; + +expwrite(contour,filename); Index: /issm/trunk-jpl/src/m/Exp/expcreatecontour.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expcreatecontour.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expcreatecontour.m (revision 12996) @@ -0,0 +1,36 @@ +function expcreatecontour(filename); +%EXPCREATECONTOUR - create a contour from a list of points +% +% expcreatecontour: from a list of (x,y) points (retrieve using ginput on an undetermined +% number of points: used RETURN key to end input), create an Argus .exp +% file holding the corresponding closed contour. +% +% Usage: +% expcreatecontour(filename) +% +% See also EXPMASTER, EXPDOC + +%Get root of filename +[path root ext ver]=fileparts(filename); + +%Get contour +disp('Click on contour points you desire. Type RETURN to end input of points'); +[x,y]=ginputquick; + +%close contour +x=[x;x(1)]; +y=[y;y(1);]; + +%plot contour +hold on; +plot(x,y,'r-'); + +%create structure for expwrite routine +a.x=x; +a.y=y; +a.name=root; +a.density=1; + +%write contour using expwrite +expwrite(a,filename); + Index: /issm/trunk-jpl/src/m/Exp/expcreateprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expcreateprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expcreateprofile.m (revision 12996) @@ -0,0 +1,31 @@ +function expcreateprofile(filename); +%EXPCREATEPROFILE - create an Argus file from a list of points +% +% expcreateprofile: from a list of (x,y) points (retrieve using ginput on an undetermined +% number of points: used RETURN key to end input), create an Argus .exp +% file holding the corresponding open profile. +% +% Usage: +% expcreateprofile(filename) +% +% See also EXPMASTER, EXPDOC + +%Get root of filename +[path root ext ver]=fileparts(filename); + +%Get profile +disp('Click on profile points you desire. Type RETURN to end input of points'); +[x,y]=ginputquick; + +%plot contour +hold on; +plot(x,y,'r-'); + +%create structure for expwrite routine +a.x=x; +a.y=y; +a.name=root; +a.density=1; + +%write profile using expwrite +expwrite(a,filename); Index: /issm/trunk-jpl/src/m/Exp/expdisp.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expdisp.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expdisp.m (revision 12996) @@ -0,0 +1,52 @@ +function expdisp(domainoutline,varargin) +%EXPDISP - plot the contours of a domain outline file +% +% This routine reads in a domain outline file (Argus format) and plots all the contours +% +% Usage: +% expdisp(domainoutline,varargin) +% expdisp(domainoutline,figurenumber,linestyle,linewidth,unitmultiplier) +% +% Example: +% expdisp('Domain.exp',1,'--r',2,10^3); +% +% See also EXPMASTER, EXPDOC + +%check nargin +if ~nargin | nargin>5 + help expdisp + error('expdisp error message: bad usage'); +end + +%parse input +if nargin<=1, + figurenumber=1; +else + figurenumber=varargin{1}; +end +if nargin<=2 + linestyle='r-'; +else + linestyle=varargin{2}; +end +if nargin<=3 + linewidth=1; +else + linewidth=varargin{3}; +end +if nargin<=4 + unitmultiplier=1; +else + unitmultiplier=varargin{4}; if isnan(unitmultiplier), unitmultiplier=1; end +end + +domain=expread(domainoutline); + +figure(figurenumber),hold on +for i=1:length(domain), + if (isnumeric(linestyle)) + plot(domain(i).x*unitmultiplier,domain(i).y*unitmultiplier,'Color',linestyle,'linewidth',linewidth); + else + plot(domain(i).x*unitmultiplier,domain(i).y*unitmultiplier,linestyle,'linewidth',linewidth); + end +end Index: /issm/trunk-jpl/src/m/Exp/expdoc.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expdoc.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expdoc.m (revision 12996) @@ -0,0 +1,36 @@ +function expdoc() +%EXPDOC - create a doc for EXP routines +% +% Usage: +% expdoc() + +disp(' '); +disp(' Utilities dedicated to ARGUS Files (''.exp'' extension)'); +disp(' expboxgen: creates a domain outline box for a .tif image for the mosaic tiff'); +disp(' usage: expboxgen(x0,y0,nx,ny,parameter_filename,box_filename)'); +disp(' x0,y0 and nx,ny are the cropping coordinates (upper left and lower right corners in the larger tiff image)'); +disp(' paramter_filename is the parameter file name for the mosaic tiff image. box_filename is self explanatory.'); +disp(' expconcatenate: display all the profiles present in an Argus file and merge them accordingly to the tips selected by the user') +disp(' usage: expconcatenate(newfile,oldfile)') +disp(' expcreatecircle: creates a closed Argus contour centered on (x,y), of radius radius_length. The contour is made of N points'); +disp(' usage: expcreatecircle(filename,x0,y0,radius_length,N)'); +disp(' expcreatecontour: creates a closed Argus contour delimited by the ''clicks'' of the user'); +disp(' usage: expcreatecontour(filename)'); +disp(' expcreateprofile: creates an Argus profile delimited by the ''clicks'' of the user'); +disp(' usage: expcreateprofile(filename)'); +disp(' expcut: display the contents of an Argus file and allow the user cut the profiles'); +disp(' usage: expcut(newfilename,oldfilename)'); +disp(' expdisp: display the contents of an Argus file'); +disp(' usage: expdisp(filename,[figure number],[line style])'); +disp(' expgen: creates an Argus file from a contour (x,y) and a flag indicating if the contour must be closed or open'); +disp(' usage: expgen(filename,contours,close_flag)'); +disp(' explink: takes a domain outline made of various segments, and links them together in one domain outline. Use expview to see end result'); +disp(' usage: explink(domainoutline,minthreshold,step)'); +disp(' exptool: allows the user to create, close, merge, remove,... Argus files and save the result in newfile'); +disp(' usage: exptool(newfile,[oldfile1],[oldfile2],[oldfile3],[...]'); +disp(' expread: reads an Argus file and build a structure that holds all the information of the file'); +disp(' usage: expread(file,close_flag)'); +disp(' expselect: display all the profiles of oldfile, the user clicks on the contour he/she wants to remove. Results saved in newfile'); +disp(' usage: expselect(newfile,oldfile)'); +disp(' expwrite: writes an Argus file from a structure given in input???'); +disp(' usage: expwrite(structure,filename)'); Index: /issm/trunk-jpl/src/m/Exp/expexcludeoutliers.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expexcludeoutliers.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expexcludeoutliers.m (revision 12996) @@ -0,0 +1,18 @@ +function excludeoutliers(newcontourname,contourname,domainname) +%EXCLUDEOUTLIERS exclude points of contour that are not within the domain contour. return new contours in a different file. +% +% Usage: excludeoutliers('NewContour.exp','Contour.exp','DomainOutline.exp'); +% +% +% See also EXPMASTER, EXPDOC + + +contour=expread(contourname); + +for i=1:length(contour), + flags=ContourToNodes(contour(i).x,contour(i).y,domainname,0); + contour(i).x=contour(i).x(find(flags)); + contour(i).y=contour(i).y(find(flags)); +end + +expwrite(contour,newcontourname); Index: /issm/trunk-jpl/src/m/Exp/expflip.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expflip.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expflip.m (revision 12996) @@ -0,0 +1,19 @@ +function expflip(domainname) +%EXPFLIP: flip orientation of all contours and domains in domainname exp file. +% +%Usage: expflip('MassFlux1.exp');a +% +% + + + + + +a=expread(domainname,1); + +for i=1:length(a), + a(i).x=flipud(a(i).x); + a(i).y=flipud(a(i).y); +end + +expwrite(a,domainname); Index: /issm/trunk-jpl/src/m/Exp/expgen.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expgen.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expgen.m (revision 12996) @@ -0,0 +1,47 @@ +function expgen(file_name,contours,close_flag); +%EXPGEN - create an Argus file from x and y arrays +% +% Create .exp domain outline type out of x,y coordinates. +% The contour defined by arrays x and y should not be closed. +% Generated domain outline will not be closed, except if close_flag is set to 1. +% +% Usage: +% expgen(file_name,contours,close_flag) +% +% See also EXPMASTER, EXPDOC + +%Check on inputs +if((close_flag~=0) & (close_flag~=1)), +error('close flag must be 0 of 1'); +end +fid=fopen(file_name,'wt'); + +for i=1:length(contours), + if(length(contours(i).x)~=length(contours(i).y)), + error('contours x and y coordinates must be of identical size'); + end + + %get density for this profile. + if isfield(contours,'density'), + density=contours(i).density; + end + + fprintf(fid,'%s\n','## Name:'); + fprintf(fid,'%s\n','## Icon:0'); + fprintf(fid,'%s\n','# Points Count Value'); + if(close_flag==0), + fprintf(fid,'%i %i\n',length(contours(i).x),density); + else + fprintf(fid,'%i %i\n',length(contours(i).x)+1,density); + end + fprintf(fid,'%s\n','# X pos Y pos'); + for j=1:length(contours(i).x), + fprintf(fid,'%f %f\n',contours(i).x(j),contours(i).y(j)); + end + + if(close_flag==1), + fprintf(fid,'%f %f\n',contours(i).x(1),contours(i).y(1)); + end + fprintf(fid,'%s\n',''); +end +fclose(fid); Index: /issm/trunk-jpl/src/m/Exp/explink.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/explink.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/explink.m (revision 12996) @@ -0,0 +1,29 @@ +function explink(domainoutline,minthreshold,step) +%EXPLINK - allow to link several segments of domain outline together +% +% Takes a domain outline made of various segments, and links them together in one +% domain outline. Use expview to see end result. +% +% Usage: +% explink(domainoutline,minthreshold,step) +% +% See also EXPMASTER, EXPDOC + +notdone=1; + +while notdone, + + for i=1:1000, + status=expconcatenate(domainoutline,minthreshold+(i-1)*step); + if status==0, + return; + end + if status==1, + break; + end + if status==-1, + continue; + end + end +end + Index: /issm/trunk-jpl/src/m/Exp/expll2xy.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expll2xy.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expll2xy.m (revision 12996) @@ -0,0 +1,37 @@ +function expll2xy(filename,sgn,central_meridian,standard_parallel) +%EXPLL2XY: switch exp argus file from lat,long to x,y +% Usage: +% expll2xy(filename,sgn,central_meridian,standard_parallel) +% - sgn = Sign of latitude +1 : north latitude (default is mer=45 lat=70) +% -1 : south latitude (default is mer=0 lat=71) + + +%Get central_meridian and standard_parallel depending on hemisphere +if nargin==4, + delta = central_meridian; + slat = standard_parallel; +elseif nargin==2 + if sgn == 1, + delta = 45; slat = 70; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 70ºN Meridian: 45º)'); + elseif sgn==-1, + delta = 0; slat = 71; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 71ºS Meridian: 0º)'); + else + error('Sign should be either +1 or -1'); + end +else + help expll2xy + error('bad usage'); +end + +%read filename: +domain=expread(filename); + +%change to x,y: +for i=1:length(domain), + [domain(i).x domain(i).y]= ll2xy(domain(i).y,domain(i).x,sgn,delta,slat); +end + +%write back to filename: +expwrite(domain,filename); Index: /issm/trunk-jpl/src/m/Exp/expmaster.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expmaster.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expmaster.m (revision 12996) @@ -0,0 +1,2 @@ +function expmaster(newfile,varargin) + disp('expmaster has been renamed exptool due to the unpopularity of its name') Index: /issm/trunk-jpl/src/m/Exp/exporientation.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/exporientation.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/exporientation.m (revision 12996) @@ -0,0 +1,12 @@ +function exporientation(filename) + +a=expread(filename); + +dx=diff(a.x); +dx=[dx;dx(end)]; + +dy=diff(a.y); +dy=[dy;dy(end)]; + +quiver(a.x,a.y,dx,dy); + Index: /issm/trunk-jpl/src/m/Exp/expremovestraightsegments.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expremovestraightsegments.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expremovestraightsegments.m (revision 12996) @@ -0,0 +1,31 @@ +function expremovestraightsegments(newfilename,filename,cutoff) +%EXPREMOVESTRAIGHTSEGMENTS: remove straight segments connecting contours. +% +% Usage: expremovestraightsegments('argus.exp',100); +% +% + +a=expread(filename,1); +newcontours=a(1); + +for i=1:length(a), + contour=a(i); + + s=sqrt(contour.x.^2+contour.y.^2); + d=diff(s); + + pos=find(abs(d)>cutoff); + pos=[0;pos;length(contour.x)]; + + for j=1:length(pos)-1, + + newcontour=contour; + newcontour.x=contour.x(pos(j)+1:pos(j+1)); + newcontour.y=contour.y(pos(j)+1:pos(j+1)); + newcontour.nods=length(newcontour.x); + newcontours(end+1)=newcontour; + end +end +newcontours=newcontours(2:end); + +expwrite(newcontours,newfilename); Index: /issm/trunk-jpl/src/m/Exp/expsplit.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expsplit.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expsplit.m (revision 12996) @@ -0,0 +1,31 @@ +function expsplit(domainoutline) +%EXPSPLIT - split exp file into sub-contours +% +% This routine reads in a domain outline file (Argus format) and plots all the contours +% This will create as many files there are contours in the domain, each file will be postfix with _i +% where i is the contour name. +% +% Usage: +% expsplit(domainoutline) +% +% Example: +% expsplit('Domain.exp'); +% +% See also EXPMASTER, EXPDOC + +%check nargin +if ~nargin | nargin>1 + help expsplit + error('expsplit error message: bad usage'); +end + +[path,root,ext]=fileparts(domainoutline); + +%Read file: +domains=expread(domainoutline,1); + +%split and write contours: +for i=1:length(domains), + subdomain=domains(i); + expwrite(subdomain,[root '_' num2str(i) ext]); +end Index: /issm/trunk-jpl/src/m/Exp/expsquare.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expsquare.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expsquare.m (revision 12996) @@ -0,0 +1,45 @@ +function expbox(filename) +%EXPBOX - Create a ARGUS file using to clicks +% +% Two clicks on a plot are used to generate a rectangular box +% This box is written in EXP format on filename +% +% Usage: +% expbox(filename) + +%check +if exist(filename,'file'), + choice=input(['A file ' filename ' already exists, do you want to modify it? (y/n)'],'s'); + if ~strcmpi(choice,'y'), + disp('no modification done ... exiting'); + return + end +end + +%Get points +disp('Click twice to define a rectangular domain. First click for upper left corner, second for lower right corner'); +[x,y]=ginput(2); + +xmiddle=mean(x); +ymiddle=mean(y); + +x1=x(1); y1=y(1); +x3=x(2); y3=y(2); + +Diag=[x1-xmiddle;y1-ymiddle]; + +Vector=[xmiddle;ymiddle]+[-Diag(2);Diag(1)]; +x2=Vector(1); y2=Vector(2); + +Vector=[xmiddle;ymiddle]-[-Diag(2);Diag(1)]; +x4=Vector(1); y4=Vector(2); + +%Build Exp structure +A=struct(); +A.nods=5; +A.density=1; +A.x=[x1 x2 x3 x4 x1]'; +A.y=[y1 y2 y3 y4 y1]'; + +%Write structure +expwrite(A,filename); Index: /issm/trunk-jpl/src/m/Exp/expswapxy.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expswapxy.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expswapxy.m (revision 12996) @@ -0,0 +1,23 @@ +function expswapxy(filename) +%EXPSWAP - swap x and y fields +% +% Usage: +% expswap(file) +% +% See also EXPMASTER, EXPDOC + + +contours=expread(filename,1); + +newcontours=contours(1); + +for i=1:length(contours), + contour=contours(i); + newcontour=contour; + newcontour.x=contour.y; + newcontour.y=contour.x; + newcontours(end+1)=newcontour; +end +newcontours=newcontours(2:end); + +expwrite(newcontours,filename); Index: /issm/trunk-jpl/src/m/Exp/exptool.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/exptool.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/exptool.m (revision 12996) @@ -0,0 +1,342 @@ +function exptool(newfile,varargin) +%EXPMASTER - allow to create, modify, add, cut, .. segments of domain outline together +% +% this routine is used to create, modify, cut,... an Argus file (.exp) +% +% exptool(newprofile,'optionname',optionvalue) +% creation of an argus file newprofile +% +% Available options: +% - include: include list of existing ARGUS files +% - color: line color (default='r') +% - selectioncolor: line color of selected profiles (default='b') +% - linestyle (default='-') +% - linewidth (default=0.2) +% - marker (default='+') +% - markersize (default=7) +% - markeredgecolor (default='r') +% +% Usage: +% exptool(newfile,varargin) +% +% Example: +% exptool('domain.exp','include',{'domain1.exp' 'domain2.exp'},'color','g','marker','+') +% +% See also EXPDOC + +%recover options +options=pairoptions(varargin{:}); + +%Some checks +if ~nargin | nargout + error('exptool usage: exptool(newfile,varargin)') +elseif exist(newfile,'file'), + %recursive call to exptool if file already exists + if ~exist(options,'include'), + exptool(newfile,'include',newfile,varargin{:}); + return; + end + + %check modification + choice=input(['A file ' newfile ' already exists, do you want to modify it? (y/n)'],'s'); + if ~strcmpi(choice,'y'), + disp('no modification done ... exiting'); + return + end +end + +%Add default options +options=addfielddefault(options,'color','r'); +options=addfielddefault(options,'selectioncolor','b'); +options=addfielddefault(options,'LineStyle','-'); +options=addfielddefault(options,'LineWidth',0.2); +options=addfielddefault(options,'Marker','+'); +options=addfielddefault(options,'MarkerSize',7); +options=addfielddefault(options,'MarkerEdgeColor','r'); + +%put all the argus profiles given in input in one structure A +A=struct([]); +numprofiles=0; +numpoints=0; +closed=[]; + +%initialize the variables with files provided by 'include' option +if exist(options,'include'), + files=getfieldvalue(options,'include'); + if ischar(files), files={files}; end + for i=1:length(files), + filename=files{i}; + if ~exist(filename,'file'), + error(['exptool error message:, ' filename ' does not exist. Exiting...']); + else + %read file + B=expread(filename); + %go through all profiles of B + for i=1:size(B,2) + %plug profile in A + if numprofiles + A(numprofiles+1)=B(i); + else + A=B(i); + end + %update numprofiles and numpoints + numpoints=numpoints+length(B(i).x); + numprofiles=numprofiles+1; + %figure out if the profile is closed or not + if (B(i).x(1)==B(i).x(end) & B(i).y(1)==B(i).y(end) & length(B(i).x)>1 ) + closed(numprofiles)=1; + else + closed(numprofiles)=0; + end + end + end + end +end + +%Get root of newfile +[path root ext]=fileparts(newfile); + +%get current figure +if ~isempty(get(0,'children')),%if there is already a figure (return the number of opened figures) + set(gcf,'Renderer','zbuffer'); %fixes a bug on Mac OS X (not needed in future Matlab version) + P=get(gcf,'position'); + F=getframe(gca); + F=F.cdata; + %get current axis + xlim=get(gca,'Xlim'); + ylim=get(gca,'Ylim'); + %recreate x_m and y_m + x_m=linspace(xlim(1),xlim(2),size(F,2)); + y_m=linspace(ylim(2),ylim(1),size(F,1)); %getframe reverse axis... + %plot the data in another figure + figure; set(gcf,'position',P); + imagesc(x_m,y_m,F); set(gca,'Ydir','normal'); + prevplot=1; + prevplot2=1; +else + figure + prevplot=0; + prevplot2=0; +end + +%plot existing profile if any +hold on + +%Build backup structre for do and redo +backup=cell(1,3); +backup{1,1}=A; +backup{1,2}=numprofiles; +backup{1,3}=numpoints; +backup{1,4}=closed; + +loop=1; +counter=1; +while loop + + %Go through A and rule out the empty profiles + list=[]; + for i=1:size(A,2); + if length(A(i).x)==0 + list(end+1)=i; + numprofiles=numprofiles-1; + end + end + A(list)=[]; + closed(list)=[]; + + %Now erase all that have been done and plot the new structure A as it is + undoplots(prevplot); + if numprofiles + prevplot2=1; + for i=1:numprofiles + if length(A(i).x)==1, + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker','o'); + else + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + end + prevplot2=prevplot2+1; + end + end + + %display menu + title('Main Menu','FontSize',14); + button=menu('Menu','add a profile (open)',...%1 + 'add a contour (closed)',... %2 + 'remove a profile',... %3 + 'modify the position of a point',... %4 + 'add points inside a profile',... %5 + 'add points at the end of a profile',... %6 + 'remove points',... %7 + 'remove several points',... %8 + 'cut a segment',... %9 + 'cut a large area',... %10 + 'merge profiles',... %11 + 'close profile',... %12 + 'undo',... %13 + 'redo',... %14 + 'quit'); %15 + + + %UNDO?? + if button==13; + if counter==1 + disp('Already at oldest change'); + else + counter=counter-1; + A=backup{counter,1}; + numprofiles=backup{counter,2}; + numpoints=backup{counter,3}; + closed=backup{counter,4}; + end + end + + %REDO?? + if button==14 + if counter==size(backup,1) + disp('Already at newest change'); + else + counter=counter+1; + A=backup{counter,1}; + numprofiles=backup{counter,2}; + numpoints=backup{counter,3}; + closed=backup{counter,4}; + end + end + + switch button + + case 1 + + [A,numprofiles,numpoints,closed]=addprofile(A,numprofiles,numpoints,closed,prevplot2,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 2 + + [A,numprofiles,numpoints,closed]=addcontour(A,numprofiles,numpoints,closed,prevplot2,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 3 + + [A,numprofiles,numpoints,closed]=removeprofile(A,numprofiles,numpoints,closed,prevplot2,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 4 + + [A,numprofiles,numpoints,closed]=modifyposition(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 5 + + [A,numprofiles,numpoints,closed]=addinsideprofile(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 6 + + [A,numprofiles,numpoints,closed]=addendprofile(A,numprofiles,numpoints,closed,prevplot2,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 7 + + [A,numprofiles,numpoints,closed]=removepoints(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 8 + + [A,numprofiles,numpoints,closed]=removeseveralpoints(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 9 + + [A,numprofiles,numpoints,closed]=cutprofile(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 10 + + [A,numprofiles,numpoints,closed]=cutarea(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + case 11 + + [A,numprofiles,numpoints,closed]=mergeprofiles(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + + case 12 + + [A,numprofiles,numpoints,closed]=closeprofile(A,numprofiles,numpoints,closed,prevplot,root,options); + counter=counter+1; + backup{counter,1}=A; + backup{counter,2}=numprofiles; + backup{counter,3}=numpoints; + backup{counter,4}=closed; + + %QUIT + case 15 + + loop=0; + + otherwise + + %do nothing + + end + +end + +hold off + +%write contour using expwrite +title('New file written, exiting...','FontSize',14); +if isempty(A) + disp('Profile empty, no file written') +else + expwrite(A,newfile); +end + +%close window +close; Index: /issm/trunk-jpl/src/m/Exp/expxy2ll.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/expxy2ll.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/expxy2ll.m (revision 12996) @@ -0,0 +1,37 @@ +function expxy2ll(filename,sgn,central_meridian,standard_parallel) +%EXPLL2XY: switch exp argus file from lat,long to x,y +% Usage: +% expxy2ll(filename,sgn,central_meridian,standard_parallel) +% - sgn = Sign of latitude +1 : north latitude (default is mer=45 lat=70) +% -1 : south latitude (default is mer=0 lat=71) + + +%Get central_meridian and standard_parallel depending on hemisphere +if nargin==4, + delta = central_meridian; + slat = standard_parallel; +elseif nargin==2 + if sgn == 1, + delta = 45; slat = 70; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 70ºN Meridian: 45º)'); + elseif sgn==-1, + delta = 0; slat = 71; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 71ºS Meridian: 0º)'); + else + error('Sign should be either +1 or -1'); + end +else + help expxy2ll + error('bad usage'); +end + +%read filename: +domain=expread(filename); + +%change to x,y: +for i=1:length(domain), + [domain(i).y domain(i).x]= xy2ll(domain(i).x,domain(i).y,sgn,delta,slat); %watch out to swap lat and long +end + +%write back to filename: +expwrite(domain,filename); Index: /issm/trunk-jpl/src/m/Exp/flowlines.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/flowlines.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/flowlines.m (revision 12996) @@ -0,0 +1,163 @@ +function flowpath=flowlines(index,x,y,u,v,x0,y0,varargin) +%FLOWLINES - compute flowlines from a given set of seed points +% +% Usage: +% flowpath=flowlines(index,x,y,u,v,x0,y0) +% +% the velocity field is given by the couple (u,v) and the coordinates +% of the seed points are (x0,y0). One can use one or several seed +% points +% +% Example: +% flowpath=flowlines(md.mesh.elements,md.mesh.x,md.mesh.y,md.vx,md.initialization.vy,x0,y0) + +%check input size +if nargin>8 | nargin<7, + help flowlines + error('flowlines error message: bad usage'); +end + +%check input +if (length(x)~=length(y) | length(x)~=length(u) | length(x)~=length(v)), + error('flowlines error message: x,y,u and v must have the same length'); +end +if length(x)<3, + error('flowlines error message: at least one element is required'); +end +if length(x0)~=length(y0), + error('flowlines error message: x0 and y0 do not have the same length'); +end + +%get maxiter and precision +if nargin==8 + maxiter=varargin{1}; +else + maxiter=200; %maximum number of iterations +end +precision=1; %division of each segment (higer precision increases number of segments) + +%check seed points +tria=TriaSearch(index,x,y,x0,y0); +pos=find(isnan(tria)); +x0(pos)=[]; +y0(pos)=[]; + +%initialize other variables +N=length(x0); +X=x0; Y=y0; +flowpath=struct('x',cell(N,1),'y',cell(N,1),'name','','density',1); +for i=1:N, + flowpath(i).x=x0(i); + flowpath(i).y=y0(i); +end +done=zeros(N,1); + +%get avegared length of each element +length_tria=1/3*(sqrt( (x(index(:,1))-x(index(:,2))).^2+(y(index(:,1))-y(index(:,2))).^2 )+... + sqrt((x(index(:,1))-x(index(:,3))).^2+(y(index(:,1))-y(index(:,3))).^2 )+... + sqrt((x(index(:,2))-x(index(:,3))).^2+(y(index(:,2))-y(index(:,3))).^2 )); + +%take velocity for each element +u=u(index)*[1;1;1]/3; +v=v(index)*[1;1;1]/3; + +%initialization: +counter=1; + +while any(~done) + + %find current triangle + queue=find(~done); + tria=TriaSearch(index,x,y,X(queue),Y(queue)); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); + for i=1:length(listnan) + %remove the last point + flowpath(queue(listnan(i))).x(end)=[]; + flowpath(queue(listnan(i))).y(end)=[]; + done(queue(listnan(i)))=1; + end + tria(listnan)=[]; + queue(listnan)=[]; + + if isempty(tria), + break; + end + + %velocity of the current triangle and norm it + ut=u(tria); vt=v(tria); normv=sqrt(ut.^2+vt.^2); + ut=ut./normv;vt=vt./normv; + + %check counter + if counter>maxiter + disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going forward']) + break + end + counter=counter+1; + + %remove stagnant point + done(queue(find(ut==0 & vt==0)))=1; + + %build next point + for i=1:length(queue) + X(queue(i))=flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision; + Y(queue(i))=flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision; + flowpath(queue(i)).x=[flowpath(queue(i)).x;flowpath(queue(i)).x(end)+ut(i)*length_tria(tria(i))/precision]; + flowpath(queue(i)).y=[flowpath(queue(i)).y;flowpath(queue(i)).y(end)+vt(i)*length_tria(tria(i))/precision]; + end +end + +%same process but reverse (vel=-vel) to have a vcomplete flow line +counter=1; +X=x0; Y=y0; +done=zeros(N,1); + +while any(~done) + + %find current triangle + queue=find(~done); + tria=TriaSearch(index,x,y,X(queue),Y(queue)); + + %check that the point is actually inside a triangle of the mesh + listnan=find(isnan(tria)); + for i=1:length(listnan) + %remove the last point + flowpath(queue(listnan(i))).x(1)=[]; + flowpath(queue(listnan(i))).y(1)=[]; + done(queue(listnan(i)))=1; + end + tria(listnan)=[]; + queue(listnan)=[]; + + if isempty(tria), + break; + end + + %velocity of the current triangle and norm it + ut=-u(tria); vt=-v(tria); normv=sqrt(ut.^2+vt.^2); + ut=ut./normv;vt=vt./normv; + + %check counter + if counter>maxiter + disp(['Maximum number of iterations (' num2str(maxiter) ') reached while going backward']) + break + end + counter=counter+1; + + %remove stagnant point + done(queue(find(ut==0 & vt==0)))=1; + + %build next point + for i=1:length(queue) + X(queue(i))=flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; + Y(queue(i))=flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; + flowpath(queue(i)).x=[flowpath(queue(i)).x(1)+ut(i)*length_tria(tria(i))/precision; flowpath(queue(i)).x]; + flowpath(queue(i)).y=[flowpath(queue(i)).y(1)+vt(i)*length_tria(tria(i))/precision; flowpath(queue(i)).y]; + end +end + +%EXP compatibility +for i=1:length(queue) + flowpath(queue(i)).name=['flowline' num2str(i)]; +end Index: /issm/trunk-jpl/src/m/Exp/ginputquick.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/ginputquick.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/ginputquick.m (revision 12996) @@ -0,0 +1,221 @@ +function [out1,out2,out3] = ginput(arg1) +%GINPUT - Graphical input from mouse. +% +% [X,Y] = GINPUT(N) gets N points from the current axes and returns +% the X- and Y-coordinates in length N vectors X and Y. The cursor +% can be positioned using a mouse (or by using the Arrow Keys on some +% systems). Data points are entered by pressing a mouse button +% or any key on the keyboard except carriage return, which terminates +% the input before N points are entered. +% +% [X,Y] = GINPUT gathers an unlimited number of points until the +% return key is pressed. +% +% [X,Y,BUTTON] = GINPUT(N) returns a third result, BUTTON, that +% contains a vector of integers specifying which mouse button was +% used (1,2,3 from left) or ASCII numbers if a key on the keyboard +% was used. +% +% Usage: +% [out1,out2,out3] = ginput(arg1) + +% Copyright 1984-2005 The MathWorks, Inc. +% $Revision: 1.1 $ $Date: 2009/04/03 22:56:26 $ + +out1 = []; out2 = []; out3 = []; y = []; +c = computer; +if ~strcmp(c(1:2),'PC') + tp = get(0,'TerminalProtocol'); +else + tp = 'micro'; +end + +if ~strcmp(tp,'none') && ~strcmp(tp,'x') && ~strcmp(tp,'micro'), + if nargout == 1, + if nargin == 1, + out1 = trmginput(arg1); + else + out1 = trmginput; + end + elseif nargout == 2 || nargout == 0, + if nargin == 1, + [out1,out2] = trmginput(arg1); + else + [out1,out2] = trmginput; + end + if nargout == 0 + out1 = [ out1 out2 ]; + end + elseif nargout == 3, + if nargin == 1, + [out1,out2,out3] = trmginput(arg1); + else + [out1,out2,out3] = trmginput; + end + end +else + + fig = gcf; + figure(gcf); + + if nargin == 0 + how_many = -1; + b = []; + else + how_many = arg1; + b = []; + if ischar(how_many) ... + || size(how_many,1) ~= 1 || size(how_many,2) ~= 1 ... + || ~(fix(how_many) == how_many) ... + || how_many < 0 + error('MATLAB:ginput:NeedPositiveInt', 'Requires a positive integer.') + end + if how_many == 0 + ptr_fig = 0; + while(ptr_fig ~= fig) + ptr_fig = get(0,'PointerWindow'); + end + scrn_pt = get(0,'PointerLocation'); + loc = get(fig,'Position'); + pt = [scrn_pt(1) - loc(1), scrn_pt(2) - loc(2)]; + out1 = pt(1); y = pt(2); + elseif how_many < 0 + error('MATLAB:ginput:InvalidArgument', 'Argument must be a positive integer.') + end + end + + % Suspend figure functions + state = uisuspend(fig); + + toolbar = findobj(allchild(fig),'flat','Type','uitoolbar'); + if ~isempty(toolbar) + ptButtons = [uigettool(toolbar,'Plottools.PlottoolsOff'), ... + uigettool(toolbar,'Plottools.PlottoolsOn')]; + ptState = get (ptButtons,'Enable'); + set (ptButtons,'Enable','off'); + end + + set(fig,'pointer','fullcrosshair'); + fig_units = get(fig,'units'); + char = 0; + + % We need to pump the event queue on unix + % before calling WAITFORBUTTONPRESS + drawnow + + while how_many ~= 0 + % Use no-side effect WAITFORBUTTONPRESS + waserr = 0; + try + keydown = wfbp; + catch + waserr = 1; + end + if(waserr == 1) + if(ishandle(fig)) + set(fig,'units',fig_units); + uirestore(state); + error('MATLAB:ginput:Interrupted', 'Interrupted'); + else + error('MATLAB:ginput:FigureDeletionPause', 'Interrupted by figure deletion'); + end + end + + ptr_fig = get(0,'CurrentFigure'); + if(ptr_fig == fig) + if keydown + char = get(fig, 'CurrentCharacter'); + button = abs(get(fig, 'CurrentCharacter')); + scrn_pt = get(0, 'PointerLocation'); + set(fig,'units','pixels') + loc = get(fig, 'Position'); + pt = [scrn_pt(1) - loc(1), scrn_pt(2) - loc(2)]; + set(fig,'CurrentPoint',pt); + else + button = get(fig, 'SelectionType'); + if strcmp(button,'open') + button = 1; + elseif strcmp(button,'normal') + button = 1; + elseif strcmp(button,'extend') + button = 2; + elseif strcmp(button,'alt') + button = 3; + else + error('MATLAB:ginput:InvalidSelection', 'Invalid mouse selection.') + end + end + pt = get(gca, 'CurrentPoint'); + + how_many = how_many - 1; + + if(char == 13) % & how_many ~= 0) + % if the return key was pressed, char will == 13, + % and that's our signal to break out of here whether + % or not we have collected all the requested data + % points. + % If this was an early breakout, don't include + % the key info in the return arrays. + % We will no longer count it if it's the last input. + break; + end + + out1 = [out1;pt(1,1)]; + y = [y;pt(1,2)]; + b = [b;button]; + end + end + + uirestore(state); + if ~isempty(toolbar) && ~isempty(ptButtons) + set (ptButtons(1),'Enable',ptState{1}); + set (ptButtons(2),'Enable',ptState{2}); + end + set(fig,'units',fig_units); + + if nargout > 1 + out2 = y; + if nargout > 2 + out3 = b; + end + else + out1 = [out1 y]; + end + + line(out1,y); + line([out1(length(out1)) out1(1)],[y(length(y)) y(1)]); + +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function key = wfbp +%WFBP Replacement for WAITFORBUTTONPRESS that has no side effects. + +fig = gcf; +current_char = []; + +% Now wait for that buttonpress, and check for error conditions +waserr = 0; +try + h=findall(fig,'type','uimenu','accel','C'); % Disabling ^C for edit menu so the only ^C is for + set(h,'accel',''); % interrupting the function. + keydown = waitforbuttonpress; + current_char = double(get(fig,'CurrentCharacter')); % Capturing the character. + if~isempty(current_char) && (keydown == 1) % If the character was generated by the + if(current_char == 3) % current keypress AND is ^C, set 'waserr'to 1 + waserr = 1; % so that it errors out. + end + end + + set(h,'accel','C'); % Set back the accelerator for edit menu. +catch + waserr = 1; +end +drawnow; +if(waserr == 1) + set(h,'accel','C'); % Set back the accelerator if it errored out. + error('MATLAB:ginput:Interrupted', 'Interrupted'); +end + +if nargout>0, key = keydown; end +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Index: /issm/trunk-jpl/src/m/Exp/manipulation/addcontour.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/addcontour.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/addcontour.m (revision 12996) @@ -0,0 +1,50 @@ +function [A,numprofiles,numpoints,closed]=addcontour(A,numprofiles,numpoints,closed,prevplot,root,options); +%ADDCONTOUR - add a closed contour +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=addcontour(A,numprofiles,numpoints,closed,prevplot,root,options) + + title('click to add a point to the new profile, RETURN to exit','FontSize',14) + hold on + + loop=1; + x=[]; + y=[]; + + while loop + + [xi,yi] = ginput(1); + + if ~isempty(xi) + x(end+1,1)=xi; + y(end+1,1)=yi; + + %plot everything + undoplots(prevplot); + plot(x,y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + plot(x(end),y(end),'MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + else + + %check that the profile is not empty + if ~isempty(x) + x(end+1)=x(1); + y(end+1)=y(1); + A(end+1).x=x; + A(end).y=y; + A(end).name=root; + A(end).density=1; + numprofiles=numprofiles+1; + numpoints=numpoints+length(x); + closed(end+1)=1; + end + + %get out + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/addendprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/addendprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/addendprofile.m (revision 12996) @@ -0,0 +1,86 @@ +function [A,numprofiles,numpoints,closed]=addendprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%ADDENDPROFILE - add point at the end of a n existing profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=addendprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting...') + return + end + if ~any(~closed) + disp('all profiles are closed') + return + end + %select a profile first + if numprofiles>1 + %first step, select a profile + isclosed=1; + title('click on a profile, RETURN to exit','FontSize',14) + while isclosed + [xi,yi] = ginput(1); + if ~isempty(xi) + %get the closest point + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + if closed(profsel) + disp('selected profile is closed, make another selection') + else + isclosed=0; + end + + else + %RETURN -> out + return + end + end + else + profsel=1; + end + + %initialize x and y + x=A(profsel).x; + y=A(profsel).y; + + %plot the selected profile + hold on + plot(x,y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + plot(x(end),y(end),'MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + loop=1; + while loop + + %first step, select a profile + title('click to add point to the selected profile, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + if ~isempty(xi) + x(end+1,1)=xi; + y(end+1,1)=yi; + + %plot everything + undoplots(prevplot); + plot(x,y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + plot(x(end),y(end),'MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize')+2,'Marker',getfieldvalue(options,'Marker')); + + else + + %check that the profile is not empty + if ~isempty(x) + A(profsel).x=x; + A(profsel).y=y; + A(profsel).name=root; + A(profsel).density=1; + numpoints=numpoints+length(x); + end + + %get out + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/addinsideprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/addinsideprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/addinsideprofile.m (revision 12996) @@ -0,0 +1,79 @@ +function [A,numprofiles,numpoints,closed]=addinsideprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%ADDINSIDEPROFILE - add apoint inside a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=addinsideprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting...') + return + end + if numpoints<2 + disp('at least two points are required, exiting...') + return + end + hold on + + %plot squares + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + loop=1; + while loop + + %first step, select a segment + title('click on a segment, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + %first click + if ~isempty(xi) + + %get the closest segment + [profsel indsel]=closestsegment(A,numprofiles,xi,yi); + + %check that at least one segment exists + if indsel==0 + disp('at least two points in one profile are required, exiting...') + return + end + + %highlight selected segment + plot([A(profsel).x(indsel) A(profsel).x(indsel+1)],[A(profsel).y(indsel) A(profsel).y(indsel+1)],... + 'color',getfieldvalue(options,'selectioncolor'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + %next click + title('click on the new point''s location, RETURN to exit','FontSize',14) + [xi,yi,but] = ginput(1); + + %second click + if ~isempty(xi) + + %add point to A + A(profsel).x=[A(profsel).x(1:indsel,1); xi; A(profsel).x(indsel+1:end,1)]; + A(profsel).y=[A(profsel).y(1:indsel,1); yi; A(profsel).y(indsel+1:end,1)]; + numpoints=numpoints+1; + + %plot new profile + undoplots(prevplot); + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + else + %RETURN->exit + return + end + else + %RETURN-> exit + return + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/addprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/addprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/addprofile.m (revision 12996) @@ -0,0 +1,48 @@ +function [A,numprofiles,numpoints,closed]=addprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%ADDPROFILE - add a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=addprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + title('click to add a point to the new profile, RETURN to exit','FontSize',14) + hold on + + loop=1; + x=[]; + y=[]; + + while loop + + [xi,yi] = ginput(1); + + if ~isempty(xi) + x(end+1,1)=xi; + y(end+1,1)=yi; + + %plot everything + undoplots(prevplot); + plot(x,y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + plot(x(end),y(end),'MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + else + + %check that the profile is not empty + if ~isempty(x) + A(end+1).x=x; + A(end).y=y; + A(end).name=root; + A(end).density=1; + numprofiles=numprofiles+1; + numpoints=numpoints+length(x); + closed(end+1)=0; + end + + %get out + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/closeprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/closeprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/closeprofile.m (revision 12996) @@ -0,0 +1,68 @@ +function [A,numprofiles,numpoints,closed]=closeprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%CLOSEPROFILE - close one or several profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=closeprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile to be closed') + return + end + + title('click on the profiles to be closed, RETURN to exit','FontSize',14) + hold on + + loop=1; + selection=[]; + + while loop + + %some checks, + if numprofiles==0 + disp('no profile present, exiting...') + return + end + if ~any(~closed), + disp('All the profiles are closed, exiting...') + return + end + + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %get closest profile + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + + if ismember(profsel,selection) + %profile was in selection, remove it from the selection + selection(find(selection==profsel))=[]; + %back to regular color + plot(A(profsel).x,A(profsel).y,... + 'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + elseif closed(profsel), + %profile already closed, do nothing + disp('selected profile aready closed, make another selection'), + else + %add the profile to the list to be closed + selection(end+1)=profsel; + %in selectioncolor + plot(A(profsel).x,A(profsel).y,... + 'color',getfieldvalue(options,'selectioncolor'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + end + else + %close the profiles + for i=1:length(selection), + A(selection(i)).x(end+1)=A(selection(i)).x(1); + A(selection(i)).y(end+1)=A(selection(i)).y(1); + numpoints=numpoints+1; + closed(selection(i))=1; + end + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/closestpoint.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/closestpoint.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/closestpoint.m (revision 12996) @@ -0,0 +1,21 @@ +function [profsel indsel]=closestpoint(A,numprofiles,xi,yi) +%CLOSESTPOINT - find the closest point of a profile +% +% This routine find the point of the profile A that is the closest +% to (xi,yi) and return the number of the profile and the number of +% the point +% +% Usage: +% [profsel indsel]=closestpoint(A,numprofiles,xi,yi) + + %loop over the points of each profile, find the closest to (xi,yi) + for i=1:numprofiles, + distance=(xi-A(i).x).^2+(yi-A(i).y).^2; + [newdistance p]=min(distance); + if ((i==1) | (newdistance1 + middles=[(A(i).x(1:end-1)+A(i).x(2:end))/2 (A(i).y(1:end-1)+A(i).y(2:end))/2]; + distance=(xi-middles(:,1)).^2+(yi-middles(:,2)).^2; + [newdistance p]=min(distance); + if (first | (newdistancep1 & p3p2 & p3 quit + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/cutprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/cutprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/cutprofile.m (revision 12996) @@ -0,0 +1,79 @@ +function [A,numprofiles,numpoints,closed]=cutprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%CUTPROFILE - cut a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=cutprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting...') + return + end + if numpoints<2 + disp('at least two points are needed') + return + end + hold on + + %plot squares + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + loop=1; + while loop + + %select a segment + title('click the segment to cut, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %get the closest segment + [profsel indsel]=closestsegment(A,numprofiles,xi,yi); + + %check that at least one segment exists + if indsel==0 + disp('at least 2 points are required'); + return, + end + + if ((closed(profsel) & length(A(profsel).x)<3) | (~closed(profsel) & length(A(profsel).x)<2)) + disp('at least 2 points are required, make another selection'); + else + %cut A + if closed(profsel) + %open the contour + A(profsel).x=[A(profsel).x(indsel+1:end-1,1);A(profsel).x(1:indsel,1)]; + A(profsel).y=[A(profsel).y(indsel+1:end-1,1);A(profsel).y(1:indsel,1)]; + numpoints=numpoints-1; + closed(profsel)=0; + else + %cut the contour in 2 profiles + A(end+1).x=A(profsel).x(indsel+1:end,1); + A(end).y=A(profsel).y(indsel+1:end,1); + A(end).name=root; + A(end).density=1; + A(profsel).x=A(profsel).x(1:indsel,1); + A(profsel).y=A(profsel).y(1:indsel,1); + numprofiles=numprofiles+1; + closed(end+1)=0; + end + + %plot new profile + undoplots(prevplot); + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + end + else + %RETURN->exit + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/mergeprofiles.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/mergeprofiles.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/mergeprofiles.m (revision 12996) @@ -0,0 +1,152 @@ +function [A,numprofiles,numpoints,closed]=mergeprofiles(A,numprofiles,numpoints,closed,prevplot,root,options); +%MERGEPROFILES - merge profiles +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile. The user must select the two tips that +% he/she wants to merge +% +% Usage: +% [A,numprofiles,numpoints,closed]=mergeprofiles(A,numprofiles,numpoints,closed,prevplot,root,options) + +hold on +loop=1; + +%Take all the tips coordinates of open profiles +counter=1; tips=[]; +for i=1:numprofiles + if ~closed(i), + %x and y coord, profile number, 1 if beginning, 2 and if end + if length(A(i).x)==1, + tips(counter,:)=[A(i).x(1) A(i).y(1) i 1]; + counter=counter+1; + else + tips(counter,:)=[A(i).x(1) A(i).y(1) i 1]; + tips(counter+1,:) = [A(i).x(end) A(i).y(end) i 2]; + counter=counter+2; + end + end +end + +if size(tips,1)<2 + disp('at least one unclosed profile is required') + return +end + +%plot the tips only +plot(tips(:,1),tips(:,2),... + 'LineStyle','none','MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); +firsttip=1; + +%loop (at least 2 clicks needed) +while loop + + %some checks + if size(tips,1)<2 + disp('at least one unclosed profiles are required') + return + end + + %select a point + if firsttip + title('click on the first tip, RETURN to exit','FontSize',14) + else + title('click on the second tip, RETURN to exit','FontSize',14) + end + + [xi,yi] = ginput(1); + + if ~isempty(xi) + + if firsttip + %find the selected tip + distance=(xi-tips(:,1)).^2+(yi-tips(:,2)).^2; + [dmin tip1]=min(distance); + numprofile1=tips(tip1,3); + firsttip=0; + + %remove tip1 from tips list + newtips=tips; + newtips(tip1,:)=[]; + + %plot selected tip + plot(tips(tip1,1),tips(tip1,2),... + 'LineStyle','none','MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + plot(A(numprofile1).x,A(numprofile1).y,... + 'color',getfieldvalue(options,'selectioncolor'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + + %second selection + else + distance=(xi-newtips(:,1)).^2+(yi-newtips(:,2)).^2; + [dmin tip2]=min(distance); + numprofile2=newtips(tip2,3); + + if numprofile1==numprofile2 + %close the profile + A(numprofile1).x(end+1)=A(numprofile1).x(1); + A(numprofile1).y(end+1)=A(numprofile1).y(1); + numpoints=numpoints+1; + closed(numprofile1)=1; + + else + + if tips(tip1,4)==1 & newtips(tip2,4)==1, + A(numprofile1).x=[flipud(A(numprofile2).x); A(numprofile1).x]; + A(numprofile1).y=[flipud(A(numprofile2).y); A(numprofile1).y]; + numprofiles=numprofiles-1; + + elseif tips(tip1,4)==1 & newtips(tip2,4)==2, + A(numprofile1).x=[A(numprofile2).x; A(numprofile1).x]; + A(numprofile1).y=[A(numprofile2).y; A(numprofile1).y]; + numprofiles=numprofiles-1; + + elseif tips(tip1,4)==2 & newtips(tip2,4)==1, + A(numprofile1).x=[A(numprofile1).x; A(numprofile2).x]; + A(numprofile1).y=[A(numprofile1).y; A(numprofile2).y]; + numprofiles=numprofiles-1; + + elseif tips(tip1,4)==2 & newtips(tip2,4)==2, + A(numprofile1).x=[A(numprofile1).x; flipud(A(numprofile2).x)]; + A(numprofile1).y=[A(numprofile1).y; flipud(A(numprofile2).y)]; + numprofiles=numprofiles-1; + end + + %delete profile2 + A(numprofile2)=[]; + closed(numprofile2)=[]; + + end + + %update tips + counter=1; tips=[]; + for i=1:numprofiles + if ~closed(i), + %x and y coord, profile number, 1 if beginning, 2 and if end + if length(A(i).x)==1, + tips(counter,:)=[A(i).x(1) A(i).y(1) i 1]; + counter=counter+1; + else + tips(counter,:)=[A(i).x(1) A(i).y(1) i 1]; + tips(counter+1,:) = [A(i).x(end) A(i).y(end) i 2]; + counter=counter+2; + end + end + end + + %plot new profile + undoplots(prevplot); + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + end + if ~isempty(tips) + plot(tips(:,1),tips(:,2),... + 'LineStyle','none','MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + %back to beginning + firsttip=1; + end + else + %RETRUN-> quit + loop=0; + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/modifyposition.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/modifyposition.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/modifyposition.m (revision 12996) @@ -0,0 +1,77 @@ +function [A,numprofiles,numpoints,closed]=modifyposition(A,numprofiles,numpoints,closed,prevplot,root,options); +%MODIFYPOSITION - modify the prosition of a point of a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=modifyposition(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting..') + return + end + + hold on + loop=1; + + %plot squares + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + while loop + + %select a point to be modified + title('click on the point to be modified, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %get the closest point + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + + %plot the point in blue + plot(A(profsel).x(indsel),A(profsel).y(indsel),... + 'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'selectioncolor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + %select new location + title('click on the new location, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %modification of its coordinates + A(profsel).x(indsel)=xi; + A(profsel).y(indsel)=yi; + + %modify the last point if the profile is closed and indsel=end or 1 + if closed(profsel) + if indsel==1 + A(profsel).x(end)=xi; + A(profsel).y(end)=yi; + elseif indsel==length(A(profsel).x) + A(profsel).x(1)=xi; + A(profsel).y(1)=yi; + end + end + + %plot new profile + undoplots(prevplot); + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + else + %RETURN-> exit + loop=0; + end + else + %RETURN-> exit + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/removepoints.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/removepoints.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/removepoints.m (revision 12996) @@ -0,0 +1,85 @@ +function [A,numprofiles,numpoints,closed]=removepoints(A,numprofiles,numpoints,closed,prevplot,root,options); +%REMOVEPOINTS - remove a point from a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=removepoints(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting...') + return + end + + hold on + loop=1; + + %plot squares + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + + end + + while loop + + %check that at least one point is present + if numpoints==0 + disp('at least one point are needed') + return + end + + %select a point to be deleted + title('click on the point to be removed, RETURN to exit','FontSize',14) + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %get the closest point + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + + %remove point of A + A(profsel).x(indsel)=[]; + A(profsel).y(indsel)=[]; + + %unclose the domain if only 2 points remaining + if closed(profsel) + if length(A(profsel).x)==3 + A(profsel).x(end)=[]; + A(profsel).y(end)=[]; + numpoints=numpoints-1; + closed(profsel)=0; + end + end + + %remove the last point if the profile is closed and indsel=end or 1 + if closed(profsel) + if indsel==1 + A(profsel).x(end)=A(profsel).x(1); + A(profsel).y(end)=A(profsel).y(1); + elseif indsel==length(A(profsel).x) + A(profsel).x(1)=A(profsel).x(end); + A(profsel).y(1)=A(profsel).y(end); + end + end + numpoints=numpoints-1; + + %plot new profile + undoplots(prevplot); + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + if length(A(i).x)==1 + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker','o'); + end + end + + else + %RETURN-> exit + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/removeprofile.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/removeprofile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/removeprofile.m (revision 12996) @@ -0,0 +1,56 @@ +function [A,numprofiles,numpoints,closed]=removeprofile(A,numprofiles,numpoints,closed,prevplot,root,options); +%REMOVEPROFILE - delete a profile +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=removeprofile(A,numprofiles,numpoints,closed,prevplot,root,options) + + title('click on the profiles to be removed, RETURN to exit','FontSize',14) + hold on + + loop=1; + selection=[]; + + while loop + + %some checks + if numprofiles==0 + disp('no profile to be removed, exiting...') + return + end + + [xi,yi] = ginput(1); + + if ~isempty(xi) + + %get closest profile + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + + if ismember(profsel,selection) + %profile was in selection, remove it + selection(find(selection==profsel))=[]; + %back to regular color + plot(A(profsel).x,A(profsel).y,... + 'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + else + %add the profile to the list to be removed + selection(end+1)=profsel; + %in selectioncolor + plot(A(profsel).x,A(profsel).y,... + 'color',getfieldvalue(options,'selectioncolor'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + end + else + %remove the profiles + selection=sort(selection); + for i=1:length(selection), + numprofiles=numprofiles-1; + numpoints=numpoints-length(A(selection(i)-(i-1)).x); + A(selection(i)-(i-1))=[]; + closed(selection(i)-(i-1))=[]; + end + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/removeseveralpoints.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/removeseveralpoints.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/removeseveralpoints.m (revision 12996) @@ -0,0 +1,130 @@ +function [A,numprofiles,numpoints,closed]=removeseveralpoints(A,numprofiles,numpoints,closed,prevplot,root,options); +%REMOVESEVERALPOINTS - remove several point +% +% this script is used by exptool as an elementary operation +% on an ARGUS profile +% +% Usage: +% [A,numprofiles,numpoints,closed]=removeseveralpoints(A,numprofiles,numpoints,closed,prevplot,root,options) + + %some checks + if numprofiles==0 + disp('no profile present, exiting...') + return + end + if numpoints<3 + disp('at least 3 points are required, exiting...') + return + end + hold on + loop=1; + + %plot squares + for i=1:numprofiles + plot(A(i).x,A(i).y,'color',getfieldvalue(options,'color'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth'),... + 'MarkerEdgeColor',getfieldvalue(options,'MarkerEdgeColor'),'MarkerSize',getfieldvalue(options,'MarkerSize'),'Marker',getfieldvalue(options,'Marker')); + end + + points=[]; + + %loop (at least 3 clicks needed) + while loop + + %some checks + if numpoints<3 + disp('at least 3 points are required, exiting...') + return + end + + %select a point + if isempty(points) + title('click on the first tip, RETURN to exit','FontSize',14) + elseif length(points)==1 + title('click on the second tip, RETURN to exit','FontSize',14) + else + title('click in the middle of the area to be removed, RETURN to exit','FontSize',14) + end + + [xi,yi] = ginput(1); + + if ~isempty(xi) + %get the closest point + %first time, look at all profiles + if isempty(points) + [profsel indsel]=closestpoint(A,numprofiles,xi,yi); + if ((closed(profsel) & length(A(profsel).x)<4) | (~closed(profsel) & length(A(profsel).x)<3)), + disp('the selected profile has less than 3 points, make another selection'); + else + selection=profsel; + points(end+1)=indsel; + plot(A(profsel).x,A(profsel).y,... + 'color',getfieldvalue(options,'selectioncolor'),'LineStyle',getfieldvalue(options,'LineStyle'),'LineWidth',getfieldvalue(options,'LineWidth')); + text(A(selection).x(indsel),A(selection).y(indsel),num2str(1),'FontSize',14,'background',[0.7 0.7 0.9]); + end + %disp(['p1= ' num2str(indsel)]), + else + %get the 2d or 3d point for the given contou + [profsel indsel]=closestpoint(A(selection),1,xi,yi); + if ismember(indsel,points) + disp('the selected points must be distinct') + else + %second click? + if length(points)==1, + points(end+1)=indsel; + text(A(selection).x(indsel),A(selection).y(indsel),num2str(2),'FontSize',14,'background',[0.7 0.7 0.9]); + %disp(['p2= ' num2str(indsel)]), + %third click? + else + p1=points(1); p2=points(2); p3=indsel; + %disp(['p3= ' num2str(indsel)]), + if p1p1 & p3p2 & p3 quit + loop=0; + end + end +end Index: /issm/trunk-jpl/src/m/Exp/manipulation/undoplots.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/manipulation/undoplots.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/manipulation/undoplots.m (revision 12996) @@ -0,0 +1,12 @@ +function undoplots(prevplot) +%UNDOPLOTS - undo plots +% +% Usage:undoplots(prevplot) + + %erase all previous plots + g=get(gca,'children'); + L=length(g); + for i=1:L-prevplot + delete(g(i)); + end +end Index: /issm/trunk-jpl/src/m/Exp/readwrite/expread.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/readwrite/expread.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/readwrite/expread.m (revision 12996) @@ -0,0 +1,81 @@ +function Struct=expread(filename); +%EXPREAD - read a file exp and build a Structure +% +% This routine reads a file .exp and build a Structure containing the +% fields x and y corresponding to the coordinates, one for the filename of +% the exp file, for the density, for the nodes, and a field closed to +% indicate if the domain is closed. +% The first argument is the .exp file to be read and the second one (optional) +% indicate if the last point shall be read (1 to read it, 0 not to). +% +% Usage: +% Struct=expread(filename) +% +% Example: +% Struct=expread('domainoutline.exp') +% Struct=expread('domainoutline.exp') +% +% See also EXPDOC, EXPWRITEASVERTICES + +%some checks +if ~exist(filename), + error(['expread error message: file ' filename ' not found!']); +end + +%initialize number of profile +count=0; + +%open file +fid=fopen(filename,'r'); + +%loop over the number of profiles +while (~feof(fid)), + + %update number of profiles + count=count+1; + + %Get file name + A=fscanf(fid,'%s %s',2); + if ~strncmp(A,'##Name:',7), break; end + if length(A)>7, + Struct(count).name=A(8:end); + else + Struct(count).name=''; + end + + %Get Icon + A=fscanf(fid,'%s %s',2); + if ~strncmp(A,'##Icon:',6), break; end + + %Get Info + A=fscanf(fid,'%s %s %s %s',4); + if ~strncmp(A,'#Points',7), break; end + + %Get number of nods and density + A=fscanf(fid,'%f %f',[1 2]); + Struct(count).nods=A(1); + Struct(count).density=A(2); + + %Get Info + A=fscanf(fid,'%s %s %s %s',5); + if ~strncmp(A,'#XposYpos',9), break; end + + %Get Coordinates + A=fscanf(fid,'%f %f',[2 Struct(count).nods]); + Struct(count).x=A(1,:)'; + Struct(count).y=A(2,:)'; + + if(Struct(count).nods~=length(Struct(count).x))error(['Profile ' num2str(count) ' reports incorrect length']); end; + + %Check if closed + if (Struct(count).nods > 1) && ... + (Struct(count).x(end) == Struct(count).x(1)) && ... + (Struct(count).y(end) == Struct(count).y(1)) + Struct(count).closed=true; + else + Struct(count).closed=false; + end +end + +%close file +fclose(fid); Index: /issm/trunk-jpl/src/m/Exp/readwrite/expwrite.m =================================================================== --- /issm/trunk-jpl/src/m/Exp/readwrite/expwrite.m (revision 12996) +++ /issm/trunk-jpl/src/m/Exp/readwrite/expwrite.m (revision 12996) @@ -0,0 +1,38 @@ +function expwrite(a,filename); +%EXPWRITE - write an Argus file from a structure given in input +% +% This routine write an Argus file form a structure containing the fields: +% x and y of the coordinates of the points. +% The first argument is the structure containing the points coordinates +% and the second one the file to be write. +% +% Usage: +% expwrite(a,filename) +% +% Example: +% expwrite(coordstruct,'domainoutline.exp') +% +% See also EXPDOC, EXPREAD, EXPWRITEASVERTICES + +fid=fopen(filename,'w'); +for n=1:length(a), + + if isfield(a,'name'), + if ~isempty(a(n).name), + fprintf(fid,'%s%s\n','## Name:',a(n).name); + else + fprintf(fid,'%s\n','## Name:'); + end + else + fprintf(fid,'%s\n','## Name:'); + end + + fprintf(fid,'%s\n','## Icon:0'); + fprintf(fid,'%s\n','# Points Count Value'); + fprintf(fid,'%i %f\n',[length(a(n).x) a(n).density]); + fprintf(fid,'%s\n','# X pos Y pos'); + fprintf(fid,'%10.10f %10.10f\n',[a(n).x a(n).y]'); + fprintf(fid,'\n',''); + +end +fclose(fid); Index: /issm/trunk-jpl/src/m/Geometry/FlagElements.m =================================================================== --- /issm/trunk-jpl/src/m/Geometry/FlagElements.m (revision 12996) +++ /issm/trunk-jpl/src/m/Geometry/FlagElements.m (revision 12996) @@ -0,0 +1,57 @@ +function flag=FlagElements(md,region), +%FLAGELEMENTS - flag the elements in an region +% +% The region can be given with an exp file, a list of elements. +% +% Usage: +% flag=FlagElements(md,region); +% +% Example: +% flag=FlagElements(md,'all'); +% flag=FlagElements(md,''); +% flag=FlagElements(md,'Domain.exp'); +% flag=FlagElements(md,'~Domain.exp'); +% flag=FlagElements(md,md.mask.elementongroundedice); + + if ischar(region), + if isempty(region), + flag=zeros(md.mesh.numberofelements,1); + invert=0; + elseif strcmpi(region,'all') + flag=ones(md.mesh.numberofelements,1); + invert=0; + else + %make sure that we actually don't want the elements outside the domain outline! + if strcmpi(region(1),'~'), + region=region(2:length(region)); + invert=1; + else + invert=0; + end + + %does the region domain outline exist or do we have to look for xlim,ylim in basinzoom? + if ~exist(region,'file'), + if (length(region)>3 & ~strcmp(region(end-3),'.exp')), + error(['Error: File ' region ' not found!']); + end + [xlim,ylim]=basinzoom('basin',region); + flag_nodes=double(md.mesh.xxlim(1) & md.mesh.yylim(1)); + flag=prod(flag_nodes(md.mesh.elements),2); + else + %ok, flag elements + flag=ContourToMesh(md.mesh.elements(:,1:3),md.mesh.x,md.mesh.y,region,'element',1); + end + end + if invert, + flag=~flag; + end + elseif isfloat(region) | islogical(region), + if size(region,1)~=md.mesh.numberofelements, + help FlagElements + error('Flaglist for region must be of same size as number of elements in model'); + end + flag=region; + else + error('Invalid region option'); + end +end Index: /issm/trunk-jpl/src/m/Geometry/FlagElements.py =================================================================== --- /issm/trunk-jpl/src/m/Geometry/FlagElements.py (revision 12996) +++ /issm/trunk-jpl/src/m/Geometry/FlagElements.py (revision 12996) @@ -0,0 +1,62 @@ +import numpy +import os +#from basinzoom import * +#from ContourToMesh import * +from MatlabFuncs import * + +def FlagElements(md,region): + """ + FLAGELEMENTS - flag the elements in an region + + The region can be given with an exp file, a list of elements. + + Usage: + flag=FlagElements(md,region); + + Example: + flag=FlagElements(md,'all'); + flag=FlagElements(md,''); + flag=FlagElements(md,'Domain.exp'); + flag=FlagElements(md,'~Domain.exp'); + flag=FlagElements(md,md.mask.elementongroundedice); + """ + + if isinstance(region,str): + if not region: + flag=numpy.zeros(md.mesh.numberofelements,'bool') + invert=0 + elif strcmpi(region,'all'): + flag=numpy.ones(md.mesh.numberofelements,'bool') + invert=0 + else: + #make sure that we actually don't want the elements outside the domain outline! + if strcmpi(region[0],'~'): + region=region[1:] + invert=1 + else: + invert=0 + + #does the region domain outline exist or do we have to look for xlim,ylim in basinzoom? + if not os.path.exists(region): + if len(region)>3 and not strcmp(region[-4:],'.exp'): + raise IOError("Error: File 'region' not found!" % region) + xlim,ylim=basinzoom('basin',region) + flag_nodes=numpy.logical_and(numpy.logical_and(md.mesh.xxlim[0]),numpy.logical_and(md.mesh.yylim[0])).astype(float) + flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1) + else: + #ok, flag elements + flag=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x,md.mesh.y,region,'element',1) + + if invert: + flag=numpy.logical_not(flag) + + elif isinstance(region,numpy.nparray) or isinstance(region,bool): + if not numpy.size(region,0)==md.mesh.numberofelements: + raise TypeError("Flaglist for region must be of same size as number of elements in model.") + flag=region + + else: + raise TypeError("Invalid region option") + + return flag + Index: /issm/trunk-jpl/src/m/Geometry/SegIntersect.m =================================================================== --- /issm/trunk-jpl/src/m/Geometry/SegIntersect.m (revision 12996) +++ /issm/trunk-jpl/src/m/Geometry/SegIntersect.m (revision 12996) @@ -0,0 +1,81 @@ +function bool=SegIntersect(seg1,seg2) +%SEGINTERSECT - test of segments intersection +% +% return 1 if the two segments intersect +% seg1=[x1 y1; x2 y2] +% seg2=[x1 y1; x2 y2] +% +% Usage: +% bool=SegIntersect(seg1,seg2) + +bool=1; + +xA=seg1(1,1); yA=seg1(1,2); +xB=seg1(2,1); yB=seg1(2,2); +xC=seg2(1,1); yC=seg2(1,2); +xD=seg2(2,1); yD=seg2(2,2); + +O2A=[xA;yA]-[xD/2+xC/2;yD/2+yC/2]; +O2B=[xB;yB]-[xD/2+xC/2;yD/2+yC/2]; +O1C=[xC;yC]-[xA/2+xB/2;yB/2+yA/2]; +O1D=[xD;yD]-[xA/2+xB/2;yB/2+yA/2]; + +n1=[yA-yB;xB-xA]; %normal vector to segA +n2=[yC-yD;xD-xC]; %normal vectot to segB + +test1=n2'*O2A; +test2=n2'*O2B; + +if test1*test2>0 + bool=0; + return; +end + +test3=n1'*O1C; +test4=n1'*O1D; + +if test3*test4>0 + bool=0; + return; +end + +%if colinear +if test1*test2==0 & test3*test4==0 & det([n1 n2])==0 + + %projection on the axis O1O2 + O2O1=[xA/2+xB/2;yB/2+yA/2]-[xD/2+xC/2;yD/2+yC/2]; + O1A=O2O1'*(O2A-O2O1); + O1B=O2O1'*(O2B-O2O1); + O1C=O2O1'*O1C; + O1D=O2O1'*O1D; + + %test if one point is included in the other segment (->bool=1) + if (O1C-O1A)*(O1D-O1A)<0 + bool=1; + return; + end + if (O1C-O1B)*(O1D-O1B)<0 + bool=1; + return; + end + if (O1A-O1C)*(O1B-O1C)<0 + bool=1; + return; + end + if (O1A-O1D)*(O1B-O1D)<0 + bool=1; + return; + end + + %test if the 2 segments have the same middle (->bool=1) + if O2O1==0 + bool=1; + return; + end + + %else + bool=0; + return; + +end + Index: /issm/trunk-jpl/src/m/Geometry/find_point.m =================================================================== --- /issm/trunk-jpl/src/m/Geometry/find_point.m (revision 12996) +++ /issm/trunk-jpl/src/m/Geometry/find_point.m (revision 12996) @@ -0,0 +1,14 @@ +function f=find_point(tabx,taby,pointx,pointy) +%FIND_POINT - find closest point +% +% find which point of the list (tabx,taby) is +% the closest to (poinx,pointy) +% +% Usage: +% f=find_point(tabx,taby,pointx,pointy) + +%Compute distance between point and cloud of points +distance=sqrt((tabx-pointx).^2+(taby-pointy).^2); + +%find index of the minimum distance and return the first one only +f=find(distance==min(min(distance)),1); Index: /issm/trunk-jpl/src/m/ImageProcessing/im_resize.m =================================================================== --- /issm/trunk-jpl/src/m/ImageProcessing/im_resize.m (revision 12996) +++ /issm/trunk-jpl/src/m/ImageProcessing/im_resize.m (revision 12996) @@ -0,0 +1,16 @@ +function newimg = im_resize(img,nw,nh) +%IM_RESIZE - resize an image using bicubic interpolation +% +% NEWIMG = IM_RESIZE(IMG,NW,NH) Given input image IMG, +% returns a new image NEWIMG of size NWxNH. +% +% Matthew Dailey 2000 + + if nargin ~= 3 + error('usage: im_resize(image,new_wid,new_ht)'); + end; + + ht_scale = size(img,1) / nh; + wid_scale = size(img,2) / nw; + + newimg = interp2(img,(1:nw)*wid_scale,(1:nh)'*ht_scale,'cubic'); Index: /issm/trunk-jpl/src/m/ImageProcessing/immerge.m =================================================================== --- /issm/trunk-jpl/src/m/ImageProcessing/immerge.m (revision 12996) +++ /issm/trunk-jpl/src/m/ImageProcessing/immerge.m (revision 12996) @@ -0,0 +1,43 @@ +function out = immerge(bg, fg, coef) +% Creates an image 'out' of same type as bg. +% 'out' has 'bg' as background, and 'fg' (transparent, +% weighted by 'coef') above 'bg'. +% Useful when one cannot use OpenGL as renderer, but still +% wants to have transparency! +% 'out', 'bg', and 'fg' are RGB images. +% +% merged = immerged(bg, fg, coef) +% - bg matrix of type double or uint8 +% - fg matrix of type double or uint8 +% - coef is a scalar between 0 and 1, or a matrix of +% such scalars, same size as 'fg' and 'bg' (AlphaData). +% +% Suggestions for future development: +% - allow to have 'coef' referring to the AlphaMap +% - allow 'coef' to take values between 1 and 64. +% +% Gauthier Fleutot 28-07-2004 +% fleutotg@esiee.fr + +intOutput = 0; % if we want the output to be of type integer + +if ~isa(bg, 'double') + bg = double(bg); % because '-' isn't defined for uint8 + intOutput = 1; +end +if ~isa(fg, 'double') + fg = double(fg); % because '-' isn't defined for uint8 +end + +dif = fg-bg; + +if size(coef) == [1 1] + out = bg + coef.*dif; +else + coef = cat(3,coef,coef,coef); % extend the coef matric in the 3rd dim. + out = bg + coef .* dif; +end + +if intOutput == 1 + out = uint8(out); +end Index: /issm/trunk-jpl/src/m/ImageProcessing/mean_congrid.m =================================================================== --- /issm/trunk-jpl/src/m/ImageProcessing/mean_congrid.m (revision 12996) +++ /issm/trunk-jpl/src/m/ImageProcessing/mean_congrid.m (revision 12996) @@ -0,0 +1,59 @@ +function res=mean_congrid(a,n,choice); +%MEAN_CONGRID - average the values around a pixel +% +% INPUT a,n,choice, where a is the matrix, and n the size of the area averaged around +% one pixel, odd number. choice=1 if the NaN values remain NaN values. +% +% Usage: +% res=mean_congrid(a,n,choice) + +s=size(a); +aa=a; +pos=find(isnan(aa)); +aa(pos)=0; + +if (mod(n,2)==0), + disp('Cannot rebin, the dimensions of the matrix and n are not compatible'); + break +end +mm=(n-1)/2; + +res=zeros(s(1),s(2)); + +for m=mm+1:s(1)-mm, + if mod(m,10)==0, + disp(m/s(1)*100); + end + + for l=mm+1:s(2)-mm, + + + if sum(sum(~isnan(a(m-mm:m+mm,l-mm:l+mm))))~=0, + res(m,l)=sum(... + sum(... + ~isnan(... + a(m-mm:m+mm,l-mm:l+mm)... + ).*... + aa(m-mm:m+mm,l-mm:l+mm)... + )... + )... + /sum(sum(~isnan(a(m-mm:m+mm,l-mm:l+mm)))); + else + res(m,l)=NaN; + end + + end +end + +if choice==1, + pos=find(isnan(a)); + res(pos)=NaN; +end + + + + + + + + Index: /issm/trunk-jpl/src/m/ImageProcessing/rebin.m =================================================================== --- /issm/trunk-jpl/src/m/ImageProcessing/rebin.m (revision 12996) +++ /issm/trunk-jpl/src/m/ImageProcessing/rebin.m (revision 12996) @@ -0,0 +1,44 @@ +function res=rebin(a,n); +%REBIN - average values of a matrix by bloc +% +% INPUT a,n, where a is the matrix, and n the size of the area averaged around +% one pixel +% +% Usage: +% res=rebin(a,n) + +s=size(a); + +if (mod(s(1)/n,2)~=0 | mod(s(2)/n,2)~=0), + disp('Cannot rebin, the dimensions of the matrix and n are not compatible'); + break +end + +res=zeros(s(1)/n,s(2)/n); + +for m=1:s(1)/n, + for l=1:s(2)/n, + if sum(sum(~isnan(a((m-1)*n+1:m*n,(l-1)*n+1:l*n))))~=0, + res(m,l)=sum(... + sum(... + ~isnan(... + a((m-1)*n+1:m*n,(l-1)*n+1:l*n)... + ).*... + a((m-1)*n+1:m*n,(l-1)*n+1:l*n)... + )... + )... + /sum(sum(~isnan(a((m-1)*n+1:m*n,(l-1)*n+1:l*n)))); + else + res(m,l)=NaN; + end + + end +end + + + + + + + + Index: /issm/trunk-jpl/src/m/Interp/FieldFindVarNames.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/FieldFindVarNames.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/FieldFindVarNames.m (revision 12996) @@ -0,0 +1,153 @@ +function Names=FieldFindVarNames(filename) +%FIELDFINDVARNAMES - find names of variables in a data set file +% +% This routines looks at the variables contained in a file and finds out +% the names of the variables that are needed for an interpolation (x,y,data) +% or (index,x,y,data) +% +% Usage: +% Names=FieldFindVarNames(filename) +% +% Example: +% Names=FieldFindVarNames('thickness.mat') +% +% See also: INTERPFROMFILE, GRIDDATA + +%some checks +if nargin~=1 | nargout~=1 + help FieldFindVarNames + error('FieldFindVarNames error message: bad usage'); +end +if ~exist(filename) + error(['FieldFindVarNames error message: file ' filename ' does not exist']); +end + +%Get variables +A=whos('-file',filename); + +%find x,y,vx and vy +xenum=NaN; yenum=NaN; dataenum=NaN; indexenum=NaN; +if length(A)==3, + isnode=1; + for i=1:3 + if strcmpi(A(i).name(1),'x'); + xenum=i; + elseif strcmpi(A(i).name(1),'y'); + yenum=i; + elseif (strncmpi(A(i).name,filename,3) | strncmpi(A(i).name,'data',4)), + dataenum=i; + else + %nothing + end + end +elseif length(A)==4, + isnode=0; + for i=1:4 + if strcmpi(A(i).name(1),'x'); + xenum=i; + elseif strcmpi(A(i).name(1),'y'); + yenum=i; + elseif (strncmpi(A(i).name,'index',5) | strncmpi(A(i).name,'elements',7)); + indexenum=i; + elseif (strncmpi(A(i).name,filename,3) | strncmpi(A(i).name,'data',4)), + dataenum=i; + else + %nothing + end + end +else + error(['FieldFindVarNames error message: file ' filename ' not supported yet (it should hold 3 variables x,y and data (for nodes) OR 4 variables x,y,index and data (for mesh))']); +end + +%2: if only one item is missing, find it by elimination +if ~isnode, + pos=find(isnan([xenum yenum indexenum dataenum])); + if length(pos)==1, + list=[xenum yenum indexenum dataenum]; list(pos)=[]; + if pos==1, + xenum=setdiff(1:4,list); + elseif pos==2, + yenum=setdiff(1:4,list); + elseif pos==3, + indexenum=setdiff(1:4,list); + elseif pos==4, + dataenum=setdiff(1:4,list); + end + end +else + pos=find(isnan([xenum yenum dataenum])); + if length(pos)==1, + list=[xenum yenum indexenum dataenum]; list(pos)=[]; + if pos==1, + xenum=setdiff(1:3,list); + elseif pos==2, + yenum=setdiff(1:3,list); + elseif pos==3, + dataenum=setdiff(1:3,list); + end + end +end + +%assum that we have found at least xenum and yenum +if ( isnan(xenum) | isnan(yenum)) + error(['FieldFindVarNames error message: file ' filename ' not supported yet (the coordinates vectors should be named x and y)']); +end + +%find index +if (~isnode & isnan(indexenum)), + for i=1:4 + lengthi=min(A(i).size); + if (lengthi==3), + indexenum=i; + end + end + if isnan(indexenum), + error(['FieldFindVarNames error message: file ' filename ' not supported yet (index not found)']); + end +end + +%4: last chance +if ~isnode, + pos=find(isnan([xenum yenum indexenum dataenum])); + if length(pos)==1, + list=[xenum yenum indexenum dataenum]; list(pos)=[]; + if pos==1, + xenum=setdiff(1:4,list); + elseif pos==2, + yenum=setdiff(1:4,list); + elseif pos==3, + indexenum=setdiff(1:4,list); + elseif pos==4, + dataenum=setdiff(1:4,list); + end + end +else + pos=find(isnan([xenum yenum dataenum])); + if length(pos)==1, + list=[xenum yenum indexenum dataenum]; list(pos)=[]; + if pos==1, + xenum=setdiff(1:3,list); + elseif pos==2, + yenum=setdiff(1:3,list); + elseif pos==3, + dataenum=setdiff(1:3,list); + end + end +end + +%last check +if isnan(dataenum) + error(['FieldFindVarNames error message: file ' filename ' not supported yet (data not found)']); +end + +%create output +Names=struct(); +Names.xname=A(xenum).name; +Names.yname=A(yenum).name; +Names.dataname=A(dataenum).name; +if ~isnode, + Names.indexname=A(indexenum).name; + Names.interp='mesh'; +else + Names.interp='node'; +end Index: /issm/trunk-jpl/src/m/Interp/FillHole.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/FillHole.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/FillHole.m (revision 12996) @@ -0,0 +1,39 @@ +function field=FillHole(index,x,y,field) +%FILLHOLE - fill mesh data that has holes in it (hole is defined by field==NaN). Get the nearest neighboors to fill the holes. +% +% Usage: +% surface=FillHole(index,x,y,surface) +% +% Example: +% md.geometry.surface=FillHole(md.mesh.elements,x,md.mesh.y,md.geometry.surface) +% + +%some checks +if nargin~=4 | nargout~=1 + help FillHole + error('FillHole error message: bad usage'); +end + +if length(x)~=length(y), + error('plugdata error message: x and y should have the same length'); +end + + +pos_hole=find(isnan(field)); +pos_full=find(~isnan(field)); + +%reduce our field to not include any holes: +field_noholes=field(pos_full); +x_noholes=x(pos_full); +y_noholes=y(pos_full); + +for i=1:length(pos_hole) + + if (mod(i,100)==0), + fprintf('\b\b\b\b\b\b\b%5.2f%s',i/length(pos_hole)*100,' %'); + end + + %search the node on the closest to i, that is not in a hole either + [d posd]=min(sqrt((x(pos_hole(i))-x_noholes).^2+(y(pos_hole(i))-y_noholes).^2)); + field(pos_hole(i))=field_noholes(posd); +end Index: /issm/trunk-jpl/src/m/Interp/InterpFromFile.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/InterpFromFile.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/InterpFromFile.m (revision 12996) @@ -0,0 +1,44 @@ +function data_out=InterpFromFile(x,y,filename,default_value) +%INTERPFROMFILE - load data and interpolate on the given nodes +% +% load a matlab file (extension .mat) which holds 3 or 4 variables +% and interpolate the data on the mesh and plug it onto the model. +% +% o 3 variables +% - a vector x (if the name of the variable do not begin with "x", an error can appear) +% - a vector y (if the name of the variable do not begin with "y", an error can appear) +% - a vector or matrix data (if the name of the variable do not begin with the field name, an error can appear) +% o 4 variables +% - a vector x (if the name of the variable do not begin with "x", an error can appear) +% - a vector y (if the name of the variable do not begin with "y", an error can appear) +% - a matrix with 3 columns (if the name of the variable do not begin with "index" or "elements", an error can appear) +% - a vector data (if the name of the variable do not begin with the field name, an error can appear) +% +% Usage: +% data=InterpFromFile(x,y,filename,default_value); +% +% Example: +% md.geometry.surface=InterpFromFile(md.mesh.x,md.mesh.y,'surfacefile.mat',0); +% +% See also: PLUGVELOCITIES, INTERPFROMGRID, INTERPFROMMESH2D, INTERPFROMMESH3D + +%some checks +if nargin~=4 | nargout~=1 + help InterpFromFile + error('plugdata error message: bad usage'); +end +if ~exist(filename) + error(['plugdata error message: file ' filename ' does not exist']); +end +if length(x)~=length(y), + error('plugdata error message: x and y should have the same length'); +end + +%load file +Names=FieldFindVarNames(filename); +Data=load(filename); +if strcmpi(Names.interp,'node'), + data_out=InterpFromGridToMesh(Data.(Names.xname),Data.(Names.yname),Data.(Names.dataname),x,y,default_value); +else + data_out=InterpFromMeshToMesh2d(Data.(Names.indexname),Data.(Names.xname),Data.(Names.yname),Data.(Names.dataname),x,y); +end Index: /issm/trunk-jpl/src/m/Interp/PatchToVec.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/PatchToVec.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/PatchToVec.m (revision 12996) @@ -0,0 +1,21 @@ +function vec=PatchToVec(Patch); +%PATCHTOVEC - converts a patch to a vector by averaging over each vertex +% +% Usage: +% vec=PatchToVec(Patch) + +%if the patch is P0: we have element values, return an element vector +switch(size(Patch.value,2)), + case 1, + vec(Patch.element)=Patch.value; + case 3, + connectivity=sparse(Patch.index(:),1,1); + value =sparse(Patch.index(:),1,Patch.value(:)); + vec=full(value./connectivity); + case 6, + connectivity=sparse(Patch.index(:),1,1); + value =sparse(Patch.index(:),1,Patch.value(:)); + vec=full(value./connectivity); + otherwise, + error('interpolation not supported yet'); + end Index: /issm/trunk-jpl/src/m/Interp/VelFindVarNames.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/VelFindVarNames.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/VelFindVarNames.m (revision 12996) @@ -0,0 +1,122 @@ +function Names=VelFindVarNames(filename) +%VELFINDVARNAMES - find names of variables in a velocity data set file +% +% This routines looks at the variables contained in a file and finds out +% the names of the variables that are needed for an interpolation (x,y,vx,vy) +% or (index,x,y,vx,vy) +% +% Usage: +% Names=VelFindVarNames(filename) +% +% Example: +% Names=VelFindVarNames('velocities.mat') +% +% See also: INTERPFROMFILE, GRIDDATA + +%some checks +if nargin~=1 | nargout~=1 + help VelFindVarNames + error('VelFindVarNames error message: bad usage'); +end +if ~exist(filename) + error(['VelFindVarNames error message: file ' filename ' does not exist']); +end + +%Get variables +A=whos('-file',filename); + +%find x,y,vx and vy +xenum=NaN; yenum=NaN; vxenum=NaN; vyenum=NaN; indexenum=NaN; +if length(A)==4, + isnode=1; + for i=1:4 + if strcmpi(A(i).name(1),'x'); + xenum=i; + elseif strcmpi(A(i).name(1),'y'); + yenum=i; + else + if (strcmpi(A(i).name(end),'x') | strncmpi(A(i).name,'vx',2)); + vxenum=i; + elseif (strcmpi(A(i).name(end),'y') | strncmpi(A(i).name,'vy',2)); + vyenum=i; + end + end + end +elseif length(A)==5, + isnode=0; + for i=1:5 + if strcmpi(A(i).name(1),'x'); + xenum=i; + elseif strcmpi(A(i).name(1),'y'); + yenum=i; + elseif (strcmpi(A(i).name(1),'index') | strcmpi(A(i).name(1),'elements')); + indexenum=i; + else + if (strcmpi(A(i).name(end),'x') | strncmpi(A(i).name,'vx',2)); + vxenum=i; + elseif (strcmpi(A(i).name(end),'y') | strncmpi(A(i).name,'vy',2)); + vyenum=i; + end + end + end +else + error(['VelFindVarNames error message: file ' filename ' not supported yet (it should hold 4 variables x,y,vx and vy (for nodes) OR 5 variables x,y,index,vx and vy (for mesh))']); +end + +%assum that we have found at least vxenum and vyenum +if ( isnan(vxenum) | isnan(vyenum)) + error(['VelFindVarNames error message: file ' filename ' not supported yet (the velocities should be named vx and vy)']); +end + +%find index +if (~isnode & isnan(indexenum)), + for i=1:5 + lengthi=min(A(i).size); + if (lengthi==3), + indexenum=i; + end + end + if isnan(indexenum), + error(['VelFindVarNames error message: file ' filename ' not supported yet (index not found)']); + end +end + +%find x y +if (isnan(xenum) | isnan(yenum)) + + %check the size + if A(vxenum).size(1)==A(vxenum).size(2), + error(['VelFindVarNames error message: file ' filename ' not supported (velocities is a square matrix, save x and y with another name)']); + end + if ~(A(vxenum).size(1)==A(vyenum).size(1) & A(vxenum).size(2)==A(vyenum).size(2)), + error(['VelFindVarNames error message: file ' filename ' not supported (vx and vy matrices do not have the same size)']); + end + + %find xenum and yenum + for i=1:4 + lengthi=max(A(i).size); + if ((i~=vxenum) & (lengthi==A(vxenum).size(1) | lengthi==A(vxenum).size(1)+1)), + yenum=i; + elseif ((i~=vxenum) & (lengthi==A(vxenum).size(2) | lengthi==A(vxenum).size(2)+1)), + xenum=i; + end + end + + %last check + if (isnan(xenum) | isnan(yenum)) + error(['plugdata error message: file ' filename ' not supported yet']); + end +end + +%create output +Names=struct(); +Names.xname=A(xenum).name; +Names.yname=A(yenum).name; +Names.vxname=A(vxenum).name; +Names.vyname=A(vyenum).name; +if ~isnode, + Names.indexname=A(indexenum).name; + Names.interp='mesh'; +else + Names.interp='node'; +end Index: /issm/trunk-jpl/src/m/Interp/plugvelocities.m =================================================================== --- /issm/trunk-jpl/src/m/Interp/plugvelocities.m (revision 12996) +++ /issm/trunk-jpl/src/m/Interp/plugvelocities.m (revision 12996) @@ -0,0 +1,41 @@ +function md=plugvelocities(md,filename,default_value) +%PLUGVELOCITIES - load velocities on a model +% +% load a matlab file (extension .mat) which holds 4 variables +% x,y,vx,vy to be plugged onto the model (or similar names) +% x and y must be vectors, vx, vy matrices +% +% Usage: +% md=plugvelocities(md,filename,default_value) +% +% Example: +% md=plugvelocities(md,'velocityfile.mat',0); +% +% See also: INTERPFROMFILE, GRIDDATA + +%some checks +if nargin~=3 | nargout~=1 + help plugvelocities + error('plugvelocities error message: bad usage'); +end +if ~exist(filename) + error(['plugvelocities error message: file ' filename ' does not exist']); +end + +%load velocities +Names=VelFindVarNames(filename); +Vel=load(filename); + +%Interpolation +if strcmpi(Names.interp,'node'), + md.inversion.vx_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,default_value); + md.inversion.vy_obs=InterpFromGridToMesh(Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,default_value); +else + md.inversion.vx_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vxname),md.mesh.x,md.mesh.y,default_value); + md.inversion.vy_obs=InterpFromMeshToMesh2d(Vel.(Names.indexname),Vel.(Names.xname),Vel.(Names.yname),Vel.(Names.vyname),md.mesh.x,md.mesh.y,default_value); +end + +md.inversion.vel_obs=sqrt(md.inversion.vx_obs.^2+md.inversion.vy_obs.^2); +md.initialization.vx=md.inversion.vx_obs; +md.initialization.vy=md.inversion.vy_obs; +md.initialization.vel=md.inversion.vel_obs; Index: /issm/trunk-jpl/src/m/Kml/exp2kml.m =================================================================== --- /issm/trunk-jpl/src/m/Kml/exp2kml.m (revision 12996) +++ /issm/trunk-jpl/src/m/Kml/exp2kml.m (revision 12996) @@ -0,0 +1,19 @@ +function exp2kml(input,output) +%EXP2KML: transform Argus exp file to kml +% +% Usage: exp2kml('temp.exp','temp2.kml') +% +% + + +%First, read exp file +domain=expread(input); + + +%then transform: +string=ge_plot(domain.x,domain.y,'name',domain.name); + +%open kml file for writing: +fid=fopen(output,'w'); +fprintf(fid,'%s',string); +fclose(fid); Index: /issm/trunk-jpl/src/m/Kml/kml2exp.m =================================================================== --- /issm/trunk-jpl/src/m/Kml/kml2exp.m (revision 12996) +++ /issm/trunk-jpl/src/m/Kml/kml2exp.m (revision 12996) @@ -0,0 +1,29 @@ +function kml2exp(input,output) +%KML2EXP: transform kml file Argus exp file. +% +% Usage: kmltoexp('temp.kml','temp2.exp') +% +% + + + + +%First, read polygon kml file. +structure=kml_shapefile(input); + +%create exp file: +domain=struct(); +for i=1:length(structure), + + if isfield(structure,'name'), + domain(end+1).name=structure(i).name; + else + domain(end+1).name='NaN'; + end + + domain(end).density=1; + domain(end).x=structure(i).X; + domain(end).y=structure(i).Y; +end +domain=domain(2:end); +expwrite(domain,output); Index: /issm/trunk-jpl/src/m/Kml/kml2expg.m =================================================================== --- /issm/trunk-jpl/src/m/Kml/kml2expg.m (revision 12996) +++ /issm/trunk-jpl/src/m/Kml/kml2expg.m (revision 12996) @@ -0,0 +1,13 @@ +function kml2expg(filename) + + [path,name,ext]=fileparts(filename); + + if strcmpi(ext,'.kmz'), + eval(['!unzip ' filename]); + eval(['!mv doc.kml ' name '.kml']); + kml2exp([name '.kml'],[name '.exp']); + expll2xy([name '.exp'],1); + end + + kml2exp([name '.kml'],[name '.exp']); + expll2xy([name '.exp'],1); Index: /issm/trunk-jpl/src/m/LatLong/ll2xy.m =================================================================== --- /issm/trunk-jpl/src/m/LatLong/ll2xy.m (revision 12996) +++ /issm/trunk-jpl/src/m/LatLong/ll2xy.m (revision 12996) @@ -0,0 +1,66 @@ +function [x,y] = ll2xy(lat,lon,sgn,central_meridian,standard_parallel) +%LL2XY - converts lat long to polar stereographic +% +% Converts from geodetic latitude and longitude to Polar +% Stereographic (X,Y) coordinates for the polar regions. +% Author: Michael P. Schodlok, December 2003 (map2ll) +% +% Usage: +% [x,y] = ll2xy(lat,lon,sgn) +% [x,y] = ll2xy(lat,lon,sgn,central_meridian,standard_parallel) +% +% - sgn = Sign of latitude +1 : north latitude (default is mer=45 lat=70) +% -1 : south latitude (default is mer=0 lat=71) + +%Get central_meridian and standard_parallel depending on hemisphere +if nargin==5, + delta = central_meridian; + slat = standard_parallel; +elseif nargin==3 + if sgn == 1, + delta = 45; slat = 70; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 70ºN Meridian: 45º)'); + elseif sgn==-1, + delta = 0; slat = 71; + disp('Info: creating coordinates in polar stereographic (Std Latitude: 71ºS Meridian: 0º)'); + else + error('Sign should be either +1 or -1'); + end +else + help ll2xy + error('bad usage'); +end + +% Conversion constant from degrees to radians +cde = 57.29577951; +% Radius of the earth in meters +re = 6378.273*10^3; +% Eccentricity of the Hughes ellipsoid squared +ex2 = .006693883; +% Eccentricity of the Hughes ellipsoid +ex = sqrt(ex2); + +latitude = abs(lat) * pi/180.; +longitude = (lon + delta) * pi/180.; + +% compute X and Y in grid coordinates. +T = tan(pi/4-latitude/2) ./ ((1-ex*sin(latitude))./(1+ex*sin(latitude))).^(ex/2); + +if (90 - slat) < 1.e-5 + rho = 2.*re*T/sqrt((1.+ex)^(1.+ex)*(1.-ex)^(1.-ex)); +else + sl = slat*pi/180.; + tc = tan(pi/4.-sl/2.)/((1.-ex*sin(sl))/(1.+ex*sin(sl)))^(ex/2.); + mc = cos(sl)/sqrt(1.0-ex2*(sin(sl)^2)); + rho = re*mc*T/tc; +end + +y = -rho .* sgn .* cos(sgn.*longitude); +x = rho .* sgn .* sin(sgn.*longitude); + +[cnt1,cnt2] = find(latitude >= pi / 2.); + +if cnt1 + x(cnt1,1) = 0.0; + y(cnt1,1) = 0.0; +end Index: /issm/trunk-jpl/src/m/LatLong/pargenerate.m =================================================================== --- /issm/trunk-jpl/src/m/LatLong/pargenerate.m (revision 12996) +++ /issm/trunk-jpl/src/m/LatLong/pargenerate.m (revision 12996) @@ -0,0 +1,45 @@ +function pargenerate(filename,xm,ym,data,varargin) +%PARGENERATE - generate parameter file for images ala Rignot +% +% Usage: +% pargenerate(filename,data,xm,ym,options); +% +% Supported options: +% - title: dataset title +% - latitude: standard latitude (degree) +% - meridian: meridian (degree) +% - format: binary format + +%process options +options=pairoptions(varargin{:}); +Title=getfieldvalue(options,'title','N/A'); +latitude=getfieldvalue(options,'latitude','N/A'); +meridian=getfieldvalue(options,'meridian','N/A'); +format=getfieldvalue(options,'format','single'); + +%Get data info +[nlines ncols]=size(data); +xmin=min(xm); +ymax=max(ym); +postx=abs(xm(2)-xm(1)); +posty=abs(ym(2)-ym(1)); + +%Open header file and get machine type +fid=fopen(filename,'wt'); +[filename, permission, machineformat, encoding] = fopen(fid); + +%write header file +fprintf(fid,'%s\n','ISSM gridded dataset parameter file'); +fprintf(fid,'%s%s\n','title: ',Title); +fprintf(fid,'%s \n','DEM_projection: PS'); +fprintf(fid,'%s%s\n','data_format: ',format); +fprintf(fid,'%s%s\n','endian: ',machineformat); +fprintf(fid,'%s%d\n','width: ',ncols); +fprintf(fid,'%s%d\n','nlines: ',nlines); +fprintf(fid,'%s%g%s\n','PS_secant_lat: ',latitude,' decimal degrees'); +fprintf(fid,'%s%g%s\n','PS_meridian_long: ',meridian,' decimal degrees'); +fprintf(fid,'%s%-15.10g\n','PS_corner_north: ',ymax); +fprintf(fid,'%s%-15.10g\n','PS_corner_east: ',xmin); +fprintf(fid,'%s%g%s\n','PS_post_north: ',postx,' m'); +fprintf(fid,'%s%g%s\n','PS_post_east: ',posty,' m'); +fclose(fid); Index: /issm/trunk-jpl/src/m/LatLong/utm2ll.m =================================================================== --- /issm/trunk-jpl/src/m/LatLong/utm2ll.m (revision 12996) +++ /issm/trunk-jpl/src/m/LatLong/utm2ll.m (revision 12996) @@ -0,0 +1,117 @@ +function [Lat,Lon] = utm2ll(xx,yy,utmzone) +% ------------------------------------------------------------------------- +% [Lat,Lon] = utm2ll(x,y,utmzone) +% +% Description: Function to convert vectors of UTM coordinates into Lat/Lon vectors (WGS84). +% Some code has been extracted from UTMIP.m function by Gabriel Ruiz Martinez. +% +% Inputs:on) +% -3.485713 7.801235 -119.955246 -17.759537 -94.799019 121.640266 +% +% Example 2: If you need Lat/Lon coordinates in Degrees, Minutes and Seconds +% [Lat, Lon]=utm2ll(x,y,utmzone); +% LatDMS=dms2mat(deg2dms(Lat)) +%LatDMS = +% 40.00 18.00 55.55 +% 46.00 17.00 2.01 +% 37.00 34.00 40.17 +% 28.00 38.00 44.33 +% 38.00 51.00 19.96 +% 25.00 3.00 42.41 +% LonDMS=dms2mat(deg2dms(Lon)) +%LonDMS = +% -3.00 29.00 8.61 +% 7.00 48.00 4.40 +% -119.00 57.00 18.93 +% -17.00 45.00 34.33 +% -94.00 47.00 56.47 +% 121.00 38.00 24.96 +% +% Author: +% Rafael Palacios +% Universidad Pontificia Comillas +% Madrid, Spain +% Version: Apr/06, Jun/06, Aug/06 +% Aug/06: corrected m-Lint warnings +%------------------------------------------------------------------------- + +% Argument checking +% +error(nargchk(3, 3, nargin)); %3 arguments required +n1=length(xx); +n2=length(yy); +n3=size(utmzone,1); +if (n1~=n2 || n1~=n3) + error('x,y and utmzone vectors should have the same number or rows'); +end +c=size(utmzone,2); +if (c~=4) + error('utmzone should be a vector of strings like "30 T"'); +end + +% Memory pre-allocation +% +Lat=zeros(n1,1); +Lon=zeros(n1,1); + +% Main Loop +% +for i=1:n1 + if (utmzone(i,4)>'X' || utmzone(i,4)<'C') + fprintf('utm2ll: Warning utmzone should be a vector of strings like "30 T", not "30 t"\n'); + end + if (utmzone(i,4)>'M') + hemis='N'; % Northern hemisphere + else + hemis='S'; + end + + x=xx(i); + y=yy(i); + zone=str2double(utmzone(i,1:2)); + + sa = 6378137.000000 ; sb = 6356752.314245; + + % e = ( ( ( sa ^ 2 ) - ( sb ^ 2 ) ) ^ 0.5 ) / sa; + e2 = ( ( ( sa ^ 2 ) - ( sb ^ 2 ) ) ^ 0.5 ) / sb; + e2cuadrada = e2 ^ 2; + c = ( sa ^ 2 ) / sb; + % alpha = ( sa - sb ) / sa; %f + % ablandamiento = 1 / alpha; % 1/f + + X = x - 500000; + + if hemis == 'S' || hemis == 's' + Y = y - 10000000; + else + Y = y; + end + + S = ( ( zone * 6 ) - 183 ); + lat = Y / ( 6366197.724 * 0.9996 ); + v = ( c / ( ( 1 + ( e2cuadrada * ( cos(lat) ) ^ 2 ) ) ) ^ 0.5 ) * 0.9996; + a = X / v; + a1 = sin( 2 * lat ); + a2 = a1 * ( cos(lat) ) ^ 2; + j2 = lat + ( a1 / 2 ); + j4 = ( ( 3 * j2 ) + a2 ) / 4; + j6 = ( ( 5 * j4 ) + ( a2 * ( cos(lat) ) ^ 2) ) / 3; + alfa = ( 3 / 4 ) * e2cuadrada; + beta = ( 5 / 3 ) * alfa ^ 2; + gama = ( 35 / 27 ) * alfa ^ 3; + Bm = 0.9996 * c * ( lat - alfa * j2 + beta * j4 - gama * j6 ); + b = ( Y - Bm ) / v; + Epsi = ( ( e2cuadrada * a^ 2 ) / 2 ) * ( cos(lat) )^ 2; + Eps = a * ( 1 - ( Epsi / 3 ) ); + nab = ( b * ( 1 - Epsi ) ) + lat; + senoheps = ( exp(Eps) - exp(-Eps) ) / 2; + Delt = atan(senoheps / (cos(nab) ) ); + TaO = atan(cos(Delt) * tan(nab)); + longitude = (Delt *(180 / pi ) ) + S; + latitude = ( lat + ( 1 + e2cuadrada* (cos(lat)^ 2) - ( 3 / 2 ) * e2cuadrada * sin(lat) * cos(lat) * ( TaO - lat ) ) * ( TaO - lat ) ) * ... + (180 / pi); + + Lat(i)=latitude; + Lon(i)=longitude; + +end Index: /issm/trunk-jpl/src/m/LatLong/xy2ll.m =================================================================== --- /issm/trunk-jpl/src/m/LatLong/xy2ll.m (revision 12996) +++ /issm/trunk-jpl/src/m/LatLong/xy2ll.m (revision 12996) @@ -0,0 +1,72 @@ +function [lat,lon] = xy2ll(x,y,sgn,central_meridian,standard_parallel) +%XY2LL - converts xy to lat long +% +% Converts Polar Stereographic (X,Y) coordinates for the polar regions to +% latitude and longitude Stereographic (X,Y) coordinates for the polar +% regions. +% Author: Michael P. Schodlok, December 2003 (map2xy.m) +% +% Usage: +% [lat,lon] = xy2ll(x,y,sgn); +% [lat,lon] = xy2ll(x,y,sgn,central_meridian,standard_parallel); +% +% - sgn = Sign of latitude +1 : north latitude (default is mer=45 lat=70) +% -1 : south latitude (default is mer=0 lat=71) + +%Get central_meridian and standard_parallel depending on hemisphere +if nargin==5, + delta = central_meridian; + slat = standard_parallel; +elseif nargin==3 + if sgn == 1, + delta = 45; slat = 70; + disp('Warning: expecting coordinates in polar stereographic (Std Latitude: 70ºN Meridian: 45º)'); + elseif sgn==-1, + delta = 0; slat = 71; + disp('Warning: expecting coordinates in polar stereographic (Std Latitude: 71ºS Meridian: 0º)'); + else + error('Sign should be either +1 or -1'); + end +else + help xy2ll + error('bad usage'); +end + +% Conversion constant from degrees to radians +cde = 57.29577951; +% Radius of the earth in meters +re = 6378.273*10^3; +% Eccentricity of the Hughes ellipsoid squared +ex2 = .006693883; +% Eccentricity of the Hughes ellipsoid +ex = sqrt(ex2); + +sl = slat*pi/180.; +rho = sqrt(x.^2 + y.^2); +cm = cos(sl) / sqrt(1.0 - ex2 * (sin(sl)^2)); +T = tan((pi / 4.0) - (sl / 2.0)) / ((1.0 - ex * sin(sl)) / (1.0 + ex * sin(sl)))^(ex / 2.0); + +if abs(slat-90.) < 1.e-5 + T = rho * sqrt((1. + ex)^(1. + ex) * (1. - ex)^(1. - ex)) / 2. / re; +else + T = rho * T / (re * cm); +end + +chi = (pi / 2.0) - 2.0 * atan(T); +lat = chi + ((ex2 / 2.0) + (5.0 * ex2^2.0 / 24.0) + (ex2^3.0 / 12.0)) * ... + sin(2 * chi) + ((7.0 * ex2^2.0 / 48.0) + (29.0 * ex2^3 / 240.0)) * ... + sin(4.0 * chi) + (7.0 * ex2^3.0 / 120.0) * sin(6.0 * chi) ; + +lat = sgn * lat; +lon = atan2(sgn * x,-sgn * y); +lon = sgn * lon; + +[res1,res2] = find(rho <= 0.1); +if res1 + lat(res1,1) = 90. * sgn; + lon(res1,1) = 0.0; +end + +lon = lon * 180. / pi; +lat = lat * 180. / pi; +lon = lon - delta; Index: /issm/trunk-jpl/src/m/Math/fixdec.m =================================================================== --- /issm/trunk-jpl/src/m/Math/fixdec.m (revision 12996) +++ /issm/trunk-jpl/src/m/Math/fixdec.m (revision 12996) @@ -0,0 +1,41 @@ +function y = fixdec(x, n) +%FIXDEC - Round towards zero with a specified number of decimals. +% +% This routine rounds the elements of X to N decimals. +% +% Usage: +% y = fixdec(x, n) +% +% Example: +% fixdec(10*sqrt(2) + i*pi/10, 4) returns 14.1421 + 0.3141i +% +% See also: FIX, FLOOR, CEIL, ROUND, FIXDIG, ROUNDDEC, ROUNDDIG. + +% Author: Peter J. Acklam +% Time-stamp: 2004-09-22 20:08:10 +0200 +% E-mail: pjacklam@online.no +% URL: http://home.online.no/~pjacklam + + % Check number of input arguments. + error(nargchk(2, 2, nargin)); + + % Quick exit if either argument is empty. + if (isempty(x) |isempty(n)) + y = []; + return + end + + % Get size of input arguments. + size_x = size(x); + size_n = size(n); + scalar_x = all(size_x == 1); % True if x is a scalar. + scalar_n = all(size_n == 1); % True if n is a scalar. + + % Check size of input arguments. + if ~scalar_x & ~scalar_n & ~isequal(size_x, size_n) + error(['When both arguments are non-scalars they must have' ... + ' the same size']); + end + + f = 10.^n; + y = fix(x .* f) ./ f; Index: /issm/trunk-jpl/src/m/Math/isnans.m =================================================================== --- /issm/trunk-jpl/src/m/Math/isnans.m (revision 12996) +++ /issm/trunk-jpl/src/m/Math/isnans.m (revision 12996) @@ -0,0 +1,15 @@ +function returnvalue=isnans(array) +%ISNANS: figure out if an array is nan. wrapper to isnan from matlab which stupidly does not allow this test for structures! +% +% Usage: isnans(array) +% +% See also : ISNAN + + +if isstruct(array), + returnvalue=0; +elseif iscell(array) + returnvalue=0; +else + returnvalue=isnan(array); +end Index: /issm/trunk-jpl/src/m/Math/isnans.py =================================================================== --- /issm/trunk-jpl/src/m/Math/isnans.py (revision 12996) +++ /issm/trunk-jpl/src/m/Math/isnans.py (revision 12996) @@ -0,0 +1,18 @@ +import numpy + +def isnans(array): + """ + ISNANS: figure out if an array is nan. wrapper to isnan from matlab which stupidly does not allow this test for structures! + + Usage: isnans(array) + + See also : ISNAN + """ + + if isinstance(array,(tuple,list,dict)): + returnvalue=0 + else: + returnvalue=numpy.isnan(array) + + return returnvalue + Index: /issm/trunk-jpl/src/m/Math/round_ice.m =================================================================== --- /issm/trunk-jpl/src/m/Math/round_ice.m (revision 12996) +++ /issm/trunk-jpl/src/m/Math/round_ice.m (revision 12996) @@ -0,0 +1,38 @@ +function new_x=round_ice(x,numnonzeros) +%ROUND_ICE - rounds up x so that it has only numnonzeros non zero digits +% +% numnonzeros must be an integer larger or equal to 1 +% +% Usage: +% new_x=round_ice(x,numnonzeros) + +%some checks +if (nargin ~=2 | nargout>1), + error('round_ice usage: new_x=round_ice(x,numonzeros)'); +end +if ~isnumeric(x) + error('round_ice error message: x must be a number and numzeros an integer'); +end +if round(numnonzeros)~=numnonzeros + error('round_ice error message: numnonzeros must be an integer larger or equal to 1') +end +if any(numnonzeros<1) + error('round_ice error message: numnonzeros must be an integer larger or equal to 1') +end +if (length(numnonzeros)~=1 & size(numnonzeros)~=size(x)) + error('round_ice error message: numnonzeros must be an integer larger or equal to 1 or a list of integers of length length(x)') +end + +%figure out how long x is +lengthx=ceil(log10(abs(x))); + +%if x contains 0, lengthx=-Inf +lengthx(isinf(lengthx))=1; + +%get its sign +si=sign(x); + +%rule out zeros +new_x=si.*round(abs(x).*10.^(-lengthx+numnonzeros)).*10.^(lengthx-numnonzeros); + + Index: /issm/trunk-jpl/src/m/Meca/carter.m =================================================================== --- /issm/trunk-jpl/src/m/Meca/carter.m (revision 12996) +++ /issm/trunk-jpl/src/m/Meca/carter.m (revision 12996) @@ -0,0 +1,28 @@ +function attenuation=carter(temperature) +%CARTER - attenuation as a function of temperature +% +% TWO WAY - Attenuation (in dB/m) as a function of temperature (K) +% From Carter at al. 2007 (Radar-based subglacial lake classification in Antarctica) +% Figure 4 +% +% Usage: +% attenuation=carter(temperature) + +if(temperature<0) + error('input temperature should be in Kelvin (positive)'); +end +T=temperature-273.15; + +Temp=[-50 -45 -40 -35 -30 -25 -20 -15 -10 -5 0]'; +A=[0.0015 0.002 0.003 0.0042 0.0055 0.0083 0.012 0.0175 0.026 0.038 0.055]'; + +%Now, do a cubic fit between Temp and B: +[cfun,gof,output]=fit(Temp,A,'cubicspline'); +%breaks=cfun.p.breaks; +%coeff=cfun.p.coefs; + +%Calculate attenuation +attenuation=cfun(T); + +%Make it a 2 way attenuation +attenuation=2*attenuation; Index: /issm/trunk-jpl/src/m/Meca/lithostaticpressure.m =================================================================== --- /issm/trunk-jpl/src/m/Meca/lithostaticpressure.m (revision 12996) +++ /issm/trunk-jpl/src/m/Meca/lithostaticpressure.m (revision 12996) @@ -0,0 +1,7 @@ +function pressure=lithostaticpressure(rho_ice,g,s,z); +%LITHOSTATICPRESSURE - compute the lithostatic pressure +% +% Usage: +% pressure=lithostacticpressure(rho_ice,g,surface,z) + +pressure=rho_ice*g*(s-z); Index: /issm/trunk-jpl/src/m/Meca/paterson.m =================================================================== --- /issm/trunk-jpl/src/m/Meca/paterson.m (revision 12996) +++ /issm/trunk-jpl/src/m/Meca/paterson.m (revision 12996) @@ -0,0 +1,42 @@ +function rigidity=paterson(temperature) +%PATERSON - figure out the rigidity of ice for a given temperature +% +% rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). +% temperature is in Kelvin degrees +% +% Usage: +% rigidity=paterson(temperature) + +if(temperature<0) + error('input temperature should be in Kelvin (positive)'); +end +T=temperature-273.15; + +%The routine below is equivalent to: + +% n=3; T=temperature-273; +% %From paterson, +% Temp=[0;-2;-5;-10;-15;-20;-25;-30;-35;-40;-45;-50]; +% A=[6.8*10^-15;2.4*10^-15;1.6*10^-15;4.9*10^-16;2.9*10^-16;1.7*10^-16;9.4* +% 10^-17;5.1*10^-17;2.7*10^-17;1.4*10^-17;7.3*10^-18;3.6*10^-18];;%s-1(kPa-3) +% %Convert into rigidity B +% B=A.^(-1/n)*10^3; %s^(1/3)Pa +% %Now, do a cubic fit between Temp and B: +% fittedmodel=fit(Temp,B,'cubicspline'); +% rigidity=fittedmodel(temperature); + +rigidity=zeros(length(T),1); +pos1=find(T<=-45); rigidity(pos1)=10^8*(-0.000292866376675*(T(pos1)+50).^3+ 0.011672640664130*(T(pos1)+50).^2 -0.325004442485481*(T(pos1)+50)+ 6.524779401948101); +pos2=find(-45<=T & T<-40); rigidity(pos2)=10^8*(-0.000292866376675*(T(pos2)+45).^3+ 0.007279645014004*(T(pos2)+45).^2 -0.230243014094813*(T(pos2)+45)+ 5.154964909039554); +pos3=find(-40<=T & T<-35); rigidity(pos3)=10^8*(0.000072737147457*(T(pos3)+40).^3+ 0.002886649363879*(T(pos3)+40).^2 -0.179411542205399*(T(pos3)+40)+ 4.149132666831214); +pos4=find(-35<=T & T<-30); rigidity(pos4)=10^8*(-0.000086144770023*(T(pos4)+35).^3+ 0.003977706575736*(T(pos4)+35).^2 -0.145089762507325*(T(pos4)+35)+ 3.333333333333331); +pos5=find(-30<=T & T<-25); rigidity(pos5)=10^8*(-0.000043984685769*(T(pos5)+30).^3+ 0.002685535025386*(T(pos5)+30).^2 -0.111773554501713*(T(pos5)+30)+ 2.696559088937191); +pos6=find(-25<=T & T<-20); rigidity(pos6)=10^8*(-0.000029799523463*(T(pos6)+25).^3+ 0.002025764738854*(T(pos6)+25).^2 -0.088217055680511*(T(pos6)+25)+ 2.199331606342181); +pos7=find(-20<=T & T<-15); rigidity(pos7)=10^8*(0.000136920904777*(T(pos7)+20).^3+ 0.001578771886910*(T(pos7)+20).^2 -0.070194372551690*(T(pos7)+20)+ 1.805165505978111); +pos8=find(-15<=T & T<-10); rigidity(pos8)=10^8*(-0.000899763781026*(T(pos8)+15).^3+ 0.003632585458564*(T(pos8)+15).^2 -0.044137585824322*(T(pos8)+15)+ 1.510778053489523); +pos9=find(-10<=T & T<-5); rigidity(pos9)=10^8*(0.001676964325070*(T(pos9)+10).^3- 0.009863871256831*(T(pos9)+10).^2 -0.075294014815659*(T(pos9)+10)+ 1.268434288203714); +pos10=find(-5<=T & T<-2); rigidity(pos10)=10^8*(-0.003748937622487*(T(pos10)+5).^3+0.015290593619213*(T(pos10)+5).^2 -0.048160403003748*(T(pos10)+5)+ 0.854987973338348); +pos11=find(-2<=T); rigidity(pos11)=10^8*(-0.003748937622488*(T(pos11)+2).^3-0.018449844983174*(T(pos11)+2).^2 -0.057638157095631*(T(pos11)+2)+ 0.746900791092860); + +%Now make sure that rigidity is positive +pos=find(rigidity<0); rigidity(pos)=10^6; Index: /issm/trunk-jpl/src/m/Meca/paterson.py =================================================================== --- /issm/trunk-jpl/src/m/Meca/paterson.py (revision 12996) +++ /issm/trunk-jpl/src/m/Meca/paterson.py (revision 12996) @@ -0,0 +1,50 @@ +from numpy import * + +def paterson(temperature): + + # Local Variables: pos11, pos5, pos10, temperature, pos, T, pos8, pos9, pos6, pos7, pos4, rigidity, pos2, pos3, pos1 + # Function calls: length, zeros, argwhere, paterson, error + #PATERSON - figure out the rigidity of ice for a given temperature + # + # rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). + # temperature is in Kelvin degrees + # + # Usage: + # rigidity=paterson(temperature) + + pos=argwhere(temperature<0.) + if len(pos): + print 'input temperature should be in Kelvin (positive)' + return [] + + T = temperature-273.15 + #The routine below is equivalent to: + # n=3; T=temperature-273; + # %From paterson, + # Temp=[0;-2;-5;-10;-15;-20;-25;-30;-35;-40;-45;-50]; + # A=[6.8*10^-15;2.4*10^-15;1.6*10^-15;4.9*10^-16;2.9*10^-16;1.7*10^-16;9.4* + # 10^-17;5.1*10^-17;2.7*10^-17;1.4*10^-17;7.3*10^-18;3.6*10^-18];;%s-1(kPa-3) + # %Convert into rigidity B + # B=A.^(-1/n)*10^3; %s^(1/3)Pa + # %Now, do a cubic fit between Temp and B: + # fittedmodel=fit(Temp,B,'cubicspline'); + # rigidity=fittedmodel(temperature); + + rigidity=zeros(len(T)) + pos1=argwhere(T<=-45); rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) + pos2=argwhere(logical_and(-45<=T,T<-40)); rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) + pos3=argwhere(logical_and(-40<=T,T<-35)); rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) + pos4=argwhere(logical_and(-35<=T,T<-30)); rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) + pos5=argwhere(logical_and(-30<=T,T<-25)); rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) + pos6=argwhere(logical_and(-25<=T,T<-20)); rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) + pos7=argwhere(logical_and(-20<=T,T<-15)); rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) + pos8=argwhere(logical_and(-15<=T,T<-10)); rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) + pos9=argwhere(logical_and(-10<=T,T<-5)); rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) + pos10=argwhere(logical_and(-5<=T,T<-2)); rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) + pos11=argwhere(-2<=T); rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) + + #Now make sure that rigidity is positive + pos=argwhere(rigidity<0); rigidity[pos]=1**6 + + return rigidity + Index: /issm/trunk-jpl/src/m/Mesh/BamgCall.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/BamgCall.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/BamgCall.m (revision 12996) @@ -0,0 +1,84 @@ +function md=BamgCall(md,field,hmin,hmax,gradation,epsilon), +%BAMGCALL - call bam +% +% build a metric using the Hessian of the given field +% call Bamg and the output mesh is plugged onto the model +% -hmin = minimum edge length (m) +% -hmax = maximum edge length (m) +% -gradation = maximum edge length gradation between 2 elements +% -epsilon = average error on each element (m/yr) +% +% Usage: +% md=BamgCall(md,field,hmin,hmax,gradation,epsilon); +% +% Example: +% md=BamgCall(md,md.inversion.vel_obs,1500,10^8,1.3,0.9); + +%2d geometric parameter (do not change) +scale=2/9; + +%Compute Hessian +t1=clock; fprintf('%s',' computing Hessian...'); +hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node'); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%Compute metric +t1=clock; fprintf('%s',' computing metric...'); +if length(md.nodeonwater)==md.mesh.numberofvertices, + pos=find(md.nodeonwater); +else + pos=[]; +end +metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%write files +t1=clock; fprintf('%s',' writing initial mesh files...'); +fid=fopen('carre0.met','w'); +fprintf(fid,'%i %i\n',md.mesh.numberofvertices,3); +fprintf(fid,'%i %i %i\n',metric'); +fclose(fid); + +fid=fopen('carre0.mesh','w'); + +%initialiation +fprintf(fid,'%s %i\n','MeshVersionFormatted',0); + +%dimension +fprintf(fid,'\n%s\n%i\n','Dimension',2); + +%Vertices +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]'); + +%Triangles +fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements ones(md.mesh.numberofelements,1)]'); +numberofelements1=md.mesh.numberofelements; + +%close +fclose(fid); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%call bamg +fprintf('%s\n',' call Bamg...'); +system(['bamg -ratio ' num2str(gradation) ' -splitpbedge -nbv 1000000 -M carre0.met -b carre0.mesh -o carre1.mesh']); + +%plug new mesh +t1=clock; fprintf('\n%s',' reading final mesh files...'); +A=meshread('carre1.mesh'); +md.mesh.x=A.x; +md.mesh.y=A.y; +md.z=zeros(A.nods,1); +md.mesh.elements=A.index; +md.mesh.numberofvertices=A.nods; +md.mesh.numberofelements=A.nels; +numberofelements2=md.mesh.numberofelements; +t2=clock;fprintf('%s\n\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%display number of elements +fprintf('\n%s %i',' inital number of elements:',numberofelements1); +fprintf('\n%s %i\n\n',' new number of elements:',numberofelements2); + +%clean up: +system('rm carre0.mesh carre0.met carre1.mesh carre1.mesh.gmsh'); Index: /issm/trunk-jpl/src/m/Mesh/BamgCallFromMetric.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/BamgCallFromMetric.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/BamgCallFromMetric.m (revision 12996) @@ -0,0 +1,65 @@ +function md=BamgCallFromMetric(md,metric,gradation), +%BAMGCALL - call bam +% +% call Bamg and the output mesh is plugged onto the model +% -gradation = maximum edge length gradation between 2 elements +% +% Usage: +% md=BamgCallFromMetric(md,metric,gradation); +% +% Example: +% md=BamgCall(md,metric,1500,10^8,1.3,0.9); + +%2d geometric parameter (do not change) +scale=2/9; + +%write files +t1=clock; fprintf('%s',' writing initial mesh files...'); +fid=fopen('carre0.met','w'); +fprintf(fid,'%i %i\n',md.mesh.numberofvertices,3); +fprintf(fid,'%i %i %i\n',metric'); +fclose(fid); + +fid=fopen('carre0.mesh','w'); + +%initialiation +fprintf(fid,'%s %i\n','MeshVersionFormatted',0); + +%dimension +fprintf(fid,'\n%s\n%i\n','Dimension',2); + +%Vertices +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y ones(md.mesh.numberofvertices,1)]'); + +%Triangles +fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements ones(md.mesh.numberofelements,1)]'); +numberofelements1=md.mesh.numberofelements; + +%close +fclose(fid); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%call bamg +fprintf('%s\n',' call Bamg...'); +system(['bamg -ratio ' num2str(gradation) ' -splitpbedge -nbv 1000000 -M carre0.met -b carre0.mesh -o carre1.mesh']); + +%plug new mesh +t1=clock; fprintf('\n%s',' reading final mesh files...'); +A=meshread('carre1.mesh'); +md.mesh.x=A.x; +md.mesh.y=A.y; +md.z=zeros(A.nods,1); +md.mesh.elements=A.index; +md.mesh.numberofvertices=A.nods; +md.mesh.numberofelements=A.nels; +numberofelements2=md.mesh.numberofelements; +t2=clock;fprintf('%s\n\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%display number of elements +fprintf('\n%s %i',' inital number of elements:',numberofelements1); +fprintf('\n%s %i\n\n',' new number of elements:',numberofelements2); + +%clean up: +system('rm carre0.mesh carre0.met carre1.mesh carre1.mesh.gmsh'); Index: /issm/trunk-jpl/src/m/Mesh/ComputeHessian.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/ComputeHessian.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/ComputeHessian.m (revision 12996) @@ -0,0 +1,60 @@ +function hessian=ComputeHessian(index,x,y,field,type) +%COMPUTEHESSIAN - compute hessian matrix from a field +% +% Compute the hessian matrix of a given field +% return the three components Hxx Hxy Hyy +% for each element or each node +% +% Usage: +% hessian=ComputeHessian(index,x,y,field,type) +% +% Example: +% hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vel_obs,'node') + +%some variables +numberofnodes=length(x); +numberofelements=size(index,1); + +%some checks +if length(field)~=numberofnodes & length(field)~=numberofelements, + error('ComputeHessian error message: the given field size not supported yet'); +end +if strcmpi(type,'node') & strcmpi(type,'element'), + error('ComputeHessian error message: only ''node'' or ''element'' type supported yet'); +end + +%initialization +line=index(:); +linesize=3*numberofelements; + +%get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma +[alpha beta]=GetNodalFunctionsCoeff(index,x,y); +areas=GetAreas(index,x,y); + +%comput weights that holds the volume of all the element holding the node i +weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofnodes,1); + +%compute field on nodes if on elements +if length(field)==numberofelements, + field=sparse(line,ones(linesize,1),repmat(areas.*field,3,1),numberofnodes,1)./weights ; +end + +%Compute gradient for each element +grad_elx=sum(field(index).*alpha,2); +grad_ely=sum(field(index).*beta,2); + +%Compute gradient for each node (average of the elements around) +gradx=sparse(line,ones(linesize,1),repmat(areas.*grad_elx,3,1),numberofnodes,1); +grady=sparse(line,ones(linesize,1),repmat(areas.*grad_ely,3,1),numberofnodes,1); +gradx=gradx./weights; +grady=grady./weights; + +%Compute hessian for each element +hessian=[sum(gradx(index).*alpha,2) sum(grady(index).*alpha,2) sum(grady(index).*beta,2)]; + +if strcmpi(type,'node') + %Compute Hessian on the nodes (average of the elements around) + hessian=[sparse(line,ones(linesize,1),repmat(areas.*hessian(:,1),3,1),numberofnodes,1)./weights ... + sparse(line,ones(linesize,1),repmat(areas.*hessian(:,2),3,1),numberofnodes,1)./weights ... + sparse(line,ones(linesize,1),repmat(areas.*hessian(:,3),3,1),numberofnodes,1)./weights ]; +end Index: /issm/trunk-jpl/src/m/Mesh/ComputeMetric.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/ComputeMetric.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/ComputeMetric.m (revision 12996) @@ -0,0 +1,66 @@ +function metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos) +%COMPUTEMETRIC - compute metric from an Hessian +% +% Usage: +% metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos) +% pos is contains the positions where the metric is wished to be maximized (water?) +% +% Example: +% metric=ComputeMetric(hessian,2/9,10^-1,100,10^5,find(md.nodeonwater) + +%first, find the eigen values of eah line of H=[hessian(i,1) hessian(i,2); hessian(i,2) hessian(i,3)] +a=hessian(:,1); b=hessian(:,2); d=hessian(:,3); +lambda1=0.5*((a+d)+sqrt(4*b.^2+(a-d).^2)); +lambda2=0.5*((a+d)-sqrt(4*b.^2+(a-d).^2)); +pos1=find(lambda1==0); +pos2=find(lambda2==0); +pos3=find(b==0 & lambda1==lambda2); + +%Modify the eigen values to control the shape of the elements +lambda1=min(max(abs(lambda1)*scale/epsilon,1/hmax^2),1/hmin^2); +lambda2=min(max(abs(lambda2)*scale/epsilon,1/hmax^2),1/hmin^2); + +%compute eigen vectors +norm1=sqrt(8*b.^2+2*(d-a).^2+2*(d-a).*sqrt((a-d).^2+4*b.^2)); +v1x=2*b./norm1; +v1y=((d-a)+sqrt((a-d).^2+4*b.^2))./norm1; +norm2=sqrt(8*b.^2+2*(d-a).^2-2*(d-a).*sqrt((a-d).^2+4*b.^2)); +v2x=2*b./norm2; +v2y=((d-a)-sqrt((a-d).^2+4*b.^2))./norm2; + +v1x(pos3)=1; v1y(pos3)=0; +v2x(pos3)=0; v2y(pos3)=1; + +%Compute new metric (for each node M=V*Lambda*V^-1) +metric=full([(v1x.*v2y-v1y.*v2x).^(-1).*(lambda1.*v2y.*v1x-lambda2.*v1y.*v2x) ... + (v1x.*v2y-v1y.*v2x).^(-1).*(lambda1.*v1y.*v2y-lambda2.*v1y.*v2y) ... + (v1x.*v2y-v1y.*v2x).^(-1).*(-lambda1.*v2x.*v1y+lambda2.*v1x.*v2y)]); + +%some corrections for 0 eigen values +metric(pos1,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos1),1); +metric(pos2,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos2),1); + +%take care of water elements +metric(pos,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos),1); + +%take care of NaNs if any (use Matlab eig in a loop) +[pos posj]=find(isnan(metric)); clear posj; +if ~isempty(pos), + fprintf(' %i %s',length(pos),'NaN found in the metric. Use Matlab routine...'); + for i=1:length(pos) + H=[hessian(pos(i),1) hessian(pos(i),2) + hessian(pos(i),2) hessian(pos(i),3)]; + [u,v]=eig(full(H)); + lambda1=v(1,1); + lambda2=v(2,2); + v(1,1)=min(max(abs(lambda1)*scale/epsilon,1/hmax^2),1/hmin^2); + v(2,2)=min(max(abs(lambda2)*scale/epsilon,1/hmax^2),1/hmin^2); + + metricTria=u*v*u^(-1); + metric(pos(i),:)=[metricTria(1,1) metricTria(1,2) metricTria(2,2)]; + end +end + +if any(isnan(metric)), + error('ComputeMetric error message: NaN in the metric despite our efforts...') +end Index: /issm/trunk-jpl/src/m/Mesh/ElementsFromEdge.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/ElementsFromEdge.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/ElementsFromEdge.m (revision 12996) @@ -0,0 +1,15 @@ +function edgeelements=ElementsFromEdge(elements,A,B) +%ELEMENTSFROMEDGE: find elements connected to one edge defined by nodes A and B +% +% Usage: edgeelements=ElementsFromEdge(elements,A,B) +% +% Eg: edgeelements=ElementsFromEdge(md.mesh.elements,tip1,tip2) +% +% +edgeelements=find(... +(elements(:,1)==A & elements(:,2)==B )| ... +(elements(:,1)==A & elements(:,3)==B )| ... +(elements(:,2)==A & elements(:,3)==B )| ... +(elements(:,2)==A & elements(:,1)==B )| ... +(elements(:,3)==A & elements(:,1)==B )| ... +(elements(:,3)==A & elements(:,2)==B )); Index: /issm/trunk-jpl/src/m/Mesh/FixMesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/FixMesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/FixMesh.m (revision 12996) @@ -0,0 +1,45 @@ +function [index2 x2 y2 value2]=FixMesh(index,x,y,value) +%FixMesh fix mesh with broken triangles, orphan vertices, etc ... +% +% Usage: +% [index2 x2 y2 value2]=FixMesh(index,x,y,value) +% where index,x,y is a delaunay triangulation, +% value is a field on the input triangulation, with values at the vertices +% index2,x2,y2,value2 is the repaired triangulation, with new values on new vertices +% +% + +%duplicate inputs +index2=index; +x2=x; +y2=y; +value2=value; + +%First, look for orphan vertices, and take them out. +flags=zeros(length(x2),1); flags(index2)=1; +orphans=find(flags==0); + +while ~isempty(orphans), + + %take the first orphan, the lower numbered, and take it out + orphan=orphans(1); + + %first x,y,value + x2(orphan)=[]; + y2(orphan)=[]; + value2(orphan)=[]; + + %now, the index: + pos=find(index2>orphan); index2(pos)=index2(pos)-1; + + %look again for orphans on new mesh + flags=zeros(length(x2),1);flags(index2)=1; + orphans=find(flags==0); +end + +%Check all triangles are well oriented. +aires=GetAreas(index2,x2,y2); +pos=find(aires<0); +temp=index2(pos,1); +index2(pos,1)=index2(pos,2); +index2(pos,2)=temp; Index: /issm/trunk-jpl/src/m/Mesh/GetAreas.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/GetAreas.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/GetAreas.m (revision 12996) @@ -0,0 +1,51 @@ +function areas=GetAreas(index,x,y,varargin) +%GETAREAS - compute areas or volumes of elements +% +% compute areas of triangular elements or volumes +% of pentahedrons +% +% Usage: +% areas =GetAreas(index,x,y); +% volumes=GetAreas(index,x,y,z); +% +% Examples: +% areas =GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); +% volumes=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y,md.z); + +%get number of elements and number of nodes +nels=size(index,1); +nods=length(x); +if nargin==4, z=varargin{1}; end + +%some checks +if nargout~=1 | (nargin~=3 & nargin~=4), + help GetAreas + error('GetAreas error message: bad usage') +end +if ((length(y)~=nods) | (nargin==4 & length(z)~=nods)), + error('GetAreas error message: x,y and z do not have the same length') +end +if max(index(:))>nods, + error(['GetAreas error message: index should not have values above ' num2str(nods) ]) +end +if (nargin==3 & size(index,2)~=3), + error('GetAreas error message: index should have 3 columns for 2d meshes.') +end +if (nargin==4 & size(index,2)~=6), + error('GetAreas error message: index should have 6 columns for 3d meshes.') +end + +%initialization +areas=zeros(nels,1); +x1=x(index(:,1)); x2=x(index(:,2)); x3=x(index(:,3)); +y1=y(index(:,1)); y2=y(index(:,2)); y3=y(index(:,3)); + +%compute the volume of each element +if nargin==3, + %compute the surface of the triangle + areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))); +else + %V=area(triangle)*1/3(z1+z2+z3) + thickness=mean(z(index(:,4:6)),2)-mean(z(index(:,1:3)),2); + areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))).*thickness; +end Index: /issm/trunk-jpl/src/m/Mesh/GetCharacteristicLength.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/GetCharacteristicLength.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/GetCharacteristicLength.m (revision 12996) @@ -0,0 +1,45 @@ +function length=GetCharacteristicLength(index,x,y,varargin) +%GETCHARACTERISTICLENGTH - compute characteristic length for a mesh +% +% compute characteristic lengths of every element of a mesh. +% +% Usage: +% length =GetCharacteristicLength(index,x,y); +% length =GetCharacteristicLength(index,x,y,z); +% +% Examples: +% length =GetCharacteristicLength(md.mesh.elements,md.mesh.x,md.mesh.y); +% length =GetCharacteristicLength(md.mesh.elements,md.mesh.x,md.mesh.y,md.z); + + +%get number of elements and number of nodes +nels=size(index,1); +nods=numel(x); + +%some checks +if nargout~=1 | (nargin~=3 & nargin~=4), + help GetCharacteristicLength + error('GetCharacteristicLength error message: bad usage') +end +if ((numel(y)~=nods) | (nargin==4 & numel(z)~=nods)), + error('GetCharacteristicLength error message: x,y and z do not have the same length') +end +if max(index(:))>nods, + error(['GetCharacteristicLength error message: index should not have values above ' num2str(nods) ]) +end +if (nargin==3 & size(index,2)~=3), + error('GetCharacteristicLength error message: index should have 3 columns for 2d meshes.') +end +if (nargin==4 & size(index,2)~=6), + error('GetCharacteristicLength error message: index should have 6 columns for 3d meshes.') +end + +%get areas or volumes. +areas=GetAreas(index,x,y,varargin{:}); + +%for a 2d mesh: +if nargin==3, + length=sqrt(2*areas); +else + error('not supported yet'); +end Index: /issm/trunk-jpl/src/m/Mesh/GetNodalFunctionsCoeff.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/GetNodalFunctionsCoeff.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/GetNodalFunctionsCoeff.m (revision 12996) @@ -0,0 +1,56 @@ +function [alpha beta varargout]=GetNodalFunctionsCoeff(index,x,y) +%GETNODELFUNCTIONSCOEFF - compute nodal functions coefficients +% +% Compute the coefficients alpha beta and optionaly gamma of +% 2d triangular elements. For each element, the nodal function +% is defined as: +% N(x,y)=sum(i=1:3) alpha_i * x + beta_i * y + gamma_i +% +% Usage: +% [alpha beta]=GetNodalFunctionsCoeff(index,x,y); +% [alpha beta gamma]=GetNodalFunctionsCoeff(index,x,y); +% +% Example: +% [alpha beta gamma]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.y); + +%make columns out of x and y +x=x(:); y=y(:); + +%get nels and nods +nels=size(index,1); +nods=length(x); + +%some checks +if nargin~=3 | (nargout~=2 & nargout~=3), + help GetNodalFunctionsCoeff + error('GetNodalFunctionsCoeff error message: bad usage') +end +if length(y)~=nods, + error('GetNodalFunctionsCoeff error message: x and y do not have the same length') +end +if max(index(:))>nods, + error(['GetNodalFunctionsCoeff error message: index should not have values above ' num2str(nods) ]) +end +if size(index,2)~=3, + error('GetNodalFunctionsCoeff error message: only 2d meshes supported. index should have 3 columns.') +end + +%initialize output +alpha=zeros(nels,3); +beta=zeros(nels,3); + +%compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma +x1=x(index(:,1)); x2=x(index(:,2)); x3=x(index(:,3)); +y1=y(index(:,1)); y2=y(index(:,2)); y3=y(index(:,3)); +invdet=1./(x1.*(y2-y3)-x2.*(y1-y3)+x3.*(y1-y2)); + +%get alpha and beta +alpha=[invdet.*(y2-y3) invdet.*(y3-y1) invdet.*(y1-y2)]; +beta =[invdet.*(x3-x2) invdet.*(x1-x3) invdet.*(x2-x1)]; + +%get gamma if requested +if nargout==3, + gamma=zeros(nels,3); + gamma=[invdet.*(x2.*y3-x3.*y2) invdet.*(y1.*x3-y3.*x1) invdet.*(x1.*y2-x2.*y1)]; + varargout{1}=gamma; +end Index: /issm/trunk-jpl/src/m/Mesh/MergeMetrics.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/MergeMetrics.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/MergeMetrics.m (revision 12996) @@ -0,0 +1,15 @@ +function metric=MergeMetrics(metric1,metric2) + +M1xx=metric1(:,1); M1xy=metric1(:,2); M1yy=metric1(:,3); +M1lambda1=0.5*((M1xx+M1yy)+sqrt(4*M1xy.^2+(M1xx-M1yy).^2)); +M1lambda2=0.5*((M1xx+M1yy)-sqrt(4*M1xy.^2+(M1xx-M1yy).^2)); +lambda1=min(M1lambda1,M1lambda2); + +M2xx=metric1(:,1); M2xy=metric1(:,2); M2yy=metric1(:,3); +M2lambda1=0.5*((M2xx+M2yy)+sqrt(4*M2xy.^2+(M2xx-M2yy).^2)); +M2lambda2=0.5*((M2xx+M2yy)-sqrt(4*M2xy.^2+(M2xx-M2yy).^2)); +lambda2=min(M2lambda2,M2lambda2); + +metric=metric1; +pos=find(lambda2=0-epsilon) & (area_2>=0-epsilon) & (area_3>=0-epsilon)); + + num_elements=length(pos); + + node_in_element(i,1:num_elements)=pos; + node_in_element(i,end)=num_elements; +end Index: /issm/trunk-jpl/src/m/Mesh/ProfileProjectOntoMesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/ProfileProjectOntoMesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/ProfileProjectOntoMesh.m (revision 12996) @@ -0,0 +1,66 @@ +function mesh_profile=ProfileProjectOntoMesh(md,profile) +%PROFILEPROJECTONTOMESH: project a profile (made of arbitrary points) onto a mesh, so that we end +% up with a list of segments self contained onto elements. +% +% Usage: mesh_profile=ProfileProjectOntoMesh(md,profile) +% +% See also intersections.m + +%make a curve out of the mesh, to use the intersections routine. +rows=[md.mesh.elements md.mesh.elements(:,1)]'; rows=rows(:); +x=md.mesh.x(rows); +y=md.mesh.y(rows); + +%[x0,y0] = intersections(profile.x,profile.y,x,y,1); +[x0,y0,indices,j] = intersections(profile.x,profile.y,x,y); + +% sort intersections to create segments in order and continuous along profile +[indices,isort]=sort(indices); +j =j (isort); +x0=x0(isort); +y0=y0(isort); + +%process x0,y0 so they do not include profile.x or profile.y +processed_indices=[]; +processed_x=[]; +processed_y=[]; +for i=1:numel(indices), + if(((indices(i)-floor(indices(i)))~=0) && ((ceil(indices(i))-indices(i))~=0)) + processed_indices=[processed_indices;floor(indices(i))]; + processed_x=[processed_x;x0(i)]; + processed_y=[processed_y;y0(i)]; + end +end + +%now merge profile.x,profile.y with processed_x,processed_y, at locations processed_indices: +newx=profile.x; +newy=profile.y; + +count=1; +for i=1:numel(profile.x), + pos=find(processed_indices==i); + if ~isempty(pos), + newx=[newx(1:count); processed_x(pos); newx(count+1:end)]; + newy=[newy(1:count); processed_y(pos); newy(count+1:end)]; + count=count+length(pos)+1; + end +end + +%now, for each node, figure out which element it belongs to. +node_in_element=NodeInElement(newx,newy,md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.vertexconnectivity); + +% eliminate nodes that don't fall in any element +% (profile may start and/or end externally and/or cross holes in the model) + +ind=find(node_in_element(:,9)>0); +newx=newx(ind,:); +newy=newy(ind,:); +node_in_element=node_in_element(ind,:); + +mesh_profile=[newx(1:end-1) newy(1:end-1) newx(2:end) newy(2:end) zeros(length(newy(2:end)),1)]; + +%find which element each segment belongs to. +for i=1:length(newx)-1, + common=intersect(node_in_element(i,1:node_in_element(i,end)), node_in_element(i+1,1:node_in_element(i+1,end))); + mesh_profile(i,end)=common(1); +end Index: /issm/trunk-jpl/src/m/Mesh/YamsCall.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/YamsCall.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/YamsCall.m (revision 12996) @@ -0,0 +1,104 @@ +function md=YamsCall(md,field,hmin,hmax,gradation,epsilon), +%YAMSCALL - call yams +% +% build a metric using the Hessian of the given field +% call Yams and the output mesh is plugged onto the model +% -hmin = minimum edge length (m) +% -hmax = maximum edge length (m) +% -gradation = maximum edge length gradation between 2 elements +% -epsilon = average error on each element (m/yr) +% +% Usage: +% md=YamsCall(md,field,hmin,hmax,gradation,epsilon); +% +% Example: +% md=YamsCall(md,md.inversion.vel_obs,1500,10^8,1.3,0.9); + +%2d geometric parameter (do not change) +scale=2/9; + +%Compute Hessian +t1=clock; fprintf('%s',' computing Hessian...'); +hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,field,'node'); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%Compute metric +t1=clock; fprintf('%s',' computing metric...'); +if length(md.mask.vertexonwater)==md.mesh.numberofvertices, + pos=find(md.mask.vertexonwater); +else + pos=[]; +end +metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%write files +t1=clock; fprintf('%s',' writing initial mesh files...'); +save -ascii carre0.met metric + +fid=fopen('carre0.mesh','w'); + +%initialiation +fprintf(fid,'\n%s\n%i\n','MeshVersionFormatted',1); + +%dimension +fprintf(fid,'\n%s\n%i\n','Dimension',2); + +%Vertices +fprintf(fid,'\n%s\n%i\n\n','Vertices',md.mesh.numberofvertices); +fprintf(fid,'%8g %8g %i\n',[md.mesh.x md.mesh.y zeros(md.mesh.numberofvertices,1)]'); + +%Triangles +fprintf(fid,'\n\n%s\n%i\n\n','Triangles',md.mesh.numberofelements); +fprintf(fid,'%i %i %i %i\n',[md.mesh.elements zeros(md.mesh.numberofelements,1)]'); +numberofelements1=md.mesh.numberofelements; + +%Deal with rifts +if ~isnan(md.rifts.riftstruct), + + %we have the list of triangles that make up the rift. keep those triangles around during refinement. + triangles=[]; + for i=1:size(md.rifts.riftstruct,1), + triangles=[triangles md.rifts(i).segments(:,3)']; + end + + fprintf(fid,'\n\n%s\n%i\n\n','RequiredTriangles',length(triangles)); + fprintf(fid,'%i\n',triangles); +end + +%close +fclose(fid); +t2=clock;fprintf('%s\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%call yams +fprintf('%s\n',' call Yams...'); +if ispc + %windows + system(['yams2-win -O 1 -v -0 -ecp -hgrad ' num2str(gradation) ' carre0 carre1']); +elseif ismac + %Macosx + system(['yams2-osx -O 1 -v -0 -ecp -hgrad ' num2str(gradation) ' carre0 carre1']); +else + %Linux + system(['yams2-linux -O 1 -v -0 -ecp -hgrad ' num2str(gradation) ' carre0 carre1']); +end + +%plug new mesh +t1=clock; fprintf('\n%s',' reading final mesh files...'); +Tria=load('carre1.tria'); +Coor=load('carre1.coor'); +md.mesh.x=Coor(:,1); +md.mesh.y=Coor(:,2); +md.mesh.z=zeros(size(Coor,1),1); +md.mesh.elements=Tria; +md.mesh.numberofvertices=size(Coor,1); +md.mesh.numberofelements=size(Tria,1); +numberofelements2=md.mesh.numberofelements; +t2=clock;fprintf('%s\n\n',[' done (' num2str(etime(t2,t1)) ' seconds)']); + +%display number of elements +fprintf('\n%s %i',' inital number of elements:',numberofelements1); +fprintf('\n%s %i\n\n',' new number of elements:',numberofelements2); + +%clean up: +system('rm carre0.mesh carre0.met carre1.tria carre1.coor carre1.meshb'); Index: /issm/trunk-jpl/src/m/Mesh/argusmesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/argusmesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/argusmesh.m (revision 12996) @@ -0,0 +1,96 @@ +function md=argusmesh(md,infile) +%ARGUSMESH - load an Argus mesh onto a model +% +% Convert an Argus mesh contained in a file into +% fields needed for the mesh in a model md. +% +% Usage: +% md=argusmesh(md,infile) +% +% Example: +% md=argusmesh(md,'TriMesh.exp') + +%some argument check: +if nargin~=2 | nargout~=1, + help argustomodel; + error('argustomodel error message: bad usage'); +end + +%determine root of infile: strip extension +[a,root,b,c]=fileparts(infile); + +%inform user we start the script: +disp([' Translating argus file ''' infile ''' into matlab model object']); + +%open infile: +fileid=fopen(infile,'r'); +if fileid==-1, + error(['Could not open file ' infile ' for reading']); +end + +%Read first line of the argus mesh: node and element parameters +[buffer,bytecount]=fscanf(fileid,'%i %i %i %i',[1 4]); +if bytecount~=4, + error(['Problem reading ' infile ' file at line #1']); +end +nel=buffer(1); +nods=buffer(2); +num_element_parameters=buffer(3); +num_node_parameters=buffer(4); +disp([' argus model ''' root ''' contains ' num2str(nel) ' elements and ' num2str(nods) ' nodes.']); + +%initialize elements and nodes +elements=zeros(nel,3); +element_parameters=zeros(nel,num_element_parameters); +x=zeros(nods,1); +y=zeros(nods,1); +z=zeros(nods,1); +node_parameters=zeros(nods,num_node_parameters); + +%read nodes: +format_string='%s %i %f %f '; +for n=1:num_node_parameters, + format_string=[format_string ' %i ']; +end + +for n=1:nods, + [buffer,bytecount]=fscanf(fileid,format_string,[1,num_node_parameters+4]); + x(n)=buffer(3); + y(n)=buffer(4); + node_parameters(n,:)=buffer(5:length(buffer)); +end + +%read elements: +format_string='%s %i %i %i %i'; +for n=1:num_element_parameters, + format_string=[format_string ' %i ']; +end +for n=1:nel, + [buffer,bytecount]=fscanf(fileid,format_string,[1,num_element_parameters+5]); + elements(n,:)=buffer(3:5); + element_parameters(n,:)=buffer(6:length(buffer)); +end + +%Create a name and a note for this model: +notes=['Model created by Argus from input file: ' infile ' and parameter file: ' root '.par on: ' date]; +name=root; + +%Finally, use model constructor to build a complete model: +md.mesh.elements=elements; +md.mesh.x=x; +md.mesh.y=y; +md.z=z; +md.mesh.numberofvertices=size(md.mesh.x,1); +md.mesh.numberofelements=size(md.mesh.elements,1); +md.mesh.vertexonbed=ones(md.mesh.numberofvertices,1); +md.mesh.vertexonsurface=ones(md.mesh.numberofvertices,1); +md.mesh.elementonbed=ones(md.mesh.numberofelements,1); +md.mesh.elementonsurface=ones(md.mesh.numberofelements,1); +md.mesh.dimension=2; +md=addnote(md,notes); + +%Add segments and nodes on boundary +md.mesh.segments=findsegments(md); +md.mesh.vertexonboundary=zeros(md.mesh.numberofvertices,1); +md.mesh.vertexonboundary(md.mesh.segments(:,1))=1; +md.mesh.vertexonboundary(md.mesh.segments(:,2))=1; Index: /issm/trunk-jpl/src/m/Mesh/intersections.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/intersections.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/intersections.m (revision 12996) @@ -0,0 +1,279 @@ +function [x0,y0,iout,jout] = intersections(x1,y1,x2,y2,robust) +%INTERSECTIONS Intersections of curves. +% Computes the (x,y) locations where two curves intersect. The curves +% can be broken with NaNs or have vertical segments. +% +% Example: +% [X0,Y0] = intersections(X1,Y1,X2,Y2,ROBUST); +% +% where X1 and Y1 are equal-length vectors of at least two points and +% represent curve 1. Similarly, X2 and Y2 represent curve 2. +% X0 and Y0 are column vectors containing the points at which the two +% curves intersect. +% +% ROBUST (optional) set to 1 or true means to use a slight variation of the +% algorithm that might return duplicates of some intersection points, and +% then remove those duplicates. The default is true, but since the +% algorithm is slightly slower you can set it to false if you know that +% your curves don't intersect at any segment boundaries. Also, the robust +% version properly handles parallel and overlapping segments. +% +% The algorithm can return two additional vectors that indicate which +% segment pairs contain intersections and where they are: +% +% [X0,Y0,I,J] = intersections(X1,Y1,X2,Y2,ROBUST); +% +% For each element of the vector I, I(k) = (segment number of (X1,Y1)) + +% (how far along this segment the intersection is). For example, if I(k) = +% 45.25 then the intersection lies a quarter of the way between the line +% segment connecting (X1(45),Y1(45)) and (X1(46),Y1(46)). Similarly for +% the vector J and the segments in (X2,Y2). +% +% You can also get intersections of a curve with itself. Simply pass in +% only one curve, i.e., +% +% [X0,Y0] = intersections(X1,Y1,ROBUST); +% +% where, as before, ROBUST is optional. + +% Version: 1.10, 25 February 2008 +% Author: Douglas M. Schwarz +% Email: dmschwarz=ieee*org, dmschwarz=urgrad*rochester*edu +% Real_email = regexprep(Email,{'=','*'},{'@','.'}) + + +% Theory of operation: +% +% Given two line segments, L1 and L2, +% +% L1 endpoints: (x1(1),y1(1)) and (x1(2),y1(2)) +% L2 endpoints: (x2(1),y2(1)) and (x2(2),y2(2)) +% +% we can write four equations with four unknowns and then solve them. The +% four unknowns are t1, t2, x0 and y0, where (x0,y0) is the intersection of +% L1 and L2, t1 is the distance from the starting point of L1 to the +% intersection relative to the length of L1 and t2 is the distance from the +% starting point of L2 to the intersection relative to the length of L2. +% +% So, the four equations are +% +% (x1(2) - x1(1))*t1 = x0 - x1(1) +% (x2(2) - x2(1))*t2 = x0 - x2(1) +% (y1(2) - y1(1))*t1 = y0 - y1(1) +% (y2(2) - y2(1))*t2 = y0 - y2(1) +% +% Rearranging and writing in matrix form, +% +% [x1(2)-x1(1) 0 -1 0; [t1; [-x1(1); +% 0 x2(2)-x2(1) -1 0; * t2; = -x2(1); +% y1(2)-y1(1) 0 0 -1; x0; -y1(1); +% 0 y2(2)-y2(1) 0 -1] y0] -y2(1)] +% +% Let's call that A*T = B. We can solve for T with T = A\B. +% +% Once we have our solution we just have to look at t1 and t2 to determine +% whether L1 and L2 intersect. If 0 <= t1 < 1 and 0 <= t2 < 1 then the two +% line segments cross and we can include (x0,y0) in the output. +% +% In principle, we have to perform this computation on every pair of line +% segments in the input data. This can be quite a large number of pairs so +% we will reduce it by doing a simple preliminary check to eliminate line +% segment pairs that could not possibly cross. The check is to look at the +% smallest enclosing rectangles (with sides parallel to the axes) for each +% line segment pair and see if they overlap. If they do then we have to +% compute t1 and t2 (via the A\B computation) to see if the line segments +% cross, but if they don't then the line segments cannot cross. In a +% typical application, this technique will eliminate most of the potential +% line segment pairs. + + +% Input checks. +error(nargchk(2,5,nargin)) + +% Adjustments when fewer than five arguments are supplied. +switch nargin + case 2 + robust = true; + x2 = x1; + y2 = y1; + self_intersect = true; + case 3 + robust = x2; + x2 = x1; + y2 = y1; + self_intersect = true; + case 4 + robust = true; + self_intersect = false; + case 5 + self_intersect = false; +end + +% x1 and y1 must be vectors with same number of points (at least 2). +if sum(size(x1) > 1) ~= 1 || sum(size(y1) > 1) ~= 1 || ... + length(x1) ~= length(y1) + error('X1 and Y1 must be equal-length vectors of at least 2 points.') +end +% x2 and y2 must be vectors with same number of points (at least 2). +if sum(size(x2) > 1) ~= 1 || sum(size(y2) > 1) ~= 1 || ... + length(x2) ~= length(y2) + error('X2 and Y2 must be equal-length vectors of at least 2 points.') +end + + +% Force all inputs to be column vectors. +x1 = x1(:); +y1 = y1(:); +x2 = x2(:); +y2 = y2(:); + +% Compute number of line segments in each curve and some differences we'll +% need later. +n1 = length(x1) - 1; +n2 = length(x2) - 1; +xy1 = [x1 y1]; +xy2 = [x2 y2]; +dxy1 = diff(xy1); +dxy2 = diff(xy2); + +% Determine the combinations of i and j where the rectangle enclosing the +% i'th line segment of curve 1 overlaps with the rectangle enclosing the +% j'th line segment of curve 2. +[i,j] = find(repmat(min(x1(1:end-1),x1(2:end)),1,n2) <= ... + repmat(max(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(max(x1(1:end-1),x1(2:end)),1,n2) >= ... + repmat(min(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(min(y1(1:end-1),y1(2:end)),1,n2) <= ... + repmat(max(y2(1:end-1),y2(2:end)).',n1,1) & ... + repmat(max(y1(1:end-1),y1(2:end)),1,n2) >= ... + repmat(min(y2(1:end-1),y2(2:end)).',n1,1)); + +% For one segment in x1,y1, i and j are returned as row vectors. They +% need to be column vectors, or iout and jout below will err out. +% (jes, 6/11/10) + +if (size(i,1) == 1) + i=i'; +end +if (size(j,1) == 1) + j=j'; +end + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +% At the same time we can remove redundant combinations of i and j in the +% case of finding intersections of a line with itself. +if self_intersect + remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)) | j <= i + 1; +else + remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +end +i(remove) = []; +j(remove) = []; + +% Initialize matrices. We'll put the T's and B's in matrices and use them +% one column at a time. AA is a 3-D extension of A where we'll use one +% plane at a time. +n = length(i); +T = zeros(4,n); +AA = zeros(4,4,n); +AA([1 2],3,:) = -1; +AA([3 4],4,:) = -1; +AA([1 3],1,:) = dxy1(i,:).'; +AA([2 4],2,:) = dxy2(j,:).'; +B = -[x1(i) x2(j) y1(i) y2(j)].'; + +% Loop through possibilities. Trap singularity warning and then use +% lastwarn to see if that plane of AA is near singular. Process any such +% segment pairs to determine if they are colinear (overlap) or merely +% parallel. That test consists of checking to see if one of the endpoints +% of the curve 2 segment lies on the curve 1 segment. This is done by +% checking the cross product +% +% (x1(2),y1(2)) - (x1(1),y1(1)) x (x2(2),y2(2)) - (x1(1),y1(1)). +% +% If this is close to zero then the segments overlap. + +% If the robust option is false then we assume no two segment pairs are +% parallel and just go ahead and do the computation. If A is ever singular +% a warning will appear. This is faster and obviously you should use it +% only when you know you will never have overlapping or parallel segment +% pairs. + +if robust + overlap = false(1,n); + warning_state = warning('off','MATLAB:singularMatrix'); + % Use try-catch to guarantee original warning state is restored. + try + lastwarn('') + for k = 1:n + T(:,k) = AA(:,:,k)\B(:,k); + [unused,last_warn] = lastwarn; + lastwarn('') + if strcmp(last_warn,'MATLAB:singularMatrix') + % Force in_range(k) to be false. + T(1,k) = NaN; + % Determine if these segments overlap or are just parallel. + overlap(k) = rcond([dxy1(i(k),:);xy2(j(k),:) - xy1(i(k),:)]) < eps; + end + end + warning(warning_state) + catch + warning(warning_state) + rethrow(lasterror) + end + % Find where t1 and t2 are between 0 and 1 and return the corresponding + % x0 and y0 values. + in_range = T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) <= 1 & T(2,:) <= 1; + % For overlapping segment pairs the algorithm will return an + % intersection point that is at the center of the overlapping region. + if any(overlap) + ia = i(overlap); + ja = j(overlap); + % set x0 and y0 to middle of overlapping region. + T(3,overlap) = (max(min(x1(ia),x1(ia+1)),min(x2(ja),x2(ja+1))) + ... + min(max(x1(ia),x1(ia+1)),max(x2(ja),x2(ja+1)))).'/2; + T(4,overlap) = (max(min(y1(ia),y1(ia+1)),min(y2(ja),y2(ja+1))) + ... + min(max(y1(ia),y1(ia+1)),max(y2(ja),y2(ja+1)))).'/2; + selected = in_range | overlap; + else + selected = in_range; + end + xy0 = T(3:4,selected).'; + + % Remove duplicate intersection points. + [xy0,index] = unique(xy0,'rows'); + x0 = xy0(:,1); + y0 = xy0(:,2); + + % Compute how far along each line segment the intersections are. + if nargout > 2 + sel_index = find(selected); + sel = sel_index(index); + iout = i(sel) + T(1,sel).'; + jout = j(sel) + T(2,sel).'; + end +else % non-robust option + for k = 1:n + [L,U] = lu(AA(:,:,k)); + T(:,k) = U\(L\B(:,k)); + end + + % Find where t1 and t2 are between 0 and 1 and return the corresponding + % x0 and y0 values. + in_range = T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) < 1 & T(2,:) < 1; + x0 = T(3,in_range).'; + y0 = T(4,in_range).'; + + % Compute how far along each line segment the intersections are. + if nargout > 2 + iout = i(in_range) + T(1,in_range).'; + jout = j(in_range) + T(2,in_range).'; + end +end + +% Plot the results (useful for debugging). +% plot(x1,y1,x2,y2,x0,y0,'ok'); Index: /issm/trunk-jpl/src/m/Mesh/isconnected.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/isconnected.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/isconnected.m (revision 12996) @@ -0,0 +1,13 @@ +function flag=isconnected(elements,A,B) +%ISCONNECTED: are two nodes connected by a triangulation? +% +% Usage: flag=isconnected(elements,A,B) +% +% + +elements=ElementsFromEdge(elements,A,B); +if isempty(elements), + flag=0; +else + flag=1; +end Index: /issm/trunk-jpl/src/m/Mesh/meshread.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/meshread.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/meshread.m (revision 12996) @@ -0,0 +1,41 @@ +function Struct=meshread(filename); + +%some checks +if ~exist(filename), + error(['meshread error message: file ' filename ' not found!']); +end + +fid=fopen(filename,'r'); + +while (~feof(fid)), + + A=fscanf(fid,'%s',1); + + if strcmp(A,'MeshVersionFormatted'); + Struct.Version=fscanf(fid,'%s',1); + + elseif strcmp(A,'Dimension'), + Struct.Dimension=fscanf(fid,'%i',1); + + elseif strcmp(A,'Vertices'), + Struct.nods=fscanf(fid,'%i',1); + A=fscanf(fid,'%f %f %f',[3 Struct.nods]); + Struct.x=A(1,:)'; + Struct.y=A(2,:)'; + + elseif strcmp(A,'Triangles'), + Struct.nels=fscanf(fid,'%i',1); + A=fscanf(fid,'%i %i %i',[4 Struct.nels]); + Struct.index=A(1:3,:)'; + + elseif strcmp(A,'Quadrilaterals'), + Struct.nels=fscanf(fid,'%i',1); + A=fscanf(fid,'%i %i %i %i',[5 Struct.nels]); + Struct.index=A(1:4,:)'; + else + %do nothing + + end +end + +fclose(fid); Index: /issm/trunk-jpl/src/m/Mesh/rifttipsonmesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/rifttipsonmesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/rifttipsonmesh.m (revision 12996) @@ -0,0 +1,26 @@ +function tips=rifttipsonmesh(md,riftoutline) +%RIFTTIPSONMESH: identify, using a rift outline, the nodes that are tips of +% rifts. + +%read rifts from outline file +rifts=expread(riftoutline,1); + +tips=[]; + +for i=1:length(rifts), + rift=rifts(i); + + x_tip=rift.x(1); + y_tip=rift.y(1); + + index=find_point(md.mesh.x,md.mesh.y,x_tip,y_tip); + tips(end+1)=index; + + x_tip=rift.x(end); + y_tip=rift.y(end); + + index=find_point(md.mesh.x,md.mesh.y,x_tip,y_tip); + tips(end+1)=index; + +end + Index: /issm/trunk-jpl/src/m/Mesh/roundmesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/roundmesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/roundmesh.m (revision 12996) @@ -0,0 +1,34 @@ +function md=roundmesh(md,radius,resolution) +%ROUNDMESH - create an unstructured round mesh +% +% This script will generate a structured round mesh +% - radius : specifies the radius of the circle in meters +% - resolution : specifies the resolution in meters +% +% Usage: +% md=roundmesh(md,radius,resolution) + +%First we have to create the domain outline + +%Get number of points on the circle +pointsonedge=floor((2*pi*radius) / resolution); + +%Calculate the cartesians coordinates of the points +x_list=ones(pointsonedge,1); y_list=ones(pointsonedge,1); +theta=(0:2*pi/pointsonedge:2*pi*(1-1/pointsonedge))'; +x_list=radius*x_list.*cos(theta); +y_list=radius*y_list.*sin(theta); +A=struct('x',x_list,'y',y_list,'density',1); +expgen('RoundDomainOutline.exp',A,1); + +%Call Bamg +md=triangle(md,'RoundDomainOutline.exp',resolution); +%md=bamg(md,'domain','RoundDomainOutline.exp','hmin',resolution); + +%move the closest node to the center +[mini pos]=min(md.mesh.x.^2+md.mesh.y.^2); +md.mesh.x(pos)=0; +md.mesh.y(pos)=0; + +%delete domain +delete('RoundDomainOutline.exp') Index: /issm/trunk-jpl/src/m/Mesh/squaremesh.m =================================================================== --- /issm/trunk-jpl/src/m/Mesh/squaremesh.m (revision 12996) +++ /issm/trunk-jpl/src/m/Mesh/squaremesh.m (revision 12996) @@ -0,0 +1,78 @@ +function md=squaremesh(md,Lx,Ly,nx,ny) +%SQUAREMESH - create a structured square mesh +% +% This script will generate a structured square mesh +% Lx and Ly are the dimension of the domain (in meters) +% nx anx ny are the number of nodes in the x and y direction +% The coordinates x and y returned are in meters. +% +% Usage: +% [md]=squaremesh(md,Lx,Ly,nx,ny) + +%get number of elements and number of nodes +nel=(nx-1)*(ny-1)*2; +nods=nx*ny; + +%initialization +segments=zeros(0,3); +index=zeros(nel,3); +x=zeros(nx*ny,1); +y=zeros(nx*ny,1); + +%create coordinates +for n=1:nx, + for m=1:ny, + x((n-1)*ny+m)=(n-1); + y((n-1)*ny+m)=(m-1); + end +end + +%create index +for n=1:(nx-1) + for m=1:(ny-1), + A=(n-1)*ny+m; + B=A+1; + C=n*ny+m; + D=C+1; + index((n-1)*(ny-1)*2+2*(m-1)+1,:)=[A C B]; + index((n-1)*(ny-1)*2+2*m,:)=[B C D]; + end +end + +%Scale x and y +x=x/max(x)*Lx; +y=y/max(y)*Ly; + +%create segments +segments=zeros(2*(nx-1)+2*(ny-1),3); +%left edge: +segments(1:ny-1,:)=[[2:ny]' [1:ny-1]' 2*[1:ny-1]'-1]; +%right edge: +segments(ny:2*(ny-1),:)=[[ny*(nx-1)+1:nx*ny-1]' [ny*(nx-1)+2:nx*ny]' 2*[(ny-1)*(nx-2)+1:(nx-1)*(ny-1)]']; +%front edge: +segments(2*(ny-1)+1:2*(ny-1)+(nx-1),:)=[[2*ny:ny:ny*nx]' [ny:ny:ny*(nx-1)]' [2*(ny-1):2*(ny-1):2*(nx-1)*(ny-1)]']; +%back edge +segments(2*(ny-1)+(nx-1)+1:2*(nx-1)+2*(ny-1),:)=[[1:ny:(nx-2)*ny+1]' [ny+1:ny:ny*(nx-1)+1]' [1:2*(ny-1):2*(nx-2)*(ny-1)+1]']; + +%plug coordinates and nodes +md.mesh.x=x; +md.mesh.y=y; +md.mesh.z=zeros(nods,1); +md.mesh.numberofvertices=nods; +md.mesh.vertexonboundary=zeros(nods,1);md.mesh.vertexonboundary(segments(:,1:2))=1; +md.mesh.vertexonbed=ones(nods,1); +md.mesh.vertexonsurface=ones(nods,1); + +%plug elements +md.mesh.elements=index; +md.mesh.segments=segments; +md.mesh.numberofelements=nel; +md.mesh.elementonbed=ones(nel,1); +md.mesh.elementonsurface=ones(nel,1); + +%Now, build the connectivity tables for this mesh. +md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices); +md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity); + +%plug other field +md.mesh.dimension=2; Index: /issm/trunk-jpl/src/m/Miscellaneous/create_region.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/create_region.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/create_region.m (revision 12996) @@ -0,0 +1,15 @@ +function create_region(name) +%CREATE_REGION - create region ???? +% +% very temporary function. +% +% Usage: +% create_region(name) + +eval(['mkdir ' name]); +eval(['cd ' name ]); +!mkdir Delivery Exp_Par Results +cd Exp_Par +!cp ../../RonneShelf/Exp_Par/* ./ +!rm -rf Hole* +eval(['!mv Ronne.par ' name '.par']); Index: /issm/trunk-jpl/src/m/Miscellaneous/findarg.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/findarg.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/findarg.m (revision 12996) @@ -0,0 +1,51 @@ +function vals=findarg(arglist,field) +%FINDARG - find argument associated to a field in a list +% +% This function parses through an argument list (typically varargin in a routine) +% looking for a character array equal to field. Once this is found, we return the +% next value in the varargin (if possible). +% Because field might appear several times in the argument list, we return a structure +% holding all these values. +% Note that all comparisons to field value are case independent. +% +% Usage: +% vals=findarg(arglist,field) +% +% Example: +% routine foobar calls vals=findarg('Data',varargin) +% with varargin='Data',1,'Data','foo','Plot','velocity','Arrow',4 +% findarg would return the following structure: vals(1).value=1, vals(2).value='foo'; + +%some argument checking: +if ((nargin==0) | (nargout==0)), + help findarg; + error('findarg error message'); +end + +if ~ischar(field), + error('findarg error message: field should be a string'); +end + +if ~iscell(arglist), + error('findarg error message: argument list should be a cell array.'); +end + +%Recover data to plot +founddata=0; + +for i=1:(length(arglist)-1), %data in arglist comes in pairs, hence the -1. + if ischar(arglist{i}), + if (strcmpi(arglist{i},field)), + founddata=founddata+1; + if founddata==1, + vals.value=arglist{i+1}; + else + vals(end+1).value=arglist{i+1}; + end + end + end +end + +if founddata==0, + vals=[]; +end Index: /issm/trunk-jpl/src/m/Miscellaneous/issmdoc.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/issmdoc.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/issmdoc.m (revision 12996) @@ -0,0 +1,15 @@ +%Quick documentation for ISSM + +%First get ISSM tier: +ISSM_DIR=issmdir; + +disp(sprintf('\n%s',' A comprehensive documentation is available on http://issm.jpl.nasa.gov')); +disp(sprintf('\n%s',' Example: how to create a square ice shelf')); +disp(sprintf('%s',' go to ',ISSM_DIR,'/examples/SquareIceshelf')); +disp(sprintf('%s',' md=model; %creates a new empty model structure')); +disp(sprintf('%s',' md=triangle(md,''DomainOutline.exp'',50000); %creates a mesh of the domain outline with a resolution of 50000m')); +disp(sprintf('%s',' md=setmask(md,''all'',''''); %defines the glacier system as an ice shelf (no island)')); +disp(sprintf('%s',' md=parameterize(md,''Square.par''); %fills all the other fields of the model')); +disp(sprintf('%s',' md=setflowequation(md,''macayeal'',''all''); %defines all elements as MacAyeal''s')); +disp(sprintf('%s',' md=solve(md,DiagnosticSolutionEnum); %generate the velocity field')); +disp(sprintf('%s',' plotmodel(md,''data'',md.results.DiagnosticSolution.Vel); %displays the velocity (type plotdoc for plotmodel help)')); Index: /issm/trunk-jpl/src/m/Miscellaneous/netcdf.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/netcdf.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/netcdf.m (revision 12996) @@ -0,0 +1,136 @@ +function S = netcdf(File,varargin) +% Function to read NetCDF files +% S = netcdf(File) +% Input Arguments +% File = NetCDF file to read +% Optional Input Arguments: +% 'Var',Var - Read data for VarArray(Var), default [1:length(S.VarArray)] +% 'Rec',Rec - Read data for Record(Rec), default [1:S.NumRecs] +% Output Arguments: +% S = Structure of NetCDF data organised as per NetCDF definition +% Notes: +% Only version 1, classic 32bit, NetCDF files are supported. By default +% data are extracted into the S.VarArray().Data field for all variables. +% To read the header only call S = netcdf(File,'Var',[]); +% +% SEE ALSO +% --------------------------------------------------------------------------- +S = []; + +try + if exist(File,'file') fp = fopen(File,'r','b'); + else fp = []; error('File not found'); end + if fp == -1 error('Unable to open file'); end + +% Read header + Magic = fread(fp,4,'uint8=>char'); + if strcmp(Magic(1:3),'CDF') error('Not a NetCDF file'); end + if uint8(Magic(4))~=1 error('Version not supported'); end + S.NumRecs = fread(fp,1,'uint32=>uint32'); + S.DimArray = DimArray(fp); + S.AttArray = AttArray(fp); + S.VarArray = VarArray(fp); + +% Setup indexing to arrays and records + Var = ones(1,length(S.VarArray)); + Rec = ones(1,S.NumRecs); + for i = 1:2:length(varargin) + if strcmp(upper(varargin{i}),'VAR') Var=Var*0; Var(varargin{i+1})=1; + elseif strcmp(upper(varargin{i}),'REC') Rec=Rec*0; Rec(varargin{i+1})=1; + else error('Optional input argument not recognised'); end + end + if sum(Var)==0 fclose(fp); return; end + +% Read non-record variables + Dim = double(cat(2,S.DimArray.Dim)); + ID = double(cat(2,S.VarArray.Type)); + + for i = 1:length(S.VarArray) + D = Dim(S.VarArray(i).DimID+1); N = prod(D); RecID{i}=find(D==0); + if isempty(RecID{i}) + if length(D)==0 D = [1,1]; N = 1; elseif length(D)==1 D=[D,1]; end + if Var(i) + S.VarArray(i).Data = ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D); + fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8'); + else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end + else S.VarArray(i).Data = []; end + end + +% Read record variables + for k = 1:S.NumRecs + for i = 1:length(S.VarArray) + if ~isempty(RecID{i}) + D = Dim(S.VarArray(i).DimID+1); D(RecID{i}) = 1; N = prod(D); + if length(D)==1 D=[D,1]; end + if Var(i) & Rec(k) + S.VarArray(i).Data = cat(RecID{i},S.VarArray(i).Data,... + ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D)); + if N > 1 fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8'); end + else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end + end + end + end + + fclose(fp); +catch + Err = lasterror; fprintf('%s\n',Err.message); + if ~isempty(fp) && fp ~= -1 fclose(fp); end +end + +% --------------------------------------------------------------------------------------- +% Utility functions + +function S = Size(ID) +% Size of NetCDF data type, ID, in bytes + S = subsref([1,1,2,4,4,8],struct('type','()','subs',{{ID}})); + +function T = Type(ID) +% Matlab string for CDF data type, ID + T = subsref({'int8','char','int16','int32','single','double'},... + struct('type','{}','subs',{{ID}})); + +function N = Pad(Num,ID) +% Number of elements to read after padding to 4 bytes for type ID + N = (double(Num) + mod(4-double(Num)*Size(ID),4)/Size(ID)).*(Num~=0); + +function S = String(fp) +% Read a CDF string; Size,[String,[Padding]] + S = fread(fp,Pad(fread(fp,1,'uint32=>uint32'),1),'uint8=>char').'; + +function A = ReOrder(A,S) +% Rearrange CDF array A to size S with matlab ordering + A = permute(reshape(A,fliplr(S)),fliplr(1:length(S))); + +function S = DimArray(fp) +% Read DimArray into structure + if fread(fp,1,'uint32=>uint32') == 10 % NC_DIMENSION + for i = 1:fread(fp,1,'uint32=>uint32') + S(i).Str = String(fp); + S(i).Dim = fread(fp,1,'uint32=>uint32'); + end + else fread(fp,1,'uint32=>uint32'); S = []; end + +function S = AttArray(fp) +% Read AttArray into structure + if fread(fp,1,'uint32=>uint32') == 12 % NC_ATTRIBUTE + for i = 1:fread(fp,1,'uint32=>uint32') + S(i).Str = String(fp); + ID = fread(fp,1,'uint32=>uint32'); + Num = fread(fp,1,'uint32=>uint32'); + S(i).Val = fread(fp,Pad(Num,ID),[Type(ID),'=>',Type(ID)]).'; + end + else fread(fp,1,'uint32=>uint32'); S = []; end + +function S = VarArray(fp) +% Read VarArray into structure + if fread(fp,1,'uint32=>uint32') == 11 % NC_VARIABLE + for i = 1:fread(fp,1,'uint32=>uint32') + S(i).Str = String(fp); + Num = double(fread(fp,1,'uint32=>uint32')); + S(i).DimID = double(fread(fp,Num,'uint32=>uint32')); + S(i).AttArray = AttArray(fp); + S(i).Type = fread(fp,1,'uint32=>uint32'); + S(i).VSize = fread(fp,1,'uint32=>uint32'); + S(i).Begin = fread(fp,1,'uint32=>uint32'); % Classic 32 bit format only + end + else fread(fp,1,'uint32=>uint32'); S = []; end Index: /issm/trunk-jpl/src/m/Miscellaneous/netcdf2struct.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/netcdf2struct.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/netcdf2struct.m (revision 12996) @@ -0,0 +1,27 @@ +function S=netcdf2struct(File) +%NETCDF2STRUCT - load netcdf file and convert to a matlab structure +% +% Usage: +% S=netcdf2struct(File); + +%Read netcdf file +data=netcdf(File); + +%initialize output +S=struct(); + +%All the variables are in VarArray field +variables=data.VarArray; +for i=1:size(variables,2), + fieldname=deblank(variables(i).Str); + fieldvalue=double(squeeze(variables(i).Data)); + S.(fieldname)=fieldvalue; +end + +%All the variables are in AttArray field +variables=data.AttArray; +for i=1:size(variables,2), + fieldname=deblank(variables(i).Str); + fieldvalue=double(variables(i).Val); + S.(fieldname)=fieldvalue; +end Index: /issm/trunk-jpl/src/m/Miscellaneous/structtoobj.m =================================================================== --- /issm/trunk-jpl/src/m/Miscellaneous/structtoobj.m (revision 12996) +++ /issm/trunk-jpl/src/m/Miscellaneous/structtoobj.m (revision 12996) @@ -0,0 +1,16 @@ +function obj=structtoobj(obj,S), +%Convert struct to object + + %Get object and structure fields + structfields=fields(S); + objprops =properties(class(obj)); + + %recover object properties + for i=1:length(structfields), + fieldname =structfields{i}; + if ismember(fieldname,objprops), + fieldvalue=getfield(S,fieldname); + obj=setfield(obj,fieldname,fieldvalue); + end + end +end Index: /issm/trunk-jpl/src/m/Model/loadmodel.m =================================================================== --- /issm/trunk-jpl/src/m/Model/loadmodel.m (revision 12996) +++ /issm/trunk-jpl/src/m/Model/loadmodel.m (revision 12996) @@ -0,0 +1,46 @@ +function varargout=loadmodel(path) +%LOADMODEL - load a model using built-in load module +% +% check that model prototype has not changed. if so, adapt to new model prototype. +% +% Usage: +% md=loadmodel(path) +% loadmodel path + +%check nargout +if nargout>1, + error('loadmodel usage error: md=loadmodel(path)'); +end + +%check existence +if exist(path,'file') + %do nothing +elseif exist([path '.mat'],'file') + %add extension + path = [path '.mat']; +else + error(['loadmodel error message: file ' path ' does not exist']); +end + +try, + %recover model on file and name it md + warning off MATLAB:unknownElementsNowStruc; + warning off MATLAB:load:classNotFound + struc=load(path,'-mat'); + warning on MATLAB:unknownElementsNowStruc; + warning on MATLAB:load:classNotFound + + name=char(fieldnames(struc)); + if size(name,1)>1, + error(['loadmodel error message: file ' path ' contains several variables. Only one model should be present.']); + end + md=struc.(name); + if nargout, + varargout{1}=md; + else + assignin('caller',name,md); + end +catch me + disp(getReport(me)) + error(['could not load model ' path]); +end Index: /issm/trunk-jpl/src/m/Model/loadmodellist.m =================================================================== --- /issm/trunk-jpl/src/m/Model/loadmodellist.m (revision 12996) +++ /issm/trunk-jpl/src/m/Model/loadmodellist.m (revision 12996) @@ -0,0 +1,50 @@ +function varargout=loadmodellist(path) +%LOADMODELLIST- load a model using built-in load module +% +% check that modellist prototype has not changed. if so, adapt to new modellist prototype. +% +% Usage: +% mds=loadmodellist(path) +% loadmodellist path + +%check nargout +if nargout>1, + error('loadmodellist usage error: mds=loadmodellist(path)'); +end +%check existence +if ~exist(path) + error(['loadmodellist error message: file ' path ' does not exist']); +end + +%check that the file is readable +[stat,mess]=fileattrib(path); +if( stat==0 | mess.UserRead~=1), + error(['loadmodellist error message: file ' path ' is not readable (permission dinied).']); +end + +%check number of variables +if length(whos('-file',path))>1, + error(['loadmodellist error message: file ' path ' contains several variables. Only one model should be present.']); +end + +try, + struc=load(path,'-mat'); + + %get name of model variable + fieldname=char(fieldnames(struc)); + mds=eval(['struc.' fieldname]); + if ~strcmpi(class(mds),'model'), + mds2=modellist; + mds2=structtomodel(mds2,mds); + mds=mds2; + clear mds2; + end + if nargout, + varargout{1}=mds; + else + assignin('caller',fieldname,mds); + end +catch me + disp(getReport(me)) + error(['could not load model ' path]); +end Index: /issm/trunk-jpl/src/m/Numerics/cfl_step.m =================================================================== --- /issm/trunk-jpl/src/m/Numerics/cfl_step.m (revision 12996) +++ /issm/trunk-jpl/src/m/Numerics/cfl_step.m (revision 12996) @@ -0,0 +1,23 @@ +function maxtime=cfl_step(md,vx,vy); +%CFL_STEP - return the maximum time step for the model in years +% +% Dt < 0.5 / ( u/Dx +v/Dy ) +% +% Usage: +% maxtime=cfl_step(md,vx,vy); +% +% Example: +% dt=cfl_step(md,md.results.DiagnosticSolution.Vx,md.results.DiagnosticSolution.Vy) + +%Check length of velocities +if size(vx,1)~=md.mesh.numberofvertices & size(vy,1)~=md.mesh.numberofvertices, + error('timestpes error message: size of velocity components must be the same as md.mesh.numberofvertices'); +end + +index=md.mesh.elements; +edgex=max(md.mesh.x(index),[],2)-min(md.mesh.x(index),[],2); +edgey=max(md.mesh.y(index),[],2)-min(md.mesh.y(index),[],2); +vx=max(abs(vx(index)),[],2); +vy=max(abs(vy(index)),[],2); + +maxtime=1/2*min(1./(vx./edgex+vy./edgey)); Index: /issm/trunk-jpl/src/m/OS/ismumps.m =================================================================== --- /issm/trunk-jpl/src/m/OS/ismumps.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/ismumps.m (revision 12996) @@ -0,0 +1,33 @@ +function flag=ismumps() +%ISMUMPS - figure out if MUMPS package was compiled with ISSM +% +% Usage: +% flag=ismumps(); + + +configfile=[issmdir() '/bin/config.h']; %should find it in the install target +if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); +end + +%go through the file, and recover the line we want +flag=2; +fid=fopen(configfile,'r'); +if(fid==-1), error(['could not open file: ' configfile]); end + +while(true), + tline=fgets(fid); + if ~ischar(tline), break, end + if strncmp(tline,'/* #undef _HAVE_MUMPS_ */',25), + flag=0; + break; + end + if strncmp(tline,'#define _HAVE_MUMPS_',20), + flag=1; + break; + end +end +fclose(fid); +if flag==2, + error('could not determine whether MUMPS was or was not compiled'); +end Index: /issm/trunk-jpl/src/m/OS/ismumps.py =================================================================== --- /issm/trunk-jpl/src/m/OS/ismumps.py (revision 12996) +++ /issm/trunk-jpl/src/m/OS/ismumps.py (revision 12996) @@ -0,0 +1,37 @@ +import os +from issmdir import * +from MatlabFuncs import * + +def ismumps(): + """ + ISMUMPS - figure out if MUMPS package was compiled with ISSM + + Usage: + flag=ismumps(); + """ + + configfile=os.path.join(issmdir(),'bin','config.h') #should find it in the install target + if not os.path.exists(configfile): + raise RuntimeError("File '%s' not found. ISSM has not been configured yet!" % configfile) + + #go through the file, and recover the line we want + flag=2 + try: + fid=open(configfile,'r') + except IOError as e: + raise IOError("could not open file: '%s'" % configfile) + + for tline in fid: + if strncmp(tline,'/* #undef _HAVE_MUMPS_ */',25): + flag=0 + break + if strncmp(tline,'#define _HAVE_MUMPS_',20): + flag=1 + break + + fid.close() + if flag==2: + raise RuntimeError("could not determine whether MUMPS was or was not compiled.") + + return flag + Index: /issm/trunk-jpl/src/m/OS/ispetsc.m =================================================================== --- /issm/trunk-jpl/src/m/OS/ispetsc.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/ispetsc.m (revision 12996) @@ -0,0 +1,33 @@ +function flag=ispetsc() +%ISPETSC - figure out if PETSC package was compiled with ISSM +% +% Usage: +% flag=ispetsc(); + + +configfile=[issmdir() '/bin/config.h']; %should find it in the install target +if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); +end + +%go through the file, and recover the line we want +flag=2; +fid=fopen(configfile,'r'); +if(fid==-1), error(['could not open file: ' configfile]); end + +while(true), + tline=fgets(fid); + if ~ischar(tline), break, end + if strncmp(tline,'/* #undef _HAVE_PETSC_ */',25), + flag=0; + break; + end + if strncmp(tline,'#define _HAVE_PETSC_',20), + flag=1; + break; + end +end +fclose(fid); +if flag==2, + error('could not determine whether PETSC was or was not compiled'); +end Index: /issm/trunk-jpl/src/m/OS/ispetsc.py =================================================================== --- /issm/trunk-jpl/src/m/OS/ispetsc.py (revision 12996) +++ /issm/trunk-jpl/src/m/OS/ispetsc.py (revision 12996) @@ -0,0 +1,37 @@ +import os +from issmdir import * +from MatlabFuncs import * + +def ispetsc(): + """ + ISPETSC - figure out if PETSC package was compiled with ISSM + + Usage: + flag=ispetsc(); + """ + + configfile=os.path.join(issmdir(),'bin','config.h') #should find it in the install target + if not os.path.exists(configfile): + raise RuntimeError("File '%s' not found. ISSM has not been configured yet!" % configfile) + + #go through the file, and recover the line we want + flag=2 + try: + fid=open(configfile,'r') + except IOError as e: + raise IOError("could not open file: '%s'" % configfile) + + for tline in fid: + if strncmp(tline,'/* #undef _HAVE_PETSC_ */',25): + flag=0 + break + if strncmp(tline,'#define _HAVE_PETSC_',20): + flag=1 + break + + fid.close() + if flag==2: + raise RuntimeError("could not determine whether PETSC was or was not compiled.") + + return flag + Index: /issm/trunk-jpl/src/m/OS/issmbbftpin.m =================================================================== --- /issm/trunk-jpl/src/m/OS/issmbbftpin.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmbbftpin.m (revision 12996) @@ -0,0 +1,48 @@ +function issmbbftpin(host, login,port,numstreams,path, packages) +%BBFTPIN get packages from host, using bbftp. assuming unix system here. +% +% usage: scpin(host,packages,path) +% +% + +%first get hostname +hostname=oshostname(); + +%first be sure packages are not in the current directory, this could conflict with pscp on windows. +%get initial warning mode +state=warning('query', 'all'); +%remove warnings in case the files do not exist +warning off +for i=1:numel(packages), + delete(packages{i}); +end +%back to initial warning state +warning(state); + +%if hostname and host are the same, do a simple copy +if strcmpi(hostname,host), + + for i=1:numel(packages), + success=copyfile([path '/' packages{i}]); %keep going, even if success=0 + end + +else + + %build a string of the type: bbftp -s -u elarour -e 'setnbstream 8; cd /nobackupp10/elarour/Testing/Interactive3/; get Antarctica.outbin' pfe1.nas.nasa.gov + command=['!bbftp -s -V -u ' login ' -e ''setnbstream 8; cd ' path '; ']; + for i=1:length(packages), + command=[command 'get ' packages{i} ';']; + end + command=[command ''' pfe1.nas.nasa.gov']; + + eval(command); + + %check bbftp worked + for i=1:numel(packages), + if ~exist(['./' packages{i}]), + error('scpin error message: could not call scp on *nix system'); + end + end + + +end Index: /issm/trunk-jpl/src/m/OS/issmbbftpout.m =================================================================== --- /issm/trunk-jpl/src/m/OS/issmbbftpout.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmbbftpout.m (revision 12996) @@ -0,0 +1,30 @@ +function issmbbftpout(host,path,login,port,numstreams,packages) +%BBFTPOUT put packages onto host, using bbftp. assuming unix system here. +% +% usage: bbftpout(host,path,login,port,numstream,packages) +% +% + +%get hostname +hostname=oshostname(); + +%if hostname and host are the same, do a simple copy +if strcmpi(host,hostname), + for i=1:numel(packages), + here=pwd; + eval(['cd ' path]) + system(['rm -rf ' packages{i} ]); + system(['ln -s ' here '/' packages{i} ' .']); + eval(['cd ' here]); + end +else + + %build a string of the type: bbftp -s -u elarour -e 'setnbstream 8; cd /nobackupp10/elarour/Testing/Interactive3/; put Antarctica.tar.gz' pfe1.nas.nasa.gov + command=['!bbftp -s -V -u ' login ' -e ''setnbstream 8; cd ' path '; '] + for i=1:length(packages), + command=[command 'put ' packages{i} ';']; + end + command=[command ''' pfe1.nas.nasa.gov']; + + eval(command); +end Index: /issm/trunk-jpl/src/m/OS/issmscpin.m =================================================================== --- /issm/trunk-jpl/src/m/OS/issmscpin.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmscpin.m (revision 12996) @@ -0,0 +1,78 @@ +function scpin(host, login,port,path, packages) +%SCPIN get packages from host, using scp on unix, and pscp on windows +% +% usage: scpin(host,packages,path) +% +% + +%first get hostname +hostname=oshostname(); + +%first be sure packages are not in the current directory, this could conflict with pscp on windows. +%get initial warning mode +state=warning('query', 'all'); +%remove warnings in case the files do not exist +warning off +for i=1:numel(packages), + delete(packages{i}); +end +%back to initial warning state +warning(state); + +%if hostname and host are the same, do a simple copy +if strcmpi(hostname,host), + + for i=1:numel(packages), + success=copyfile([path '/' packages{i}]); %keep going, even if success=0 + end + +else + + if ispc, + %use the putty project pscp.exe: it should be in the path. + + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, + error('scpin error message: could not find ISSM_DIR_WIN environment variable'); + end + ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + + for i=1:numel(packages), + [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' host ':' path '/' packages{i} ' ./']); + if status, + error('scpin error message: could not call putty pscp'); + end + end + + else + %just use standard unix scp + %string to copy multiple files using scp: + if numel(packages)==1, + string=packages{1}; + else + string='\{'; + for i=1:numel(packages)-1, + string=[string packages{i} ',']; + end + string=[string packages{end} '\}']; + end + + + if port, + eval(['!scp -P ' num2str(port) ' ' login '@localhost:' path '/' string ' ./']); + else + eval(['!scp ' login '@' host ':' path '/' string ' ./']); + end + + %check scp worked + for i=1:numel(packages), + if ~exist(['./' packages{i}]), + error('scpin error message: could not call scp on *nix system'); + end + end + end +end Index: /issm/trunk-jpl/src/m/OS/issmscpin.py =================================================================== --- /issm/trunk-jpl/src/m/OS/issmscpin.py (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmscpin.py (revision 12996) @@ -0,0 +1,76 @@ +import socket +import platform +import subprocess +import os +import shutil +from MatlabFuncs import * + +def scpin(host, login,port,path, packages): + """ + SCPIN get packages from host, using scp on unix, and pscp on windows + + usage: scpin(host,packages,path) + """ + + #first get hostname + hostname=socket.gethostname().lower().split('.')[0] + + #first be sure packages are not in the current directory, this could conflict with pscp on windows. + #remove warnings in case the files do not exist + for package in packages: + try: + os.remove(package) + except OSError as e: + pass + + #if hostname and host are the same, do a simple copy + if strcmpi(hostname,host): + + for package in packages: + try: + shutil.copy(os.path.join(path,package),os.getcwd()) #keep going, even if success=0 + except OSError as e: + pass + + else: + + if 'Windows' in platform.system(): + #use the putty project pscp.exe: it should be in the path. + + #get ISSM_DIR variable + if 'ISSM_DIR_WIN' in os.environ: + ISSM_DIR=os.environ['ISSM_DIR_WIN'][1:-2] + else: + raise OSError("scpin error message: could not find ISSM_DIR_WIN environment variable.") + + username=raw_input('Username: (quoted string) ') + key=raw_input('Key: (quoted string) ') + + for package in packages: + try: + subprocess.check_call('%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s:%s %s' % (ISSM_DIR,username,key,host,os.path.join(path,package),os.getcwd()),shell=True) + except CalledProcessError as e: + raise CalledProcessError("scpin error message: could not call putty pscp.") + + else: + #just use standard unix scp + #string to copy multiple files using scp: + if len(packages)==1: + string=packages[0] + else: + string='{' + for package in packages: + string+=packages[i]+',' + string=string[:-1]+'}' + + + if port: + subprocess.call('scp -P %d %s@localhost:%s %s' % (port,login,os.path.join(path,string),os.getcwd),shell=True) + else: + subprocess.call('scp %s@%s:%s %s' % (login,host,os.path.join(path,string),os.getcwd),shell=True) + + #check scp worked + for package in packages: + if not os.path.exists(os.path.join('.',package)): + raise OSError("scpin error message: could not call scp on *nix system.") + Index: /issm/trunk-jpl/src/m/OS/issmscpout.m =================================================================== --- /issm/trunk-jpl/src/m/OS/issmscpout.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmscpout.m (revision 12996) @@ -0,0 +1,57 @@ +function issmscpout(host,path,login,port,packages) +%SCPOUT send packages to a host, using scp on unix, and pscp on windows +% +% usage: scpout(host,path,packages) +% +% + +%get hostname +hostname=oshostname(); + +%if hostname and host are the same, do a simple copy + +if strcmpi(host,hostname), + for i=1:numel(packages), + here=pwd; + eval(['cd ' path]) + system(['rm -rf ' packages{i} ]); + system(['ln -s ' here '/' packages{i} ' .']); + eval(['cd ' here]); + end +else + if ispc, + %use the putty project pscp.exe: it should be in the path. + + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, + error('scpout error message: could not find ISSM_DIR_WIN environment variable'); + end + ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + + for i=1:numel(packages), + [status,result]=system([ISSM_DIR '/externalpackages/ssh/pscp.exe -l "' username '" -pw "' key '" ' packages{i} ' ' host ':' path]); + if status, + error('scpout error message: could not call putty pscp'); + end + end + + else + %just use standard unix scp + %create string of packages being sent + string=''; + for i=1:numel(packages), + string=[string ' ' packages{i}]; + end + string=[string ' ']; + + if port, + eval(['!scp -P ' num2str(port) ' ' string ' ' login '@localhost:' path]); + else + eval(['!scp ' string ' ' login '@' host ':' path]); + end + end +end Index: /issm/trunk-jpl/src/m/OS/issmscpout.py =================================================================== --- /issm/trunk-jpl/src/m/OS/issmscpout.py (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmscpout.py (revision 12996) @@ -0,0 +1,58 @@ +import socket +import platform +import subprocess +import os +import shutil +from MatlabFuncs import * + +def issmscpout(host,path,login,port,packages): + """ + SCPOUT send packages to a host, using scp on unix, and pscp on windows + + usage: scpout(host,path,packages) + """ + + #get hostname + hostname=socket.gethostname().lower().split('.')[0] + + #if hostname and host are the same, do a simple copy + + if strcmpi(host,hostname): + for package in packages: + here=os.getcwd() + os.chdir(path) + shutil.rmtree(package) + subprocess.call('ln -s %s %s' % (os.path.join(here,package),path),shell=True) + os.chdir(here) + else: + if 'Windows' in platform.system(): + #use the putty project pscp.exe: it should be in the path. + + #get ISSM_DIR variable + if 'ISSM_DIR_WIN' in os.environ: + ISSM_DIR=os.environ['ISSM_DIR_WIN'][1:-2] + else: + raise OSError("scpout error message: could not find ISSM_DIR_WIN environment variable.") + + username=raw_input('Username: (quoted string) ') + key=raw_input('Key: (quoted string) ') + + for package in packages: + try: + subprocess.check_call('%s/externalpackages/ssh/pscp.exe -l "%s" -pw "%s" %s %s:%s' % (ISSM_DIR,username,key,package,host,path),shell=True) + except CalledProcessError as e: + raise CalledProcessError("scpout error message: could not call putty pscp.") + + else: + #just use standard unix scp + #create string of packages being sent + string='' + for package in packages: + string+=' '+package + string+=' ' + + if port: + subprocess.call('scp -P %d %s %s@localhost:%s' % (port,string,login,path),shell=True) + else: + subprocess.call('scp %s %s@%s:%s' % (string,login,host,path),shell=True) + Index: /issm/trunk-jpl/src/m/OS/issmssh.m =================================================================== --- /issm/trunk-jpl/src/m/OS/issmssh.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmssh.m (revision 12996) @@ -0,0 +1,37 @@ +function issmssh(host,login,port,command) +%ISSMSSH - wrapper for OS independent ssh command. +% +% usage: +% issmssh(host,command) + +%first get hostname +hostname=oshostname(); + +%if same as host, just run the command. +if strcmpi(host,hostname), + system(command); +else + if ispc, + %use the putty project plink.exe: it should be in the path. + + %get ISSM_DIR variable + [status,ISSM_DIR]=system('echo [%ISSM_DIR_WIN%]'); + if status, + error('issmssh error message: could not find ISSM_DIR_WIN environment variable'); + end + ISSM_DIR=ISSM_DIR(2:end-2); + + username=input('Username: (quoted string) '); + key=input('Key: (quoted string) '); + + system([ISSM_DIR '/externalpackages/ssh/plink.exe -ssh -l "' username '" -pw "' key '" ' host ' "' command '"']); + + else + %just use standard unix ssh + if port, + eval(['!ssh -l ' login ' -p ' num2str(port) ' localhost "' command '"']); + else + eval(['!ssh -l ' login ' ' host ' "' command '"']); + end + end +end Index: /issm/trunk-jpl/src/m/OS/issmssh.py =================================================================== --- /issm/trunk-jpl/src/m/OS/issmssh.py (revision 12996) +++ /issm/trunk-jpl/src/m/OS/issmssh.py (revision 12996) @@ -0,0 +1,42 @@ +import socket +import platform +import subprocess +import os +from MatlabFuncs import * + +def issmssh(host,login,port,command): + """ + ISSMSSH - wrapper for OS independent ssh command. + + usage: + issmssh(host,command) + """ + + #first get hostname + hostname=socket.gethostname().lower().split('.')[0] + + #if same as host, just run the command. + if strcmpi(host,hostname): + subprocess.call(command,shell=True) + else: + if 'Windows' in platform.system(): + #use the putty project plink.exe: it should be in the path. + + #get ISSM_DIR variable + if 'ISSM_DIR_WIN' in os.environ: + ISSM_DIR=os.environ['ISSM_DIR_WIN'][1:-2] + else: + raise OSError("issmssh error message: could not find ISSM_DIR_WIN environment variable.") + + username=raw_input('Username: (quoted string) ') + key=raw_input('Key: (quoted string) ') + + subprocess.call('%s/externalpackages/ssh/plink.exe -ssh -l "%s" -pw "%s" %s "%s"' % (ISSM_DIR,username,key,host,command),shell=True); + + else: + #just use standard unix ssh + if port: + subprocess.call('ssh -l %s -p %d localhost "%s"' % (login,port,command),shell=True) + else: + subprocess.call('ssh -l %s %s "%s"' % (login,host,command),shell=True) + Index: /issm/trunk-jpl/src/m/OS/listfiles.m =================================================================== --- /issm/trunk-jpl/src/m/OS/listfiles.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/listfiles.m (revision 12996) @@ -0,0 +1,22 @@ +function list=listfiles() +%LISTFILES list files inside a directory +% this is very OS dependent. +% +% usage: list=listfiles; +% +% +% see also LS DIR + +%use dir, as it seems to act OS independent + +first_list=dir; +list={}; + +for i=1:numel(first_list), + if ( ~strcmpi(first_list(i).name,'.') &... + ~strcmpi(first_list(i).name,'..') &... + ~strcmpi(first_list(i).name,'NightlyRun') &... + ~strcmpi(first_list(i).name,'.svn')), + list{end+1}=first_list(i).name; + end +end Index: /issm/trunk-jpl/src/m/OS/listfilesparallel.m =================================================================== --- /issm/trunk-jpl/src/m/OS/listfilesparallel.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/listfilesparallel.m (revision 12996) @@ -0,0 +1,15 @@ +function list=listfilesparallel(rank,numprocs) +%LISTFILESPARALLEL list files inside a directory, depending on rank and number of processors running this routine. +% this is very OS dependent. +% +% usage: list=listfilesparallel(rank,numprocs); +% +% +% see also LS DIR LISTFILES + +list=listfiles'; +numfiles=numel(list); + +%we now have a list, split it between all the processors. +[i1,i2]=parallelrange(rank,numprocs,numfiles); +list=list(i1:i2); Index: /issm/trunk-jpl/src/m/OS/oshostname.m =================================================================== --- /issm/trunk-jpl/src/m/OS/oshostname.m (revision 12996) +++ /issm/trunk-jpl/src/m/OS/oshostname.m (revision 12996) @@ -0,0 +1,22 @@ +function hostname=oshostname() +%OSHOSTNAME figure out hostname, irrespective of os type +% +% usage: hostname=oshostname(); +% +% + +if ispc, + [status,hostname]=system('hostname | sed ''s/-//g''');hostname=hostname(1:end-1); + + if status, + error('oshostname error message: could not run hostname command on windows os'); + end + +else + [status,hostname]=system(['hostname -s | sed ''s/-//g''']); + if status, + error('oshostname error message: could not run hostname command on *nix os'); + end + hostname=hostname(1:end-1); + hostname=ddewhite(hostname); +end Index: /issm/trunk-jpl/src/m/Plot/plot2patch.m =================================================================== --- /issm/trunk-jpl/src/m/Plot/plot2patch.m (revision 12996) +++ /issm/trunk-jpl/src/m/Plot/plot2patch.m (revision 12996) @@ -0,0 +1,16 @@ +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: /issm/trunk-jpl/src/m/Plot/squarezoom.m =================================================================== --- /issm/trunk-jpl/src/m/Plot/squarezoom.m (revision 12996) +++ /issm/trunk-jpl/src/m/Plot/squarezoom.m (revision 12996) @@ -0,0 +1,20 @@ +function squarezoom() +%SQUAREZOOM - zoom on a part of a figure +% +% Usage: +% squarezoom() + +disp('Click twice to define a square where you want to zoom. First click for upper left corner, second for lower right corner'); +[x,y]=ginput(2); +dx=x(2)-x(1); +dy=y(1)-y(2); + +if dx>dy, + delta=dx-dy; + xlim([x(1) x(2)]); + ylim([y(2)-delta/2 y(1)+delta/2]); +else + delta=dy-dx; + xlim([x(1)-delta/2 x(2)+delta/2]); + ylim([y(2) y(1)]); +end Index: /issm/trunk-jpl/src/m/Shell/flaimdir.m =================================================================== --- /issm/trunk-jpl/src/m/Shell/flaimdir.m (revision 12996) +++ /issm/trunk-jpl/src/m/Shell/flaimdir.m (revision 12996) @@ -0,0 +1,7 @@ +function FLAIM_DIR=flaimdir() +%ISSMDIR - Get FLAIM installation directory +% +% Usage: +% FLAIM_DIR=flaimdir() + +FLAIM_DIR=[issmdir '/externalpackages/flaim/install']; Index: /issm/trunk-jpl/src/m/Shell/issmdir.m =================================================================== --- /issm/trunk-jpl/src/m/Shell/issmdir.m (revision 12996) +++ /issm/trunk-jpl/src/m/Shell/issmdir.m (revision 12996) @@ -0,0 +1,18 @@ +function ISSM_DIR=issmdir() +%ISSMDIR - Get ISSM_DIR environment variable +% +% Usage: +% ISSM_DIR=issmdir() + +if ~ispc, + ISSM_DIR =getenv('ISSM_DIR'); +else + ISSM_DIR =getenv('ISSM_DIR_WIN'); + if strcmpi(ISSM_DIR(end),'/') | strcmpi(ISSM_DIR(end),'\'), + ISSM_DIR = ISSM_DIR(1:end-1); %shave off the last '/' + end +end + +if (isempty(ISSM_DIR)), + error('issmdir error message: ''ISSM_DIR'' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!'); +end Index: /issm/trunk-jpl/src/m/Shell/issmdir.py =================================================================== --- /issm/trunk-jpl/src/m/Shell/issmdir.py (revision 12996) +++ /issm/trunk-jpl/src/m/Shell/issmdir.py (revision 12996) @@ -0,0 +1,24 @@ +import platform +import os +from MatlabFuncs import * + +def issmdir(): + """ + ISSMDIR - Get ISSM_DIR environment variable + + Usage: + ISSM_DIR=issmdir() + """ + + if not 'Windows' in platform.system(): + ISSM_DIR =os.environ['ISSM_DIR'] + else: + ISSM_DIR =os.environ['ISSM_DIR_WIN'] + if strcmpi(ISSM_DIR[-1],'/') or strcmpi(ISSM_DIR[-1],'\\'): + ISSM_DIR = ISSM_DIR[:-1] #shave off the last '/' + + if not ISSM_DIR: + raise RuntimeError("issmdir error message: 'ISSM_DIR' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!") + + return ISSM_DIR + Index: /issm/trunk-jpl/src/m/Shell/jplsvn.m =================================================================== --- /issm/trunk-jpl/src/m/Shell/jplsvn.m (revision 12996) +++ /issm/trunk-jpl/src/m/Shell/jplsvn.m (revision 12996) @@ -0,0 +1,15 @@ +function JPL_SVN=jplsvn() +%ISSMDIR - Get JPL_SVN environment variable +% +% Usage: +% JPL_SVN=jplsvn() + +if ~ispc, + JPL_SVN =getenv('JPL_SVN'); +else + JPL_SVN =getenv('JPL_SVN_WIN'); +end + +if (isempty(JPL_SVN)), + error('jplsvn error message: ''JPL_SVN'' environment variable is empty! You should define JPL_SVN in your .cshrc or .bashrc'); +end Index: /issm/trunk-jpl/src/m/Shell/ucisvn.m =================================================================== --- /issm/trunk-jpl/src/m/Shell/ucisvn.m (revision 12996) +++ /issm/trunk-jpl/src/m/Shell/ucisvn.m (revision 12996) @@ -0,0 +1,15 @@ +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: /issm/trunk-jpl/src/m/String/ddeblank.m =================================================================== --- /issm/trunk-jpl/src/m/String/ddeblank.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/ddeblank.m (revision 12996) @@ -0,0 +1,29 @@ +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: /issm/trunk-jpl/src/m/String/ddewhite.m =================================================================== --- /issm/trunk-jpl/src/m/String/ddewhite.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/ddewhite.m (revision 12996) @@ -0,0 +1,30 @@ +function sout = ddewhite(s) +%DDEWHITE Double dewhite. Strip both leading and trailing whitespace. +% +% DDEWHITE(S) removes leading and trailing white space and any null +% characters from the string S. A null character is one that has an absolute +% value of 0. +% +% See also DEWHITE, DEBLANK, DDEBLANK. + +% Author: Peter J. Acklam +% Time-stamp: 2003-10-13 11:12:57 +0200 +% E-mail: pjacklam@online.no +% URL: http://home.online.no/~pjacklam + + error(nargchk(1, 1, nargin)); + if ~ischar(s) + error('Input must be a string (char array).'); + end + + if isempty(s) + sout = s; + return; + end + + [r, c] = find(~isspace(s)); + if size(s, 1) == 1 + sout = s(min(c) : max(c)); + else + sout = s(:, min(c) : max(c)); + end Index: /issm/trunk-jpl/src/m/String/dewhite.m =================================================================== --- /issm/trunk-jpl/src/m/String/dewhite.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/dewhite.m (revision 12996) @@ -0,0 +1,30 @@ +function sout = dewhite(s) +%DEWHITE Dewhite. Strip trailing whitespace. +% +% DEWHITE(S) removes leading and trailing white space and any null characters +% from the string S. A null character is one that has an absolute value of +% 0. +% +% See also DDEWHITE, DEBLANK, DDEBLANK. + +% Author: Peter J. Acklam +% Time-stamp: 2003-10-13 11:12:52 +0200 +% E-mail: pjacklam@online.no +% URL: http://home.online.no/~pjacklam + + error(nargchk(1, 1, nargin)); + if ~ischar(s) + error( 'Input must be a string (char array).' ); + end + + if isempty(s) + sout = s; + return; + end + + [r, c] = find(~isspace(s)); + if size(s, 1) == 1 + sout = s(1:max(c)); + else + sout = s(:,1:max(c)); + end Index: /issm/trunk-jpl/src/m/String/discardnum.m =================================================================== --- /issm/trunk-jpl/src/m/String/discardnum.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/discardnum.m (revision 12996) @@ -0,0 +1,14 @@ +function string2=discardnum(string) +%DISCARDNUM - ?????? +% +% Usage: +% string2=discardnum(string) + +string2=string; + +for i=1:length(string), + if (((string(i)-0) <=57) & ((string(i)-0) >=48)), + string2=string(1:i-1); + break; + end +end Index: /issm/trunk-jpl/src/m/String/ismemberi.m =================================================================== --- /issm/trunk-jpl/src/m/String/ismemberi.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/ismemberi.m (revision 12996) @@ -0,0 +1,26 @@ +function flag=ismemberi(string,list), +%ISMEMBERI - return 1 if a string belongs to a list (case insensitive) +% +% same function as Matlab's ismember except that it +% is case insensitive +% +% Usage: +% flag=ismemberi(string,list); +% +% Example: +% flag=ismemberi('test','{'test1','test2','test3'}); + +if ~iscell(list) + error('ismemberi error message: the list of string must be a cell!') +end + +%initialize output +flag=0; + +%go through the list +for i=1:length(list), + if strcmpi(string,list{i}), + flag=i; + return + end +end Index: /issm/trunk-jpl/src/m/String/issmprintf.m =================================================================== --- /issm/trunk-jpl/src/m/String/issmprintf.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/issmprintf.m (revision 12996) @@ -0,0 +1,13 @@ +function issmprintf(flag,format,varargin) +%ISSMPRINTF - display string in solution sequences. wrapper to disp and sprintf. +% +% Usage: +% issmprintf(flag,format,string) +% flag can be used to switch display on and off +% +% Example: +% issmprintf(1,'%s\n','string to display'); + +if flag, + disp(sprintf(format,varargin{:})); +end Index: /issm/trunk-jpl/src/m/String/logoutput.m =================================================================== --- /issm/trunk-jpl/src/m/String/logoutput.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/logoutput.m (revision 12996) @@ -0,0 +1,7 @@ +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)); Index: /issm/trunk-jpl/src/m/String/strsplit.m =================================================================== --- /issm/trunk-jpl/src/m/String/strsplit.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/strsplit.m (revision 12996) @@ -0,0 +1,91 @@ +function splittedstring = strsplit(inpstr,delimiter) +%STRSPLIT - split a tring of delimiter separated values +% +% This function should be used to split a string of delimiter separated +% values. If all values are numerical values the returned matrix is a +% double array but if there is one non numerical value a cell array is +% returned. You can check this with the iscell() function. +% inpstr: string containing delimiter separatede numerical values, eg +% 3498,48869,23908,34.67 +% Output: An x by 1 matrix containing the splitted values +% Delimiter: optional, if omitted the delimiter is , (comma) +% +% Usage: +% output = strsplit(inpstr[,delimiter]) +% + +% mailto: gie.spaepen@ua.ac.be + + + +%Check input arguments +if(nargin < 1) + error('There is no argument defined'); +else + if(nargin == 1) + strdelim = ','; + %Verbose off!! disp 'Delimiter set to ,'; + else + strdelim = delimiter; + end +end + +%deblank string +deblank(inpstr); + +%Get number of substrings +idx = findstr(inpstr,strdelim); +if size(idx) == 0 + disp 'No delimiter in string, inputString is returned'; + splittedstring = inpstr; +else + %Define size of the indices + sz = size(idx,2); + %Define splittedstring + tempsplit = {}; + %Loop through string and itinerate from delimiter to delimiter + for i = 1:sz + %Define standard start and stop positions for the start position, + %choose 1 as startup position because otherwise you get an array + %overflow, for the endposition you can detemine it from the + %delimiter position + strtpos = 1; + endpos = idx(i)-1; + %If i is not the beginning of the string get it from the delimiter + %position + if i ~= 1 + strtpos = idx(i-1)+1; + end + %If i is equal to the number of delimiters get the last element + %first by determining the lengt of the string and then replace the + %endpos back to a standard position + if i == sz + endpos = size(inpstr,2); + tempsplit(i+1) = {inpstr(idx(i)+1 : endpos)}; + endpos = idx(i)-1; + end + %Add substring to output: splittedstring a cell array + tempsplit(i) = {inpstr(strtpos : endpos)}; + end + %Flag + isallnums = 1; + %Check is there are NaN values if matrix elements are converted to + %doubles + for i = 1:size(tempsplit,2) + tempdouble = str2double(tempsplit(i)); + if(isnan(tempdouble)) + isallnums = 0; + end + end + %If isallnums = 1 then return a double array otherwise return a cell + %array + if(isallnums == 1) + for i = 1:size(tempsplit,2) + splittedstring(i) = str2double(tempsplit(i)); + end + else + splittedstring = tempsplit; + end + + +end Index: /issm/trunk-jpl/src/m/String/strsplit_strict.m =================================================================== --- /issm/trunk-jpl/src/m/String/strsplit_strict.m (revision 12996) +++ /issm/trunk-jpl/src/m/String/strsplit_strict.m (revision 12996) @@ -0,0 +1,37 @@ +function splittedstring = strsplit(inpstr,delimiter) +%STRSPLIT - split a tring of delimiter separated values +% +% Usage: +% output = strsplit_strict(inpstr,delimiter) + + +%Check input arguments +if(nargin ~= 2) + error('There is no argument defined'); +end + +%deblank string +deblank(inpstr); + +%Get number of substrings +idx = findstr(inpstr,delimiter); +if size(idx) == 0 + splittedstring = {inpstr}; +else + sz = size(idx,2); + splittedstring = {}; + %Loop through string and itinerate from delimiter to delimiter + for i = 1:sz + strtpos = 1; + endpos = idx(i)-1; + if i ~= 1 + strtpos = idx(i-1)+1; + end + if i == sz + endpos = size(inpstr,2); + splittedstring(i+1) = {inpstr(idx(i)+1 : endpos)}; + endpos = idx(i)-1; + end + splittedstring(i) = {inpstr(strtpos : endpos)}; + end +end Index: /issm/trunk-jpl/src/m/consistency/checkfield.m =================================================================== --- /issm/trunk-jpl/src/m/consistency/checkfield.m (revision 12996) +++ /issm/trunk-jpl/src/m/consistency/checkfield.m (revision 12996) @@ -0,0 +1,195 @@ +function md = checkfield(md,fieldname,varargin) +%CHECKFIELD - check field consistency +% +% Used to check model consistency. +% Available options: +% - NaN: 1 if check that there is no NaN +% - size: [lines cols], NaN for non checked dimensions +% - >: greater than provided value +% - >=: greater or equal to provided value +% - <: smallerthan provided value +% - <=: smaller or equal to provided value +% - < vec: smallerthan provided values on each vertex +% - forcing: 1 if check forcing consistency (size and time) +% - values: cell of strings or vector of acceptable values +% - numel: list of acceptable number of elements +% - cell: 1 if check that is cell +% - empty: 1 if check that non empty +% - message: overloaded error message +% +% Usage: +% md = checkfield(md,fieldname,options); +% +% Example: +% md = checkfield(md,'mesh.elementonbed','size',[md.mesh.numberofelements 1],'values',[0 1]); +% md = checkfield(md,'diagnostic.icefront','size',[NaN 4],'NaN',1); +% md = checkfield(md,'diagnostic.icefront(:,end)','values',[0 1 2]); + +%get options +options=pairoptions(varargin{:}); + +%get field from model +eval(['field=md.' fieldname ';']); + +%check empty +if exist(options,'empty') + if isempty(field), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' is empty'])); + end +end + +%Check size +if exist(options,'size') + fieldsize=getfieldvalue(options,'size'); + if isnan(fieldsize(1)), + if (size(field,2)~=fieldsize(2)), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have ' num2str(fieldsize(2)) ' columns'])); + end + elseif isnan(fieldsize(2)), + if (size(field,1)~=fieldsize(1)), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have ' num2str(fieldsize(1)) ' lines'])); + end + else + if ((size(field,1)~=fieldsize(1)) | (size(field,2)~=fieldsize(2))) + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' size should be ' num2str(fieldsize(1)) ' x ' num2str(fieldsize(2))])); + end + end +end + +%Check numel +if exist(options,'numel') + fieldnumel=getfieldvalue(options,'numel'); + if ~ismember(numel(field),fieldnumel), + if length(fieldnumel)==1 + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' size should be ' sprintf('%g ',fieldnumel) ])); + elseif length(fieldnumel)==2 + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' size should be ' num2str(fieldnumel(1)) ' or ' num2str(fieldnumel(2)) ])); + else + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' size should be ' sprintf('%g, ',fieldnumel(1:end-1)) ' or ' num2str(fieldnumel(end)) ])); + end + end +end + +%check NaN +if getfieldvalue(options,'NaN',0); + field2=reshape(field,prod(size(field)),1); + if any(isnan(field2)), + md = checkmessage(md,getfieldvalue(options,'message',... + ['NaN values found in field ''' fieldname ''''])); + end +end + +%check cell +if getfieldvalue(options,'cell',0); + if ~iscell(field), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should be a cell'])); + end +end + +%check values +if exist(options,'values') + fieldvalues=getfieldvalue(options,'values'); + if iscell(fieldvalues), %strings + if ischar(field) | iscell(fieldvalues), + if any(~ismember(field,fieldvalues)), + if length(fieldvalues)==1 + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' value should be ''' fieldvalues{1} ''''])); + elseif length(fieldvalues)==2 + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' values should be ''' fieldvalues{1} ''' or ''' fieldvalues{2} ''''])); + else + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have values in ' sprintf('''%s'', ',fieldvalues{1:end-1}) 'or ''' fieldvalues{end} ''''])); + end + end + else + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should be one of the following strings: ' sprintf('''%s'', ',fieldvalues{1:end-1}) 'or ''' fieldvalues{end} ''''])); + end + else + field2=reshape(field,prod(size(field)),1); + if isnumeric(field), + if any(~ismember(field2,fieldvalues)), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have values in [' num2str(fieldvalues) ']'])); + end + else + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should be a number in [' num2str(fieldvalues) ']'])); + end + end +end + +%check greater +if exist(options,'>=') + lowerbound=getfieldvalue(options,'>='); + field2=reshape(field,prod(size(field)),1); + if any(field2') + lowerbound=getfieldvalue(options,'>'); + field2=reshape(field,prod(size(field)),1); + if any(field2<=lowerbound), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have values above ' num2str(lowerbound(1,1))])); + end +end + +%check smaller +if exist(options,'<=') + upperbound=getfieldvalue(options,'<='); + field2=reshape(field,prod(size(field)),1); + if any(field2>upperbound), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have values below ' num2str(upperbound(1,1))])); + end +end +if exist(options,'<') + upperbound=getfieldvalue(options,'<'); + field2=reshape(field,prod(size(field)),1); + if any(field2>=upperbound), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have values below ' num2str(upperbound(1,1))])); + end +end + +%check file +if getfieldvalue(options,'file',0), + if ~exist(field,'file') + md = checkmessage(md,['file provided in ''' fieldname ''': ''' field ''' does not exist']); + end +end + +%Check forcings (size and times) +if getfieldvalue(options,'forcing',0), + if size(field,1)==md.mesh.numberofvertices, + if ~size(field,2)==1, + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have only one column as there are md.mesh.numberofvertices lines'])); + end + elseif size(field,1)==md.mesh.numberofvertices+1 + if any(field(end,:)~=sort(field(end,:))), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' columns should be sorted chronologically'])); + end + if any(field(end,1:end-1)==field(end,2:end)), + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' columns must not contain duplicate timesteps'])); + end + else + md = checkmessage(md,getfieldvalue(options,'message',... + ['field ''' fieldname ''' should have md.mesh.numberofvertices or md.mesh.numberofvertices+1 lines'])); + end +end Index: /issm/trunk-jpl/src/m/consistency/checkfield.py =================================================================== --- /issm/trunk-jpl/src/m/consistency/checkfield.py (revision 12996) +++ /issm/trunk-jpl/src/m/consistency/checkfield.py (revision 12996) @@ -0,0 +1,156 @@ +import numpy +import os +from pairoptions import * +from MatlabFuncs import * + +def checkfield(md,fieldname,*args): + """ + CHECKFIELD - check field consistency + + Used to check model consistency. + Available options: + - NaN: 1 if check that there is no NaN + - size: [lines cols], NaN for non checked dimensions + - >: greater than provided value + - >=: greater or equal to provided value + - <: smallerthan provided value + - <=: smaller or equal to provided value + - < vec: smallerthan provided values on each vertex + - forcing: 1 if check forcing consistency (size and time) + - values: cell of strings or vector of acceptable values + - numel: list of acceptable number of elements + - cell: 1 if check that is cell + - empty: 1 if check that non empty + - message: overloaded error message + + Usage: + md = checkfield(md,fieldname,options); + + Example: + md = checkfield(md,'mesh.elementonbed','size',[md.mesh.numberofelements 1],'values',[0 1]); + md = checkfield(md,'diagnostic.icefront','size',[NaN 4],'NaN',1); + md = checkfield(md,'diagnostic.icefront(:,end)','values',[0 1 2]); + """ + + #get options + options=pairoptions(*args) + + #get field from model +# field=getattr(md,fieldname) + exec("field=md.%s" % fieldname) + + #check empty + if options.exist('empty'): + if not field: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' is empty" % fieldname)) + + #Check size + if options.exist('size'): + fieldsize=options.getfieldvalue('size') + if len(fieldsize) == 1: + if (not numpy.size(field,0)==fieldsize[0]): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' size should be %d" % (fieldname,fieldsize[0]))) + elif len(fieldsize) == 2: + if numpy.isnan(fieldsize[0]): + if not numpy.size(field,1)==fieldsize[1]: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have %d columns" % (fieldname,fieldsize[1]))) + elif numpy.isnan(fieldsize[1]): + if not numpy.size(field,0)==fieldsize[0]: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have %d lines" % (fieldname,fieldsize[0]))) + else: + if (not numpy.size(field,0)==fieldsize[0]) or (not numpy.size(field,1)==fieldsize[1]): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' size should be %d x %d" % (fieldname,fieldsize[0],fieldsize[1]))) + + #Check numel + if options.exist('numel'): + fieldnumel=options.getfieldvalue('numel') + if not numpy.size(field) in fieldnumel: + if len(fieldnumel)==1: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' size should be %d" % (fieldname,fieldnumel))) + elif len(fieldnumel)==2: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' size should be %d or %d" % (fieldname,fieldnumel[0],fieldnumel[1]))) + else: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' size should be %s" % (fieldname,fieldnumel))) + + #check NaN + if options.getfieldvalue('NaN',0): + if True in numpy.isnan(field): + md = md.checkmessage(options.getfieldvalue('message',\ + "NaN values found in field '%s'" % fieldname)) + + #check cell + if options.getfieldvalue('cell',0): + if not isinstance(field,(tuple,list,dict)): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should be a cell" % fieldname)) + + #check values + if options.exist('values'): + fieldvalues=options.getfieldvalue('values') + if False in ismember(field,fieldvalues): + if len(fieldvalues)==1: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' value should be '%s'" % (fieldname,fieldvalues[0]))) + elif len(fieldvalues)==2: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' values should be '%s' or '%s'" % (fieldname,fieldvalues[0],fieldvalues[1]))) + else: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have values in %s" % (fieldname,fieldvalues))) + + #check greater + if options.exist('>='): + lowerbound=options.getfieldvalue('>=') + if numpy.any(field'): + lowerbound=options.getfieldvalue('>') + if numpy.any(field<=lowerbound): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have values above %d" % (fieldname,lowerbound))) + + #check smaller + if options.exist('<='): + upperbound=options.getfieldvalue('<=') + if numpy.any(field>upperbound): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have values below %d" % (fieldname,upperbound))) + if options.exist('<'): + upperbound=options.getfieldvalue('<') + if numpy.any(field>=upperbound): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have values below %d" % (fieldname,upperbound))) + + #check file + if options.getfieldvalue('file',0): + if not os.path.exists(field): + md = md.checkmessage("file provided in '%s': '%s' does not exist" % (fieldname,field)) + + #Check forcings (size and times) + if options.getfieldvalue('forcing',0): + if numpy.size(field,0)==md.mesh.numberofvertices: + if not numpy.size(field,1)==1: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have only one column as there are md.mesh.numberofvertices lines" % fieldname)) + elif numpy.size(field,0)==md.mesh.numberofvertices+1: + if not numpy.all(field[-1,:]==numpy.sort(field[-1,:])): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' columns should be sorted chronologically" % fieldname)) + if nump.any(field[-1,0:-1]==field[-1,1:]): + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' columns must not contain duplicate timesteps" % fieldname)) + else: + md = md.checkmessage(options.getfieldvalue('message',\ + "field '%s' should have md.mesh.numberofvertices or md.mesh.numberofvertices+1 lines" % fieldname)) + + return md + Index: /issm/trunk-jpl/src/m/recursivepath.m =================================================================== --- /issm/trunk-jpl/src/m/recursivepath.m (revision 12996) +++ /issm/trunk-jpl/src/m/recursivepath.m (revision 12996) @@ -0,0 +1,38 @@ +function p = recursivepath(d) +%RECURSIVEPATH - generate paths in a directory +% +% this routine is equivalent to Matlab's genpath except that it skips CVS and .svn directories +% +% Usage: +% p = recursivepath(d) + +%initialize path to be returned +p = ''; +sep=pathsep; %directory separator + +% Generate path based on given root directory +files=dir(d); +if isempty(files) + return +end + +% Add d to the path even if it is empty. +p = [p d sep]; + +% set logical vector for subdirectory entries in d +isdir = logical(cat(1,files.isdir)); + +% Recursively goes through the subdirectories of d +dirs=files(isdir); % select only directory entries from the current listing +for i=1:length(dirs) + dirname=dirs(i).name; + if ~strcmp(dirname,'.') & ... + ~strcmp(dirname,'..') & ... + ~strcmp(dirname,'.svn') & ... + ~strcmp(dirname,'CVS') & ... + ~strncmp(dirname,'@',1) & ... %Method directories not allowed in MATLAB path + ~strcmp(dirname,'private') %private directories not allowed in MATLAB path + + p = [p recursivepath(fullfile(d,dirname))]; + end +end