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Merged
merged 9 commits into from
Feb 4, 2021
Merged

Clean interface improvements #181

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65132c6
Passive clean
Jan 31, 2021
cc7fe15
api change to map_mesh_properties
Jan 31, 2021
a13b9fb
docstring
Jan 31, 2021
a4bd29a
fiddling with map_mesh
Jan 31, 2021
c972e3a
Merge branch 'Projection' into improve_clean_interface
Feb 3, 2021
2b9a5c8
handling adding nodes
Feb 4, 2021
8986da5
Merge branch 'improve_clean_interface' of https://github.com/CHLNDDEV…
Feb 4, 2021
103f0f2
Update msh.m
Feb 4, 2021
8c34a10
Update README.md
Feb 4, 2021
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121 changes: 81 additions & 40 deletions @msh/msh.m
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
title % mesh title
p % vertices
t % triangles
b % bathymetry
b % bathy
bd % land boundaries
op % open boundaries
bx % slope of bathy in x direction
Expand Down Expand Up @@ -279,10 +279,10 @@ function write(obj,fname,type)
% 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
% 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
Expand All @@ -293,25 +293,25 @@ function write(obj,fname,type)
% j) 'transect' - plot a bathy transect through GUI
% k) 'xx' - plots an arbitrary f13 attribute 'xx' by
% contains search
%
% 'type' ADDITIONALS.
%
% '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
% 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.
% 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] or;
% [num_intervals caxis_lower caxis_upper]
% ii) 'fontsize': figure fontsize
% iii) 'backcolor': figure background RGB color (where mesh
Expand All @@ -321,13 +321,14 @@ function write(obj,fname,type)
% v) 'pivot' : value in meters for which to assume is datum when
% plotting topo-bathymetry (default 0.0 m)
%

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;

projtype = [];
type = 'tri';
subdomain = [];
Expand All @@ -343,14 +344,14 @@ function write(obj,fname,type)
elseif strcmp(varargin{kk}, 'pivot')
pivot = varargin{kk+1};
elseif strcmp(varargin{kk}, 'proj')
projtype = varargin{kk+1};
projtype = varargin{kk+1};
elseif strcmp(varargin{kk},'type')
type = varargin{kk+1};
elseif strcmp(varargin{kk},'subdomain')
subdomain = 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
Expand All @@ -370,7 +371,7 @@ function write(obj,fname,type)
if strcmp(projtype,'none')
proj = 0;
end

% Handle user specified subdomain
if ~isempty(subdomain)
% i.e. is a bounding box
Expand Down Expand Up @@ -673,7 +674,7 @@ function write(obj,fname,type)
end

function plotter(cmap,round_dec,yylabel,apply_pivot)
% applies the plot for the quantiy 'q' and specific
% applies the plot for the quantiy 'q' and specific
% colormap/colorbar inputs
if proj
if mesh
Expand Down Expand Up @@ -984,7 +985,7 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
%process categorical cleaning options
if any(strcmp(varargin,'passive'))
disp('Employing passive option')
opt.db = 0.1; opt.ds = 0; opt.con = 10; opt.djc = 0;
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'))
Expand Down Expand Up @@ -2465,7 +2466,7 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
% 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,pix);
obj = map_mesh_properties(obj,'ind',pix);
end


Expand Down Expand Up @@ -3365,6 +3366,9 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
% 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);
Expand All @@ -3379,8 +3383,7 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
fem_struct.ar = fem_struct.z*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
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
Expand Down Expand Up @@ -3596,10 +3599,8 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)

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

function obj = flipEdge(obj,j,k)
Expand Down Expand Up @@ -3899,24 +3900,48 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
boundary = cell2mat(boundary');
end

function obj = map_mesh_properties(obj,ind)
% obj = map_mesh_properties(obj,ind)
% Map properties of a msh obj given a subset of integers, 'ind'.
% Assumes that the p and t components of the mesh have already
% been changed
% -> Common usage would be after receiving the indices as
% an output from the fixmesh function
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
%
% ocean depths/topography
if ~isempty(obj.b)
obj.b = obj.b(ind);
% 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 = obj.bx(ind);
obj.bx = m_old.bx(ind);
end
if ~isempty(obj.by)
obj.by = obj.by(ind);
obj.by = m_old.by(ind);
end
% open boundary info
if ~isempty(obj.op) && obj.op.nope > 0
Expand Down Expand Up @@ -3994,23 +4019,39 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
obj.f13.NumOfNodes = length(ind);
for att = 1:obj.f13.nAttr
% Get the old index for this attribute
idx_old = obj.f13.userval.Atr(att).Val(1,:);
val_old = obj.f13.userval.Atr(att).Val(2:end,:);
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 = obj.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]';
end
% Put the uservalues back into f13 struct
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 = obj.f24.Val(:,:,ind);
obj.f24.Val = m_old.f24.Val(:,:,ind);
end
% f5354
if ~isempty(obj.f5354)
idx_old = obj.f5354.nodes;
idx_old = m_old.f5354.nodes;
[~,idx_new] = intersect(idx_old,ind);
obj.f5354.nodes = idx_new;
end
Expand Down Expand Up @@ -4204,8 +4245,8 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
['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.
Expand All @@ -4219,7 +4260,7 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
% smoothed - original msh obj but patch smoothed.
%
% Author Keith R. USP, Brazil, 2020

if nargin < 2
h = impoly;
poly = h.getPosition;
Expand All @@ -4229,7 +4270,7 @@ function plotter(cmap,round_dec,yylabel,apply_pivot)
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



end % end methods
Expand Down
1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -140,6 +140,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
## Added
- `mesh2d` interface improvements to filter small polygons.
- Support for creation of `fort.20` files for forcing rivers by @Jiangchao3
- Mesh "cleaning" modes moderate and aggressive transfer nodal attributes via improvements to `msh.map_mesh_properties`

## Changed
- `msh.plot()` overhaul. All options specified via kwarg.
Expand Down