/MatlabCode/branches/Greg's Branch/Online/isosamp/iso2mesh/savesurfpoly.m

function savesurfpoly(v, f, holelist, regionlist, p0, p1, fname, forcebox)

%

% savesurfpoly(v,f,holelist,regionlist,p0,p1,fname)

%

% save a set of surfaces into poly format (for tetgen)

%

% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)

% date: 2007/11/21

%

% input:

%      v: input, surface node list, dimension (nn,3)

%         if v has 4 columns, the last column specifies mesh density near each node

%      f: input, surface face element list, dimension (be,3)

%      holelist: list of holes, each hole is represented by an internal point

%      regionlist: list of regions, similar to holelist

%      p0: coordinate of one of the end of the bounding box

%      p1: coordinate for the other end of the bounding box

%      fname: output file name

%      forcebox: non-empty: add bounding box, []: automatic

%                if forcebox is a 8x1 vector, it will be used to 

%                specify max-edge size near the bounding box corners

%

% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)

%

    dobbx=0;

    if nargin >= 8

        dobbx = ~isempty(forcebox) & all(forcebox);

    end



    if ~iscell(f) && size(f, 2) == 4

        faceid = f(:,4);

        f = f(:,1:3);

    end



    if ~iscell(f)

        edges = surfedge(f);

    else

        edges = [];

    end

    bbxnum = 0;



    nodesize = [];

    if size(v, 2) == 4

        nodesize = v(:,4);

        v = v(:,1:3);

    end

    node = v;

    loopid = [];

    if ~isempty(edges)

        loops = extractloops(edges);

        if length(loops) < 3

            error('degenerated loops detected');

        end

        seg = [0 find(isnan(loops))];

        segnum = length(seg)-1;

        newloops = [];

        for i=1:segnum

            if seg(i+1)-(seg(i)+1) == 0, continue; end

            newloops = [newloops nan bbxflatsegment(node, loops(seg(i)+1:seg(i+1)-1))];

        end

        loops = [newloops nan];



        seg = [0 find(isnan(loops))];

        segnum = length(seg)-1;

        bbxnum = 6;

        loopcount = zeros(bbxnum, 1);

        loopid = zeros(segnum, 1);

        for i = 1:segnum     % walk through the edge loops

            subloop = loops(seg(i)+1:seg(i+1)-1);

            if isempty(subloop), continue; end

            boxfacet = find(sum(abs(diff(v(subloop,:)))) < 1e-8); % find a flat loop

            if length(boxfacet) == 1   % if the loop is flat along x/y/z dir

                bf = boxfacet(1);    % no degeneracy allowed

                if sum(abs(v(subloop(1), bf)-p0(bf))) < 1e-2

                    loopcount(bf) = loopcount(bf)+1;

                    v(subloop,bf) = p0(bf);

                    loopid(i) = bf;

                elseif sum(abs(v(subloop(1), bf)-p1(bf))) < 1e-2

                    loopcount(bf+3) = loopcount(bf+3)+1;

                    v(subloop,bf) = p1(bf);

                    loopid(i) = bf+3;

                end

            end

        end

    end



    if dobbx && isempty(edges)

        bbxnum = 6;

        loopcount = zeros(bbxnum, 1);

    end



    if dobbx || ~isempty(edges)

        nn = size(v, 1);

        boxnode = [p0;p1(1) p0(2:3);p1(1:2) p0(3);p0(1) p1(2) p0(3);

            p0(1:2) p1(3);p1(1) p0(2) p1(3);p1;p0(1) p1(2:3)];

        boxelem = [

            4 nn nn+3 nn+7 nn+4;   % x=xmin

            4 nn nn+1 nn+5 nn+4;   % y=ymin

            4 nn nn+1 nn+2 nn+3;   % z=zmin

            4 nn+1 nn+2 nn+6 nn+5; % x=xmax

            4 nn+2 nn+3 nn+7 nn+6; % y=ymax

            4 nn+4 nn+5 nn+6 nn+7];% z=zmax



        node = [v;boxnode];

    end



    node = [(0:size(node,1)-1)' node];



    fp = fopen(fname, 'w');

    fprintf(fp, '#node list\n%d 3 0 0\n', length(node));

    fprintf(fp, '%d %f %f %f\n', node');



    if ~iscell(f)

        fprintf(fp, '#facet list\n%d 1\n', length(f)+bbxnum);

        elem = [3*ones(length(f), 1) f-1 ones(length(f), 1)];

        if ~isempty(elem)

            fprintf(fp,'1 0\n%d %d %d %d %d\n', elem');

        end

    else % if the surface is recorded as a cell array

        totalplc = 0;

        for i = 1:length(f)

            if ~iscell(f{i})

                totalplc = totalplc+size(f{i}, 1);

            else

                totalplc = totalplc+size(f{i}{1}, 1);

            end

        end

        fprintf(fp, '#facet list\n%d 1\n', totalplc+bbxnum);

        for i = 1:length(f)

            plcs = f{i};

            faceid = -1;

            if iscell(plcs) % if each face is a cell, use plc{2} for face id

                if length(plcs) > 1

                    faceid = plcs{2};

                end

                plcs = plcs{1};

            end

            for row = 1:size(plcs, 1);

                plc = plcs(row,:);

                if any(isnan(plc)) % we use nan to separate outter contours and holes

                    holeid = find(isnan(plc));

                    if faceid > 0

                        fprintf(fp, '%d %d %d\n%d', length(holeid)+1, length(holeid), faceid, holeid(1)-1);

                    else

                        fprintf(fp, '%d %d\n%d', length(holeid)+1, length(holeid), holeid(1)-1);

                    end

                    fprintf(fp, '\t%d', plc(1:holeid(1)-1)-1);

                    fprintf(fp, '\t1\n');

                    for j = 1:length(holeid)

                        if j == length(holeid)

                            fprintf(fp, '%d', length(plc(holeid(j)+1:end)));

                            fprintf(fp, '\t%d', plc(holeid(j)+1:end)-1);

                        else

                            fprintf(fp, '%d', length(plc(holeid(j)+1:holeid(j+1)-1)));

                            fprintf(fp, '\t%d', plc(holeid(j)+1:holeid(j+1)-1)-1);

                        end

                        fprintf(fp, '\t1\n');

                    end

                    for j = 1:length(holeid)

                        if j == length(holeid)

                            fprintf(fp, '%d %f %f %f\n', j, mean(node(plc(holeid(j)+1:end),2:4)));

                        else

                            fprintf(fp, '%d %f %f %f\n', j, mean(node(plc(holeid(j)+1:holeid(j+1)-1),2:4)));

                        end

                    end

                else

                    if faceid > 0

                        fprintf(fp, '1 0 %d\n%d', faceid, length(plc));

                    else

                        fprintf(fp, '1 0\n%d', length(plc));

                    end

                    fprintf(fp, '\t%d', plc-1);

                    fprintf(fp, '\t1\n');

                end

            end

        end

    end



    if dobbx || ~isempty(edges)

        for i = 1:bbxnum

            fprintf(fp, '%d %d 1\n', 1+loopcount(i), loopcount(i));

            fprintf(fp, '%d %d %d %d %d\n', boxelem(i,:));

            if ~isempty(edges) && loopcount(i) && ~isempty(find(loopid == i, 1))

                endid = find(loopid == i);

                for k = 1:length(endid)

                    j = endid(k);

                    subloop = loops(seg(j)+1:seg(j+1)-1);

                    fprintf(fp, '%d ', length(subloop));

                    fprintf(fp, '%d ', subloop-1);

                    fprintf(fp, '\n');

                end

                for k = 1:length(endid)

                    j = endid(k);

                    subloop = loops(seg(j)+1:seg(j+1)-1);

                    fprintf(fp, '%d %f %f %f\n', k, internalpoint(v, subloop)); %mean(v(subloop,:)));

                end

            end

        end

    end



    if size(holelist,1)

        fprintf(fp, '#hole list\n%d\n', size(holelist, 1));

        for i = 1:size(holelist, 1)

            fprintf(fp, '%d %f %f %f\n', i, holelist(i,:));

        end

    else

        fprintf(fp, '#hole list\n0\n');

    end



    if size(regionlist, 1)

        fprintf(fp, '#region list\n%d\n', size(regionlist, 1));

        for i = 1:size(regionlist, 1)

            fprintf(fp, '%d %f %f %f %d\n', i, regionlist(i,:), i);

        end

    end

    fclose(fp);



    if ~isempty(nodesize)

        if size(nodesize, 1)+size(forcebox(:), 1) == size(node, 1)

            nodesize = [nodesize; forcebox(:)];

        end

        fid = fopen(regexprep(fname, '\.poly$', '.mtr'), 'w');

        fprintf(fid, '%d 1\n', size(nodesize, 1));

        fprintf(fid, '%f\n', nodesize);

        fclose(fid);

    end

end