source: issm/trunk/src/m/model/modelextract.m@ 9714

function md2=modelextract(md1,area)
%modelextract - extract a model according to an Argus contour or flag list
%
%   This routine extracts a submodel from a bigger model with respect to a given contour
%   md must be followed by the corresponding exp file or flags list
%   It can either be a domain file (argus type, .exp extension), or an array of element flags. 
%   If user wants every element outside the domain to be 
%   modelextract2d, add '~' to the name of the domain file (ex: '~Pattyn.exp');
%   an empty string '' will be considered as an empty domain
%   a string 'all' will be considered as the entire domain
%   add an argument 0 if you do not want the elements to be checked (faster)
%
%   Usage:
%      md2=modelextract(md1,area);
%
%   Examples:
%      md2=modelextract(md,'Domain.exp');
%      md2=modelextract(md,md.mask.elementonfloatingice);
%
%   See also: EXTRUDE, COLLAPSE

%some checks
if ((nargin~=2) | (nargout~=1)),
        help modelextract
        error('modelextract error message: bad usage');
end

%get check option
if (nargin==3 & varargin{1}==0),
        checkoutline=0;
else
        checkoutline=1;
end

%first
flag_elem=FlagElements(md1,area);

%kick out all elements with 3 dirichlets
spc_elem=find(~flag_elem);
spc_node=sort(unique(md1.elements(spc_elem,:)));
flag=ones(md1.numberofnodes,1);
flag(spc_node)=0;
pos=find(sum(flag(md1.elements),2)==0);
flag_elem(pos)=0;

%extracted elements and nodes lists
pos_elem=find(flag_elem);
pos_node=sort(unique(md1.elements(pos_elem,:)));

%keep track of some fields
numberofnodes1=md1.numberofnodes;
numberofelements1=md1.numberofelements;
numberofnodes2=length(pos_node);
numberofelements2=length(pos_elem);
flag_node=zeros(numberofnodes1,1);
flag_node(pos_node)=1;

%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
Pelem=zeros(numberofelements1,1);
Pelem(pos_elem)=[1:numberofelements2]';
Pnode=zeros(numberofnodes1,1);
Pnode(pos_node)=[1:numberofnodes2]';

%renumber the elements (some node won't exist anymore)
elements_1=md1.elements;
elements_2=elements_1(pos_elem,:);
elements_2(:,1)=Pnode(elements_2(:,1));
elements_2(:,2)=Pnode(elements_2(:,2));
elements_2(:,3)=Pnode(elements_2(:,3));
if md1.dim==3,
        elements_2(:,4)=Pnode(elements_2(:,4));
        elements_2(:,5)=Pnode(elements_2(:,5));
        elements_2(:,6)=Pnode(elements_2(:,6));
end

%OK, now create the new model !

        %take every fields from model
        md2=md1;

        %automatically modify fields

        %loop over model fields
        model_fields=fields(md1);
        for i=1:length(model_fields),
                %get field
                field=md1.(model_fields{i});
                fieldsize=size(field);
                if isobject(field), %recursive call
                        object_fields=fields(md1.(model_fields{i}));
                        for j=1:length(object_fields),
                                %get field
                                field=md1.(model_fields{i}).(object_fields{j});
                                fieldsize=size(field);
                                %size = number of nodes * n
                                if fieldsize(1)==numberofnodes1
                                        md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
                                elseif (fieldsize(1)==numberofnodes1+1)
                                        md2.(model_fields(i)).(object_fields{j})=[field(pos_node,:); field(end,:)];
                                        %size = number of elements * n
                                elseif fieldsize(1)==numberofelements1
                                        md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
                                end
                        end
                else
                        %size = number of nodes * n
                        if fieldsize(1)==numberofnodes1
                                md2.(model_fields{i})=field(pos_node,:);
                        elseif (fieldsize(1)==numberofnodes1+1)
                                md2.(model_fields(i))=[field(pos_node,:); field(end,:)];
                                %size = number of elements * n
                        elseif fieldsize(1)==numberofelements1
                                md2.(model_fields{i})=field(pos_elem,:);
                        end
                end
        end

        %modify some specific fields

        %Mesh
        md2.numberofelements=numberofelements2;
        md2.numberofnodes=numberofnodes2;
        md2.elements=elements_2;

        %uppernodes lowernodes
        if md1.dim==3
                md2.uppernodes=md1.uppernodes(pos_node);
                pos=find(~isnan(md2.uppernodes));
                md2.uppernodes(pos)=Pnode(md2.uppernodes(pos));

                md2.lowernodes=md1.lowernodes(pos_node);
                pos=find(~isnan(md2.lowernodes));
                md2.lowernodes(pos)=Pnode(md2.lowernodes(pos));

                md2.upperelements=md1.upperelements(pos_elem);
                pos=find(~isnan(md2.upperelements));
                md2.upperelements(pos)=Pelem(md2.upperelements(pos));

                md2.lowerelements=md1.lowerelements(pos_elem);
                pos=find(~isnan(md2.lowerelements));
                md2.lowerelements(pos)=Pelem(md2.lowerelements(pos));
        end

        %Initial 2d mesh 
        if md1.dim==3
                flag_elem_2d=flag_elem(1:md1.numberofelements2d);
                pos_elem_2d=find(flag_elem_2d);
                flag_node_2d=flag_node(1:md1.numberofnodes2d);
                pos_node_2d=find(flag_node_2d);

                md2.numberofelements2d=length(pos_elem_2d);
                md2.numberofnodes2d=length(pos_node_2d);
                md2.elements2d=md1.elements2d(pos_elem_2d,:);
                md2.elements2d(:,1)=Pnode(md2.elements2d(:,1));
                md2.elements2d(:,2)=Pnode(md2.elements2d(:,2));
                md2.elements2d(:,3)=Pnode(md2.elements2d(:,3));

                md2.x2d=md1.x(pos_node_2d);
                md2.y2d=md1.y(pos_node_2d);
        end

        %Edges
        if size(md2.edges,2)>1, %do not use ~isnan because there are some NaNs...
                %renumber first two columns
                pos=find(~isnan(md2.edges(:,4)));
                md2.edges(:  ,1)=Pnode(md2.edges(:,1)); 
                md2.edges(:  ,2)=Pnode(md2.edges(:,2)); 
                md2.edges(:  ,3)=Pelem(md2.edges(:,3));
                md2.edges(pos,4)=Pelem(md2.edges(pos,4));
                %remove edges when the 2 vertices are not in the domain.
                md2.edges=md2.edges(find(md2.edges(:,1) & md2.edges(:,2)),:);
                %Replace all zeros by NaN in the last two columns;
                pos=find(md2.edges(:,3)==0);
                md2.edges(pos,3)=NaN;
                pos=find(md2.edges(:,4)==0);
                md2.edges(pos,4)=NaN;
                %Invert NaN of the third column with last column (Also invert first two columns!!)
                pos=find(isnan(md2.edges(:,3)));
                md2.edges(pos,3)=md2.edges(pos,4);
                md2.edges(pos,4)=NaN;
                values=md2.edges(pos,2);
                md2.edges(pos,2)=md2.edges(pos,1);
                md2.edges(pos,1)=values;
                %Finally remove edges that do not belong to any element
                pos=find(isnan(md2.edges(:,3)) & isnan(md2.edges(:,4)));
                md2.edges(pos,:)=[];
        end

        %Penalties
        if ~isnan(md2.diagnostic.vertex_pairing),
                for i=1:size(md1.diagnostic.vertex_pairing,1);
                        md2.diagnostic.vertex_pairing(i,:)=Pnode(md1.diagnostic.vertex_pairing(i,:));
                end
                md2.diagnostic.vertex_pairing=md2.diagnostic.vertex_pairing(find(md2.diagnostic.vertex_pairing(:,1)),:);
        end
        if ~isnan(md2.prognostic.vertex_pairing),
                for i=1:size(md1.prognostic.vertex_pairing,1);
                        md2.prognostic.vertex_pairing(i,:)=Pnode(md1.prognostic.vertex_pairing(i,:));
                end
                md2.prognostic.vertex_pairing=md2.prognostic.vertex_pairing(find(md2.prognostic.vertex_pairing(:,1)),:);
        end

        %recreate segments
        if md1.dim==2
                md2.nodeconnectivity=NodeConnectivity(md2.elements,md2.numberofnodes);
                md2.elementconnectivity=ElementConnectivity(md2.elements,md2.nodeconnectivity);
                md2.segments=contourenvelope(md2);
                md2.mesh.vertexonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1;
        end

        %Boundary conditions: Dirichlets on new boundary
        %Catch the elements that have not been extracted
        orphans_elem=find(~flag_elem);
        orphans_node=unique(md1.elements(orphans_elem,:))';
        %Figure out which node are on the boundary between md2 and md1
        nodestoflag1=intersect(orphans_node,pos_node);
        nodestoflag2=Pnode(nodestoflag1);
        if numel(md1.diagnostic.spcvx)>1 & numel(md1.diagnostic.spcvy)>2 & numel(md1.diagnostic.spcvz)>2,
                if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
                        md2.diagnostic.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2); 
                        md2.diagnostic.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
                else
                        md2.diagnostic.spcvx(nodestoflag2)=NaN;
                        md2.diagnostic.spcvy(nodestoflag2)=NaN;
                        disp(' ')
                        disp('!! modelextract warning: spc values should be checked !!')
                        disp(' ')
                end
                %put 0 for vz
                md2.diagnostic.spcvz(nodestoflag2)=0;
        end
        if ~isnan(md1.thermal.spctemperature),
                md2.thermal.spctemperature(nodestoflag2,1)=1;
        end

        %Diagnostic
        if ~isnan(md2.diagnostic.icefront)
                md2.diagnostic.icefront(:,1)=Pnode(md1.diagnostic.icefront(:,1)); 
                md2.diagnostic.icefront(:,2)=Pnode(md1.diagnostic.icefront(:,2)); 
                md2.diagnostic.icefront(:,end-1)=Pelem(md1.diagnostic.icefront(:,end-1));
                if md1.dim==3
                        md2.diagnostic.icefront(:,3)=Pnode(md1.diagnostic.icefront(:,3)); 
                        md2.diagnostic.icefront(:,4)=Pnode(md1.diagnostic.icefront(:,4)); 
                end
                md2.diagnostic.icefront=md2.diagnostic.icefront(find(md2.diagnostic.icefront(:,1) & md2.diagnostic.icefront(:,2) & md2.diagnostic.icefront(:,end)),:);
        end

        %Results fields
        if isstruct(md1.results),
                md2.results=struct();
                solutionfields=fields(md1.results);
                for i=1:length(solutionfields),
                        %get subfields
                        solutionsubfields=fields(md1.results.(solutionfields(i)));
                        for j=1:length(solutionsubfields),
                                field=md1.results.(solutionfields(i)).(solutionsubfields(j));
                                if length(field)==numberofnodes1,
                                        md2.results.(solutionfields(i)).(solutionsubfields(j))=field(pos_node);
                                elseif length(field)==numberofelements1,
                                        md2.results.(solutionfields(i)).(solutionsubfields(j))=field(pos_elem);
                                else
                                        md2.results.(solutionfields(i)).(solutionsubfields(j))=field;
                                end
                        end
                end
        end

%Keep track of pos_node and pos_elem
md2.mesh.extractedvertices=pos_node;
md2.mesh.extractedelements=pos_elem;