text:
classdef msh
    % MSH: Mesh class
    % Contains, handles, and builds properties of a mesh such as vertices,
    % an element table, bathymetry and ADCIRC style boundary types
    % Copyright (C) 2018  Keith Roberts & William Pringle
    %
    % Class constructor/read a mesh into a msh class.
    %
    % Options are specified as name/value pairs for this class.
    % NB: The file type is determined by suffix extension (e.g., 'fname.14')
    %
    % Usage:
    %   obj = msh(varargin)
    %
    % Examples:
    %   m = msh(); % returns a blank mesh object.
    %   m = msh('fname.14'); % reads in from a fort.14 file
    %   m = msh('fname','fname.14','aux',{'blah.13','otherfile.15'}); % reads in a fort.14 along with a fort.13 and fort.15
    %   m = msh('points', point_array, 'elements', triangle_table); % reads in from points and elements format.
    %
    % varargin options:
    %   i)   'fname' - The filename of the msh file.
    %   ii)  'points' - a num_points x 2 array of points
    %   iii) 'elements' - a num_elements x 3 array of triangles
    %         indexing into points array.
    %   iv)  'aux' - a cell-array with filenames of additional
    %         files that pair with the mesh
    %    v)  'nob' - 0/1 enable/disable the reading of
    %         boundary conditions (nodestrings).
    %         Default  = 0 [i.e., will read in boundary conditions]
    %
    %
    %   This program is free software: you can redistribute it and/or modify
    %   it under the terms of the GNU General Public License as published by
    %   the Free Software Foundation, either version 3 of the License, or
    %   (at your option) any later version.
    %
    %   This program is distributed in the hope that it will be useful,
    %   but WITHOUT ANY WARRANTY; without even the implied warranty of
    %   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    %   GNU General Public License for more details.
    %
    %   You should have received a copy of the GNU General Public License
    %   along with this program.  If not, see <http://www.gnu.org/licenses/>.
    properties
        title % mesh title
        p  % vertices
        t  % triangles
        b  % bathy
        bd % land boundaries
        op % open boundaries
        bx % slope of bathy in x direction
        by % slope of bathy in y direction
        f11 % A structure for the fort11 (initial density) values
        f13 % A struct of the fort13 attributes
        f15 % A struct of the fort15 inputs
        f19 % A struct for the fort19 non-periodic elevation bc
        f20 % A struct for the fort20 non-periodic flux/ele radiation bc
        f24 % A struct of the fort24 SAL values
        f2001 % A struct for the fort2001 non-periodic flux/ele sponge bc
        f5354 % A struct for the fort53001/54001 tidal ele/flux sponge bc
        offset63 % A struct for the offset.63 dynamicwaterlevelcorrection file
        proj   % Description of projected space (m_mapv1.4)
        coord  % Description of projected space (m_mapv1.4)
        mapvar % Description of projected space (m_mapv1.4)
        pfix   % fixed points that were constrained in msh
        egfix  % fixed eges that were constraind in msh
    end

    methods
        function obj = msh(varargin)

            % Check for m_map dir
            if exist('m_proj','file')~=2
                error('The program m_map was not found. Please read the user guide')
            end
            % Check for utilties dir
            if ~exist('inpoly.m','file')
                error('The utilities directory was not found. Please read the user guide')
            end
            % Check for dataset dir
            if exist('datasets','dir')~=7
                warning('We suggest you to place your files in a folder called datasets. Please read the user guide')
            end

            % just want a blank mesh object
            if nargin == 0
                obj.title = 'OceanMesh2D';
                return
            end

            fname = [];
            aux = {};
            nob = 0;
            % if only one arg. then assume filename of mesh file...
            if nargin == 1
                % Mesh file name
                fname = varargin{1};
            else
                % Otherwise, name value pairs specified.
                % Parse other varargin
                for kk = 1:2:length(varargin)
                    if strcmp(varargin{kk},'fname')
                        fname = varargin{kk+1};
                    elseif strcmp(varargin{kk},'points')
                        obj.p = varargin{kk+1};
                    elseif strcmp(varargin{kk},'elements')
                        obj.t = varargin{kk+1};
                    elseif strcmp(varargin{kk},'aux')
                        aux = varargin{kk+1};
                    elseif strcmp(varargin{kk},'nob')
                        nob = varargin{kk+1};
                    end
                end
            end

            % Return if we filled in points and or elements manually
            if ~isempty(obj.p) || ~isempty(obj.t)
                obj.title = 'Manual Input';
                return;
            end

            if isempty(fname)
                help(msh)
                error('See usage instructions above. Please specify the fname of the mesh as a name/value pair...');
            end

            if any(contains(fname,'.14')) || any(contains(fname,'.grd'))
                disp('INFO: An ADCIRC fort.14 file will be read...')
                bdflag = 1;
                if nob
                    bdflag = 0;
                end
                [t,p,b,op,bd,title] = readfort14(fname,bdflag);
                obj.p  = p; obj.t  = t; obj.b  = b;
                obj.bd = bd; obj.op = op;
                obj.title = title;
                % elseif any(contains(type,'otherformat'))
                % OTHER FORMAT READING GOES HERE.
            else
                % for now only handling fort.14 mesh type
                error('Please specify filename with suffix (e.g., fname.14)');
            end
            % loop over all extra files passed
            for f = 1 : length(aux)
                fname = aux{f};
                if any(contains(fname,'.13'))
                    disp('INFO: ADCIRC fort.13 file will be read...')
                    obj.f13 = readfort13(fname);
                end
                if any(contains(fname,'.15'))
                    disp('INFO: ADCIRC fort.15 file will be read...')
                    if isempty(obj.op) ||  isempty(obj.bd)
                        error('Boundary data required to read f15...also read in f14.')
                    end
                    obj.f15 = readfort15(fname,obj.op,obj.bd);
                end
                if any(contains(fname,'.24'))
                    if isempty(obj.p)
                        error('No vertices present to readfort24')
                    end
                    if isempty(obj.f15)
                        error(['No f15 present to readfort24.' ...
                            ' (make sure fort.15 is listed before' ...
                            ' fort.24 in aux cell array)'])
                    end
                    if obj.f15.ntif == 0
                        error('No constituents in f15 to readfort24')
                    end
                    disp('INFO: ADCIRC fort.24 file will be read...')
                    obj.f24 = readfort24( fname, obj.f15.ntif, ...
                        length(obj.p), {obj.f15.tipotag.name} );
                end
            end

        end

        % write mesh to disk
        function write(obj,fname,type,varargin)
            % Usage:
            % write(obj,fname,type,varargin)
            %
            % Examples:
            % write(obj);       % writes all available data to fort_1.xx (ADCIRC) files
            % write(obj,fname); % writes all available data to fname.xx (ADCIRC) files
            % write(obj,fname,'14');  % writes mesh data to fname.14 (ADCIRC) file
            % write(obj,fname,'gr3'); % writes mesh data to fname.gr3 (SCHISM) file
            % write(obj,fname,'ww3'); % writes mesh data to fname.ww3 (WaveWatchIII) file
            % write(obj,fname,{'13','14'}); % writes mesh data and f13 attribute data to fname.14 and fname.13 (ADCIRC) files
            % write(obj,fname,'24','netcdf'); % writes fort.24 SAL data to fname.24.nc netcdf file
            if nargin == 1
                fname = 'fort_1';
            end
            if nargin < 3
                if isempty(obj.p)
                    error('No mesh, cannot write.')
                end

                % renumber it use RCM by default
                %obj = renum(obj) ;

                if isempty(obj.b)
                    b_t = 0*obj.p(:,1);
                else
                    b_t = obj.b;
                end
                writefort14( [fname '.14'], obj.t, obj.p, b_t, ...
                    obj.op , obj.bd ,obj.title ) ;
                if ~isempty(obj.f13)
                    writefort13( obj.f13, [fname '.13'] );
                end
                if ~isempty(obj.f15)
                    writefort15( obj.f15, [fname '.15'], obj.bd );
                end
                if ~isempty(obj.f24)
                    writefort24( obj.f24, [fname '.24'], obj.p, varargin);
                end
                if ~isempty(obj.f5354)
                    writefort5354( obj.f5354, fname );
                end
                if ~isempty(obj.offset63)
                    writeoffset63( obj.offset63, [fname '.offset.63'] );
                end
            else
                if any(contains(type,'14')) || any(contains(type,'ww3')) || ...
                        any(contains(type,'gr3'))
                    if isempty(obj.p)
                        error('No mesh, cannot write.')
                    end
                    if isempty(obj.b)
                        b_t = 0*obj.p(:,1);
                    else
                        b_t = obj.b;
                    end
                    if any(contains(type,'14'))
                        writefort14( [fname '.14'] , obj.t, obj.p, b_t, ...
                            obj.op , obj.bd ,obj.title ) ;
                    end
                    if any(contains(type,'gr3'))
                        if ~isempty(obj.bd)
                            % schism only accepts ibtype 0 or 1 for land bcs
                            obj.bd.ibtype(obj.bd.ibtype == 21) = 1;
                            obj.bd.ibtype(obj.bd.ibtype == 20) = 0;
                        end
                        writefort14( [fname '.gr3'] , obj.t, obj.p, b_t, ...
                            obj.op , obj.bd ,obj.title ) ;
                    end
                    if any(contains(type,'ww3'))
                        writeww3( [fname '.ww3'] , obj.t, obj.p, b_t, ...
                            obj.op , obj.title ) ;
                    end
                end
                if any(contains(type,'11')) && ~isempty(obj.f11)
                    writefort11( obj.f11, [fname '.11'] );
                end
                if any(contains(type,'13')) && ~isempty(obj.f13)
                    writefort13( obj.f13, [fname '.13'] );
                end
                if any(contains(type,'15')) && ~isempty(obj.f15)
                    writefort15( obj.f15, [fname '.15'], obj.bd );
                end
                if any(contains(type,'19')) && ~isempty(obj.f19)
                    writefort19( obj.f19, [fname '.19'] );
                end
                if any(contains(type,'20')) && ~isempty(obj.f20)
                    writefort20( obj.f20, [fname '.20'] );
                end
                if any(contains(type,'2001')) && ~isempty(obj.f2001)
                    writefort19( obj.f2001, [fname '.2001'] );
                end
                if any(contains(type,'24')) && ~isempty(obj.f24)
                    writefort24( obj.f24, [fname '.24'], obj.p, varargin);
                end
                if any(contains(type,'5354')) && ~isempty(obj.f5354)
                    writefort5354( obj.f5354, fname );
                end
                if any(contains(type,'offset')) && ~isempty(obj.offset63)
                    writeoffset63( obj.offset63, [fname '.offset.63'] );
                end
            end
        end

        % general plot function
        function h = plot(obj,varargin)
            % h = plot(obj,varargin)
            %
            % 1) obj: msh object
            %
            % 2) varargin kwargs:
            %
            % 'type': plot type, choose from:
            %    a) 'tri'  - (default) plots the triangulation
            %    b) 'bd'   - same as tri but with nodestrings/boundary conditions plotted
            %    c) 'ob'   - outer boundary of the mesh
            %    d) 'b'    - plots the bathymetry
            %    e) 'slp'  - plots the bathymetric gradients
            %    f) 'reso' - plots the element circumradius (resolution) based on the projection
            %    g) 'resodx' - plots the gradient in 'reso'
            %    h) 'qual'   - plots the element quality
            %    i) 'sponge' - plots the sponge zone/strength coefficients
            %    j) 'transect' - plot a bathy transect through GUI
            %    k) 'xx' -     plots an arbitrary f13 attribute 'xx' by
            %                  contains search
            %
            % 'type' ADDITIONALS.
            %   Add the following words inside the type character string to implement desired behaviors:
            %    aa) 'notri': plot without the triangulation (used with 'bd' option)
            %    bb) 'earth': use with 'reso' option to plot resolution using element edgelengths on the Earth
            %    cc) 'log': use with options that use a colormap to plot the caxis in log space
            %    dd) 'mesh': use with options that use a colormap to plot colors on the element
            %                edges (a mesh look) instead of on the element faces (a surface look)
            %
            % 'proj': what available m_map projection to plot in e.g.,: 'equi', 'lamb', 'stereo'
            %    Select 'none' to plot without the m_map projection.
            %    Default is the projection of the msh object.
            %
            % 'subdomain': Plot a subdomain of the mesh bounded by the corner coordinates
            %           (a bounding box: [west east; south north])
            %
            % options to refine the look of the plot:
            %    i) 'colormap': number of colormap intervals and (optional) range:
            %                    [num_intervals] or;
            %                    [num_intervals caxis_lower caxis_upper]
            %   ii) 'fontsize': figure fontsize
            %  iii) 'backcolor': figure background RGB color (where mesh
            %                    doesn't exist), default is [1 1 1] => white
            %   iv) 'holdon'  : =1 to plot on existing figure (otherwise
            %                    will use new figure)
            %    v) 'pivot'   : value in meters for which to assume is datum when
            %                    plotting topo-bathymetry (default 0.0 m)
            %   'axis_limits' : Force the axes limits to be bounded by what
            %                   is passed in bbox.
            %   'cmap':         The name of the cmocean colormap
            %                    (each option has different default)
            %                    type 'help cmocean' to see all the colormaps
            %                    available

            fsz = 12; % default font size
            bgc = [1 1 1]; % default background color
            cmap_int = 10; % default num of colormap intervals
            holdon = 0;
            pivot = 0.0; % assume datum is 0.0 m
            proj = 1;
            axis_limits = []; % use mesh extents to determine plot extents
            cmap = 1; % default value is specified in plot method
            leg_ind = [];

            projtype = [];
            type = 'tri';
            subdomain = [];
            for kk = 1:2:length(varargin)
                if strcmp(varargin{kk},'fontsize')
                    fsz = varargin{kk+1};
                elseif strcmp(varargin{kk},'backcolor')
                    bgc = varargin{kk+1};
                elseif strcmp(varargin{kk},'colormap')
                    cmap_int = varargin{kk+1};
                elseif strcmp(varargin{kk},'holdon')
                    holdon = varargin{kk+1};
                elseif strcmp(varargin{kk}, 'pivot')
                    pivot = varargin{kk+1};
                elseif strcmp(varargin{kk}, 'proj')
                    projtype = varargin{kk+1};
                elseif strcmp(varargin{kk},'type')
                    type = varargin{kk+1};
                elseif strcmp(varargin{kk},'subdomain')
                    subdomain = varargin{kk+1};
                elseif strcmp(varargin{kk},'axis_limits')
                    axis_limits = varargin{kk+1};
                elseif strcmp(varargin{kk}, 'cmap')
                    cmap = varargin{kk+1};
                end
            end

            % kjr default behavior, just use what's in the .mat file
            if isempty(projtype)
                global MAP_PROJECTION MAP_VAR_LIST MAP_COORDS
                if ~isempty(obj.coord)
                    % kjr 2018,10,17; Set up projected space imported from msh class
                    MAP_PROJECTION = obj.proj ;
                    MAP_VAR_LIST   = obj.mapvar ;
                    MAP_COORDS     = obj.coord ;
                    del = 0;
                    projtype = MAP_PROJECTION.name;
                else
                    error(['no native projection in msh class, please specify the plotting projection: ' ...
                           'plot(m,''type'',''tri'',''proj'',''lamb''), or no projection: plot(m,''type'',''tri'',''proj'',''none'')'])
                end
            end

            if strcmp(projtype,'none')
               proj = 0;
            end

            % Handle user specified subdomain
            if ~isempty(subdomain)
                % i.e. is a bounding box
                subdomain = [subdomain(1,1) subdomain(2,1);
                    subdomain(1,1) subdomain(2,2); ...
                    subdomain(1,2) subdomain(2,2);
                    subdomain(1,2) subdomain(2,1); ...
                    subdomain(1,1) subdomain(2,1)];
                % Get a subdomain given by bou
                [obj,kept] = extract_subdomain(obj,subdomain,'nscreen',0);
                obj = map_mesh_properties(obj,'ind',kept);
            end

            % Set up projected space
            del = setProj(obj,proj,projtype,0,axis_limits) ;

            if del
                % This deletes any elements straddling the -180/180
                % boundary for plotting purposes (doesn't for stereo)
                xt = [obj.p(obj.t(:,1),1) obj.p(obj.t(:,2),1) ...
                      obj.p(obj.t(:,3),1) obj.p(obj.t(:,1),1)];
                dxt = diff(xt,[],2);
                obj.t(abs(dxt(:,1)) > 180 | abs(dxt(:,2)) > 180 | ...
                      abs(dxt(:,3)) > 180,:) = [];
            end

            logaxis = 0;
            idxl = strfind(type,'log');
            if ~isempty(idxl)
                logaxis = 1; type(idxl:idxl+2) = [];
            end
            mesh = 0;
            idxl = strfind(type,'mesh');
            if ~isempty(idxl)
                mesh = 1; type(idxl:idxl+3) = [];
            end
            earthres = 0;
            idxl = strfind(type,'earth');
            if ~isempty(idxl)
                earthres = 1; type(idxl:idxl+4) = [];
            end
            tri = 1;
            idxl = strfind(type,'notri');
            if ~isempty(idxl)
                tri = 0; type(idxl:idxl+4) = [];
            end

            % Make new figure if not holdon
            if ~holdon
                figure;
            end
            hold on

            switch type
                % parse aux options first
                case('tri')
                    if proj
                        m_triplot(obj.p(:,1),obj.p(:,2),obj.t);
                    else
                        simpplot(obj.p,obj.t);
                    end
                case('bd')
                    legend_names = {'open ocean boundary','outer no-flux boundary',...
                        'inner no-flux boundary','subgrid scale barriers'};
                    if tri
                        if proj
                            m_triplot(obj.p(:,1),obj.p(:,2),obj.t);
                        else
                            simpplot(obj.p,obj.t);
                        end
                    end
                    if ~isempty(obj.bd)
                        for nb = 1 : obj.bd.nbou
                            if obj.bd.ibtype(nb)  == 24 || obj.bd.ibtype(nb) == 94
                                if sum(leg_ind == 4) == 0
                                    leg_ind(end+1) = 4;
                                end
                                if proj
                                    % plot front facing
                                    m_plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'g-','linewi',1.2);
                                    % plot back facing
                                    h(4) = m_plot(obj.p(obj.bd.ibconn(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.ibconn(1:obj.bd.nvell(nb),nb),2),'y-','linewi',1.2);
                                else
                                    % plot front facing
                                    plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'g-','linewi',1.2);
                                    % plot back facing
                                    h(4) = plot(obj.p(obj.bd.ibconn(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.ibconn(1:obj.bd.nvell(nb),nb),2),'y-','linewi',1.2);
                                end
                            elseif obj.bd.ibtype(nb)  == 20
                                if sum(leg_ind == 2) == 0
                                    leg_ind(end+1) = 2;
                                end
                                if proj
                                    h(2) = m_plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'r-','linewi',1.2);
                                else
                                    h(2) = plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'r-','linewi',1.2);
                                end
                            else
                                if sum(leg_ind == 3) == 0
                                    leg_ind(end+1) = 3;
                                end
                                if proj
                                    h(3) = m_plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'g-','linewi',1.2);
                                else
                                    h(3) = plot(obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),1),...
                                        obj.p(obj.bd.nbvv(1:obj.bd.nvell(nb),nb),2),'g-','linewi',1.2);
                                end
                            end
                        end
                    end
                    if ~isempty(obj.op)
                        for nb = 1 : obj.op.nope
                            if sum(leg_ind == 1) == 0
                                leg_ind(end+1) = 1;
                            end
                            if proj
                                h(1) = m_plot(obj.p(obj.op.nbdv(1:obj.op.nvdll(nb),nb),1),...
                                    obj.p(obj.op.nbdv(1:obj.op.nvdll(nb),nb),2),'b-','linewi',3.2);
                            else
                                h(1) = plot(obj.p(obj.op.nbdv(1:obj.op.nvdll(nb),nb),1),...
                                    obj.p(obj.op.nbdv(1:obj.op.nvdll(nb),nb),2),'b-','linewi',1.2);
                            end
                        end
                    end
                    if isempty(obj.bd) && isempty(obj.op)
                        disp('boundaries are empty!');
                    end
                case('ob') % outer boundary of mesh
                    [~,bpt] = extdom_edges2(obj.t,obj.p);
                    if proj
                        m_plot(bpt(:,1),bpt(:,2),'r.');
                    else
                        plot(bpt(:,1),bpt(:,2),'r.');
                    end
                case('b')
                    if logaxis
                       q = log10(max(1,abs(obj.b))); % plot on log scale
                    else
                       q = obj.b;
                    end
                    if cmap == 1
                        cmap = '-topo';
                    end
                    plotter(cmap,1,'depth below datum [m]',true);
                    title('mesh topo-bathy');
                case('slp')
                    slp = hypot(obj.bx,obj.by);
                    if logaxis
                        q = log10(slp); % plot on log scale
                    else
                        q = slp;
                    end
                    if cmap == 1
                        cmap = 'thermal';
                    end
                    plotter(cmap,3,'topographic gradient',false);
                case('reso')
                    % Get bar lengths
                    if earthres
                        [bars,barlen] = GetBarLengths(obj,0);
                        % sort bar lengths in ascending order
                        [barlen,IA] = sort(barlen,'descend');
                        bars = bars(IA,:);
                        % get the minimum bar length for each node
                        [B1,IB] = unique(bars(:,1),'last');
                        [B2,IC] = unique(bars(:,2),'last');
                        d1 = NaN*obj.p(:,1); d2 = NaN*obj.p(:,1);
                        d1(B1) = barlen(IB); d2(B2) = barlen(IC);
                        z = min(d1,d2);
                        yylabel = 'minimum connected bar length [m]';
                    else
                        % get the points on the current projection
                        [X,Y]= m_ll2xy(obj.p(:,1),obj.p(:,2));
                        % get the circumcenter radius of each element
                        TR = triangulation(obj.t,X,Y);
                        [~,cr] = circumcenter(TR);
                        % Get the element connectivity
                        [vtoe,nne] = VertToEle(obj.t);
                        % Make sure null value adds zero contribution
                        cr(end+1) = 0;
                        vtoe(vtoe == 0) = length(obj.t) + 1;
                        % Sum up all element contributions to each node and
                        % divide by number of connected elements
                        z = sum(cr(vtoe))./nne;
                        % scale by earth radius
                        Re = 6378.137e3; z = Re*z;
                        yylabel = 'element circumradius [m]';
                    end
                    if logaxis
                        q = log10(z); % plot on log scale with base
                    else
                        q = z;
                    end
                    if cmap == 1
                        cmap = 'thermal';
                    end
                    plotter(cmap,0,yylabel,false);
                    title('mesh resolution');
                case('resodx')
                    TR = triangulation(obj.t,obj.p(:,1),obj.p(:,2));
                    [cc,cr] = circumcenter(TR);
                    for i = 1  : length(obj.t)
                        cl = cr(i) ;
                        for j = 1 :  3
                            z(obj.t(i,j),1) = cl;
                        end
                    end
                    [Hx,Hy] = Unstruc_Bath_Slope( obj.t,obj.p(:,1),obj.p(:,2),z);
                    HH = hypot(Hx,Hy);
                    if logaxis
                        q = log10(HH); % plot on log scale with base
                    else
                        q = HH;
                    end
                    if cmap == 1
                        cmap = 'balance';
                    end
                    plotter(cmap,3,'change in resolution',true);
                    title('Relaxation rate of topology');
                case('qual')
                    q = gettrimeshquan(obj.p, obj.t);
                    nq = zeros(length(obj.p),1) + 1.0 ;
                    for i = 1 : length(obj.t)
                        for j = 1 : 3
                            nm = obj.t(i,j);
                            nq(nm) = min(nq(nm),q.qm(i));
                        end
                    end
                    if logaxis
                        q = log10(nq); % plot on log scale with base
                    else
                        q = nq;
                    end
                    if cmap == 1
                       cmap = 'matter';
                    end
                    plotter(cmap,3,'area-length ratio',false);
                    title('Mesh quality metric');
                case('sponge')
                    ii = find(contains({obj.f13.defval.Atr(:).AttrName},'sponge'));
                    defval  = obj.f13.defval.Atr(ii).Val;
                    userval = obj.f13.userval.Atr(ii).Val;
                    values = userval(2,:);
                    if proj
                        m_fastscatter(obj.p(:,1),obj.p(:,2),defval(1)*ones(length(obj.p),1));
                        m_fastscatter(obj.p(userval(1,:),1),obj.p(userval(1,:),2),values');
                    else
                        fastscatter(obj.p(:,1),obj.p(:,2),defval(1)*ones(length(obj.p),1));
                        fastscatter(obj.p(userval(1,:),1),obj.p(userval(1,:),2),values');
                    end
                    if cmap == 1
                       cmap = 'deep';
                    end
                    colormap(cmocean(cmap));
                    colorbar;
                case('transect')
                    if proj
                        error('To plot transects, you must plot with proj=0!');
                    end
                    cmap = cmocean('ice',256);
                    subplot(2,1,1)
                    trisurf(obj.t,obj.p(:,1),obj.p(:,2),obj.b); view(2);
                    alpha 0.75
                    shading interp;
                    colormap(cmap); cb=colorbar; ylabel(cb,'m below geoid');
                    axis equal
                    h = imline;
                    pos = h.getPosition;
                    text(pos(1,1),pos(1,2),'Start','color','r');
                    text(pos(2,1),pos(2,2),'End','color','r');
                    [la,lo]=interpm(pos(:,2),pos(:,1),5/111e3);
                    plot(lo,la,'r.')
                    transect = [lo,la]; clearvars lo la
                    if ~isempty(obj.b)
                        F = scatteredInterpolant(obj.p(:,1),obj.p(:,2),obj.b);
                    else
                        error('Bathy must be on mesh to plot transects!');
                    end
                    bOnTransect = F(transect) ;
                    subplot(2,1,2);
                    plot(-bOnTransect,'linewi',2) ;
                    disp(mean(bOnTransect))
                    title('Bathymetry along transect');
                    ylabel('m below geoid');
                    xlabel('Points along transect')
                otherwise
                    disp(['Trying to plot arbitrary f13 attribute: ' type])
                    if ~isempty(obj.f13)
                        ii = find(contains({obj.f13.defval.Atr.AttrName},type));
                        jj = find(contains({obj.f13.userval.Atr.AttrName},type));
                        if isempty(ii)
                            error(['no f13 attribute of ' type ' found']);
                        elseif length(ii) > 1
                            disp({obj.f13.defval.Atr(ii).AttrName})
                            error(['more than one f13 attribute matched ' type]);
                        end
                        defval  = obj.f13.defval.Atr(ii).Val;
                        userval = obj.f13.userval.Atr(jj).Val;
                        defval = reshape(defval,1,[]);
                        q = obj.p(:,1)*0 + defval;
                        q(userval(1,:),:) = userval(2:end,:)';
                        % just take the inf norm
                        q = max(q,[],2);
                        if logaxis
                            q = abs(q);
                            q(q == 0) = min(q(q > 0));
                            if length(cmap_int) >= 3
                               rd = ceil(-log10(cmap_int(2)));
                            else
                               rd = ceil(-log10(min(q)));
                            end
                            q = log10(q);
                        else
                           if length(cmap_int) >= 3
                              rd = ceil(-log10((cmap_int(3)-cmap_int(2))/cmap_int(1)));
                           else
                              rd = ceil(-log10((max(q) - min(q))/cmap_int(1)));
                           end
                        end
                        if cmap == 1
                            cmap = lansey(cmap_int(1));
                        end
                        plotter(cmap,rd+1,'',false);
                        ax = gca;
                        ax.Title.String = obj.f13.defval.Atr(ii).AttrName;
                        ax.Title.Interpreter = 'none';
                    else
                        error('f13 structure is empty!');
                    end
            end
            ax = gca;
            ax.FontSize = fsz;
            ax.Color = bgc;
            if proj == 1
                % now add the box
                m_grid('FontSize',fsz,'bac',bgc);
            end
            if ~isempty(leg_ind)
                legend(h(leg_ind),legend_names(leg_ind),'location','best')
            end

            function plotter(cmap,round_dec,yylabel,apply_pivot)
               % applies the plot for the quantiy 'q' and specific
               % colormap/colorbar inputs
               if proj
                   if mesh
                      m_trimesh(obj.t,obj.p(:,1),obj.p(:,2),q);
                   else
                      m_trisurf(obj.t,obj.p(:,1),obj.p(:,2),q);
                   end
               else
                   if mesh
                      trimesh(obj.t,obj.p(:,1),obj.p(:,2),q);
                   else
                      trisurf(obj.t,obj.p(:,1),obj.p(:,2),q);
                      shading flat;
                   end
                   view(2);
               end
               numticks = cmap_int(1)+1;
               cb = colorbar;
               if logaxis
                   if length(cmap_int) >= 3
                      desiredTicks = round(10.^(linspace(...
                           log10(cmap_int(2)),...
                           log10(cmap_int(3)),numticks)),round_dec);
                   else
                      desiredTicks = round(10.^(linspace(min(q),...
                           max(q),numticks)),round_dec);
                   end
                   caxis([log10(min(desiredTicks)) log10(max(desiredTicks))]);
                   cb.Ticks     = log10(desiredTicks);
                   for tck = 1 : length(desiredTicks)
                      cb.TickLabels{tck} = num2str(desiredTicks(tck));
                   end
               else
                   if length(cmap_int) >= 3
                      desiredTicks = round(linspace(cmap_int(2),...
                           cmap_int(3),numticks),round_dec);
                   else
                      desiredTicks = round(linspace(min(q),...
                           max(q),numticks),round_dec);
                   end
                   caxis([min(desiredTicks) max(desiredTicks)]);
                   cb.Ticks = desiredTicks;
                   for tck = 1 : length(desiredTicks)
                      cb.TickLabels{tck} = num2str(desiredTicks(tck));
                   end
               end
               if apply_pivot
                  cmocean(cmap,cmap_int(1),'pivot',pivot);
               else
                  try
                     cmocean(cmap,cmap_int(1));
                  catch
                     colormap(cmap)
                  end
               end
               ylabel(cb,yylabel,'fontsize',fsz);
            end
        % EOF PLOT
        end

        % renumber mesh min. bw
        function obj=renum(obj)

            np=length(obj.p); nt=length(obj.t);
            % Calculate adjacency matrix of t
            S = sparse(obj.t(:,[1,1,2,2,3,3]),obj.t(:,[2,3,1,3,1,2]),1,np,np);
            W = sum(S,2);
            if any(W==0)
                error('Invalid mesh. Hanging nodes found. Retriangulate.');
            end
            % calc bw
            [i,j] = find(S);
            bw = max(i-j) + 1;
            disp(['Initial bandwidth is ',num2str(bw)]);

            % renumber with minimizing bw
            perm = symrcm(S);
            R    = S(perm,perm);
            prn  = obj.p(perm,:);
            if ~isempty(obj.b)
                obj.b    = obj.b(perm);
            end

            if ~isempty(obj.bx)
                obj.bx   = obj.bx(perm);
                obj.by   = obj.by(perm);
            end

            if ~isempty(obj.f24)
                obj.f24.Val = obj.f24.Val(:,:,perm);
            end

            obj.p    = prn;
            perm_inv(perm(1:np)) = ( 1 : np );
            ttemp = obj.t ;
            for ie = 1 : nt
                nm1 = ttemp(ie,1) ;
                nm2 = ttemp(ie,2) ;
                nm3 = ttemp(ie,3) ;
                ttemp(ie,1) = perm_inv(nm1);
                ttemp(ie,2) = perm_inv(nm2);
                ttemp(ie,3) = perm_inv(nm3);
            end
            obj.t = ttemp ;
            % compare bw
            [i,j] = find(R);
            bw = max(i-j) + 1;
            disp(['Renumbered bandwidth is ',num2str(bw)]);

            % renum the nodestrings
            if ~isempty(obj.op) && obj.op.nope > 0
                disp('Renumbering the elevation specified boundary nodestrings...');
                for ib = 1 : obj.op.nope
                    node = obj.op.nbdv(1:obj.op.nvdll(ib),ib);
                    obj.op.nbdv(1:obj.op.nvdll(ib),ib) = perm_inv(node);
                end
            end

            if ~isempty(obj.bd) && obj.bd.nbou > 0
                disp('Renumbering the flux boundary nodestrings...');
                for ib = 1 : obj.bd.nbou
                    tempcell{ib} = obj.bd.nbvv(1:obj.bd.nvell(ib),ib);
                end
                temp = cell2mat(tempcell');
                ex   = find(temp~=0) ;
                temp(ex) = perm_inv(temp(ex))';
                temp = mat2cell(temp,cellfun(@length,tempcell));
                nbvv = zeros(size(obj.bd.nbvv,1),size(obj.bd.nbvv,2));
                for ib = 1 : obj.bd.nbou
                    for iv = 1 : obj.bd.nvell(ib)
                        nbvv(iv,ib) = temp{ib}(iv,:);
                    end
                end
                obj.bd.nbvv = nbvv;

                % renumber the various components of the weir connectivity
                if isfield(obj.bd,'ibconn')
                    for ib = 1 : obj.bd.nbou
                        tempcell{ib} = obj.bd.ibconn(1:obj.bd.nvell(ib),ib);
                    end
                    temp = cell2mat(tempcell');
                    ex   = find(temp~=0) ;
                    temp(ex) = perm_inv(temp(ex))';
                    temp = mat2cell(temp,cellfun(@length,tempcell));
                    ibconn = zeros(size(obj.bd.nbvv,1),size(obj.bd.nbvv,2));
                    for ib = 1 : obj.bd.nbou
                        for iv = 1 : obj.bd.nvell(ib)
                            ibconn(iv,ib) = temp{ib}(iv,:);
                        end
                    end
                    obj.bd.ibconn = ibconn;
                end
            end

            if ~isempty(obj.f13)
                disp('Renumbering the fort.13...');
                for i = 1 : obj.f13.nAttr
                    idx = obj.f13.userval.Atr(i).Val(1,:);
                    idx = perm_inv(idx);
                    obj.f13.userval.Atr(i).Val(1,:) = idx;
                end
            end

            if ~isempty(obj.f5354)
                disp('Renumbering the fort.5354...');
                idx = perm_inv(obj.f5354.nodes);
                obj.f5354.nodes = idx;
            end
        end

        % interp bathy/slope
        function obj = interp(obj,geodata,varargin)
            % obj = interp(obj,geodata,varargin)
            % Puts bathy and slopes on the msh obj (a wrapper for GridData).
            % 'geodata' input may be a geodata class or a netCDF dem filename char.
            % 'geodata' may also be a cell array of geodata classes and dems and
            % interp will loop over all them.
            %
            % optional varargins are as follows (copied from GridData):
            %          K - vector of relevant nodes to search. This can
            %                         significantly speed up the calculation by either
            %                         only interpolating part of the mesh or
            %                         intepolating whole mesh but in segments. Function
            %                         automatically removes uncessary portions of DEM
            %                         Example to call:
            %                         K = find( obj.p(:,1) >= lon_min & ...
            %                                   obj.p(:,2) <= lon_max);
            %                         obj = interp(obj,dem,'K',K);
            %
            %       type - type is either 'depth', 'slope' or 'all'
            %                         'all' is the default (both slope and depth).
            %                         'slope' to gets the gradients of DEM
            %
            %     interp - interp is either the normal griddedInterpolant
            %                         options in MATLAB or is 'CA' (default). Note: 'CA'
            %                         applies linear griddedInterpolant when the DEM
            %                         and grid sizes are similar.
            %
            %          N - enlarge cell-averaging stencil by factor N (only
            %                         relevant for CA interpolation method).
            %                         default value N=1.
            %
            %        nan - 'fill' to fill in any NaNs everywhere
            %            - 'fillinside' to fill NaNs only in DEM extents
            %
            %   mindepth - ensure the minimum depth is bounded in the
            %              interpolated region
            %
            %   maxdepth - ensure the maximum depth is bounded in the
            %              interpolated region
            %
            %   ignoreOL - = 0 [default]: interpolate data without masking overland
            %              = 1          : Mask overland data which may help for seabed-only interpolation
            % slope_calc - = 'rms' [default]: Compute cell-averaged slope based on root-mean-square
            %              = 'abs'          : Compute cell-averaged slope based on mean of absolute value
            %     invert - = 0          : does not invert values of the dem
            %                             (i.e., keeps the sign of the topography the same as the dem)
            %              = 1 [default]: inverts the values of the dem
            %                             (underwater is positive depth)
            %   lut      - A look up table (lut). See nlcd and ccap in
            %              datasets/ for examples

            % if give cell of geodata or dems then interpolate all
            if iscell(geodata) || isstring(geodata)
                for i = 1:length(geodata)
                    if isempty(varargin)
                        obj = GridData(geodata{i},obj);
                    else
                        obj = GridData(geodata{i},obj,varargin);
                    end
                end
            else
                if isempty(varargin)
                    obj = GridData(geodata,obj);
                else
                    obj = GridData(geodata,obj,varargin);
                end
            end
            % Inverting if necessary
            invert = 1;
            tI = find(strcmp(varargin,'invert'));
            if ~isempty(tI)
                invert = varargin{tI+1};
            end
            % the output from GridData is underwater positive value so no
            % inversion means flipping back
            if ~invert
                obj.b = -obj.b;
            end

            % Checking the data...
            type = 'all';
            tI = find(strcmp(varargin,'type'));
            if ~isempty(tI)
                type = varargin{tI+1};
            end
            % Test for nans
            if strcmp(type,'all') || strcmp(type,'depth')
                % In depths
                Inan = sum(isnan(obj.b));
                if Inan > 0
                    warning('NaNs have been found in the bathymetry')
                end
            end
            if strcmp(type,'all') || strcmp(type,'slope')
                % In slope
                Inan = sum(isnan(obj.bx)) + sum(isnan(obj.by));
                if Inan > 0
                    warning('NaNs have been found in the slope')
                end
            end
            % Compute slope of b (not the values of bx/by)
            if strcmp(type,'all') || strcmp(type,'depth')
                [edge,elen] = GetBarLengths(obj,0);
                mbe = obj.b(edge);
                slope = abs(diff(mbe,[],2))./elen;
                disp(['Maximum topographic gradient is '  num2str(max(slope))])
                if max(slope) > 0.1
                    warning(['Maximum topographic gradient is larger than ' ...
                        '0.1, which might cause problems for simulation. ' ...
                        'Consider using the "lim_bathy_slope" msh class method']);
                end
            end
        end

        function [obj,qual] = clean(obj,varargin)
            % [obj,qual] = clean(obj,varargin)
            % obj - msh object
            % varargin - optional base cleaning type followed by optional
            % name-value pairs as listed below:
            %
            % base cleaning types: 'medium' (or 'default'), 'passive', 'aggressive'
            %
            % optional name-value pairs
            % 'db'  - boundary element cutoff quality (0 - 1)
            % 'ds'  - perform smoothing? (0 [no], 1 [direct implicit], 2 [hill-climbing])
            % 'con' - upper bound on connectivity (6-19)
            % 'djc' - dj_cutoff (0 - 1 [area portion] or > 1 [km^2])
            % 'sc_maxit' - max iterations for deletion of singly connected
            %         elements ( >= 0, if set to 0 operation not performed)
            % 'mqa' - allowable minimum element quality (0 - 1); setting
            %         this too value high may prevent convergence
            % 'nscreen' - print info to screen? (default = 1)
            % 'pfix' - fixed points to keep (default empty)
            % 'proj' -to project or not (default = 1)

            if ~isempty(varargin)
                if iscell(varargin{1}); varargin = varargin{1}; end
            end
            % keep for parsing to recursive function
            varargino = varargin;

            % Fixing up the mesh automatically
            disp('Beginning mesh cleaning and smoothing operations...');

            %process categorical cleaning options
            if any(strcmp(varargin,'passive'))
                disp('Employing passive option')
                opt.db = 0.1; opt.ds = 0; opt.con = 0; opt.djc = 0;
                opt.sc_maxit = 0; opt.mqa = 1e-4; opt.renum = 0;
                varargin(strcmp(varargin,'passive')) = [];
            elseif any(strcmp(varargin,'aggressive'))
                disp('Employing aggressive option')
                opt.db = 0.5; opt.ds = 2; opt.con = 9; opt.djc = 0.25;
                opt.sc_maxit = inf; opt.mqa = 0.5; opt.renum = 1;
                varargin(strcmp(varargin,'aggressive')) = [];
            else
                disp('Employing default (medium) option or user-specified opts')
                opt.db = 0.25; opt.ds = 2; opt.con = 9; opt.djc = 0.1;
                opt.sc_maxit = 0; opt.mqa = 0.25; opt.renum = 1;
                varargin(strcmp(varargin,'default')) = [];
                varargin(strcmp(varargin,'medium')) = [];
            end
            % set defaults
            opt.nscreen = 1; opt.projL = 1; pfixV = [];
            % process user-defined individual cleaning options
            optstring = {'nscreen','pfix','proj','con','djc','db','ds',...
                'sc_maxit','mqa','renum'};
            for ii = 1:2:length(varargin)
                jj = find(strcmp(varargin{ii},optstring));
                if isempty(jj)
                    error(['Unrecognized input option: ' varargin{ii}])
                elseif jj == 1
                    opt.nscreen = varargin{ii + 1};
                elseif jj == 2
                    pfixV = varargin{ii + 1};
                elseif jj == 3
                    opt.projL = varargin{ii + 1};
                elseif jj == 4
                    opt.con = varargin{ii + 1};
                elseif jj == 5
                    opt.djc  = varargin{ii + 1};
                elseif jj == 6
                    opt.db = varargin{ii + 1};
                elseif jj == 7
                    opt.ds  = varargin{ii + 1};
                elseif jj == 8
                    opt.sc_maxit  = varargin{ii + 1};
                elseif jj == 9
                    opt.mqa  = varargin{ii + 1};
                elseif jj == 10
                    obj.renum = varargin{ii + 1};
                end
            end

            % display options
            disp('INFO: The following cleaning options have been enabled..')
            disp(opt)
            disp(['length of pfix = ' num2str(length(pfixV))])

            if opt.projL
                global MAP_PROJECTION MAP_VAR_LIST MAP_COORDS
                if ~isempty(obj.coord)
                    MAP_PROJECTION = obj.proj ;
                    MAP_VAR_LIST   = obj.mapvar ;
                    MAP_COORDS     = obj.coord ;
                end
                % transform to projected coordinates
                [obj.p(:,1),obj.p(:,2)] =  m_ll2xy(obj.p(:,1),obj.p(:,2));
                if ~isempty(pfixV)
                    [pfixV(:,1),pfixV(:,2)] = m_ll2xy(pfixV(:,1),pfixV(:,2));
                end
            end

            % "fix" mesh and carry
            obj = fixmeshandcarry(obj);

            LT = size(obj.t,1);

            if opt.db
                while 1
                    % Begin by just deleting poor mesh boundary elements
                    tq = gettrimeshquan(obj.p,obj.t);
                    % Get the elements that have a boundary bar
                    bdbars = extdom_edges2(obj.t,obj.p);
                    bdnodes = unique(bdbars(:));
                    vtoe = VertToEle(obj.t);
                    bele = unique(vtoe(:,bdnodes)); bele(bele == 0) = [];
                    tqbou = tq.qm(bele);
                    % Delete those boundary elements with quality < opt.db
                    if min(tqbou) >= opt.db; break; end
                    obj.t(bele(tqbou < opt.db),:) = [];
                    obj = fixmeshandcarry(obj);
                end
                if opt.nscreen
                    disp(['Deleted ' num2str(LT-size(obj.t,1)) ...
                        ' bad boundary elements'])
                end
                % kjr, collapse small triangles together
                [obj.p,obj.t] = ...
                    collapse_thin_triangles(obj.p,obj.t,opt.db);
            end

            % Make mesh traversable
            obj = Make_Mesh_Boundaries_Traversable(obj,opt.djc,opt.nscreen);

            % Delete elements with single edge connectivity
            obj = Fix_single_connec_edge_elements(obj,opt.sc_maxit,opt.nscreen);

            % Renumber the mesh here
            if opt.renum
                obj = renum(obj);
            end

            % Reduce the mesh connectivity to maximum of con-1
            % May not always work without error
            if opt.con > 6
                try
                    obj = bound_con_int(obj,opt.con);
                catch
                    warning('Could not reduce connectivity mesh');
                end
            end

            % Now do the smoothing if required
            if opt.ds
                if opt.ds == 2
                    % Perform the hill-climbing smoothing
                    [obj.p,~,obj.t,~] = smooth2(obj.p,[],obj.t);
                else
                    % Perform the direct smoothing
                    [obj.p,obj.t] = direct_smoother_lur(obj.p,obj.t,...
                        pfixV,opt.nscreen);
                end
            end

            % Checking and displaying element quality
            tq = gettrimeshquan( obj.p, obj.t);
            mq_m = mean(tq.qm);
            mq_l = min(tq.qm);
            mq_s = std(tq.qm);
            mq_l3sig = mq_m - 3*mq_s;
            qual = [mq_m,mq_l3sig,mq_l];
            LTn = size(obj.t,1);

            if mq_l < opt.mqa && LT ~= LTn
                % Need to clean it again
                disp('Poor or overlapping elements, cleaning again')
                disp(['(Min Qual = ' num2str(mq_l) ')'])
                % repeat without projecting (already projected)
                ii = find(strcmp(varargino,'proj'), 1);
                if ~isempty(ii)
                    varargino{ii+1} = 0;
                else
                    varargino{end+1} = 'proj';
                    varargino{end+1} = 0;
                end
                ii = find(strcmp(varargino,'pfix'), 1);
                if ~isempty(ii)
                    varargino{ii+1} = pfixV;
                end
                obj = clean(obj,varargino(:));
            elseif opt.nscreen
                disp(['number of nodes is ' num2str(length(obj.p))])
                disp(['mean quality is ' num2str(mq_m)])
                disp(['min quality is ' num2str(mq_l)])
            end

            % Do the transformation back
            if opt.projL
                [obj.p(:,1),obj.p(:,2)] = m_xy2ll(obj.p(:,1),obj.p(:,2));
            end
        end

        function obj = lim_bathy_slope(obj,dfdx,overland)
            %obj = lim_bathy_slope(obj,dfdx,overland)
            % overland = 0; limits both bathy and topography
            % overland = 1; limits only topography
            % overland = -1; limits only bathy
            if nargin < 3
                overland  = 0;
            end
            if overland == 0
                % Call bathy then topo
                obj = lim_bathy_slope(obj,dfdx,-1);
                obj = lim_bathy_slope(obj,dfdx,+1);
                return
            end

            % Limit to topo or bathymetric slope to dfdx on the edges
            imax = 100;
            [edge,elen] = GetBarLengths(obj,0);
            bt = obj.b;
            if overland == -1
                I = bt < 0;
                word = 'bathymetric';
            elseif overland == 1
                I = bt > 0;
                word = 'topographic';
            end
            bt(I) = 0;
            bt(~I) = -overland*bt(~I);
            [bnew,flag] = limgrad(edge,elen,bt,dfdx,imax);
            if flag
                obj.b(~I) = -overland*bnew(~I);
                disp(['Successfully limited ' word ' slope to ' ...
                    num2str(dfdx) ' in limgrad function'])
            else
                warning(['Could not limit ' word ' slope to  ' ...
                    num2str(dfdx) ' in limgrad function'])
            end
        end

        % re-direct makens to make_bc
        function obj = makens(obj,type,varargin)
            % 'makens' is deprecated. Please use 'make_bc'
            obj = make_bc(obj,type,varargin);
        end

        % make_bc: make boundary conditions
        function obj = make_bc(obj,type,varargin)
            % obj = make_bc(obj,type,varargin)
            %
            % Applies boundary conditions to the mesh.
            % Uses the ADCIRC formatting and 'ibtype' integers
            % that refer to the boundary condition type.
            %
            % obj: msh class obj
            % type: 'auto', 'outer', 'inner', 'delete', or 'weirs'
            %
            % ---------
            % 'auto' - automatically applies elevation and no-flux bcs to mesh based on geodata class
            %     NB: Use 'auto_outer' option to only apply bcs to the outermost
            %     polygon and ignore the islands
            % varargins:
            % varargin{1}: geodata class
            %     NB: User may supply an empty varargin{1} if you have interpolated depths
            %     to your mesh in which case the 'depth' based classification will be enforced
            % varargin{2} (optional): method of classification:
            %    - 'distance': classifies as ocean based on distance to shoreline
            %    - 'depth': classifies as ocean based on depth
            %    - 'both' [default]: must satisfy both depth and distance criteria
            % varargin{3} (optional):
            %    - if varargin{2} is 'distance' or 'both': the distance in geographic degrees
            %      from shoreline beyond which edge is classifed as ocean (default is 10*gdat.gridspace)
            %    - if varargin{2} is 'depth': the depth below which a boundary is
            %      classifed as ocean (default is 10 m)
            % varargin{4} (optional):
            %    - if varargin{2} is 'both': the depth below which a boundary is
            %      classifed as ocean (default is 10 m)
            %    - if varargin{2} is not 'both': the minimum number of
            %      vertices for a boundary to be classifed as ocean (default is 10)
            % varargin{5} (optional):
            %    - if varargin{2} is 'both': the minimum number of
            %      vertices for a boundary to be classifed as ocean (default is 10)
            %
            % ---------
            % 'outer' - applies user-defined bc to a segment of the outer mesh polygon
            % varargins:
            % varargin{1}: direction (0 = anti-clockwise, 1 = clockwise)
            % varargin{2} (optional): vertex # to start at
            % varargin{3} (optional): vertex # to end at
            % varargin{4} (optional): flux (1) or elevation (2) nodestring
            % varargin{5} (optional): if flux, no-flux (20) or river (22) flux nodestring
            %
            % ---------
            % 'inner' - applies no-flux bcs to all inner mesh polygons (i.e., islands)
            % varargins:
            % varargin{1} (optional): ibtype to set (default = 21)
            %
            % ---------
            % 'weirs' - applies weir bcs to all weirs passed in your gdat.
            % varargins:
            % varargin{1}: geodata class that had crestlines passed.
            %
            % ---------
            % 'delete' - deletes a user-clicked land/mainland boundary condition from a msh.
            % varargins:
            % index of land/mainland boundary to delete

            if nargin < 2
                error('Needs type: one of "auto", "outer", "inner", "delete", or "weirs"')
            end
            if iscell(varargin{1})
                varargin = varargin{1};
            end
            L = 1e3;
            switch type
                case{'auto','auto_outer'}
                    % automatically applies elevation and no-flux bcs to mesh based on geodata class
                    outer_only = false;
                    if contains(type,'outer'); outer_only = true; end
                    if isempty(varargin)
                        error('must supply a geodata class for "auto" as third input')
                    end
                    gdat = varargin{1};
                    if isempty(gdat)
                        disp(['gdat is empty: enforcing the ' ...
                            'depth-based "auto" option.'])
                        classifier = 'depth';
                    else
                        if ~isa(gdat,'geodata')
                            error('third input must be a geodata class for "auto"')
                        end
                        dist_lim = 10*gdat.gridspace;
                        classifier = 'both';
                    end
                    depth_lim = -10;
                    cut_lim = 10;
                    if length(varargin) > 1 && ~isempty(varargin{2})
                        classifier = varargin{2};
                    end
                    switch classifier
                        case{'distance'}
                            if length(varargin) > 2 && ~isempty(varargin{3})
                                dist_lim = varargin{3};
                            end
                            if length(varargin) > 3 && ~isempty(varargin{4})
                                cut_lim = varargin{4};
                            end
                        case('depth')
                            if (isempty(obj.b) || sum(obj.b) == 0) && ...
                                    (isempty(gdat) || isempty(gdat.Fb))
                                if isempty(obj.b) || sum(obj.b) == 0
                                    warning('No depths on the mesh')
                                end
                                if ~isempty(gdat) && isempty(gdat.Fb)
                                    warning('No DEM info in gdat')
                                end
                                error('Cannot use "depth" classification criteria for above reasons')
                            end
                            if length(varargin) > 2 && ~isempty(varargin{3})
                                depth_lim = -varargin{3};
                            end
                            if length(varargin) > 3 && ~isempty(varargin{4})
                                cut_lim = varargin{4};
                            end
                        case('both')
                            if (isempty(obj.b) || sum(obj.b) == 0) && ...
                                    (isempty(gdat) || isempty(gdat.Fb))
                                if isempty(obj.b) || sum(obj.b) == 0
                                    warning('No depths on the mesh')
                                end
                                if ~isempty(gdat) && isempty(gdat.Fb)
                                    warning('No DEM info in gdat')
                                end
                                error('Cannot use "both" classification criteria for above reasons')
                            end
                            if length(varargin) > 2 && ~isempty(varargin{3})
                                dist_lim = varargin{3};
                            end
                            if length(varargin) > 3 && ~isempty(varargin{4})
                                depth_lim = -varargin{4};
                            end
                            if length(varargin) > 4 && ~isempty(varargin{5})
                                cut_lim = varargin{4};
                            end
                    end

                    % Check for global mesh
                    Le = find(obj.p(:,1) < -179, 1);
                    Ri = find(obj.p(:,1) > 179, 1);
                    if ~isempty(Le) && ~isempty(Ri)
                        error('Detected global mesh, cannot apply "auto" makens. Try "inner" option')
                    end

                    % Get the boundary edges and mid-points
                    etbv  = extdom_edges2(obj.t,obj.p);
                    x = obj.p(:,1); y = obj.p(:,2);
                    x_mid = mean(x(etbv),2);
                    y_mid = mean(y(etbv),2);
                    eb_mid = [x_mid, y_mid];
                    clear x y x_mid y_mid

                    % classify each boundary edge
                    % eb_class is 1 if it is classed as ocean
                    switch classifier
                        case{'both','distance'}
                            % process gdat info
                            land = [];
                            if ~isempty(gdat.mainland)
                                land = gdat.mainland;
                                land(isnan(land(:,1)),:) = [];
                            end
                            if ~isempty(gdat.inner)
                                inner = gdat.inner;
                                inner(isnan(inner(:,1)),:) = [];
                                land = [land; inner];
                            end
                            if ~isempty(land)
                               [~,ldst] = ourKNNsearch(land',eb_mid',1);
                            else
                               % set distance to be larger than dist_lim
                               % everywhere when no land exists
                               ldst = eb_mid(:,1)*0 + 2*dist_lim
                            end
                            eb_class = ldst > dist_lim;
                            if strcmp(classifier,'both')
                                % ii) based on depth
                                if ~isempty(obj.b) && sum(abs(obj.b)) > 0
                                    eb_depth = -mean(obj.b(etbv),2);
                                elseif ~isempty(gdat)
                                    eb_depth = gdat.Fb(eb_mid);
                                end
                                eb_class = eb_class & eb_depth < depth_lim;
                            end
                        case('depth')
                            % ii) based on depth
                            if ~isempty(obj.b) && sum(abs(obj.b)) > 0
                                eb_depth = -mean(obj.b(etbv),2);
                            elseif ~isempty(gdat)
                                eb_depth = gdat.Fb(eb_mid);
                            end
                            eb_class = eb_depth < depth_lim;
                    end

                    [polys,poly_idxs] = extdom_polygon(etbv,obj.p,1);

                    % classify each boundary polygon.
                    nope = 0; neta = 0; nbou  = 0; nvel  = 0;
                    npolys = length(polys);

                    for i = 1:npolys
                        % Get the edge numbers for this polygon
                        idv = poly_idxs{i};
                        poly_ed = [idv(1:end-1) idv(2:end)];
                        eb_class_t = 0*poly_ed(:,1);
                        % make sure that the order of polygon and
                        % the order of the edges in etbv are the same
                        [~,ed_id1,poly_id1] = intersect(etbv,poly_ed,'rows','stable');
                        eb_class_t1 = eb_class(ed_id1);
                        eb_class_t(poly_id1) = eb_class_t1;
                        [~,ed_id2,poly_id2] = intersect(fliplr(etbv),poly_ed,'rows','stable');
                        eb_class_t2 = eb_class(ed_id2);
                        eb_class_t(poly_id2) = eb_class_t2;

                        % check if part of polygon is an ocean
                        eb_sum = sum(eb_class_t);
                        if eb_sum > 0
                            % % Consists of both ocean and mainland

                            % If a boundary segment is composed of both
                            % ocean and mainland, then the whole segment is
                            % 'cut up' into segments. Special care is
                            % taken to ensure the ocean
                            % type boundary starts following then by mainland
                            % etc.
                            Cuts  = find(diff(eb_class_t) ~= 0);

                            % Do not include open boundary that is
                            % smaller than cutlim vertices across
                            rm = false(length(Cuts),1);
                            if eb_class_t(1)
                                st = 2;
                            else
                                st = 1;
                            end
                            for ii = st:2:length(Cuts)
                                if ii == length(Cuts)
                                    if length(idv) - Cuts(ii) + ...
                                            Cuts(1) - 1  < cut_lim
                                        rm([1 end]) = 1;
                                    end
                                else
                                    if Cuts(ii+1) - Cuts(ii) < cut_lim
                                        rm(ii:ii+1) = 1;
                                    end
                                end
                            end
                            Cuts(rm) = [];

                            ns = 1;
                            for ii = 1:length(Cuts)+1
                                if ii > length(Cuts)
                                    idv_t = [idv(ns:end); idv(1)];
                                else
                                    ne = Cuts(ii);
                                    idv_t = idv(ns:ne);
                                    ns = ne;
                                end
                                if mod(ii,2) == eb_class_t(1)
                                    % make this segment mainland
                                    nope = nope + 1;
                                    nvdll(nope) = length(idv_t);
                                    neta = neta + nvdll(nope);
                                    ibtypee(nope) = 0;
                                    nbdv(1:nvdll(nope),nope) = idv_t';
                                else
                                    % make this segment ocean
                                    nbou = nbou + 1;
                                    nvell(nbou) = length(idv_t);
                                    nvel = nvel + nvell(nbou);
                                    ibtype(nbou) = 20;
                                    nbvv(1:nvell(nbou),nbou) = idv_t';
                                end
                            end
                            if outer_only
                                break;
                            end
                        else
                            % % polygon is an island
                            nbou = nbou + 1;
                            nvell(nbou) = length(idv);
                            nvel = nvel + nvell(nbou);
                            nbvv(1:nvell(nbou),nbou) = idv';
                            ibtype(nbou) = 21;
                        end
                    end

                    % enter our results in the msh op and bd fields
                    if nope > 0
                        % ocean boundary
                        obj.op.nope = nope ;
                        obj.op.neta = neta ;
                        obj.op.nvdll = nvdll ;
                        obj.op.ibtype = ibtypee ;
                        obj.op.nbdv = nbdv;
                    end

                    if nbou > 0
                        % land boundary
                        obj.bd.nbou = nbou ;
                        obj.bd.nvel = nvel ;
                        obj.bd.nvell = nvell ;
                        obj.bd.ibtype = ibtype ;
                        obj.bd.nbvv = nbvv ;
                    end

                case('auto_old')
                    % % keeping the old auto for regression
                    if isempty(varargin)
                        error('third input must be a geodata class for auto makens')
                    end
                    gdat = varargin{1};
                    if ~isa(gdat,'geodata')
                        error('third input must be a geodata class for auto makens')
                    end
                    cutlim = 10; depthlim = 10;
                    if length(varargin) > 1 && ~isempty(varargin{2})
                        cutlim = varargin{2};
                    end
                    if length(varargin) > 2 && ~isempty(varargin{3})
                        depthlim = varargin{3};
                    end
                    % Check for global mesh
                    Le = find(obj.p(:,1) < -179, 1);
                    Ri = find(obj.p(:,1) > 179, 1);
                    if ~isempty(Le) && ~isempty(Ri)
                        error('Detected global mesh, cannot apply "auto" makens. Try "inner" option')
                    end

                    % Get the boundaries
                    [etbv,~]  = extdom_edges2(obj.t,obj.p);
                    [~,poly_idx] = extdom_polygon(etbv,obj.p,1);

                    outerbox = gdat.outer(1:find(isnan(gdat.outer(:,1)),1,'first'),:);
                    if ~isempty(gdat.mainland)
                        mainland = gdat.mainland;
                        mainland(isnan(mainland(:,1)),:) = [];
                    end
                    if ~isempty(gdat.inner)
                        inner = gdat.inner;
                        inner(isnan(inner(:,1)),:) = [];
                    end

                    % Get geodata outer and mainland polygons
                    nope = 0; neta = 0; nbou  = 0; nvel  = 0;
                    island_check = true; mainland_been = false;

                    % loop through all the polygons
                    for poly_count = 1 : length(poly_idx)
                        idv = poly_idx{poly_count};
                        %
                        if ~mainland_been
                            [~,odst] = ourKNNsearch(outerbox(1:end-1,:)',obj.p(idv,:)',1);
                            if ~isempty(gdat.mainland)
                                [~,mdst] = ourKNNsearch(mainland',obj.p(idv,:)',1);
                            else
                                mdst = 1e4;
                            end
                        end
                        if ~isempty(gdat.inner)
                            if island_check
                                [~,idst] = ourKNNsearch(inner',obj.p(idv,:)',1);
                                if min(odst) < min(idst) || ...
                                        min(mdst) < min(idst)
                                    island_check = false;
                                end
                            end
                            if island_check || mainland_been
                                % must be an island
                                nbou = nbou + 1;
                                nvell(nbou) = length(idv);
                                nvel = nvel + nvell(nbou);
                                nbvv(1:nvell(nbou),nbou) = idv';
                                ibtype(nbou) = 21;
                                continue
                            end
                        end
                        mainland_been = true;
                        if ~isempty(gdat.mainland)
                            % set the bathy values
                            if ~isempty(gdat.Fb)
                                zvalue = gdat.Fb(obj.p(idv,:));
                            else
                                % Dummy all underwater
                                zvalue = 0*obj.p(idv,1) - 1e4;
                            end

                            % find the boundaries that are mainland
                            main = mdst < odst | zvalue > -depthlim;

                            % indices of switch
                            Cuts  = find(diff(main) ~= 0);

                            % Do not include open boundary that is
                            % smaller than cutlim vertices across
                            rm = false(length(Cuts),1);
                            if main(1); st = 1; else; st = 2; end
                            for ii = st:2:length(Cuts)
                                if ii == length(Cuts)
                                    if length(main) - Cuts(ii) + ...
                                            Cuts(1) - 1  < cutlim
                                        rm([1 end]) = 1;
                                    end
                                else
                                    if Cuts(ii+1) - Cuts(ii) < cutlim
                                        rm(ii:ii+1) = 1;
                                    end
                                end
                            end
                            Cuts(rm) = [];

                            if isempty(Cuts)
                                if sum(main)/length(main) > 0.5
                                    % get mainland
                                    nbou = nbou + 1;
                                    nvell(nbou) = length(idv);
                                    nvel = nvel + nvell(nbou);
                                    ibtype(nbou) = 20;
                                    nbvv(1:nvell(nbou),nbou) = idv';
                                else
                                    % get ocean
                                    nope = nope + 1;
                                    nvdll(nope) = length(idv);
                                    neta = neta + nvdll(nope);
                                    ibtypee(nope) = 0;
                                    nbdv(1:nvdll(nope),nope) = idv';
                                end
                            else
                                % loop through each cut
                                for loop = 1:length(Cuts)
                                    if loop < length(Cuts)
                                        idv_temp = idv(Cuts(loop):Cuts(loop+1));
                                    else
                                        % need to loop back to start
                                        idv_temp = [idv(Cuts(loop):end); idv(1:Cuts(1))];
                                    end
                                    % Break up idv_temp into L chunks
                                    N = ceil(length(idv_temp)/L);
                                    LE = ceil(length(idv_temp)/N);
                                    ns = 1;
                                    for nn = 1:N
                                        ne = min(ns + LE - 1,length(idv_temp));
                                        idv_t = idv_temp(ns:ne);
                                        if ~main(Cuts(loop)+1)
                                            % Get ocean
                                            nope = nope + 1;
                                            nvdll(nope) = length(idv_t);
                                            neta = neta + nvdll(nope);
                                            ibtypee(nope) = 0;
                                            nbdv(1:nvdll(nope),nope) = idv_t;
                                        else
                                            % Get mainland
                                            nbou = nbou + 1;
                                            nvell(nbou) = length(idv_t);
                                            nvel = nvel + nvell(nbou);
                                            ibtype(nbou) = 20;
                                            nbvv(1:nvell(nbou),nbou) = idv_t;
                                        end
                                        ns = ne + 1;
                                    end
                                end
                            end
                        else
                            % must be ocean
                            nope = nope + 1;
                            nvdll(nope) = length(idv);
                            neta = neta + nvdll(nope);
                            ibtypee(nope) = 0;
                            nbdv(1:nvdll(nope),nope) = idv';
                        end
                    end

                    if nope > 0
                        % ocean boundary
                        obj.op.nope = nope ;
                        obj.op.neta = neta ;
                        obj.op.nvdll = nvdll ;
                        obj.op.ibtype = ibtypee ;
                        obj.op.nbdv = nbdv;
                    end

                    if nbou > 0
                        % land boundary
                        obj.bd.nbou = nbou ;
                        obj.bd.nvel = nvel ;
                        obj.bd.nvell = nvell ;
                        obj.bd.ibtype = ibtype ;
                        obj.bd.nbvv = nbvv ;
                    end

                case{'inner','islands'}

                    nbou = 0;
                    nvel = 0;
                    ibt = 21;
                    if ~isempty(varargin)
                        ibt = varargin{1};
                    end
                    disp(['setting ibtype to ' num2str(ibt)])

                    [etbv,~]  = extdom_edges2(obj.t,obj.p);
                    [poly,poly_idx,max_ind] = extdom_polygon(etbv,obj.p,1);

                    % the largest polygon will be a combination of ocean and mainland
                    % boundaries. Deal with this first, then remove it from the polygon
                    poly(max_ind) = [];
                    poly_idx(max_ind) = [];

                    % loop through the remaining polygons
                    nvell = zeros(1,length(poly)); ibtype = nvell + ibt;
                    nbvv  = zeros(max(cellfun('length',poly_idx)),length(poly));
                    for nbou = 1 : length(poly)
                        vso = poly{nbou};
                        idv = poly_idx{nbou};
                        % islands
                        nvell(nbou) = length(vso);
                        nvel = nvel + nvell(nbou);
                        nbvv(1:nvell(nbou),nbou) = int32(idv');
                    end
                    nbvv = int32(nbvv);

                    % ocean boundary
                    if isempty(obj.op)
                        obj.op.nope = 0 ;
                        obj.op.neta = 0 ;
                        obj.op.nvdll = 0 ;
                        obj.op.ibtype = 0 ;
                        obj.op.nbdv = 0;
                    end

                    % land boundary
                    if nbou == 0
                        disp('No islands found!')
                    else
                        if isempty(obj.bd)
                            obj.bd.nbou = nbou ;
                            obj.bd.nvel = nvel ;
                            obj.bd.nvell = nvell ;
                            obj.bd.ibtype = ibtype ;
                            obj.bd.nbvv = nbvv ;
                        else
                            obj.bd.nbou = obj.bd.nbou + nbou ;
                            obj.bd.nvel = obj.bd.nvel + nvel ;
                            maxold = max(obj.bd.nvell);
                            maxnew = max(nvell);
                            if maxold < maxnew
                                obj.bd.nbvv(end+1:end+maxnew-maxold,:) = 0;
                            elseif maxold > maxnew
                                nbvv(end+1:end+maxold-maxnew,:) = 0;
                            end
                            obj.bd.nvell = [obj.bd.nvell nvell];
                            obj.bd.ibtype = [obj.bd.ibtype ibtype];
                            obj.bd.nbvv = [obj.bd.nbvv nbvv];
                        end
                    end

                case('outer')
                    if isempty(varargin)
                        error('must specify direction of boundary in third entry')
                    end
                    dir = varargin{1};

                    [bnde,bpts] = extdom_edges2(obj.t,obj.p);

                    if length(varargin) < 3
                        % use this to figure out the vstart and vend
                        figure, plot(bpts(:,1),bpts(:,2),'k.');
                        %hold on; fastscatter(obj.p(:,1),obj.p(:,2),obj.b) ;
                        caxis([-10 10]) ; axis equal ;
                        title('use data cursor to identify vstart and vend');
                        dcm_obj = datacursormode(gcf);
                        set(dcm_obj,'UpdateFcn',{@myupdatefcn2,bpts})

                        % Use data cursor to get the values of the boundary nodes.
                        vstart=input('Enter the value for vstart : ');
                        vend=input('Enter the value for vend : ');

                        bndidx = unique(bnde(:));
                        vstart = bndidx(vstart);
                        vend   = bndidx(vend);
                    else
                        vstart = varargin{2}; vend = varargin{3};
                        if length(varargin) >= 4
                            type = varargin{4};
                            if length(varargin) >= 5
                                type2 = varargin{5};
                            else
                                type2 = type;
                            end
                            [~,~,obj.op,obj.bd] = extract_boundary(vstart,vend,bnde,obj.p,...
                                dir,obj.op,obj.bd,type,type2); %<--updates op and bd.
                            return;
                        end
                    end
                    [~,~,obj.op,obj.bd] = extract_boundary(vstart,vend,bnde,obj.p,...
                        dir,obj.op,obj.bd); %<--updates op and bd.

                case('delete')

                    temp = obj.bd.nbvv;
                    bounodes=obj.bd.nbvv ;
                    idx=sum(bounodes~=0);
                    bounodes=bounodes(:) ;
                    bounodes(bounodes==0)=[] ;
                    boupts = obj.p(bounodes,:) ;
                    idx2=[0,cumsum(idx)]'+1;
                    k = 0 ;
                    for i = 1 : length(idx2)-1
                        k = k + 1 ;
                        bounodes(idx2(i):idx2(i+1)-1,2) = k ;
                    end

                    if isempty(varargin)
                        % have the user select the nodestring '
                        plot(obj,'type','bd','proj','none') ;

                        dcm_obj = datacursormode(gcf);
                        title('use data cursor to select nodestring to be deleted');
                        pause
                        c_info = getCursorInfo(dcm_obj);
                        [tmp(:,1),tmp(:,2)]=m_ll2xy(boupts(:,1),boupts(:,2));
                        idx3 = ourKNNsearch(boupts',c_info.Position',1)  ;
                        del = bounodes(idx3,2) ;  %<- get the nodestring index
                        pltid = temp(:,del) ; pltid(pltid==0)=[] ;
                        hold on; m_plot(obj.p(pltid,1),obj.p(pltid,2),'r-','linewi',2) ;
                    else
                        del = varargin{1};
                    end
                    disp(['Deleting boundary with index ',num2str(del)]) ;

                    obj.bd.nbvv(:,del)=[];
                    if isfield(obj.bd,'ibconn')
                        obj.bd.ibconn(:,del)=[];
                        obj.bd.barinht(:,del)=[];
                        obj.bd.barincfsb(:,del)=[];
                        obj.bd.barincfsp(:,del)=[];
                    end
                    num_delnodes = idx(del) ;
                    obj.bd.nbou = obj.bd.nbou - 1 ;
                    obj.bd.nvell(del)=[] ;
                    obj.bd.ibtype(del)=[] ;
                    obj.bd.nvel = obj.bd.nvel - num_delnodes ;

                case('weirs')
                    if isempty(varargin)
                        error('Third input must be a geodata class obj')
                    end
                    gdat = varargin{1};
                    if ~isa(gdat,'geodata')
                        error('The third input must be a geodata class object you used create the mesh with.')
                    end
                    ar = 0; hts = 0; count = 0;
                    if length(varargin) > 1 && ~isempty(varargin{2})
                        ar = varargin{2};
                    end
                    if length(varargin) > 2 && ~isempty(varargin{3})
                        hts = varargin{3};
                    end

                    % identifying and adding internal weir type boundaries (ibtype=24)
                    for ii = 1 : length(gdat.ibconn_pts) % for each weir
                        [front_nn, d1] = ourKNNsearch(obj.p',gdat.ibconn_pts{ii}(:,1:2)',1);
                        [back_nn,  d2] = ourKNNsearch(obj.p',gdat.ibconn_pts{ii}(:,3:4)',1);
                        rm = d1 > 1e-9 & d2 > 1e-9;
                        front_nn(rm) = [] ; back_nn(rm) = [] ;
                        nn = [front_nn,back_nn] ;
                        for iii = 1 : length(nn)
                            rm2(iii,1)=length(unique(nn(iii,:)))~=2 ;
                        end
                        front_nn(rm2) = [] ; back_nn(rm2) = [] ;
                        clearvars rm2 ;
                        %                         % visualize node pairs
                        %                         plot(obj,'tri',0) ;
                        %                         hold on; plot(obj.p(front_nn,1),obj.p(front_nn,2),'r.') ;
                        %                         hold on; plot(obj.p(back_nn,1),obj.p(back_nn,2),'gs') ;

                        % add to the boundary struct
                        if  ~isempty(obj.bd)
                            % unpack current boundaries
                            nbou   = obj.bd.nbou;
                            nvel   = obj.bd.nvel;
                            nvell  = obj.bd.nvell;
                            nbvv   = obj.bd.nbvv;
                            ibtype = obj.bd.ibtype;

                            % append on the weir
                            nbou = nbou + 1;
                            nvell(nbou) = length(front_nn) ; % only list front facing nodes in nbvv for barriers
                            nvel = nvel + nvell(nbou);
                            nbvv(1:nvell(nbou),nbou) = front_nn;
                            ibtype(nbou) = 24;

                            % repackage it
                            obj.bd.nbou   = nbou ;
                            obj.bd.nvel   = nvel ;
                            obj.bd.nvell  = nvell ;
                            obj.bd.ibtype = ibtype ;
                            obj.bd.nbvv   = nbvv ;
                        else
                            % create a new boundary struct
                            % initialize arrays
                            nbou  = 0 ;
                            nvel  = 0 ;
                            nvell = [] ;
                            ibtype= [] ;
                            nbvv  = [] ;

                            % append on the weir
                            nbou = nbou + 1;
                            nvell(nbou) = length(front_nn) ; % only list front facing nodes in nbvv for barriers
                            nvel = nvel + nvell(nbou);
                            nbvv(1:nvell(nbou),nbou) = front_nn;
                            ibtype(nbou) = 24;

                            % package it
                            obj.bd.nbou   = nbou ;
                            obj.bd.nvel   = nvel ;
                            obj.bd.nvell  = nvell ;
                            obj.bd.ibtype = ibtype ;
                            obj.bd.nbvv   = nbvv ;
                        end

                        % either append or create new weir connectivity tables
                        if isfield(obj.bd,'ibconn')
                            % then append
                            ibconn    = obj.bd.ibconn ;
                            barinht   = obj.bd.barinht ;
                            barincfsb = obj.bd.barincfsb ;
                            barincfsp = obj.bd.barincfsp ;
                            ibconn(1:nvell(nbou),nbou) = back_nn ; % only list back facing nodes in ibconn for barriers
                            % Opt 1) ask the user for a dataset to give the
                            % crestline (barinht) ;
                            if ar == 0
                                ar = input('Type 1 to enter weir crest height or type 2 to specify dataset...') ;
                                if ar==1
                                    % fixed value for weir crests
                                    ht = input('Enter value in meters ABOVE the geoid for the height of the weir...') ;
                                    disp('-----------------------------------------------------------') ;
                                elseif ar==2
                                    % working on it !
                                    %
                                    error('NOT WORKING YET')
                                end
                            else
                                count = count + 1;
                                ht = hts(count);
                            end
                            barinht(1:nvell(nbou),nbou) =  ht ;
                            barincfsb(1:nvell(nbou),nbou) = 1 ; % these are standard values
                            barincfsp(1:nvell(nbou),nbou) = 1 ; % these are standard values
                        else
                            % then create new
                            ibconn = nbvv*0 ;
                            ibconn(1:nvell(nbou),nbou) = back_nn ;  % only list back facing nodes in ibconn for barriers
                            barinht =  [] ;
                            barincfsb = [];
                            barincfsp = [] ;
                            % Opt 1) ask the user for a dataset to give the crestline
                            % height (barinht)
                            if ar == 0
                                ar = input('Type 1 to enter weir crest height or type 2 to specify dataset...') ;
                                if ar==1
                                    % fixed value for weir crests
                                    ht = input('Enter value in meters ABOVE the geoid for the height of the weir...') ;
                                    disp('-----------------------------------------------------------') ;
                                elseif ar==2
                                    % working on it !
                                    %
                                    error('NOT WORKING YET')
                                end
                            else
                                count = count + 1;
                                ht = hts(count);
                            end
                            barinht(1:nvell(nbou),nbou)   = ht ;
                            barincfsb(1:nvell(nbou),nbou) = 1 ; % these are standard values
                            barincfsp(1:nvell(nbou),nbou) = 1 ; % these are standard values
                        end
                        % now add them back
                        obj.bd.ibconn    = ibconn ;
                        obj.bd.barinht   = barinht ;
                        obj.bd.barincfsb = barincfsb ;
                        obj.bd.barincfsp = barincfsp ;
                    end
                otherwise
                    error(['unrecognized type = ',type])
            end

            function txt = myupdatefcn2(~,event_obj,myarray)
                pos = get(event_obj,'Position');
                ind = find(abs(myarray(:,1)-pos(1))<eps & abs(myarray(:,2)-pos(2))<eps);
                txt = {['X: ',num2str(pos(1))],...
                    ['Y: ',num2str(pos(2))],...
                    ['Index: ',num2str(ind')]};
            end
        end

        function [p1,t1,pw,tw]=extractWeirs(p1,t1,obj)
            % Return the points and elements associated with the weirs
            % while removing these elements and nodes from the obj.
            weir_nodes = [];
            for ii = 1:obj.bd.nbou
                if obj.bd.ibtype(ii) ~= 24; continue; end
                nodes = full(obj.bd.nbvv(1:obj.bd.nvell(ii),ii));
                nodes2 = full(obj.bd.ibconn(1:obj.bd.nvell(ii),ii));
                weir_nodes = [weir_nodes; nodes; nodes2];
            end
            %  retrieve elements connected to weir nodes
            vtoe = VertToEle(t1);
            connec_eles = vtoe(:,weir_nodes);
            connec_eles(connec_eles == 0) = [];
            connec_eles = unique(connec_eles)';
            tw = t1(connec_eles,:);
            % retrieve all other elements
            unconnec_eles = setdiff([1:length(t1)]',connec_eles);
            tn = t1(unconnec_eles,:);
            p1o = p1;
            [p1,t1] = fixmesh(p1,tn);
            % ensure that the new obj1 is traversable
            objn = msh(); objn.t = t1; objn.p = p1;
            objn = Make_Mesh_Boundaries_Traversable(objn,0,1);
            % add the deleted elements into the weir triangulation
            twadd = setdiff(t1,objn.t,'rows');
            [~,~,I] = intersect(p1(twadd,:),p1o,'rows','stable');
            if ~isempty(I)
                twadd = reshape(I,[length(I)/3 3]);
            end
            % finalize the weir mesh and the obj1 mesh
            [pw,tw] = fixmesh(p1o,[tw; twadd]);
            p1 = objn.p; t1 = objn.t;
            % clear unnecessary vars from memory
            clear vtoe unconnec_eles connec_eles objn p1o
        end

        function merge = plus(obj1,obj2,type,cleanargin)
            % merge = plus(obj1,obj2,type,cleanargin)
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%
            % Merge together two meshes contained in the msh objects obj1
            % and obj2. It uses MATLAB's implementation of the Boywer-Watson
            % incremental triangulation and then applies mesh cleaning
            % algorithms to "fix" the intersection zone between meshes.
            %
            % NOTE: msh obj1 can contain fixed points and these will be
            % preserved in the merger.
            %
            % HINT: if you intend to use this a priori, perhaps you should
            % ensure the mesh size functions are similar.
            %
            % INPUTS:
            % obj1: msh() class of inset mesh (INSET MUST BE FIRST).
            % obj2: msh() class of base mesh.
            % type: = 'arb' (default), best for merging arbitrary non-matching
            %          overlapping meshes that have similar resolutions.
            %          Updates boundary of obj2 (for removal of
            %          triangles) after removing intersection(obj1,obj2)
            %          from obj2.
            %       = 'arb+', good for avoiding holes when merging
            %          arbitrary  non-matching overlapping meshes with
            %          disparate resolution/mesh size functions.
            %          Does not update boundary of obj2 (for removal of
            %          triangles) after removing intersection(obj1,obj2)
            %          from obj2
            %       = 'match', assumes a perfect match and that obj1 can be
            %          simply appended to obj2.
            %       = 'matche', will attempt to extract a portion from obj2
            %          that is inside obj1 before matching these together
            %          i.e., that obj1 and obj2 having matching vertices.
            % cleanargin: = a cell-array of arguments for the clean
            %          operator. Default is {'passive'} for 'match(e)' type
            %          and {'djc',0,'sc_maxit',0} for 'arb(+)' type.
            %          Specify an empty [] cleanargin to avoid cleaning.
            %
            % Note special cleanargin options:
            %        1) 'prune_djc' - specify the djc for the pruned obj2
            %           (obj2 minus intersection with obj1) - 0.01 by default
            %        2) 'lock_dis' - specify the distance in degrees from
            %           the intersection at which to lock points. Note that
            %           the user can also specify fixed points in the
            %           individual msh obj "pfix" field to lock specific points.
            %
            % OUPUTS:
            % merge: a msh object in which the msh obj1's connectivity and
            % bathymetry is carried over (along with fixed points
            % from obj1 and obj2).
            %
            % kjr, und, chl, sept. 2017 Version 1.0.
            % kjr, und, chl, oct. 2018, Version 1.5
            % kjr, usp. july 2019. Support for carrying over weirs and pfix.
            % wjp, inserting the 'tight' options optimizied for certain
            % situations
            % kjr, usp. nov 2019. Better merging wrt to fixed constraints.
            %                     now collapses thin triangles incrementally
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%

            %%%%%%%%%%% Parsing inputs %%%%%%%%%%%%%%%%%%%%%%%%%%%%
            if nargin < 3
                type = 'arb';
            end
            prune_djc = 0.01;
            lock_dis = 0;
            options = {'arb','arb+','match','matche'};
            if sum(strcmp(options,type)) == 0
                error('type does not match any of arb, arb+, match, matche')
            else
                disp(['Implementing merge type = ',type])
            end
            if nargin < 4
                if strcmp(type,'match') || strcmp(type,'matche')
                    cleanargin = {'passive','pfix',[]};
                else
                    cleanargin = {'djc',0,'sc_maxit',0,'proj',0,'pfix',[]};
                end
            else
                if isempty(cleanargin)
                    disp('No cleaning of mesh will occur');
                else
                    if ~iscell(cleanargin)
                        error('cleanargin must be a cell')
                    end
                    if strcmp(type(1:3),'arb')
                        if sum(strcmp(cleanargin,'proj')) == 0
                            cleanargin{end+1} = 'proj';
                            cleanargin{end+1} = 0;
                        end
                        if sum(strcmp(cleanargin,'djc')) == 0
                            cleanargin{end+1} = 'djc';
                            cleanargin{end+1} = 0;
                        end
                        if sum(strcmp(cleanargin,'sc_maxit')) == 0
                            cleanargin{end+1} = 'sc_maxit';
                            cleanargin{end+1} = 0;
                        end
                    end
                    if sum(strcmp(cleanargin,'pfix')) == 0
                        cleanargin{end+1} = 'pfix';
                        cleanargin{end+1} = [];
                    end
                    pI = find(strcmp(cleanargin,'prune_djc'));
                    if ~isempty(pI)
                        prune_djc = cleanargin{pI+1};
                        cleanargin(pI:pI+1) = [];
                    end
                    pI = find(strcmp(cleanargin,'lock_dis'));
                    if ~isempty(pI)
                        lock_dis = cleanargin{pI+1};
                        cleanargin(pI:pI+1) = [];
                    end
                end
            end
            % Get location of pfix in the cleanargin
            pfix_loc = find(strcmp(cleanargin,'pfix'))+1;
            % Displaying to screen
            disp(['cleaning options: ' cleanargin])
            if strcmp(type(1:3),'arb')
                disp(['The djc for the pruned obj2 is: ' num2str(prune_djc)])
                if lock_dis > 0
                    disp(['Locking points a distance of ' ...
                        num2str(lock_dis) ' deg away from intersection'])
                else
                    disp(['Locking points more than 2*maximum edge ' ...
                        'length in obj1 away from intersection'])
                end
            end
            %%%%%%%%%%%%%%% end of parsing inpiuts %%%%%%%%%%

            p1 = obj1.p; t1 = obj1.t;
            p2 = obj2.p; t2 = obj2.t;

            pfix1 = obj1.pfix; nfix1 = length(pfix1);
            pfix2 = obj2.pfix; nfix2 = length(pfix2);

            % all combined edge constraints
            nfix    = nfix1+nfix2 ;
            pfixx   = [pfix1; pfix2] ;

            global MAP_PROJECTION MAP_COORDS MAP_VAR_LIST
            if ~isempty(obj2.coord)
                if any(min(obj1.p) < min(obj2.p)) || ...
                   any(max(obj1.p) > max(obj2.p))
                    objt = obj2; objt.p = [objt.p; obj1.p];
                    objt.p(1,:) = min(objt.p) - 1e-3;
                    objt.p(2,:) = max(objt.p) + 1e-3;
                    setProj(objt,1,obj2.proj.name);
                else
                    % kjr 2018,10,17; Set up projected space imported from msh class
                    MAP_PROJECTION = obj2.proj ;
                    MAP_VAR_LIST   = obj2.mapvar ;
                    MAP_COORDS     = obj2.coord ;
                end
            else
                if max(abs(obj2.p(:,2)) > 85)
                    projname = 'stereo';
                else
                    projname = 'trans';
                end
                setProj(obj2,1,projname);
            end

            % check to see if we can do the trivial merge
            extract = 0;
            if strcmp(type,'matche')
                extract = 1;
            elseif ~strcmp(type,'match')
                try
                    cell2 = extdom_polygon(extdom_edges2(t2,p2),p2,-1,0);
                    poly_vec2 = cell2mat(cell2');
                    [edges2] = Get_poly_edges(poly_vec2);
                catch
                    error('Mesh 2 is invalid. Please execute msh.clean on object');
                end
                in = inpoly(obj1.p,poly_vec2,edges2);
                if sum(in) == 0
                    disp('no points in obj1 found in obj2, switch to "match" case')
                    type = 'match';
                end
            end

            switch(type)
                case {'match','matche'}
                    %% Matching meshes - may be overlapping but there are
                    %% vertices that uniquely match so that the overlapping
                    %% can be extracted and then obj1, obj2 concentated together
                    % extract the inner region of obj1 (inset) from obj2 (base)
                    % assuming that the inset fits perfectly in the base
                    obj1o = obj1;
                    if extract
                        [p1(:,1),p1(:,2)] = m_ll2xy(p1(:,1),p1(:,2)) ;
                        [p2(:,1),p2(:,2)] = m_ll2xy(p2(:,1),p2(:,2)) ;
                        obj1.p = p1; obj2.p = p2;
                        bou = get_boundary_of_mesh(obj1,1);
                        [~,outer] = max(cellfun(@length,bou));
                        [obj2,ind] = extract_subdomain(obj2,bou{outer},...
                                           'centroid',1,'keep_inverse',1);
                        obj2 = map_mesh_properties(obj2,'ind',ind);
                        [obj2.p(:,1),obj2.p(:,2)] = m_xy2ll(obj2.p(:,1),obj2.p(:,2));
                        obj2 = obj2.clean(cleanargin);
                        clear ind
                    end
                    % concatenate
                    m1 = cat(obj1o,obj2);
                    merge = msh(); merge.p = m1.p; merge.t = m1.t;
                    obj1 = obj1o;
                    clear m1 obj1o
                otherwise
                    %% Abitrary non-matching overlapping meshes
                    % Project both meshes into the space of the global mesh
                    [p1(:,1),p1(:,2)] = m_ll2xy(p1(:,1),p1(:,2)) ;
                    [p2(:,1),p2(:,2)] = m_ll2xy(p2(:,1),p2(:,2)) ;
                    if nfix > 0
                        [pfixx(:,1),pfixx(:,2)] = m_ll2xy(pfixx(:,1),pfixx(:,2));
                    end

                    % checking for weirs in obj1 to keep
                    if ~isempty(obj1.bd) && any(obj1.bd.ibtype == 24)
                        disp('Weirs found in obj1, extracting to ensure they are preserved')
                        [p1,t1,pwin1,twin1] = extractWeirs(p1,t1,obj1);
                    end

                    % checking for weirs in obj2 to keep
                    if ~isempty(obj2.bd) && any(obj2.bd.ibtype == 24)
                        disp('Weirs found in obj2, extracting to ensure they are preserved')
                        [p2,t2,pwin2,twin2] = extractWeirs(p2,t2,obj2);
                    end

                    disp('Forming outer boundary for base...')
                    try
                        cell2 = extdom_polygon(extdom_edges2(t2,p2),p2,-1,0);
                        poly_vec2 = cell2mat(cell2');
                        [edges2] = Get_poly_edges(poly_vec2);
                    catch
                        error('Mesh 2 is invalid. Please execute msh.clean on object');
                    end

                    disp('Forming outer boundary for inset...')
                    try
                        [cell1] = extdom_polygon(extdom_edges2(t1,p1),p1,-1,0);
                        poly_vec1 = cell2mat(cell1');
                        [edges1] = Get_poly_edges(poly_vec1);
                    catch
                        error('Mesh 1 is invalid. Please execute msh.clean on object');
                    end

                    % Delete the region in the global mesh that is in the
                    % intersection with inset.
                    disp('Deleting intersection...');
                    in1 = inpoly(p2(t2(:,1),:),poly_vec1,edges1);
                    in2 = inpoly(p2(t2(:,2),:),poly_vec1,edges1);
                    in3 = inpoly(p2(t2(:,3),:),poly_vec1,edges1);
                    t2(in1 & in2 & in3,:) = [];
                    % We need to delete straggling elements that are
                    % generated through the above deletion step
                    pruned2 = msh() ; pruned2.p = p2; pruned2.t = t2;
                    pruned2 = Make_Mesh_Boundaries_Traversable(...
                        pruned2,prune_djc,1);
                    t2 = pruned2.t; p2 = pruned2.p;
                    % get new poly_vec2
                    if strcmp(type,'arb')
                        cell2 = extdom_polygon(extdom_edges2(t2,p2),p2,-1,0);
                        poly_vec2 = cell2mat(cell2');
                        [edges2] = Get_poly_edges(poly_vec2);
                    end

                    disp('Merging...')
                    DTbase = delaunayTriangulation(p1);
                    DTbase.Points(end+(1:length(p2)),:) = p2;
                    if nfix > 0
                        bdx = ourKNNsearch(DTbase.Points',pfixx',1);
                    else
                        bdx = [];
                    end

                    % Prune triangles outside both domains.
                    disp('Pruning...')
                    for ii = 1:2
                        % The loop makes sure to remove only small connectivity for the boundaries
                        if ii == 2
                            % To remove small connectivity or bad elements
                            [~, enum] = VertToEle(tm);
                            bdbars = extdom_edges2(tm,pm);
                            bdnodes = unique(bdbars(:));
                            I = find(enum <= 4);
                            nn = setdiff(I',[bdx; bdnodes]);
                            DTbase.Points(unique(nn),:) = [];
                        end

                        pm = DTbase.Points; tm = DTbase.ConnectivityList;

                        pmid = (pm(tm(:,1),:)+pm(tm(:,2),:)+pm(tm(:,3),:))/3;

                        %in1 is inside the inset boundary polygon
                        in1 = inpoly(pmid,poly_vec1,edges1);

                        %in2 is inside the global boundary polygon
                        in2 = inpoly(pmid,poly_vec2,edges2);

                        % remove triangles that aren't in the global mesh or
                        % aren't in the inset mesh
                        del = (~in1 & ~in2);
                        tm(del,:) = [];
                    end

                    merge = msh() ; merge.p = pm; merge.t = tm ;

                    if ~isempty(cleanargin)
                        % convert to degrees to calculate distance
                        [t_p1(:,1),t_p1(:,2)] = m_xy2ll(p1(:,1),p1(:,2));
                        [t_mrg(:,1),t_mrg(:,2)] = m_xy2ll(merge.p(:,1),merge.p(:,2));
                        [t_p2(:,1),t_p2(:,2)] = m_xy2ll(p2(:,1),p2(:,2));
                        if lock_dis == 0
                            % lock anything vertices more than 2*dmax away
                            % from intersection
                            [~,dst] = ourKNNsearch(t_p1',t_p1',2);
                            dmax = max(dst(:,2));
                            lock_dis = 2*dmax;
                        end
                        % determining the locked vertices
                        [~,dst1] = ourKNNsearch(t_p1',t_mrg',1);
                        [~,dst2] = ourKNNsearch(t_p2',t_mrg',1);
                        locked = [merge.p(dst1 > lock_dis | dst2 > lock_dis,:); pfixx];
                        cleanargin{pfix_loc} = locked;
                        % iteration is done in clean if smoothing creates neg quality
                        merge = clean(merge,cleanargin);
                    end
                    clear pm tm pmid p1 t1 p2 t2

                    merge.pfix  = pfixx ;
                    % edges don't move but they are no longer valid after merger
                    merge.egfix = [];

                    % put the weirs from obj1 back into merge
                    if ~isempty(obj1.bd) && any(obj1.bd.ibtype == 24)
                        disp('Putting the weirs from obj1 back into merged mesh')
                        wm = msh(); wm.p = pwin1; wm.t = twin1;
                        merge = cat(merge,wm);
                    end

                    % put the weirs from obj2 back into merge
                    if ~isempty(obj2.bd) && any(obj2.bd.ibtype == 24)
                        disp('Putting the weirs from obj2 back into merged mesh')
                        wm = msh(); wm.p = pwin2; wm.t = twin2;
                        merge = cat(merge,wm);
                    end

                    % convert back to lat-lon wgs84
                    [merge.p(:,1),merge.p(:,2)] = ...
                        m_xy2ll(merge.p(:,1),merge.p(:,2));

                    if nfix > 0
                        [merge.pfix(:,1),merge.pfix(:,2)] = ...
                            m_xy2ll(pfixx(:,1),pfixx(:,2));
                    end
            end

            merge.proj    = MAP_PROJECTION ;
            merge.coord   = MAP_COORDS ;
            merge.mapvar  = MAP_VAR_LIST ;

            % Check element order
            merge = CheckElementOrder(merge);

            if ~isempty(cleanargin) && ...
                    (strcmp(type,'match') || strcmp(type,'matche'))
                % let's clean if match type
                merge = clean(merge,cleanargin);
            end

            % Carry over bathy and gradients
            if ~isempty(obj1.b) && ~isempty(obj2.b)
                disp('Carrying over bathy and slope values.')
                merge.b = 0*merge.p(:,1);
                [idx1,dst1] = ourKNNsearch(obj1.p',merge.p',1);
                [idx2,dst2] = ourKNNsearch(obj2.p',merge.p',1);
                merge.b( dst1 <= dst2) = obj1.b( idx1(dst1 <= dst2));
                merge.b( dst2 <  dst1 ) = obj2.b( idx2(dst2 <  dst1) );
                if ~isempty(obj1.bx) && ~isempty(obj2.bx)
                    merge.bx = 0*merge.b; merge.by = 0*merge.b;
                    merge.bx(dst2 < dst1) = obj2.bx(idx2(dst2 < dst1));
                    merge.bx(dst1 <= dst2) = obj1.bx(idx1(dst1 <= dst2));
                    merge.by(dst2 < dst1) = obj2.by(idx2(dst2 < dst1));
                    merge.by(dst1 <= dst2) = obj1.by(idx1(dst1 <= dst2));
                end
            end

            if ~isempty(obj1.f13)
                disp('Carrying over obj1 f13 data + any corresponding obj2 f13 data')
                if ~isempty(obj2.f13)
                   ob2name = {obj2.f13.userval.Atr.AttrName};
                else
                   ob2name = {};
                end
                merge.f13 = obj1.f13;
                merge.f13.NumOfNodes = size(merge.p,1);
                for ii = 1:merge.f13.nAttr
                    attname = merge.f13.userval.Atr(ii).AttrName;
                    idx1 = obj1.f13.userval.Atr(ii).Val(1,:)';
                    val1 = obj1.f13.userval.Atr(ii).Val(2:end,:)';
                    idx1 = ourKNNsearch(merge.p',obj1.p(idx1,:)',1);
                    jj = find(contains(ob2name,attname));
                    if ~isempty(jj)
                       disp(['Carrying over obj1 and obj2 ' attname])
                       idx2 = obj2.f13.userval.Atr(jj).Val(1,:)';
                       val2 = obj2.f13.userval.Atr(jj).Val(2:end,:)';
                       idx2 = ourKNNsearch(merge.p',obj2.p(idx2,:)',1);
                       idx = [idx1; idx2];
                       val = [val1; val2];
                    else
                       disp(['Carrying over obj1 ' attname])
                       idx = idx1; val = val1;
                    end
                    [idx,I] = sort(idx,'ascend');
                    userval = [double(idx) val(I,:)];
                    merge.f13.userval.Atr(ii).Val = userval';
                end
            end

            if ~isempty(obj1.bd) && any(obj1.bd.ibtype == 24)
                disp('Carrying over weir nodestrings from obj1.')
                merge = carryoverweirs(merge,obj1);
            end

            if ~isempty(obj2.bd) && any(obj2.bd.ibtype == 24)
                disp('Carrying over weir nodestrings from obj2.')
                if exist('obj2o','var'); obj2 = obj2o; end
                merge = carryoverweirs(merge,obj2);
            end

            disp('NB: f15, obj2 f13 data not in obj1, non-weir nodestrings etc. are not carried over.')

        end

        function obj = cat(obj,obj1)
            % obj = cat(obj,obj1)
            % cat two non-overlapping meshes
            pin = obj1.p; tin = obj1.t;
            [~,d] = ourKNNsearch(pin',pin',2);
            d = max(d,[],2); mind = min(d);
            [idx,d] = ourKNNsearch(obj.p',pin',1);
            ind = 1:size(pin,1);
            LIA = ismember(tin(:),ind(d < mind));
            tin(LIA) = idx(tin(LIA));
            tin(~LIA) = tin(~LIA) + length(obj.p);
            obj.p = [obj.p; pin];
            obj.t = [obj.t; tin];
            % append to b and bx, by to avoid error in fixmeshandcarry
            if ~isempty(obj.b)
                obj.b = [obj.b; NaN(size(pin,1),1)];
            end
            if ~isempty(obj.bx)
                obj.bx = [obj.bx; NaN(size(pin,1),1)];
                obj.by = [obj.by; NaN(size(pin,1),1)];
            end
            obj = fixmeshandcarry(obj);
        end

        function obj = trim(obj,threshold)
            % obj = trim(obj,threshold)
            % trim a mesh excluding elevations above the threshold
            % (given threshold should be positive for overland)
            if isempty(obj.b) || all(obj.b == 0)
                error('need bathy on mesh')
            end
            bem = max(obj.b(obj.t),[],2);   % only trim when all vertices
            obj.t(bem < -threshold,:) = []; % of element are above the threshold.
            obj = fixmeshandcarry(obj);
        end

        function obj = fixmeshandcarry(obj)
            % obj = fixmeshandcarry(obj);
            % "fixes" mesh and carries mesh properties over
            % e.g., b, bx, by, f13, f24, f5354 dat
            [obj.p,obj.t,pix] = fixmesh(obj.p,obj.t);
            % carry over...
            obj = map_mesh_properties(obj,'ind',pix);
        end

        function obj = CheckElementOrder(obj,proj)
            if nargin == 1
                proj = 0;
            end
            vx = obj.p(:,1); vy = obj.p(:,2);
            xt = [vx(obj.t(:,1)) vx(obj.t(:,2)) ...
                vx(obj.t(:,3)) vx(obj.t(:,1))];
            yt = [vy(obj.t(:,1)) vy(obj.t(:,2)) ...
                vy(obj.t(:,3)) vy(obj.t(:,1))];
            dxt = diff(xt,[],2);
            dyt = diff(yt,[],2);
            for ii = 1:3
                iii = ii - 1; if iii == 0; iii = 3; end
                I = abs(dxt(:,ii)) > 180 & abs(dxt(:,iii)) > 180;
                xt(I,ii) = xt(I,ii) + 360*sign(dxt(I,ii));
            end
            xt(:,end) = xt(:,1);
            % Get new diff
            dxt = diff(xt,[],2);
            Area = dxt(:,3).*-dyt(:,2) + dxt(:,2).*dyt(:,3);
            if ~isempty(find(Area < 0, 1))
                disp([num2str(sum(Area < 0)) ...
                    ' elements found that are not in counterclockwise order'])
                if proj
                    global MAP_PROJECTION MAP_VAR_LIST MAP_COORDS
                    % kjr 2018,10,17; Set up projected space imported from msh class
                    MAP_PROJECTION = obj.proj ;
                    MAP_VAR_LIST   = obj.mapvar ;
                    MAP_COORDS     = obj.coord ;
                    [pt(:,1),pt(:,2)] = m_ll2xy(obj.p(:,1),obj.p(:,2));
                else
                    pt = obj.p;
                end
                [~,tt] = fixmesh(pt,obj.t);
                obj.t(Area < 0,:) = tt(Area < 0,:);
                obj = CheckElementOrder(obj,~proj);
            else
                disp('All elements now in counterclockwise order')
            end
        end

        function obj = carryoverweirs(obj,obj1)
            idx1 = nearest_neighbor_map(obj, obj1,'precise');
            if isempty(obj.bd)
                obj.bd.nbou=0;
                obj.bd.nvell=[];
                obj.bd.nvel=[];
                obj.bd.nbvv=[];
                obj.bd.ibconn=[];
                obj.bd.ibtype=[];
                obj.bd.barinht=[];
                obj.bd.barincfsb=[];
                obj.bd.barincfsp=[];
            end
            % starting boundary number
            startBou = obj.bd.nbou + 1 ;
            % number of new weir boundaries
            jj = obj1.bd.ibtype == 24;
            obj.bd.nbou =  obj.bd.nbou + sum(jj);
            % types of boundaries
            obj.bd.ibtype = [obj.bd.ibtype obj1.bd.ibtype(jj)];
            % new boundaries come after what's already on
            obj.bd.nvell = [obj.bd.nvell obj1.bd.nvell(jj)];
            % nvel is twice the number of nodes on each boundary
            obj.bd.nvel = 2*sum(obj.bd.nvell);
            % nbvv is a matrix of boundary nodes
            [nr1,nc1]=size(obj.bd.nbvv);
            nc2 = sum(jj); nr2 = sum(obj1.bd.nvell(jj));
            nbvv_old = obj.bd.nbvv;
            ibconn_old = obj.bd.ibconn;
            barinht_old = obj.bd.barinht;
            barincfsb_old = obj.bd.barincfsb;
            barincfsp_old = obj.bd.barincfsp;

            obj.bd.nbvv = zeros(max(nr1,nr2),max(nc1,nc1+nc2));
            obj.bd.ibconn = zeros(max(nr1,nr2),max(nc1,nc1+nc2));
            obj.bd.barinht = zeros(max(nr1,nr2),max(nc1,nc1+nc2));
            obj.bd.barincfsb = zeros(max(nr1,nr2),max(nc1,nc1+nc2));
            obj.bd.barincfsp = zeros(max(nr1,nr2),max(nc1,nc1+nc2));

            obj.bd.nbvv(1:nr1,1:nc1)=nbvv_old;
            obj.bd.ibconn(1:nr1,1:nc1)=ibconn_old;
            obj.bd.barinht(1:nr1,1:nc1)=barinht_old;
            obj.bd.barincfsb(1:nr1,1:nc1)=barincfsb_old;
            obj.bd.barincfsp(1:nr1,1:nc1)=barincfsp_old;

            % remap
            jj = find(jj);
            for ii = startBou:obj.bd.nbou
                idx = ii - (startBou-1) ;
                idx = jj(idx);
                nodes =  full(obj1.bd.nbvv(1:obj1.bd.nvell(idx),idx));
                nodes2 = full(obj1.bd.ibconn(1:obj1.bd.nvell(idx),idx));

                obj.bd.nbvv(1:obj.bd.nvell(ii),ii)   = idx1(nodes);
                obj.bd.ibconn(1:obj.bd.nvell(ii),ii) = idx1(nodes2);
                obj.bd.barinht(1:obj.bd.nvell(ii),ii) = ...
                               obj1.bd.barinht(1:obj1.bd.nvell(idx),idx);
                obj.bd.barincfsb(1:obj.bd.nvell(ii),ii) = ...
                               obj1.bd.barincfsb(1:obj1.bd.nvell(idx),idx);
                obj.bd.barincfsp(1:obj.bd.nvell(ii),ii) = ...
                               obj1.bd.barincfsp(1:obj1.bd.nvell(idx),idx);
            end
        end

        function [out1,barlen,bars] = CalcCFL(obj,dt,type)
            if isempty(obj.b)
                error('Bathymetry is required to estimate the Courant number');
            end
            if nargin < 3
                % use spherical haversine distances
                type = 0;
            end

            g      = 9.81;        % gravity
            [bars,barlen] = GetBarLengths(obj,type);
            % sort bar lengths in ascending order
            [barlen,IA] = sort(barlen,'ascend');
            bars = bars(IA,:);
            % get the minimum bar length for each node
            [B1,IB] = unique(bars(:,1),'first');
            [B2,IC] = unique(bars(:,2),'first');
            d1 = NaN*obj.p(:,1); d2 = NaN*obj.p(:,1);
            d1(B1) = barlen(IB); d2(B2) = barlen(IC);
            d = min(d1,d2);

            % wavespeed in ocean (second term represents orbital
            % velocity at 0 degree phase for 1-m amp. wave).
            U = sqrt(g*max(obj.b,1)) + sqrt(g./max(obj.b,1));
            if nargin > 1 && ~isempty(dt)
                % Get CFL from input dt
                CFL = dt*U(:)./d;  % <-- from the wave celerity
                out1 = CFL;
            else
                CFL = 1.0;
                dt = d.*CFL./U; % <-- from the wave celerity
                out1 = dt;
            end
        end

        function [bars,barlen] = GetBarLengths(obj,type)
            % [bars,barlen] = GetBarLengths(obj,type)
            % Get bars and bar lengths of the elements in msh object
            % set type = 0 for bar lengths computed using Harvesine formula
            % set type = 1 for bar lengths computed using CCP with
            % correction factor for x-direction
            if nargin < 2
                type = 0;
            end
            bars = [obj.t(:,[1,2]); obj.t(:,[1,3]); obj.t(:,[2,3])]; % Interior bars duplicated
            bars = unique(sort(bars,2),'rows');                      % Bars as node pairs
            if nargout == 1; return; end
            if type == 0
                % Compute based on Haversine spherical earth distances
                long   = zeros(length(bars)*2,1);
                lat    = zeros(length(bars)*2,1);
                long(1:2:end) = obj.p(bars(:,1),1);
                long(2:2:end) = obj.p(bars(:,2),1);
                lat(1:2:end)  = obj.p(bars(:,1),2);
                lat(2:2:end)  = obj.p(bars(:,2),2);
                % Get spherical earth distances for bars
                barlen = m_lldist(long,lat);
                barlen = barlen(1:2:end)*1e3;  % L = Bar lengths in meters
            elseif type == 1
                % Compute based on CPP with sfac correction factor for x-direction
                sfea = obj.p(:,2); sfac = cosd(mean(sfea)) ./ cosd(sfea);
                sfacelemid = mean(sfac(obj.t),2);
                vtoe = VertToEle(obj.t);
                vtoe(vtoe == 0) = length(obj.t) + 1;
                sfacelemid(end+1) = NaN;
                conbar1 = vtoe(:,bars(:,1));
                conbar2 = vtoe(:,bars(:,2));
                sfacbar1 = max(sfacelemid(conbar1));
                sfacbar2 = max(sfacelemid(conbar2));
                sfac = max(sfacbar1,sfacbar2)';
                % add safety factor for high latitudes (this is quite critical)
                sfac = sfac.*ceil(sfac/10);
                [x, y] = CPP_conv( obj.p(:,1), obj.p(:,2) );
                barlen = hypot(diff(x(bars),[],2)./sfac,diff(y(bars),[],2));
            end

            function [ x,y ] = CPP_conv( lon,lat )
                %CPP_conv Converts lat and lon to x and y
                lon0 =  mean(lon) * pi/180; lat0 = mean(lat) * pi/180;

                R = 6378206.4;
                lonr = lon * pi/180; latr = lat * pi/180;
                x = R * (lonr - lon0) * cos(lat0);
                y = R * latr;
            end
        end

        function obj = bound_courant_number(obj,dt,cr_max,cr_min,varargin)
            % obj = bound_courant_number(obj,dt,cr_max,cr_min,varargin)
            % Decimate/refine a mesh to achieve Cr max/min bounds for
            % optimal numerical performance.
            %
            % Takes a mesh and removes and adds nodes to produce an updated
            % mesh that satisfies the given timestep requirements of the
            % user (i.e., cr_min > Cr(obj) < cr_max)
            %
            %                       INPUTS
            % dt is the desired timestep to run the simulation (in seconds)
            % cr_max is the desired maximum Courant number (optional,
            % default is 0.5). Set to zero to skip.
            % cr_min is the desired minimum Courant number (optional,
            % default is 0). Set to zero to skip.
            % varargin(1) is maximum number of iterations (maxIT) to attempt bound.
            % by default this is 10.
            %
            %                       OUTPUTS
            % obj is a mesh where the regions that were modified now
            % respect the Courant bounds.

            % AUTHORSHIP:
            % kjr, chl, und, 2017 (originally checktimestep)
            % kjr, chl, und, 2018 <--updated for projected spaces
            % wjp, chl, und, 2019 <--updates to carry over slopes and
            % using the msh clean, and CFL calc type option
            % kjr, poli, usp 2020 <--Rewrote and generalized. Now add and as well as delete
            %                        to achieve min and max. Courant bound.

            % Set up input args and catch errors.
            if nargin < 2
                help bound_courant_number
                error('Please supply correct input args...See help printout above');
            end

            % no cr_max, use default
            if nargin < 3
                cr_max = 0.5;
            end

            % no cr_min supplied
            if nargin < 4
                cr_min = 0;
            end
            % else both cr_max and cr_min have been supplied
            % determine number of maximum iterations
            if nargin > 4
                maxIT = varargin{1};
            else
                maxIT = 10;
            end

            disp(['Desired time step is ' num2str(dt) ' s'])

            %% Deal with any projection information for accurate bar
            % length calculations.
            type  = 0;       %<-- 0 == Haversine, 1 == CPP with correction factor

            % Conduct initial check of Courant number to return early if possible
            Cr = real(CalcCFL(obj,dt,type));
            if max(Cr) <= cr_max && min(Cr) >= cr_min
               disp('Courant number constraints are already satisfied')
               return
            end

            % deleting boundary conditions which are difficult to recompute when
            % the triangulation changes
            obj.bd = []; obj.op = [];

            if ~isempty(obj.coord)
                % kjr 2018,10,17; Set up projected space imported from msh class
                global MAP_PROJECTION MAP_VAR_LIST MAP_COORDS
                MAP_PROJECTION = obj.proj ;
                MAP_VAR_LIST   = obj.mapvar ;
                MAP_COORDS     = obj.coord ;
            else
                lon_mi = min(obj.p(:,1)); lon_ma = max(obj.p(:,1));
                lat_mi = min(obj.p(:,2)); lat_ma = max(obj.p(:,2));
                m_proj('Trans','lon',[lon_mi lon_ma],'lat',[lat_mi lat_ma]) ;
            end

            %% Project into space..
            [obj.p(:,1),obj.p(:,2)] = m_ll2xy(obj.p(:,1),obj.p(:,2));

            %% Make bathy interpolant for reprojection later on.
            F = scatteredInterpolant(obj.p(:,1),obj.p(:,2),obj.b,...
                'linear','nearest');

            % OPTIONALLY BOUND THE MAXIMUM COURANT NUMBER BY DELETING
            if cr_max > eps % if cr_max is set to 0 this is skipped
                disp(['Editing the mesh to bound max. Courant number to ' num2str(cr_max)])
                it  = 0; % iteration counter

                if ~isempty(obj.pfix)
                    [pf(:,1),pf(:,2)] = m_ll2xy(obj.pfix(:,1),obj.pfix(:,2));
                else
                    pf = [];
                end
                con = 9;
                badnump = 1e10;
                tic
                while 1
                    [obj.p(:,1),obj.p(:,2)] = m_xy2ll(obj.p(:,1),obj.p(:,2));
                    Cr = real(CalcCFL(obj,dt,type));
                    [obj.p(:,1),obj.p(:,2)] = m_ll2xy(obj.p(:,1),obj.p(:,2));
                    bad = Cr > cr_max;
                    badnum = sum(bad);

                    display(['Number of maximum Cr bound violations ',num2str(badnum)]);
                    disp(['Max Cr is : ',num2str(max(Cr))]);
                    if it == maxIT; break; end
                    if badnum == 0; break; end
                    if badnump - badnum <= 0; con = con + 1; end
                    it = it + 1;
                    obj = DecimateTria(obj,bad);
                    % Clean up the new mesh (already projected) without direct
                    % smoothing (we have used local smooting in DecmimateTria
                    obj = clean(obj,'passive','proj',0,'pfix',pf,'con',con);
                    % Overwrite the nearest-neighbour interp of b in clean with linear interp
                    obj.b = F(obj.p(:,1),obj.p(:,2));
                    badnump = badnum;
                end
                toc
                disp(['Achieved max Cr of ',num2str(max(Cr)),...
                    ' after ',num2str(it),' iterations.']);
            end

            % OPTIONALLY BOUND THE MINIMUM COURANT NUMBER BY REFINING
            if cr_min > eps %if cr_min is set to 0 this is skipped
                disp(['Editing the mesh to bound min. Courant number to ' num2str(cr_min)])
                it  = 0; % iteration counter

                if ~isempty(obj.pfix)
                    [pf(:,1),pf(:,2)] = m_ll2xy(obj.pfix(:,1),obj.pfix(:,2));
                else
                    pf = [];
                end

                tic
                while 1
                    [obj.p(:,1),obj.p(:,2)] = m_xy2ll(obj.p(:,1),obj.p(:,2));
                    Cr = real(CalcCFL(obj,dt,type));
                    [obj.p(:,1),obj.p(:,2)] = m_ll2xy(obj.p(:,1),obj.p(:,2));
                    bad = Cr < cr_min;
                    badnum = sum(bad);

                    display(['Number of minimum Cr bound violations ',num2str(badnum)]);
                    disp(['Min. Cr is : ',num2str(min(Cr))]);
                    if it == maxIT; break; end
                    if badnum == 0; break; end
                    it = it + 1;

                    % save old msh object for mapping
                    obj_old = obj;

                    % refine select elements using an octree approach
                    obj = RefineTrias(obj_old,bad);

                    % map back properties
                    obj = map_mesh_properties(obj,'msh_old',obj_old);

                    % put bathy back on with linear interp
                    obj.b = F(obj.p(:,1),obj.p(:,2));

                end
            end

            % find nans
            if ~isempty(find(isnan(obj.b), 1))
                warning('NaNs in bathy found')
            end

            % convert back to lat-lon wgs84
            [obj.p(:,1),obj.p(:,2)] = m_xy2ll(obj.p(:,1),obj.p(:,2));

            % Check Element order
            obj = CheckElementOrder(obj);

            % Call itself recursively to make sure both criteria are satisifed
            obj = bound_courant_number(obj,dt,cr_max,cr_min,maxIT);

            % Last display message
            disp(['All msh attributes have been carried over except for boundary ' ...
                  'conditions which need to be recomputed. Since the triangulation ' ...
                  'has changed it may pay to recompute other attributes as well']);
            return;

            function obj = DecimateTria(obj,bad)
                % helper function to delete triangles to achieve max. Cr
                % bound.
                m_old = obj; % save original mesh object for mapping
                % form outer polygon of mesh for cleaning up.
                poly_cell = get_boundary_of_mesh(obj,1);
                % Deleting any polylines less than three points (last point is NaN)
                poly_cell(cellfun(@length,poly_cell) < 4) = [];
                poly_vec1 = cell2mat(poly_cell');
                clear poly_cell
                [edges1]  = Get_poly_edges(poly_vec1);
                % delete the points that violate the cfl, locally retriangulate, and then locally smooth
                DTbase = delaunayTriangulation(obj.p(:,1),obj.p(:,2));
                DTbase.Points(find(bad),:) = [];
                pm   = DTbase.Points; tm = DTbase.ConnectivityList;
                pmid = (pm(tm(:,1),:)+pm(tm(:,2),:)+pm(tm(:,3),:))/3;
                in1  = inpoly(pmid,poly_vec1,edges1);
                tm(~in1,:) = []; [pm,tm] = fixmesh(pm,tm);
                % Delete shitty boundary elements iteratively
                badbound = 1;
                while ~isempty(find(badbound, 1))
                    tq1 = gettrimeshquan(pm,tm);
                    % Get the elements that have a boundary bar
                    bnde = extdom_edges2(tm,pm);
                    bdnodes = unique(bnde(:));
                    vtoe = VertToEle(tm);
                    bele = unique(vtoe(:,bdnodes)); bele(bele == 0) = [];
                    tqbou = tq1.qm(bele);
                    badbound = bele(tqbou < 0.1);
                    % Delete those boundary elements with quality < 0.1
                    tm(badbound,:) = [];
                end
                [pm,tm] = fixmesh(pm,tm);
                if sum(bad) < size(pm,1)*0.1
                    % find all the points nearby each "bad" point.
                    idx = ourKNNsearch(pm',obj.p(find(bad),:)',12);
                    idx = idx(:);
                    idx = unique(idx);
                    constr = setdiff((1:length(pm))',idx);
                    [pm,tm] = smoothmesh(pm,tm,constr,50,0.01);
                else
                    warning('Adapation would result in potentially catastrophic lose of connectivity, try adapting to a smaller timestep');
                end
                obj.p = pm; obj.t = tm;
                obj = map_mesh_properties(obj,'msh_old',m_old);
            end

            function obj = RefineTrias(obj,bad)
                % helper function to refine triangles to achieve min.
                % Courant bound
                ptemp = obj.p; ttemp = obj.t;
                [vtoe,nne]=VertToEle(ttemp);
                badTrias = vtoe(:,bad);
                badTrias(badTrias==0)=[];
                badTrias=unique(badTrias);
                edges = [ttemp(:,[1,2]); ttemp(:,[1,3]); ttemp(:,[2,3])];
                edges = unique(sort(edges,2),'rows');
                yesrefine = false(length(ttemp),1);
                yesrefine(badTrias,:)=true;
                tnum=ones(length(ttemp),1);
                [pnew,~,tnew] = tridiv2(ptemp,edges,ttemp,tnum,yesrefine);
                obj.p = pnew; obj.t = tnew;
            end

        end

        function obj = CheckTimestep(obj,dt,varargin)
            % This function has been deprecated. Use "bound_courant_number" instead.
            % obj = CheckTimestep(obj,dt,varargin)
            % varargin(1) is desired CFL (< 1) or maximum iterations (> 1)
            % varargin(2) is desired dj_cutoff
            %
            % Decimate mesh to achieve CFL condition for stability.
            %
            % Takes a mesh and removes triangles and nodes to produce a mesh
            % that satisfies the given timestep requirements of the user by
            % incrementally modifying the triangulation nearby each edge
            % that violates the CFL.
            % kjr, chl, und, 2017
            % kjr, chl, und, 2018 <--updated for projected spaces
            % wjp, chl, und, 2019 <--updates to carry over slopes and
            % using the msh clean, and CFL calc type option

            error('This function has been deprecated. Use "bound_courant_number" instead')

        end

        function [] = GatherStationsFromKML(obj,kmlfile,ofname,varargin)
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            % Read a kml file created in google maps to get coordinates of
            % stations that lie within the meshes extents.
            % (Note we can move the stations to reasonable locations off land etc in google
            % maps before exporting to kml).
            %
            %
            % Inputs:
            %     obj     - msh object
            %     kmlfile - kml filename dowloaded from William Pringle's tidal database.
            %     ofname  - filename of csv containing stations that fall within the mesh.
            %     const (optional)  - A cell-array of constitutents to validate against.
            %                         By default will be all major 8 (
            %                         {'M2','S2','N2','K2','K1','O1','P1','Q1'});
            %     Source (optional) - A cell-array of the source databases
            %                        in order of priority/reliability. By default it is:
            %                        sources = {'Truth_Pelagic','Truth_Shelf','NOAA','JMA','AUS_Tides',...
            %                        'KHAO','GESLA','UHSLC_Fast','Truth_Coast',...
            %                        'Various_Publications','ST727','IHO',};
            % Outputs:
            %
            % Author: William Pringle
            % Changes by Keith Roberts: merged code into msh class and added input parser for name/value pairs, 2018-03-22
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            %% Variables to set
            if nargin < 3, error('Not enough input arguments!'); end

            if ~isempty(varargin)
                names = {'const','Source'};
                for ii = 1:length(names)
                    ind = find(~cellfun(@isempty,strfind(varargin(1:2:end),names{ii})));
                    if ~isempty(ind)
                        if ii == 1
                            const = varargin{ind*2};
                        else
                            Source = varargin{ind*2};
                        end
                    end
                end

            else
                % Set the constituents we wanna look at
                const = {'M2','S2','N2','K2','K1','O1','P1','Q1'};
                Source = {'Truth_Pelagic','Truth_Shelf','NOAA','JMA','AUS_Tides',...
                    'KHAO','GESLA','UHSLC_Fast','Truth_Coast',...
                    'Various_Publications','ST727','IHO',};
            end

            %% Reading the kml
            T = [];
            for kml = kmlfile
                kmlS = kml2struct(kml{1});
                % Getting rid of unnecessary shit
                T_n = struct2table(kmlS);
                T_n.Geometry = [];
                T_n.BoundingBox = [];
                %T.Description = [];
                T_n = T_n(:,[1 3 4 2 5]);
                T_n.Source = T_n.StyleUrl;
                T_n.StyleUrl = [];
                T = [T; T_n];
            end

            %% Convert description to amp and phases
            obs = NaN(height(T),length(const)*2);
            for i = 1:height(T)
                if strcmp(T.Source{i}(end-5:end),'0288D1') % light blue
                    T.Source{i} = 'Truth_Pelagic';
                elseif strcmp(T.Source{i}(end-5:end),'FFEA00') % yellow
                    T.Source{i} = 'Truth_Shelf';
                elseif strcmp(T.Source{i}(end-5:end),'0F9D58') % green
                    T.Source{i} = 'Truth_Coast';
                elseif strcmp(T.Source{i}(end-5:end),'757575') % grey
                    T.Source{i} = 'NOAA';
                elseif strcmp(T.Source{i}(end-5:end),'673AB7') % dark purple
                    T.Source{i} = 'JMA';
                elseif strcmp(T.Source{i}(end-5:end),'FF5252') % coral
                    T.Source{i} = 'KHAO';
                elseif strcmp(T.Source{i}(end-5:end),'7CB342') % light green
                    T.Source{i} = 'GESLA';
                elseif strcmp(T.Source{i}(end-5:end),'A52714') % medium red
                    T.Source{i} = 'UHSLC_Fast';
                elseif strcmp(T.Source{i}(end-5:end),'FFD600') % austrlian gold
                    T.Source{i} = 'AUS_Tides';
                elseif strcmp(T.Source{i}(end-5:end),'880E4F') % dark blue
                    T.Source{i} = 'ST727';
                elseif strcmp(T.Source{i}(end-5:end),'3949AB') % dark blue
                    T.Source{i} = 'IHO';
                elseif strcmp(T.Source{i}(end-5:end),'9C27B0') % light purple
                    T.Source{i} = 'Various_Publications';
                end
                Descrip = T.Description(i); Descrip = Descrip{1};
                cc = 0;
                for c = const
                    cc = cc + 1;
                    % Get position in description of the constituent
                    Positions = regexp(Descrip,[c{1} '_']);
                    Positions = find(~cellfun(@isempty,Positions));
                    if isempty(Positions); continue; end
                    if length(Positions) > 2
                        % M2 seasonal shit
                        Positions(1:2) = [];
                    end
                    amp = Descrip(Positions(1));
                    s = strfind(amp,' ');
                    obs(i,cc*2-1) = str2double(amp{1}(s{1}+1:end));
                    phs = Descrip(Positions(2));
                    s = strfind(phs,' ');
                    obs(i,cc*2) = str2double(phs{1}(s{1}+1:end));
                end
            end
            % Make names
            for ii = 1:length(const)
                const_names{2*ii-1} = [const{ii} '_amp'];
                const_names{2*ii} = [const{ii} '_phs'];
            end
            T1 = array2table(obs,'VariableNames',const_names);
            T.Description = [];
            % Combine
            T = [T T1];

            %% Only keep stations within our domain
            bnde = extdom_edges2(obj.t,obj.p);
            poly = extdom_polygon(bnde,obj.p,0);

            k=0; poly_vec=[];
            for i = 1 : length(poly)
                for ii = 1 : length(poly{i})
                    k = k + 1;
                    poly_vec(k,:) = poly{i}(ii,:);
                end
                k = k + 1;
                poly_vec(k,:) = [NaN,NaN];
            end
            edges = Get_poly_edges(poly_vec);
            in = inpoly([T.Lon,T.Lat],poly_vec,edges);
            T = T(in,:);
            %% Delete duplicates
            radius = 0.08/60; % only take one station within 1 min box
            [~,IA] = uniquetol([T.Lon T.Lat],radius,'ByRows',true,...
                'DataScale',1,'OutputAllIndices',true);
            % Just initialise T_new randomly
            T_new = T(1:length(IA),:);
            delete = []; nn = 0;
            for ii = 1:length(IA)
                T_temp = T(IA{ii},:);
                % We want to pick the source in heirachial order
                for s = Source
                    exp_s = regexp(T_temp.Source,s{1});
                    exp_s = find(~cellfun(@isempty,exp_s));
                    if ~isempty(exp_s)
                        if length(exp_s) > 1
                        end
                        T_new(ii,:) = T_temp(exp_s,:);
                        break
                    end
                end
                if isempty(exp_s)
                    nn = nn + 1;
                    delete(nn) = ii;
                end
            end
            T_new(delete,:) = [];
            % sorting
            [~,IA] = sort(T_new.Name);
            T_new = T_new(IA,:);
            [~,IA] = sort(T_new.Source);
            T_new = T_new(IA,:);

            %% Write to the .csv
            % Output table of the names and positions
            writetable(T_new(IA,:),ofname)
            %             %% Populate the f15
            %             % elevation
            %             obj.f15.nstae = obj.f15.nstae + numel(find(Sta_type(:,1)));
            %             obj.f15.elvstaloc = [obj.f15.elvstaloc;
            %                 [Sta_lon(Sta_type(:,1) == 1) ...
            %                 Sta_lat(Sta_type(:,1) == 1)]];
            %             obj.f15.elvstaname = [obj.f15.elvstaname;
            %                 strcat(Sta_name(Sta_type(:,1) == 1),' ID:',...
            %                 Sta_ID(Sta_type(:,1) == 1))];

        end

        function [ef,efx,efy]=reconstructEdgefx(obj,efdx)
            % Given a msh object, reconstruct the edge function resolution
            % with a resolution equal to efdx in WGS84 degrees.
            efdx = efdx/111e3;

            TR = triangulation(obj.t,obj.p(:,1),obj.p(:,2));
            [~,cr] = circumcenter(TR);

            for i = 1  : length(obj.t)
                cl = cr(i) ;
                for j = 1 :  3
                    z(obj.t(i,j)) = cl;
                end
            end

            bbox = [min(obj.p); max(obj.p)]';
            [efx,efy] = ndgrid(bbox(1,1):efdx:bbox(1,2),...
                bbox(2,1):efdx:bbox(2,2));
            F = scatteredInterpolant(obj.p(:,1),obj.p(:,2),z','linear','linear');

            ef = F(efx,efy);

            bnde = extdom_edges2(obj.t,obj.p);
            poly1=extdom_polygon(bnde,obj.p,1);
            for i = 1 : length(poly1)
                poly1{i} = [poly1{i} ; NaN NaN];
            end
            poly_vec1=cell2mat(poly1');
            edges1=Get_poly_edges(poly_vec1);
            in = inpoly([efx(:),efy(:)],poly_vec1,edges1);
            ef(~in) = NaN;
        end

        function [centroids,bc] = baryc(obj)
            centroids = (obj.p(obj.t(:,1),:)+obj.p(obj.t(:,2),:)+obj.p(obj.t(:,3),:))/3;
            if nargout > 1 && ~isempty(obj.b)
                bc = (obj.b(obj.t(:,1))+obj.b(obj.t(:,2))+obj.b(obj.t(:,3)))/3;
            end
        end

        function [obj3] = minus(obj1,obj2)
            % Given two overlapping triangulations described in msh objects
            % obj1 and obj2, remove the triangles in obj1 with centroids
            % that are in the boundary of obj2.
            % Here the notion of "in" is defined as being with the polygon
            % that is the boundary of obj2.
            %
            % NOTE: The first mesh must define a region that inclues the region
            % of obj2 but not the entitery, otherwise the algorithm removes
            % all of obj1 and segfaults.
            % Author: keith, und, chl, 2018
            bnde = extdom_edges2(obj2.t,obj2.p);
            poly = extdom_polygon(bnde,obj2.p,-1);
            polyc= cell2mat(poly');
            edges=Get_poly_edges(polyc);

            centroids = baryc(obj1) ;
            in = inpoly(centroids,polyc,edges);

            tempp = obj1.p;
            tempt = obj1.t;

            tempt(in,:) = [] ;
            [tempp,tempt]=fixmesh(tempp,tempt) ;

            obj3 = msh();
            obj3.p = tempp; obj3.t = tempt;
            obj3 = renum(obj3);

        end

        function obj = bound_con_int(obj,nvl) %nvu,
            %  bound_con_int updates all interior nodes that are connected
            %  to more than 7 nodes and less than 21 so that every node is
            %  connected to at most 7 nodes. It also makes sure there are no
            %  small connectivity less than 5 nodes. A springing routine is used locally
            %  to help smooth out the updates.  Note that specifying NVL one can
            %  fix nodes with connectivity of NVL or higher and leave the others.
            %
            %  NOTE:  fem_struct.nei should already be a component, if not one is
            %         computed.
            %
            %
            %  Variables
            %  fem_struct -- is the finite element structure from the opnml suite.
            %  fem -- the updated finite element structure.
            %        Note:  fem.x,fem.y,fem.z,fem.e, fem.nei, and fem.ar
            %                  get updated.
            %               fem.bnd does not need to be updated.
            %  nvl -- lower limit of connectivity to fix should be 8 <= nvl <= 20
            %  nvu -- upper limit of connectivity to fix should be 4 usually
            %
            %  Usage -- fem = reduce_con_int(fem_struct);
            %
            %  Name: reduce_con_int.m
            %  Written by: Ben Holladay (SEAP Student 2004)
            %  Date: June 22,2004
            %  Modified:  Aug. 30, 2004, Chris Massey
            %             Jan. 10, 2006, Chris Massey
            %             Aug. 15, 2006, Chris Massey  - Cleaned up comments.
            %             Sept. 19, 2006, Chris Massey -- fixed bug
            %             Aug. 22, 2007, Chris Massey -- fixed bug
            %             Apr. 25, 2018, Chris Massey -- Added nvl option to fix nodes
            %                with connectivity higher than or equal to nvl.
            %             Apr. 26, 2018, Keith Roberts--Merged into msh class for
            %             OceanMesh software
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

            % save object for mapping
            obj_old = obj;

            % convert msh obj to fem_struct
            bnde=extdom_edges2(obj.t,obj.p);
            fem_struct.x = obj.p(:,1);
            fem_struct.y = obj.p(:,2);
            fem_struct.e = obj.t;
            if ~isempty(obj.b)
                fem_struct.z = obj.b;
            else
                fem_struct.z = obj.p(:,1)*0;
            end
            fem_struct.bnd = bnde;
            fem_struct.ar  = fem_struct.z*0.0;
            fem_struct.name= 'temp';
            if ~isempty(obj.f15) || ~isempty(obj.f13)
                warning('Reduce nodal connectivity will migrate your nodal attributes using nearest neighbor interpolation and earse your control file.');
            end

            %Ensure the appropriate number of input arguements is given, checks that the
            %fem_struct is valid.
            if nargin == 0
                error('Not enough input arguments; need a valid fem_struct.');
            end
            if ~is_valid_struct(fem_struct)
                error('Input argument to reduce_con_bnd must be a valid fem_struct.');
            end
            %             % Make sure that the upper limit of connectivity count falls
            %             % no larger than 4 nodes
            %             if nargin < 2
            %                 if nvl > 4
            %                     disp('Connectivity Upper Limit must not be greater than 4. Resetting');
            %                     nvu = 4;
            %                 end
            %             else
            %                 nvu = 4;
            %             end

            %Make sure that the lower limit of connecitivity count falls between
            % 8 and 20 nodes
            if nargin == 2
                if nvl < 8
                    disp('Connectivity Lower Limit must be at least 8.  Resetting');
                    nvl = 8;
                end
                if nvl > 20
                    disp('Connectivity Lower Limit must not be greater than 20. Resetting');
                    nvl = 20;
                end
            else
                nvl = 8;
            end

            %Sets the intial fem_struct variables and determines the max
            %connectivity. Displays errors if the connectivity is to high.

            % List of all nodes not on the boundary;
            tmpnodes = setdiff(1:1:length(fem_struct.x),unique(fem_struct.bnd(:)));
            bndrynodes = unique(fem_struct.bnd(:));

            nelems = size(fem_struct.e,1);

            % Determine if fem_struct.nei is present, if not added it.
            try
                nc = size(fem_struct.nei(tmpnodes,:),2);
            catch
                disp(' ');
                disp('A neighbor list was not present in the finite element structure.');
                disp('One is being added now.');
                fem_struct.nei = ele2nei(fem_struct.e,fem_struct.x,fem_struct.y);
                disp(' ');
                disp('The neigbor list was successfully added.');
                nc = size(fem_struct.nei(tmpnodes,:),2);
            end

            nelems_orig = nelems;
            nnodes_orig = length(fem_struct.x);
            nc_orig = nc;

            [~,J1] = find(fem_struct.nei(bndrynodes,:)~=0);
            highbndry = max(J1);
            clear J1

            %nsmall = any(fem_struct.nei(j,nvu+1));

            if nc > 21
                error(['The connectivity is too high and must be brought down to at least',...
                    '20 by hand.']);
            end

            if nc <= nvl-1
                disp(['The grids nodal connectivity is not higher than ',num2str(nvl),', nothing will be done.']);
                disp('Returning the original mesh.');
                return
            end

            disp(' ')
            disp('NOTE: NO UPDATING IS DONE FOR BOUNDARY NODES.');
            disp(' ')

            %Begins loop to update nodes.
            tempr = size(fem_struct.nei,2);
            if tempr < nvl-1 %7
                tempr = 0;
            else
                tmpr = length(find(fem_struct.nei(tmpnodes,nvl)~=0));
            end
            imax = 20;i = 1;
            i2flag = 1;
            fixedint=[];
            disp('Beginning the update loop')
            disp(' ')
            while tempr ~= 0 && i <= imax
                disp(['Pass number ',num2str(i,'%4.0f'),' through the loop'])

                %tmpnodes2 = tmpnodes;
                %iupdnn=find(fem_struct.nei(tmpnodes,nvl)~=0);  %nodes with high connectivity
                %tmpnodes = tmpnodes(iupdnn);
                %clear tmpnodes2
                nnodes = size(fem_struct.nei(tmpnodes,:),1);

                j2 = 1;
                while j2 <= nnodes
                    jj = tmpnodes(j2);
                    temp2 = fem_struct.nei(jj,nvl); %8;
                    if  temp2 ~= 0
                        testnei = fem_struct.nei(jj,:);
                        % TCM -- Begin -- 09/19/2006
                        %temp1 = sum(ismember((fem_struct.nei(j,:)),0)); TCM
                        %tempnc = nc - temp1; TCM
                        tempnc = sum(~ismember((fem_struct.nei(jj,:)),0)); %TCM
                        % TCM -- END -- 09/19/2006

                        disp(['Updating node number ',num2str(jj),' using',' fix ',num2str(tempnc)]);
                        switch tempnc
                            case {13,14,15,16,17,18,19,20}
                                fem_struct = update1320nbr(fem_struct,jj);
                            case 12
                                fem_struct = update12nbr(fem_struct,jj);
                            case 11
                                fem_struct = update11nbr(fem_struct,jj);
                            case 10
                                fem_struct = update10nbr(fem_struct,jj);
                            case 9
                                fem_struct = update9nbr(fem_struct,jj);
                            case 8
                                fem_struct = update8nbr(fem_struct,jj);
                            otherwise
                                disp('Already fixed.')
                        end
                        if sum(testnei) == sum(fem_struct.nei(jj,:)) %?? What is this test?
                            fixedint(i2flag) = jj;
                            temp1 = find(fem_struct.nei(jj,:) ~= 0,1,'last');
                            fixedintnei(i2flag) = temp1;
                            i2flag = i2flag + 1;
                        end
                    end
                    if size(fem_struct.nei,2) < nvl %8
                        j2 = nnodes + 1;
                    else
                        j2 = j2 + 1;
                    end
                end

                %Check if any nodes where added to the do not update lists.
                try
                    fixedint = fixedint;
                    fixedintnei = fixedintnei;
                catch
                    fixedint = 1:0;
                    fixedintnei = 1:0;
                end

                %Create do not update list for interior nodes.

                %newnei = fem_struct.nei(fixedint,:);
                %temp1 = ismember(fem_struct.nei(fixedint,:),0);
                %temp2 = sum(temp1,2);
                %temp3 = [(size(fem_struct.nei,2))-temp2];
                %temp4 = fixedintnei' - temp3;
                %temp5 = find(temp4 < 0);
                %fixedint(temp5) = [];
                %fixedintnei(temp5) = [];
                %temp6 = size(temp5,1);
                %i2flag = i2flag - temp6;

                int = setdiff(1:length(fem_struct.x),bndrynodes);

                tmpnodes = setdiff(int,fixedint);

                i = i + 1;
                %tmpnodes = setdiff(1:1:length(fem_struct.x),unique(fem_struct.bnd(:)));
                if size(fem_struct.nei,2) > nvl-1
                    tempr = length(find(fem_struct.nei(tmpnodes,nvl) ~= 0));
                else
                    tempr = 0;
                end
            end

            %Creates the output structure.
            fem = fem_struct;
            [~,J1] = find(fem_struct.nei(tmpnodes,:)~=0);
            highint = max(J1);

            fem.nei = fem.nei(:,1:max(highint,highbndry));
            fem = el_areas(fem);

            % Display a message that we reached the maximum number of loop iterations
            % prior to minimizing the interior nodal connectivity list
            if i>imax && highint > nvl-1 %7
                disp(' ')
                disp(['Maximum loop iteration count of ',num2str(imax),' was',...
                    ' exceeded before all interior nodes']);
                disp('reached their miniminal connecitvity.');
            end

            % Display a summary of mesh updates.
            disp(' ')
            disp([num2str(size(fem.e,1)-nelems_orig),' elements have been added']);
            disp([num2str(length(fem.x)-nnodes_orig),' nodes have been added']);
            disp(['Maximum interior nodal connectivity was reduced from ',...
                num2str(nc_orig), ' to ',num2str(highint),'.']);
            disp(['The maximum nodal connectivity for a boundary node',...
                ' is ',num2str(highbndry),'.']);
            disp(' ');

            % kjr convert back to msh obj.
            obj.p = [fem_struct.x,fem_struct.y];
            obj.t = fem_struct.e;
            obj = map_mesh_properties(obj,'msh_old',obj_old);
        end

        function obj = flipEdge(obj,j,k)
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            %Line_swap is mesh refining tool that swaps an edge that two elements
            % share. It reconnects the elements so that the edge they share has been
            % flipped. This routine only operates on one line at a time and can only be
            % used if the two elements share an edge. This routine can operate on any
            % elemnet, even boundry elements, unless the new elements formed by the line
            % swap would overlap existing elements. No nodes are moved by this routine.
            % The fem.e and fem.ar are the only fields that are updated. If no .nei file
            % is present then none will be generated; however, if one is present then
            % it will be updated to reflect the new connectivity.
            %
            % Calls: is_valid_struct.m
            %
            % Usage: fem = line_swap(fem_struct,j,k);
            %
            % Variables:
            %  fem -- the new split finite element mesh.
            %  fem_struct -- the finite element grid structure from the opnml suite.
            %          Note: fem_struct.nei will not be generated if not present
            %  j -- element number for one element used in the line swap.
            %  k -- element number for one element used in the line swap.
            %          Note: j and k can be interchanged.
            %
            % Filename: line_swap.m
            % Created by: Ben Holladay
            % Date: June 8, 2005
            % Last Modified:
            %       Oct. 26, 2007 -- Chris Massey, NRL 7322
            %       Changed when line swap can not be performed due to mesh tangling,
            %       from an error call to a display message and return original fem.
            % Last Modified:
            %       Added into msh class for OceanMesh2D software--kjr, chl, und,
            %       April 2018.
            %%%
            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

            % convert msh obj to fem_struct
            bnde=extdom_edges2(obj.t,obj.p);
            fem_struct.x = obj.p(:,1);
            fem_struct.y = obj.p(:,2);
            fem_struct.e = obj.t;
            if ~isempty(obj.b)
                fem_struct.z = obj.b;
            else
                fem_struct.z = obj.p(:,1)*0;
            end
            fem_struct.bnd = bnde;
            fem_struct.ar  = obj.b*0.0;
            fem_struct.name= 'temp';
            if ~isempty(obj.f15) || ~isempty(obj.f13)
                warning('Reduce nodal connectivity will erase your nodal attributes and control file. Go on?');
                pause
            end

            %Ensure the apropriate number of input arguements is given, checks that the
            %fem_struct is valid.
            if nargin == 0
                error('Not enough input arguments; need a fem_struct and two element numbers.');
            end
            if ~is_valid_struct(fem_struct)
                error('Input argument to line swap must be a valid fem_struct.');
            end
            if nargin == 1
                error(['Input arguments must include a valid fem_struct and two element ' , ...
                    'numbers that share an edge.']);
            elseif nargin == 2
                error('Two element numbers must be given.');
            elseif nargin == 3
                if j <= 0 | j > size(fem_struct.e,1) | j ~= floor(j)
                    error(['Element numbers must positive integers that are less than ',...
                        'the maximum number of elements.']);
                end
                if k <= 0 | k > size(fem_struct.e,1) | k ~= floor(k)
                    error(['Element numbers must positive integers that are less than ',...
                        'the maximum number of elements.']);
                end
            else
                error('Too many input arguments.');
            end

            %Sets the intial fem_struct variables.
            x = fem_struct.x;
            y = fem_struct.y;
            enodes = fem_struct.e;
            ar = fem_struct.ar;

            %Determine if the elements share a common edge.
            elems = enodes([j;k],:);
            comp = unique(intersect(elems(1,:),elems(2,:)));
            if length(comp) < 2
                error('The elements do not share a common edge.');
            end

            %Indentify each node for swapping.
            [nodes,ti,tj] = unique(elems);
            temp1 = setdiff((1:6),ti);
            temp1 = elems(temp1);
            temp2 = setdiff(nodes,temp1);

            %Determine if the angle between the elements is too big for line_swap to
            %effectively operate on it.
            a2 = (x(enodes([j;k],3))-x(enodes([j;k],2))).^2+(y(enodes([j;k],3))-y(enodes([j;k],2))).^2;
            b2 = (x(enodes([j;k],1))-x(enodes([j;k],3))).^2+(y(enodes([j;k],1))-y(enodes([j;k],3))).^2;
            c2 = (x(enodes([j;k],2))-x(enodes([j;k],1))).^2+(y(enodes([j;k],2))-y(enodes([j;k],1))).^2;
            A = (180/pi)*acos((b2+c2-a2)./(2*sqrt(b2).*sqrt(c2)));
            B = (180/pi)*acos((c2+a2-b2)./(2*sqrt(c2).*sqrt(a2)));
            C = (180/pi)*acos((a2+b2-c2)./(2*sqrt(a2).*sqrt(b2)));
            ang = [A,B,C];
            temp3 = find(temp1(1) == elems);
            temp4 = find(temp1(2) == elems);
            temp5 = ang(temp3);
            temp6 = ang(temp4);
            temp5 = sum(temp5);
            temp6 = sum(temp6);
            if temp5 >= 180 | temp6 >= 180
                disp(['The line cannot be swapped because the new elements would '...
                    'create overlapping elements.']);
                fem = fem_struct;
                return
            elseif temp5 >= 135 | temp6 >= 135
                disp(['Warning: The elements created will contain large angles.']);
            end
            clear a2 b2 c2 A B C ang

            %Swap the lines in the enodes list.
            temp3 = setdiff(elems(1,:),temp1);
            temp4 = setdiff(elems(2,:),temp1);
            temp5 = find(elems(1,:) == temp1(1));
            elems(1,temp5) = temp4;
            temp6 = find(elems(2,:) == temp1(2));
            elems(2,temp6) = temp3;
            clear temp5 temp6;

            %Recomputes the areas for the new elements.
            xnodes = x(elems);
            ynodes = y(elems);
            temparea = 0.5*(xnodes(:,1).*(ynodes(:,2)-ynodes(:,3))+xnodes(:,2).*...
                (ynodes(:,3)-ynodes(:,1))+xnodes(:,3).*(ynodes(:,1)-ynodes(:,2)));
            clear xnodes ynodes x y;

            %Addes the new elements and areas to the global lists.
            enodes([j;k,],:) = elems;
            ar([j;k]) = temparea(:);
            clear elems temparea;

            %Create the output structure.
            fem = fem_struct;
            fem.e = enodes;
            fem.ar = ar;

            %Updates the nei if present.
            try
                nei = fem_struct.nei;
                nei = [nei,zeros((size(nei,1)),1)];
                tempnei = nei([temp1(:);temp2(:)],:);
                temp3 = find(tempnei(1,:) == temp1(2));
                temp4 = setdiff(1:(size(tempnei,2)),temp3);
                tempnei(1,:) = ([tempnei(1,temp4),0]);
                temp3 = find(tempnei(2,:) == temp1(1));
                temp4 = setdiff(1:(size(tempnei,2)),temp3);
                tempnei(2,:) = ([tempnei(2,temp4),0]);
                temp3 = find(tempnei(3,:) == temp1(1) | tempnei(3,:) == temp1(2));
                if abs(temp3(1)-temp3(2)) == 1
                    tempnei(3,:) = [tempnei(3,(1:temp3(1))),temp2(2),tempnei(3,((temp3(2)):(end-1)))];
                else
                    tempnei(3,:) = [temp2(2),tempnei(3,(1:end-1))];
                end
                temp3 = find(tempnei(4,:) == temp1(1) | tempnei(4,:) == temp1(2));
                if abs(temp3(1)-temp3(2)) == 1
                    tempnei(4,:) = [tempnei(4,(1:temp3(1))),temp2(1),tempnei(4,((temp3(2)):(end-1)))];
                else
                    tempnei(4,:) = [temp2(1),tempnei(4,(1:end-1))];
                end
                nei([temp1(:);temp2(:)],:) = tempnei;
                temp3 = find(nei(:,end) ~= 0);
                if isempty(temp3) == 1
                    nei = nei(:,(1:end-1));
                end
                temp3 = find(nei(:,end) ~= 0);
                if isempty(temp3) == 1
                    nei = nei(:,(1:end-1));
                end
                fem.nei = nei;
            catch
            end

            % kjr convert back to msh obj.
            obj.p = []; obj.b = []; obj.t =[];
            obj.p = [fem_struct.x,fem_struct.y];
            obj.b = fem_struct.z;
            obj.t = fem_struct.e;
        end

        function mfixed = MergeFP(muw,mfp)
            %%%%%%%
            % Merges a watertight mesh muw with a mesh that contains both
            % over and underwater sections mfp. This method assumes mfp has
            % been created by edge locking the shoreline and using fixed
            % points.
            %
            % INPUTS:
            % muw: watertight msh object
            % mfp: watertight msh with the floodplain using edge locking
            %
            % OUTPUTS:
            % mfixed: a final merged msh that seamlessly mates with the
            % underwater mesh.
            % kjr, April 2019

            m3 = mfp - muw ;

            dt = delaunayTriangulation(muw.p) ;

            dt.Points(end+(1:length(m3.p)),:) = m3.p ;

            tmp = mfp;

            tmp.p = dt.Points ; tmp.t = dt.ConnectivityList;

            % delete points outside mfp and muw
            bnde = extdom_edges2(mfp.t,mfp.p) ;
            polyt=extdom_polygon(bnde,mfp.p,-1,0,20) ;
            polyt=cell2mat(polyt') ;

            ee   = Get_poly_edges(polyt) ;
            bc   = baryc(tmp) ;
            infp   = inpoly(bc,polyt,ee) ;

            bnde = extdom_edges2(muw.t,muw.p) ;
            polyt=extdom_polygon(bnde,muw.p,-1,0,20) ;
            polyt=cell2mat(polyt') ;

            ee   = Get_poly_edges(polyt) ;
            bc   = baryc(tmp) ;
            inuw   = inpoly(bc,polyt,ee) ;

            tmp.t(~infp & ~inuw,:) = [] ;

            [tmp.p,tmp.t] = fixmesh(tmp.p,tmp.t) ;

            mfixed = tmp ;

            mfixed = renum(mfixed) ;

        end

        function [pfix,egfix] = extractFixedConstraints(obj)
            %%%%%%%
            % Extract boundary of mesh in no order.
            % INPUTS: msh_obj
            % OUTPUTS: the points and edges of the mesh
            % NOTE: You can visualize these constraints by
            % drawedge2(pfix,egfix);
            % kjr, April 2019
            [egfix,pfix] = extdom_edges2(obj.t,obj.p) ;
            if ~isempty(obj.op) && obj.op.nope > 0
                disp('detected ocean boundary, removing these fixed points')
                ocean = unique(obj.op.nbdv(:));
                [~,IA] = intersect(egfix(:,1),ocean);
                [~,IB] = intersect(egfix(:,2),ocean);
                DEL1 = unique([IA;IB]);
                egfix(DEL1,:) = [];
                pfix = obj.p(unique(egfix(:)),:);
            end
            egfix = renumberEdges(egfix) ;
        end

        function [boundary, bou_index] = get_boundary_of_mesh(obj,ascell)
            % [boundary, bou_index] = get_boundary_of_mesh(obj,ascell)
            %
            % Returns the boundary of the mesh and/or the mesh indices of
            % the boundary
            %
            % INPUTS: msh_obj
            % OUTPUTS: msh boundary in one of two forms:
            %   1) NaN-delimited vector in a "walking" order (ascell == 0 [default])
            %   2) A cell for each polygon (ascell = 1)
            %
            % kjr, April 2019
            % wjp, Oct 2020
            %
            if nargin < 2 || isempty(ascell)
                ascell = 0;
            end
            bnde = extdom_edges2(obj.t,obj.p) ;
            try
                [boundary,bou_index] = extdom_polygon(bnde,obj.p,-1) ;
            catch
                warning('ALERT: Boundary of mesh is not walkable. Returning polylines.');
                [boundary,bou_index] = extdom_polygon(bnde,obj.p,-1,1) ;
            end
            if ascell; return; end
            boundary = cell2mat(boundary');
            bou_index = cell2mat(bou_index');
        end

        function obj = map_mesh_properties(obj,varargin)
            % obj = map_mesh_properties(obj,varargin)
            % Map properties of a msh obj (e.g., bathymetry, f13) given a subset of integers, 'ind'.
            % Assumes that the msh.p and msh.t components of the mesh have already
            % been changed. A common usage would be after receiving the indices as
            % an output from the `fixmesh` function. However, these mapping indices can also be derived
            % from nearest neighbor interpolation
            %
            % Usage:
            %   obj = map_mesh_properties(obj,'ind',index_mapping);
            %   obj = map_mesh_properties(obj,'msh_old',old_msh_object);
            %
            % varargin options:
            %   i)   'ind' - A mapping from an old mesh to a new mesh.
            %                the old mesh and new mesh ideally
            %                shouldn't have changed much
            %   ii)  'msh_old' - an old mesh object from which `ind` are calculated to perform the mapping
            %

            % Name value pairs specified.
            % Parse other varargin
            ind = [];
            m_old = obj;
            for kk = 1:2:length(varargin)
                if strcmp(varargin{kk},'msh_old')
                    m_old = varargin{kk+1};
                elseif strcmp(varargin{kk},'ind')
                    ind = varargin{kk+1};
                end
            end
            if isempty(ind)
                ind = nearest_neighbor_map(m_old, obj);
            end
            if ~isempty(m_old.b)
                obj.b = m_old.b(ind);
            end
            % topographic gradients
            if ~isempty(obj.bx)
                obj.bx = m_old.bx(ind);
            end
            if ~isempty(obj.by)
                obj.by = m_old.by(ind);
            end
            % open boundary info
            if ~isempty(obj.op) && obj.op.nope > 0
                for ib = 1 : obj.op.nope
                    idx_old = obj.op.nbdv(1:obj.op.nvdll(ib),ib);
                    % Only keep idx_old that is common to ind and map to ind
                    [~,~,idx_new] = intersect(idx_old,ind,'stable');
                    % if a polygon
                    if ~isempty(idx_new) && ...
                            length(idx_new) == length(idx_old)-1 && idx_old(end) == idx_old(1)
                        idx_new(end+1) = idx_new(1);
                    end
                    % Get the new length of this boundary
                    obj.op.nvdll(ib) = length(idx_new);
                    % Reset and reload the nbdv for this boundary
                    obj.op.nbdv(:,ib) = 0;
                    obj.op.nbdv(1:obj.op.nvdll(ib),ib) = idx_new;
                end
                obj.op.neta = sum(obj.op.nvdll);
                if obj.op.neta == 0
                    % Remove open boundary info...
                    obj.op = [];
                else
                    % Remove zero length boundary and unnessary part from the nbdv
                    obj.op.nbdv = obj.op.nbdv(1:max(obj.op.nvdll),:);
                    zero_bound = obj.op.nvdll == 0;
                    obj.op.nope = sum(~zero_bound);
                    obj.op.ibtype(zero_bound) = [];
                    obj.op.nvdll(zero_bound) = [];
                    obj.op.nbdv(:,zero_bound) = [];
                end
            end
            % land boundary info
            if ~isempty(obj.bd) && obj.bd.nbou > 0
                for ib = 1 : obj.bd.nbou
                    nvell_old = obj.bd.nvell(ib);
                    idx_old = obj.bd.nbvv(1:nvell_old,ib);
                    % Only keep idx_old that is common to ind and map to ind
                    [~,idx_new] = ismember(idx_old,ind); % allows for repeats
                    idx_new(idx_new == 0) = [];
                    % Get the new length of this boundary
                    obj.bd.nvell(ib) = length(idx_new);
                    % Reset and reload the nbdv for this boundary
                    obj.bd.nbvv(:,ib) = 0;
                    obj.bd.nbvv(1:obj.bd.nvell(ib),ib) = idx_new;
                    %
                    % Proceed only if the ibconn field exists and if ibtype
                    % is one of 4, 5, 24, 25
                    if ~isfield(obj.bd,'ibconn'); continue; end
                    if obj.bd.ibtype(ib) ~= 4 && obj.bd.ibtype(ib) ~= 5 && ...
                       obj.bd.ibtype(ib) ~= 24 && obj.bd.ibtype(ib) ~= 25
                       continue;
                    end
                    idx_old = obj.bd.ibconn(1:nvell_old,ib);
                    % Only keep idx_old that is common to ind and map to ind
                    [~,idx_new] = ismember(idx_old,ind);
                    idx_new(idx_new == 0) = [];
                    nconn = length(idx_new);
                    % Check the new length of this boundary
                    if nconn ~=  obj.bd.nvell(ib)
                        warning(['ibconn of subset has a different length to nbvv. ' ...
                                 'Setting boundary length to smallest of the two. ' ...
                                 'To avoid this message make sure the weir is fully within the subset.'])
                        disp(['boundary number = ' num2str(ib)])
                        disp(['length of nbvv = ', num2str(obj.bd.nvell(ib))])
                        disp(['length of ibconn = ' num2str(nconn)])
                        obj.bd.nvell(ib) = min(nconn,obj.bd.nvell(ib));
                    end
                    % Reset and reload the ibconn for this boundary
                    obj.bd.ibconn(:,ib) = 0;
                    obj.bd.ibconn(1:obj.bd.nvell(ib),ib) = idx_new(1:obj.bd.nvell(ib));
                end
                obj.bd.nvel = sum(obj.bd.nvell);
                if obj.bd.nvel == 0
                    % Remove land boundary info...
                    obj.bd = [];
                else
                    % Remove unnessary part from the nbdv
                    obj.bd.nbvv = obj.bd.nbvv(1:max(obj.bd.nvell),:);
                    obj.bd.nbvv(:,obj.bd.nvell == 0) = [];
                    if isfield(obj.bd,'ibconn')
                        obj.bd.ibconn = obj.bd.ibconn(1:max(obj.bd.nvell),:);
                        obj.bd.barinht = obj.bd.barinht(1:max(obj.bd.nvell),:);
                        obj.bd.barincfsb = obj.bd.barincfsb(1:max(obj.bd.nvell),:);
                        obj.bd.barincfsp = obj.bd.barincfsp(1:max(obj.bd.nvell),:);
                        obj.bd.ibconn(:,obj.bd.nvell == 0) = [];
                        obj.bd.barinht(:,obj.bd.nvell == 0) = [];
                        obj.bd.barincfsb(:,obj.bd.nvell == 0) = [];
                        obj.bd.barincfsp(:,obj.bd.nvell == 0) = [];
                    end
                    obj.bd.ibtype(obj.bd.nvell == 0) = [];
                    obj.bd.nvell(obj.bd.nvell == 0) = [];
                    obj.bd.nbou = length(obj.bd.nvell);
                end
            end
            % f13
            if ~isempty(m_old.f13)
                obj.f13 = m_old.f13;
                obj.f13.NumOfNodes = length(ind);
                for att = 1:obj.f13.nAttr
                    % Get the old index for this attribute
                    idx_old = m_old.f13.userval.Atr(att).Val(1,:);
                    val_old = m_old.f13.userval.Atr(att).Val(2:end,:);
                    % Only keep idx and val that is common to ind and map to ind
                    [~,ind_new,idx_new] = intersect(idx_old,ind);
                    val_new = val_old(:,ind_new);

                    % find indices of new nodes
                    [~,ind_added] = setdiff(obj.p,m_old.p,'rows');
                    if ~isempty(ind_added)
                        defval  = m_old.f13.defval.Atr(att).Val;
                        userval = m_old.f13.userval.Atr(att).Val;
                        defval = reshape(defval,1,[]);
                        values = m_old.p(:,1)*0 + defval;
                        values(userval(1,:),:) = userval(2:end,:)';
                        % for the new indices give the closest value in m_old
                        % for any given nodal attribute
                        tmp = ourKNNsearch(m_old.p',obj.p(ind_added,:)',1);
                        val_new2 = values(tmp,:);
                        idx_new = [idx_new; ind_added];
                        val_new = [val_new'; val_new2]';
                        [idx_new, C] = unique(idx_new);
                        val_new = val_new(:,C);
                    end
                    % Put the uservalues back into f13 struct
                    obj.f13.userval.Atr(att).AttrName = m_old.f13.userval.Atr(att).AttrName;
                    obj.f13.userval.Atr(att).Val = [idx_new'; val_new];
                    obj.f13.userval.Atr(att).usernumnodes = length(idx_new);
                end
            end
            % f24
            if ~isempty(obj.f24)
                obj.f24.Val = m_old.f24.Val(:,:,ind);
            end
            % f5354
            if ~isempty(obj.f5354)
                idx_old = m_old.f5354.nodes;
                [~,idx_new] = intersect(idx_old,ind);
                obj.f5354.nodes = idx_new;
            end
            % EOF
        end

        function obj = pruneOverlandMesh(obj,elev,djc)
            %%%%%%%
            % Removes overland extent greater than certain elevation about
            % geoid of the mesh.
            % INPUTS: msh_obj and height above the geoid whereby elements with
            % an average depth greater than elev are pruned from the mesh.
            % OUTPUS: a msh_obj with the overland extents removed.
            % april 2019, kjr
            if nargin < 3
                djc = 0.25;
            end
            [obj.p(:,1),obj.p(:,2)] =  m_ll2xy(obj.p(:,1),obj.p(:,2));
            Fb = scatteredInterpolant(obj.p(:,1),obj.p(:,2),obj.b,'linear','nearest') ;
            c = (obj.b(obj.t(:,1),:)+obj.b(obj.t(:,2),:)+obj.b(obj.t(:,3),:))/3;
            obj.t(c < -elev,:) = [];
            [pp,tt] = fixmesh(obj.p,obj.t) ;
            obj.p = pp; obj.t = tt;
            obj = Make_Mesh_Boundaries_Traversable(obj,djc,1);
            obj = renum(obj) ;
            obj.b = Fb(obj.p) ;
            [obj.p(:,1),obj.p(:,2)] =  m_xy2ll(obj.p(:,1),obj.p(:,2));
        end

        function obj = interpFP(obj,gdat,muw,gdatuw,minb,CAN)
            %%%%%%%
            % Interpolate topography onto a mesh with floodplain
            % Interpolates bathymetry underwater using a grid-scale
            % averaging with a minimum depth of 1-m.
            % Then it uses a 3x multipler for grid-scale averaging
            % to interpolate overland topography.
            % Finally, it updates the bathymetry on the outputted msh
            % to match the underwater and the overland sections.
            %
            %%%%%%%
            % INPUTS
            % obj: msh_obj to interpolate topograhy/bathy on
            % gdat:geodata obj that contains DEM (could be cell-array of
            % gdats)
            % muw: msh_obj of only the watertight portion of the domain
            %
            %%%%%%%
            % OUTPUTS:
            % a msh_obj with bathy/topo on its vertices
            %
            % kjr, april 2019

            % parsing some inputs (or set to default)
            if nargin < 5
                minb = 1;
            end
            if nargin < 6
                CAN = 3;
            end

            bnde = extdom_edges2(muw.t,muw.p) ;
            bou = extdom_polygon(bnde,muw.p,-1) ;
            bou = cell2mat(bou') ;

            dmy1 = obj; % land + uw

            ee = Get_poly_edges(bou);
            in = inpoly(dmy1.p,bou,ee) ;

            % get the "on"
            on = ismembertol(dmy1.p,muw.p,1e-5,'ByRows',true);

            obj.b = (1:length(obj.p(:,1)))'*0 ;

            if ~iscell(gdat); gdat = {gdat}; end

            for i = 1 : length(gdat)
                if isempty(gdat{i}.Fb)
                    disp(['Entry ',num2str(i), ' does not contain DEM, skipping']);
                    continue
                end
                if i == 1
                    in2 = true(size(obj.b));
                else
                    in2 = inpoly(dmy1.p,gdat{i}.boubox(1:end-1,:)) ;
                end
                dmy1 = interp(obj,gdatuw(i),'type','depth','ignoreOL',1);

                dmy2 = interp(obj,gdat(i),'type','depth','N',CAN) ; % use smooth overland

                if ~isempty(gdat{i}.mainlandb) || ~isempty(gdat{i}.innerb)
                    riverbound = [];
                    if ~isempty(gdat{i}.mainlandb)
                        notlakem = find(~contains(gdat{i}.mainlandb_type,'lake'));
                        isnan1 = find(isnan(gdat{i}.mainlandb(:,1)));
                        for l = 1:length(notlakem)
                            if notlakem(l) == 1; isn1 = 1; else
                                isn1 = isnan1(notlakem(l)-1)+1; end
                            isn2 = isnan1(notlakem(l))-1;
                            riverbound = [riverbound; ...
                                gdat{i}.mainlandb(isn1:isn2,:)];
                        end
                    end
                    if ~isempty(isempty(gdat{i}.innerb))
                        notlakei = find(~contains(gdat{i}.innerb_type,'lake'));
                        isnan1 = find(isnan(gdat{i}.innerb(:,1)));
                        for l = 1:length(notlakei)
                            if notlakei(l) == 1; isn1 = 1; else
                                isn1 = isnan1(notlakei(l)-1)+1; end
                            isn2 = isnan1(notlakei(l))-1;
                            riverbound = [riverbound; ...
                                gdat{i}.innerb(isn1:isn2,:)];
                        end
                    end

                    % kjr 2018,10,17; Set up projected space imported from msh class
                    dmyriver = dmy2;
                    dmyriver.p = [dmyriver.p; riverbound(:,1:2)];
                    setProj(dmyriver,1,obj.proj.name)
                    [rvb(:,1),rvb(:,2)] = ...
                        m_ll2xy(riverbound(:,1),riverbound(:,2));
                    [dmp(:,1),dmp(:,2)] = m_ll2xy(dmy2.p(:,1),dmy2.p(:,2));
                    F = scatteredInterpolant(rvb(:,1),rvb(:,2),...
                        riverbound(:,3),'natural','nearest');
                    offset = F(dmp);
                    % change above land
                    dmy2.b = min(0,dmy2.b + offset);
                    % change minb based on river height
                    minb = max(1,dmy1.b*0 + minb - offset);
                end
                uw = in | on | dmy1.b > 0;
                dmy1.b = max(dmy1.b,minb); % bound the depth by minb
                obj.b(uw & in2,1) = dmy1.b(uw & in2,1) ;
                obj.b(~uw & in2,1) = dmy2.b(~uw & in2,1) ;

            end

        end

        function poly = get_poly(obj, auto)
            % obj = get_poly(obj, auto)
            % Get the walkable polygon around a hole in the
            % mesh by clicking the starting point.
            % Common use case would be to re-mesh an area of the mesh.
            %
            % Input(s)
            % obj - msh object
            % auto - whether user clicks or not to draw polygon
            %
            % Return(s)
            % poly - a cell-array of polygons
            %
            % See also Examples/Example_12_Remeshing_Patches.m
            %
            % Created by Keith Roberts, 2020, USP
            dir = 1;

            if nargin < 3
                auto = 1;
            end

            [bnde,bpts] = extdom_edges2(obj.t,obj.p);

            if auto == 1
                [poly] = extdom_polygon(bnde,obj.p,dir);
            else
                % use this to figure out the vstart and vend
                figure, plot(bpts(:,1),bpts(:,2),'k.');
                %hold on; fastscatter(obj.p(:,1),obj.p(:,2),obj.b) ;
                caxis([-10 10]) ; axis equal ;
                title('Use the data cursor to identify the starting point');
                dcm_obj = datacursormode(gcf);
                set(dcm_obj,'UpdateFcn',{@myupdatefcn2,bpts})

                % Use data cursor to get the values of the boundary nodes.
                vstart=input('Enter the index for the starting point : ');

                bndidx = unique(bnde(:));
                vstart = bndidx(vstart);
                vend = vstart; % assume start is end

                [poly,~,~,~] = extract_boundary(vstart,vend,bnde,obj.p,dir,[],[],0,0);
            end

            function txt = myupdatefcn2(~,event_obj,myarray)
                pos = get(event_obj,'Position');
                ind = find(abs(myarray(:,1)-pos(1))<eps & abs(myarray(:,2)-pos(2))<eps);
                txt = {['X: ',num2str(pos(1))],...
                    ['Y: ',num2str(pos(2))],...
                    ['Index: ',num2str(ind')]};
            end
        end

        function [smoothed] = mesh_patch_smoother(obj, poly)
            % obj = mesh_patch_smoother(obj, poly)
            % Smooth a patch of elements perserving the boundaries of the patch.
            % If poly is not supplied, prompts the user to draw it.
            %
            % Inputs
            % obj - msh object.
            % poly - a single polygon (does not require to be NaN-delimited).
            %
            % Outputs
            % smoothed - original msh obj but patch smoothed.
            %
            % Author Keith R. USP, Brazil, 2020

            if nargin < 2
                h = impoly;
                poly = h.getPosition;
            end
            sub1  = extract_subdomain(obj, poly,'keep_inverse',0);
            sub2  = extract_subdomain(obj, poly,'keep_inverse',1);
            sub1 = clean(sub1, {'ds',2,'mqa',1e-4,'djc',0.0,'con',5,'db',0,'sc_maxit',0});
            smoothed = plus(sub1,sub2,'match',{'djc',0.0,'ds',0,'db',0,'con',5,'mqa',1e-4,'sc_maxit',0});
        end

        function obj= remove_attribute(obj, attrname)
            % obj = remove_attribute(obj, attrname)
            % Remove the attribute 'attrname' from the f13 field.
            %
            % Inputs
            % obj - msh object.
            % attrname - character string of the attribute name (or part of it).
            %        Warning: All 'contains' string matches will be removed
            % Outputs
            % obj - msh object with f13 attribute removed.
            %
            % Author WJP, Mar, 2021

            def_cell = {obj.f13.defval.Atr.AttrName};
            ii = find(contains(def_cell,attrname));
            disp(['Removing attribute(s): ' def_cell{ii}])
            obj.f13.defval.Atr(ii) = [];
            %
            user_cell = {obj.f13.userval.Atr.AttrName};
            ii = find(contains(user_cell,attrname));
            obj.f13.userval.Atr(ii) = [];
            %
            obj.f13.nAttr = length(obj.f13.defval.Atr);
        end

    end % end methods

end % end class

author: CHLNDDEV