Index: Damkjer/Damkjer_Research.sln =================================================================== --- Damkjer/Damkjer_Research.sln (revision 12) +++ Damkjer/Damkjer_Research.sln (revision 13) @@ -36,5 +36,9 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Util", "Util\Util.vcxproj", "{20FE2624-C64F-D61A-BD8F-1725A8E68A42}" EndProject -Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "VpTreeAPI", "MATLAB\VpTreeAPI\VpTreeAPI.vcxproj", "{1B676DFD-587D-21CB-803A-A85006F79AEC}" +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "VpTreeAPI", "Util\MATLAB\VpTreeAPI\VpTreeAPI.vcxproj", "{60D16805-4012-4602-742C-4578A6C2DE6E}" +EndProject +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "test_SplayTree", "Util\Dictionaries\test\TestSplayTree.vcxproj", "{344E49A2-518C-23E5-9358-09928FD326E3}" +EndProject +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "SplayTreeAPI", "Util\MATLAB\SplayTreeAPI\SplayTreeAPI.vcxproj", "{3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}" EndProject Global @@ -133,20 +137,52 @@ {20FE2624-C64F-D61A-BD8F-1725A8E68A42}.Release|x64.ActiveCfg = Release|x64 {20FE2624-C64F-D61A-BD8F-1725A8E68A42}.Release|x64.Build.0 = Release|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Debug|Win32.ActiveCfg = Debug|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Debug|Win32.Build.0 = Debug|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Debug|x64.ActiveCfg = Debug|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Debug|x64.Build.0 = Debug|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.DebugOMP|Win32.ActiveCfg = DebugOMP|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.DebugOMP|Win32.Build.0 = DebugOMP|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.DebugOMP|x64.ActiveCfg = DebugOMP|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.DebugOMP|x64.Build.0 = DebugOMP|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.OpenMP|Win32.ActiveCfg = OpenMP|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.OpenMP|Win32.Build.0 = OpenMP|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.OpenMP|x64.ActiveCfg = OpenMP|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.OpenMP|x64.Build.0 = OpenMP|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Release|Win32.ActiveCfg = Release|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Release|Win32.Build.0 = Release|Win32 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Release|x64.ActiveCfg = Release|x64 - {1B676DFD-587D-21CB-803A-A85006F79AEC}.Release|x64.Build.0 = Release|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Debug|Win32.ActiveCfg = Debug|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Debug|Win32.Build.0 = Debug|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Debug|x64.ActiveCfg = Debug|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Debug|x64.Build.0 = Debug|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.DebugOMP|Win32.ActiveCfg = DebugOMP|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.DebugOMP|Win32.Build.0 = DebugOMP|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.DebugOMP|x64.ActiveCfg = DebugOMP|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.DebugOMP|x64.Build.0 = DebugOMP|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.OpenMP|Win32.ActiveCfg = OpenMP|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.OpenMP|Win32.Build.0 = OpenMP|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.OpenMP|x64.ActiveCfg = OpenMP|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.OpenMP|x64.Build.0 = OpenMP|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Release|Win32.ActiveCfg = Release|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Release|Win32.Build.0 = Release|Win32 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Release|x64.ActiveCfg = Release|x64 + {60D16805-4012-4602-742C-4578A6C2DE6E}.Release|x64.Build.0 = Release|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.Debug|Win32.ActiveCfg = Debug|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.Debug|Win32.Build.0 = Debug|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.Debug|x64.ActiveCfg = Debug|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.Debug|x64.Build.0 = Debug|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.DebugOMP|Win32.ActiveCfg = DebugOMP|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.DebugOMP|Win32.Build.0 = DebugOMP|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.DebugOMP|x64.ActiveCfg = DebugOMP|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.DebugOMP|x64.Build.0 = DebugOMP|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.OpenMP|Win32.ActiveCfg = OpenMP|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.OpenMP|Win32.Build.0 = OpenMP|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.OpenMP|x64.ActiveCfg = OpenMP|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.OpenMP|x64.Build.0 = OpenMP|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.Release|Win32.ActiveCfg = Release|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.Release|Win32.Build.0 = Release|Win32 + {344E49A2-518C-23E5-9358-09928FD326E3}.Release|x64.ActiveCfg = Release|x64 + {344E49A2-518C-23E5-9358-09928FD326E3}.Release|x64.Build.0 = Release|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Debug|Win32.ActiveCfg = Debug|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Debug|Win32.Build.0 = Debug|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Debug|x64.ActiveCfg = Debug|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Debug|x64.Build.0 = Debug|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.DebugOMP|Win32.ActiveCfg = DebugOMP|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.DebugOMP|Win32.Build.0 = DebugOMP|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.DebugOMP|x64.ActiveCfg = DebugOMP|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.DebugOMP|x64.Build.0 = DebugOMP|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.OpenMP|Win32.ActiveCfg = OpenMP|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.OpenMP|Win32.Build.0 = OpenMP|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.OpenMP|x64.ActiveCfg = OpenMP|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.OpenMP|x64.Build.0 = OpenMP|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Release|Win32.ActiveCfg = Release|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Release|Win32.Build.0 = Release|Win32 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Release|x64.ActiveCfg = Release|x64 + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution @@ -158,9 +194,11 @@ {A1B0D6A4-C217-4E4D-8832-EB81D59F2283} = {27DB8DBD-623B-4593-80F3-9F25F07BBA1A} {20FE2624-C64F-D61A-BD8F-1725A8E68A42} = {27DB8DBD-623B-4593-80F3-9F25F07BBA1A} - {1B676DFD-587D-21CB-803A-A85006F79AEC} = {3411130C-FC3A-47AD-9277-EEA9BDA15D28} + {60D16805-4012-4602-742C-4578A6C2DE6E} = {3411130C-FC3A-47AD-9277-EEA9BDA15D28} + {3C2B4717-4B1D-6843-E0DD-80DFD7B0ECD2} = {3411130C-FC3A-47AD-9277-EEA9BDA15D28} {75486221-5693-30A9-18E4-ECC307F92A68} = {3093F2E8-7C3B-4B90-8E92-C0C235FB979A} {FF08AA20-7D15-AEAB-9915-1FA343E8C993} = {3093F2E8-7C3B-4B90-8E92-C0C235FB979A} {72785A79-5BD2-AAE4-6386-93F74C7E248D} = {3093F2E8-7C3B-4B90-8E92-C0C235FB979A} {84624C89-966E-4948-1393-64F0D0965AC0} = {3093F2E8-7C3B-4B90-8E92-C0C235FB979A} + {344E49A2-518C-23E5-9358-09928FD326E3} = {3093F2E8-7C3B-4B90-8E92-C0C235FB979A} EndGlobalSection EndGlobal Index: Damkjer/PointProcessing/SpatialAnalyzer/nbrspanalyze.m =================================================================== --- Damkjer/PointProcessing/SpatialAnalyzer/nbrspanalyze.m (revision 13) +++ Damkjer/PointProcessing/SpatialAnalyzer/nbrspanalyze.m (revision 13) @@ -0,0 +1,228 @@ +% NbrSpAnalyze Point Cloud Spatial Analysis +% +% File: spanalize.m +% +% Description: +% Perform local feature attribution via eigenspace analysis. +% +% Limitations: +% No known limitations. +% +% Synopsis: +% [classes] = spanalyse(queries, database, ...) +% +% Inputs: +% queries - . +% database - . +% +% Option strings may be provided as abbreviations as long as they resolve to +% a unique option. +% +% 'neighbors' - . +% 'radius' - . +% 'counts' - . +% 'steps' - . +% +% Outputs: +% classes - Structure containing the spatial analysis classifications. +% +% Toolbox requirements: +% None. +% +% Code requirements: +% None. +% +% Data requirements: +% None. +% +% References: +% None. +% +% See Also: +% None. +% + +% Copyright (C) 2013 Kristian L. Damkjer. +% +% Software History: +% 2013-JAN-28 K. Damkjer +% Initial Coding. +% 2013-FEB-04 K. Damkjer +% Change output to a struct for easier referencing. +% + +%****************************************************************************** +% spanalyze +%****************************************************************************** +function [ classes ] = nbrspanalyze( points, neighborhoods, varargin ) + % Perform local feature attribution via eigenspace analysis. + % + % Parameters: + % queries - . + % + % database - . + % + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % classes - Structure containing the spatial analysis classifications. + % + + maketimebar = false; + + if (~isempty(varargin) && strcmp('timebar',varargin{1})) + maketimebar = true; + end + + % Sizing metrics + dimensions=size(points, 1); + elements=size(neighborhoods, 2); + + % Pre-allocate classes + norms=zeros(dimensions, elements); + feats=zeros(dimensions, elements); + biases=zeros(1,elements); + ints=zeros(1,elements); + + % This process may take a while. Display time bar while processing. + if (maketimebar) + msg='Analyzing Neighborhoods...'; + tstart=tic; + h = timebar(1, elements, msg, tstart); + end + + % Step through the queries in chunks. + step=1000; + + if (maketimebar) + tic; + end + + for elem=1:step:elements + + last=min(elem+step-1,elements); + + NN=neighborhoods(elem:last); + + cells=cell(1,length(NN)); + + for n=1:length(NN) + cells{n}=points(:,NN{n})'; + end + + [covs,bias,inty]=fastcov(cells); + + % Compute the neighborhood covariance eigenvalues. + [V,D]=par_eig(covs); + + for nbr=1:length(NN) + + % skip underconstrained neighborhoods (possible with radius searches) + if (length(NN{nbr})<5 || any(any(isnan(covs{nbr})))) + continue; + end + + [~,index]=min(abs(D{nbr})); + A=V{nbr}; + norms(:,elem+nbr-1)=abs(A(:,index)); + + % Option 1: Define features as eigenvalues + % feats(:,elem+nbr-1)=sort(D{nbr},'descend'); + + % Option 2: Define features as singular values. Eigenvalues are not + % guaranteed to be in any order. We want them in descending order. + % + % max is to get rid of pesky negative zeros. + feats(:,elem+nbr-1)=sqrt(max(sort(D{nbr},'descend'),0)); + + biases(elem+nbr-1)=bias{nbr}; + ints(elem+nbr-1)=inty{nbr}; + end + + % Update the time bar. + if (maketimebar && toc > 1) + tic; + h = timebar(elem, elements, msg, tstart, h); + end + end + + % Close the time bar, if still open. + if (maketimebar && all(ishghandle(h, 'figure'))) + close(h); + end + + % Compute Normalized Features + energy=sum(feats,1); + nfeats=bsxfun(@times,feats',1./energy')'; + nfeats(isnan(nfeats))=1; + + % Compute Omnivariance +% omnivar=prod(feats,1).^(1/dimensions); + omnivar=prod(feats.*feats,1).^(1/dimensions); +% omnivar=prod(nfeats,1).^(1/dimensions); + + % Compute Eigen Entropy + entropy=-sum(nfeats.*log(nfeats))./log(dimensions); + entropy(entropy==1)=0; + + % Compute Eigen Structure + structure=1-entropy; + + % Compute Fractional Anisotropy + evmeans=mean(feats,1); + evdevs=feats-repmat(evmeans,dimensions,1); + numer=dimensions.*sum(evdevs.^2,1); + denom=(dimensions-1).*sum(feats.^2,1); + fa=(numer./denom).^(1/2); + + % Compute Anisotropy + ani=(feats(1,:)-feats(dimensions,:))./(feats(1,:)); + + % Compute Isotropy + iso=1-ani; + + % Compute dimensional degree + dims=zeros(size(feats)); + dims(1:dimensions-1,:)=(feats(1:dimensions-1,:)-feats(2:dimensions,:))./... + repmat(feats(1,:),dimensions-1,1); + dims(dimensions,:)=iso; + + % Compute Dimensional Embedding + [~,label]=max(dims,[],1); + + % Compute dimensional entropy +% alpha=[dims;iso]; + alpha=dims; + de=-sum(alpha.*log(alpha))./log(dimensions); + + if (~isreal(de)) + disp('de...'); + disp(de); + disp('feats...'); + disp(feats); + disp('eigs...'); + disp(feats.*feats); + end + + % Populate feature classes + classes.features=feats; + classes.normals=norms; + classes.dimensionality=dims; + classes.isotropy=iso; + classes.anisotropy=ani; + classes.FA=fa; + classes.entropy=entropy; + classes.structure=structure; + classes.omnivariance=omnivar; + classes.labeling=label; + classes.biases=biases; + classes.intensity=ints; + classes.de=de; + +end Index: Damkjer/PointProcessing/SpatialAnalyzer/spanalyze.m =================================================================== --- Damkjer/PointProcessing/SpatialAnalyzer/spanalyze.m (revision 12) +++ Damkjer/PointProcessing/SpatialAnalyzer/spanalyze.m (revision 13) @@ -55,5 +55,5 @@ % spanalyze %****************************************************************************** -function [ classes ] = spanalyze( queries, database, varargin ) +function [ classes ] = spanalyze( queries, points, varargin ) % Perform local feature attribution via eigenspace analysis. % @@ -87,4 +87,7 @@ ints=zeros(1,elements); + % Build database + database=VpTree(points); + % This process may take a while. Display time bar while processing. msg='Computing Structure Tensors...'; @@ -131,135 +134,138 @@ end - % Compute neighborhood covariance, intensity and bias values. - if (isempty(userParams.counts) && isempty(userParams.steps)) +% % Compute neighborhood covariance, intensity and bias values. +% if (isempty(userParams.counts) && isempty(userParams.steps)) % Not using adaptive neighborhoods. cells=cell(1,length(NN)); for n=1:length(NN) - cells{n}=queries(:,NN{n})'; + cells{n}=points(:,NN{n})'; end [covs,bias,inty]=fastcov(cells); - elseif (~isempty(userParams.counts)) - % Using variable neighbor count based adaptive neighborhoods. - - % TODO: Conoslidate the common functionality in adaptive methods into - % a single function. - - tempfeats=zeros(dimensions,size(NN,1)); - tempde=zeros(length(userParams.counts),size(NN,1)); - - tempcovs=cell(length(userParams.counts),1); - tempbias=cell(length(userParams.counts),1); - tempinty=cell(length(userParams.counts),1); - - % Compute candidiate values (HACKY) - for c=1:length(userParams.counts) - cells=cell(1,length(NN)); - - for n=1:length(NN) - cells{n}=queries(:,NN{n}(1:userParams.counts(c)))'; - end - - [tempcovs{c},tempbias{c},tempinty{c}]=fastcov(cells); - - for nbr=1:size(NN,1) - [~,D]=par_eig(tempcovs{c}{nbr}); - tempfeats(:,nbr)=sort(diag(D),'descend'); - end - - % Compute dimensional degree - % Do not use the following definition based on singular values: - % tempdims=(sqrt(tempfeats(1:dimensions-1,:))-... - % sqrt(tempfeats(2:dimensions,:)))./... - % repmat(sqrt(tempfeats(1,:)),dimensions-1,1); - tempdims=(tempfeats(1:dimensions-1,:)-... - tempfeats(2:dimensions,:))./... - repmat(tempfeats(1,:),dimensions-1,1); - - % Compute isotropy - tempiso=(tempfeats(dimensions,:))./(tempfeats(1,:)); - - % Compute dimensional entropy - tempalpha=[tempdims;tempiso]; - tempde(c,:)=-sum(tempalpha.*log(tempalpha))./log(dimensions); - end - - % Minimize on dimensional entropy (HACKY) - [~,ind]=min(tempde); - - covs=tempcovs{ind}; - bias=tempbias{ind}; - inty=tempinty{ind}; - elseif (~isempty(userParams.steps)) - % Using variable neighborhood radii based adaptive neighborhoods. - - % TODO: Conoslidate the common functionality in adaptive methods into - % a single function. - - tempfeats=zeros(dimensions,size(NN,1)); - tempde=zeros(length(userParams.steps),size(NN,1)); - - tempcovs=cell(length(userParams.steps),1); - tempbias=cell(length(userParams.steps),1); - tempinty=cell(length(userParams.steps),1); - - % Compute candidiate values (HACKY) - for c=1:length(userParams.steps) - - nbrs=cell(1,length(DISTS)); - - for n=1:length(DISTS) - nbrs{n}=sum(DISTS{n} <= userParams.steps(c))'; - end - - cells=cell(1,length(NN)); - - for n=1:length(NN) - cells{n}=queries(:,NN{n}(DISTS{n} <= userParams.steps(c)))'; - end - - [tempcovs{c},tempbias{c},tempinty{c}]=fastcov(cells); - - for nbr=1:size(NN,1) - if (nbrs{nbr}<5) - continue; - end - - [~,D]=par_eig(tempcovs{c}{nbr}); - tempfeats(:,nbr)=sort(diag(D),'descend'); - end - - % Compute dimensional degree - % Do not use the following definition based on singular values: - % tempdims=(sqrt(tempfeats(1:dimensions-1,:))-... - % sqrt(tempfeats(2:dimensions,:)))./... - % repmat(sqrt(tempfeats(1,:)),dimensions-1,1); - tempdims=(tempfeats(1:dimensions-1,:)-... - tempfeats(2:dimensions,:))./... - repmat(tempfeats(1,:),dimensions-1,1); - - % Compute isotropy - tempiso=(tempfeats(dimensions,:))./(tempfeats(1,:)); - - % Compute dimensional entropy - tempalpha=[tempdims;tempiso]; - tempde(c,:)=-sum(tempalpha.*log(tempalpha))./log(dimensions); - end - - % Minimize on dimensional entropy (HACKY) - [~,ind]=nanmin(tempde); - - covs=tempcovs{ind}; - bias=tempbias{ind}; - inty=tempinty{ind}; - else - error('Unhandled Condition'); - end + +% elseif (~isempty(userParams.counts)) +% +% % Using variable neighbor count based adaptive neighborhoods. +% +% % TODO: Conoslidate the common functionality in adaptive methods into +% % a single function. +% +% tempfeats=zeros(dimensions,size(NN,1)); +% tempde=zeros(length(userParams.counts),size(NN,1)); +% +% tempcovs=cell(length(userParams.counts),1); +% tempbias=cell(length(userParams.counts),1); +% tempinty=cell(length(userParams.counts),1); +% +% % Compute candidiate values (HACKY) +% for c=1:length(userParams.counts) +% cells=cell(1,length(NN)); +% +% for n=1:length(NN) +% cells{n}=points(:,NN{n}(1:userParams.counts(c)))'; +% end +% +% [tempcovs{c},tempbias{c},tempinty{c}]=fastcov(cells); +% +% for nbr=1:size(NN,1) +% [~,D]=par_eig(tempcovs{c}{nbr}); +% tempfeats(:,nbr)=sort(diag(D),'descend'); +% end +% +% % Compute dimensional degree +% % Do not use the following definition based on singular values: +% % tempdims=(sqrt(tempfeats(1:dimensions-1,:))-... +% % sqrt(tempfeats(2:dimensions,:)))./... +% % repmat(sqrt(tempfeats(1,:)),dimensions-1,1); +% tempdims=(tempfeats(1:dimensions-1,:)-... +% tempfeats(2:dimensions,:))./... +% repmat(tempfeats(1,:),dimensions-1,1); +% +% % Compute isotropy +% tempiso=(tempfeats(dimensions,:))./(tempfeats(1,:)); +% +% % Compute dimensional entropy +% tempalpha=[tempdims;tempiso]; +% tempde(c,:)=-sum(tempalpha.*log(tempalpha))./log(dimensions); +% end +% +% % Minimize on dimensional entropy (HACKY) +% [~,ind]=min(tempde); +% +% covs=tempcovs{ind}; +% bias=tempbias{ind}; +% inty=tempinty{ind}; +% elseif (~isempty(userParams.steps)) +% +% % Using variable neighborhood radii based adaptive neighborhoods. +% +% % TODO: Conoslidate the common functionality in adaptive methods into +% % a single function. +% +% tempfeats=zeros(dimensions,size(NN,1)); +% tempde=zeros(length(userParams.steps),size(NN,1)); +% +% tempcovs=cell(length(userParams.steps),1); +% tempbias=cell(length(userParams.steps),1); +% tempinty=cell(length(userParams.steps),1); +% +% % Compute candidiate values (HACKY) +% for c=1:length(userParams.steps) +% +% nbrs=cell(1,length(DISTS)); +% +% for n=1:length(DISTS) +% nbrs{n}=sum(DISTS{n} <= userParams.steps(c))'; +% end +% +% cells=cell(1,length(NN)); +% +% for n=1:length(NN) +% cells{n}=points(:,NN{n}(DISTS{n} <= userParams.steps(c)))'; +% end +% +% [tempcovs{c},tempbias{c},tempinty{c}]=fastcov(cells); +% +% for nbr=1:size(NN,1) +% if (nbrs{nbr}<5) +% continue; +% end +% +% [~,D]=par_eig(tempcovs{c}{nbr}); +% tempfeats(:,nbr)=sort(diag(D),'descend'); +% end +% +% % Compute dimensional degree +% % Do not use the following definition based on singular values: +% % tempdims=(sqrt(tempfeats(1:dimensions-1,:))-... +% % sqrt(tempfeats(2:dimensions,:)))./... +% % repmat(sqrt(tempfeats(1,:)),dimensions-1,1); +% tempdims=(tempfeats(1:dimensions-1,:)-... +% tempfeats(2:dimensions,:))./... +% repmat(tempfeats(1,:),dimensions-1,1); +% +% % Compute isotropy +% tempiso=(tempfeats(dimensions,:))./(tempfeats(1,:)); +% +% % Compute dimensional entropy +% tempalpha=[tempdims;tempiso]; +% tempde(c,:)=-sum(tempalpha.*log(tempalpha))./log(dimensions); +% end +% +% % Minimize on dimensional entropy (HACKY) +% [~,ind]=nanmin(tempde); +% +% covs=tempcovs{ind}; +% bias=tempbias{ind}; +% inty=tempinty{ind}; +% else +% error('Unhandled Condition'); +% end % Compute the neighborhood covariance eigenvalues. [V,D]=par_eig(covs); - for nbr=1:size(NN,1) + for nbr=1:length(NN) % skip underconstrained neighborhoods (possible with radius searches) @@ -302,6 +308,6 @@ % Compute Omnivariance - omnivar=prod(feats,1).^(1/dimensions); -% omnivar=prod(feats.*feats,1).^(1/dimensions); +% omnivar=prod(feats,1).^(1/dimensions); + omnivar=prod(feats.*feats,1).^(1/dimensions); % omnivar=prod(nfeats,1).^(1/dimensions); @@ -333,8 +339,9 @@ % Compute Dimensional Embedding - [~,embed]=max([dims;iso],[],1); - + [~,label]=max(dims,[],1); + % Compute dimensional entropy - alpha=[dims;iso]; +% alpha=[dims;iso]; + alpha=dims; de=-sum(alpha.*log(alpha))./log(dimensions); @@ -349,5 +356,5 @@ classes.structure=structure; classes.omnivariance=omnivar; - classes.embedding=embed; + classes.labeling=label; classes.biases=biases; classes.intensity=ints; @@ -441,4 +448,10 @@ userParams = struct('radius', 0, 'neighbors', 0, 'counts', [], 'steps', []); + + if isempty(varargin) + error('Damkjer:InvalidOptions', ... + ['A neighborhood size must be specified, either directly or '... + 'via optional parameters.']); + end if length(varargin) == 1 || ~isnumeric(varargin{2}) Index: Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m =================================================================== --- Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m (revision 13) +++ Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m (revision 13) @@ -0,0 +1,578 @@ +% Thin_Dyn Point Cloud Thinning (Dyn et al) +% +% File: thin_Dyn.m +% +% Description: +% Perform thinning according to Dyn 2004. +% +% Limitations: +% No known limitations. +% +% Synopsis: +% [results] = spanalyse(points, threshold, ...) +% +% Inputs: +% points - . +% threshold - must be positive. between 0-1, treated as percentage, > 1 +% points. +% +% Option strings may be provided as abbreviations as long as they resolve to +% a unique option. +% +% 'neighbors' - . +% 'radius' - . +% 'counts' - . +% 'steps' - . +% +% Outputs: +% results - Thinned point cloud. +% +% Toolbox requirements: +% None. +% +% Code requirements: +% None. +% +% Data requirements: +% None. +% +% References: +% Dyn reference. +% +% See Also: +% None. +% + +% Copyright (C) 2013 Kristian L. Damkjer. +% +% Software History: +% 2013-DEC-28 Initial coding. +% + +%****************************************************************************** +% thin_Dyn +%****************************************************************************** +function [ results ] = thin_Damkjer( points, threshold, varargin ) + % Perform local feature attribution via eigenspace analysis. + % + % Parameters: + % points - . + % + % threshold - . + % + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % classes - Structure containing the spatial analysis classifications. + % + + userParams = parseInputs(varargin{:}); % Parse Inputs + + % Make sure we have unique points... we barf otherwise... + disp('Culling duplicate points...'); + tstart=tic; + points = unique(points.','rows').'; + disp(['...done in ' num2str(toc(tstart)) 's']); + + disp('Indexing points...'); + tstart=tic; + database = VpTree(points); + queries = points; + disp(['...done in ' num2str(toc(tstart)) 's']); + + database.excludeWithin(0.001); % Set mm precision on searches. + + % Sizing metrics + dimensions=size(queries, 1); + elements=size(queries, 2); + + nbrs = cell(1,elements); + + %*** + % CREATE NEIGHBORHOODS + %*** + + % This process may take a while. Display time bar while processing. + msg='Creating Neigborhoods...'; + tstart=tic; + h = timebar(1, elements, msg, tstart); + + disp(msg); + + % Step through the queries in chunks. + step=1000; + + tic; + + for elem=1:step:elements + + % The last available element may be closer than elem + step. + last=min(elem+step-1,elements); + + % Get the nearest neighbors of elem + if (userParams.radius > 0 && userParams.neighbors <= 0) + % Perform a fixed radius search + nbrs(elem:last)=database.rnn(queries(:,elem:last),... + userParams.radius); + elseif (userParams.radius <= 0 && userParams.neighbors > 0) + % Search unconstrained neighbors + nbrs(elem:last)=database.knn(queries(:,elem:last),... + userParams.neighbors); + elseif (userParams.radius > 0 && userParams.neighbors > 0) + % Search constrained to radius + nbrs(elem:last)=database.knn(queries(:,elem:last),... + userParams.neighbors,... + 'lim',userParams.radius); + elseif (~isempty(userParams.counts) && userParams.radius <= 0) + % Search unconstrained neighbors + nbrs(elem:last)=database.knn(queries(:,elem:last),... + max(userParams.counts)); + elseif (~isempty(userParams.counts) && userParams.radius > 0) + % Search constrained to radius + nbrs(elem:last)=database.knn(queries(:,elem:last),... + max(userParams.counts),... + 'lim',userParams.radius); + elseif (~isempty(userParams.steps)) + % Perform a fixed radius search + [nbrs(elem:last),DISTS]=database.rnn(queries(:,elem:last),... + max(userParams.steps)); + end + + % Update the time bar. + if (toc > 1) + tic; + h = timebar(elem, elements, msg, tstart, h); + end + end + + % Close the time bar, if still open. + if (all(ishghandle(h, 'figure'))) + close(h); + end + + disp(['...done in ' num2str(toc(tstart)) 's']); + +%% Obsolete code + %*** + % COMPUTE DUAL NEIGHBORHOODS (THIS IS SLOW. LET'S MEX IT) + %*** + +% % This process may take a while. Display time bar while processing. +% msg='Computing Dual Neigborhoods...'; +% tstart=tic; +% h = timebar(1, elements, msg, tstart); +% +% disp(msg); +% +% tic; +% for elem=1:elements +% +% % Build up dual set +% for nbr=1:length(nbrs{elem}) +% n = nbrs{elem}(nbr); +% duals{n}=[duals{n}(:); elem]; +% end +% +% % Update the time bar. +% if (toc > 1) +% tic; +% h = timebar(elem, elements, msg, tstart, h); +% end +% end +% +% % Close the time bar, if still open. +% if (all(ishghandle(h, 'figure'))) +% close(h); +% end +% +% disp(['...done in ' num2str(toc(tstart)) 's']); +%% + %*** + % COMPUTE DUAL NEIGHBORHOODS -- MEX'D + %*** + + disp('Computing Dual Neigborhoods...'); + tstart=tic; + duals=fastsetdual(nbrs); + disp(['...done in ' num2str(toc(tstart)) 's']); + + %*** + % COMPUTE SIGNIFICANCES + %*** + disp('Computing Significances...'); + tstart=tic; + + feats = nbrspanalyze(points, nbrs, 'timebar'); + + disp(['...done in ' num2str(toc(tstart)) 's']); + + sigs = feats.de; +% sigs = sqrt(feats.biases.*feats.de); +% sigs = 0.5 * (feats.biases + feats.de); + + %*** + % PARTITION THE DATA SET + %*** + + disp('Partition by Label...'); + tstart=tic; + + parts = cell(1,dimensions); + + for dim=1:dimensions + parts{dim}=uint64(find(feats.labeling==dim)); + end + + [~,idx]=sort(cellfun('length',parts),'ascend'); + parts=parts(idx); + + disp(['...done in ' num2str(toc(tstart)) 's']); + + %*** + % THIN BY LABEL + %*** + + fraction=0; + + removed=zeros(1,elements-threshold); + dual_size=zeros(1,elements-threshold); + current=1; + + removed_wgts=cell(1,3); + fellback = 0; + + for dim=1:dimensions + desired = threshold * length(parts{dim}) / elements + fraction; + tau = floor(desired); + fraction = desired-tau; + heap = SplayTree(sigs(parts{dim}),parts{dim}); + n = length(parts{dim})-tau; + + removed_wgts{dim}=zeros(1,n); + +% tau=threshold; +% heap = SplayTree(feats.de); +% n = length(feats.de) - tau; +% removed_wgts=zeros(1,n); + + msg=['Thin Dimension ' num2str(dim) '(' num2str(length(parts{dim})) ... + '->' num2str(tau) ')...']; +% msg='Thin...'; + tstart=tic; + h = timebar(1, n, msg, tstart); + + disp(msg); + tic; + + for x=1:n +% if false + + % Remove Element + [wgt, idx]=heap.pop_head(); + + removed(current)=idx; + removed_wgts{dim}(x)=wgt; + + % Find neighborhoods that contain removed element + neighborhoods=sort(duals{idx}, 'ascend'); + dual_size(current)=length(neighborhoods); + + % The removed element neighborhood is eliminated, so it no longer + % contains the neighbors. Update the neighbor duals appropriately. + neighbors=nbrs{idx}; + + for nbr=1:length(neighbors) + duals{neighbors(nbr)}=duals{neighbors(nbr)}(duals{neighbors(nbr)}~=idx); + end + + % The fallback neighborhood is identical for all neighborhoods, but + % may be expensive to compute. Allow it to be lazily instantiated. + fallback_pool = []; + + % Replace removed element in each neighborhood with nearest neighbor + for hood=1:length(neighborhoods) + + % Build up the list of potential new neighbors +% disp('building candidates...'); + +%% Obsolete code +% nbr_pool=unique(vertcat(nbrs{nbrs{neighborhoods(hood)}})); +% nbr_pool=setdiff(nbr_pool, idx); +% nbr_pool=setdiff(nbr_pool, nbrs{neighborhoods(hood)}); +%% + nbr_pool=fastsetunion({nbrs{nbrs{neighborhoods(hood)}}}); + non_nbrs=fastsetunion({nbrs{neighborhoods(hood)},idx,neighborhoods(hood)}); + nbr_pool=nbr_pool(~ismembc(nbr_pool(:), non_nbrs(:))); + + if (isempty(nbr_pool)) + if (isempty(fallback_pool)) + fallback_pool = uint64(find(~ismember(1:size(points,2),removed))); + end + fellback = fellback + 1; + nbr_pool = fallback_pool; + nbr_pool=nbr_pool(~ismembc(nbr_pool(:), non_nbrs(:))); + end + + + % Find the closest +% disp('finding closest...'); + +%% Obsolete code +% % Don't use VP Tree for single nearest neighbor... overhead not +% % worth it. +% locdb = VpTree(points(:,nbr_pool)); +% nn=locdb.knn(points(:,idx),1); +% new_idx=nn{1} +%% + [~,new_idx]=min(sum((bsxfun(@minus, points(:,nbr_pool), ... + points(:,idx))).^2, 1)); + + % Update the neighborhood +% disp('updating neighborhood...'); + + if (length(nbr_pool(new_idx)) ~= length(nbrs{neighborhoods(hood)}(nbrs{neighborhoods(hood)}==idx))) + neighborhoods + size(fallback_pool) + non_nbrs + nbr_pool + nbr_pool(new_idx) + + nbrs{neighborhoods(hood)}(nbrs{neighborhoods(hood)}==idx) + + error('What happened?'); + end + + nbrs{neighborhoods(hood)}(nbrs{neighborhoods(hood)}==idx) = ... + nbr_pool(new_idx); + + % Update the dual +% disp('updating dual...'); + duals{nbr_pool(new_idx)}(end + 1,1) = neighborhoods(hood); + +% disp(nbrs{neighborhoods(hood)}); +% disp(duals{nbr_pool(new_idx)}); + end + + duals{idx}=[]; + + % Update analysis for elements +% disp('updating analysis...'); + locfeats = nbrspanalyze(points, nbrs(neighborhoods)); + + locsigs = locfeats.de; +% locsigs = sqrt(locfeats.biases.*locfeats.de); +% locsigs = 0.5 * (locfeats.biases + locfeats.de); + + % Update heap, where required +% size(neighborhoods') +% +% if (size(sigs(neighborhoods)) ~= size(neighborhoods')) +% sigsize=size(sigs(neighborhoods)) +% nbrsize=size(neighborhoods') +% error('Stop'); +% end + +% sigs(neighborhoods) +% neighborhoods' +% locsigs + + updates=parts{dim}(ismember(parts{dim},neighborhoods)); + sig_upd=locsigs(ismember(neighborhoods,updates)); + + if (length(updates) ~= length(sig_upd)) + fellback + neighborhoods + updates + sig_upd + error('OK, seriously!'); + end + + heap.erase(sigs(updates),updates); + heap.insert(sig_upd,updates); + sigs(neighborhoods)=locsigs; + feats.de(neighborhoods)=locfeats.de; + feats.biases(neighborhoods)=locfeats.biases; + + current = current + 1; + + % Update the time bar. + if (toc > 1) + tic; + h = timebar(x, n, msg, tstart, h); + end + end + + % Close the time bar, if still open. + if (all(ishghandle(h, 'figure'))) + close(h); + end + + disp(['...done in ' num2str(toc(tstart)) 's']); + end + + disp(['Generated fallback neighborhood pool ' num2str(fellback) ' time(s).']); + + x_max=max(cellfun(@length, removed_wgts)); + y=nan(length(removed_wgts),x_max); + + for dim=1:dimensions + y(dim,1:length(removed_wgts{dim}))=removed_wgts{dim}; + end + +% x_max=length(removed_wgts); +% y = removed_wgts; + + figure, plot(1:x_max,y); +% figure, semilogx(1:x_max,y); + + figure, plot(1:length(dual_size),dual_size); + + results = points(:,~ismember(1:size(points,2),removed)); + +end + +%****************************************************************************** +% parseInputs +%****************************************************************************** +function [userParams] = parseInputs(varargin) + % Support function to parse inputs into userParams structure + % + % Parameters: + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % userParams - . + + userParams = struct('radius', 0, 'neighbors', 0, 'counts', [], 'steps', []); + + if isempty(varargin) + error('Damkjer:InvalidOptions', ... + ['A neighborhood size must be specified, either directly or '... + 'via optional parameters.']); + end + + if length(varargin) == 1 || ~isnumeric(varargin{2}) + value = varargin{1}; + + if (isscalar(value) && ... + isreal(value) && ... + value >= 5) + userParams.neighbors = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Number of Neighbors must be a real valued positive '... + 'integer greater or equal to 5: ' num2str(value)]); + end + + varargin(1) = []; + end + + % Parse the Property/Value pairs + if rem(length(varargin), 2) ~= 0 + error('Damkjer:PropertyValueNotPair', ... + ['Additional arguments must take the form of Property/Value '... + 'pairs']); + end + + propertyNames = {'neighbors', 'radius', 'counts', 'steps'}; + + while ~isempty(varargin) + property = varargin{1}; + value = varargin{2}; + + % If the property has been supplied in a shortened form, lengthen it + iProperty = find(strncmpi(property, propertyNames, length(property))); + + if isempty(iProperty) + error('Damkjer:InvalidProperty', 'Invalid Property'); + elseif length(iProperty) > 1 + error('Damkjer:AmbiguousProperty', ... + 'Supplied shortened property name is ambiguous'); + end + + property = propertyNames{iProperty}; + + switch property + case 'neighbors' + if (isscalar(value) && ... + isreal(value) && ... + value >= 5) + userParams.neighbors = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Number of Neighbors must be a real valued positive '... + 'integer greater or equal to 5']); + end + case 'radius' + if (isscalar(value) && ... + isnumeric(value) && ... + isreal(value) && ... + value > 0) + userParams.radius = value; + else + error('Damkjer:InvalidRadius', ... + 'Radius must be a real valued positive scalar'); + end + case 'counts' + if (isvector(value) && ... + isreal(value) && ... + issorted(value) && ... + all(value >= 5)) + userParams.counts = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Counts must be a sorted vector of real valued positive '... + 'integers greater or equal to 5']); + end + case 'steps' + if (isvector(value) && ... + isreal(value) && ... + issorted(value) && ... + all(value > 0)) + userParams.steps = value; + else + error('Damkjer:InvalidSteps', ... + ['Steps must be a sorted vector of real valued positive '... + 'values']); + end + end + + varargin(1:2) = []; + end + + % Check for mutually exclusive options. + if (~isempty(userParams.counts) && userParams.neighbors >= 5) + error('Damkjer:MutExOpts', ... + '''neighbors'' and ''counts'' options are mutually exclusive'); + end + + if (~isempty(userParams.steps) && userParams.radius > 0) + error('Damkjer:MutExOpts', ... + '''steps'' and ''radius'' options are mutually exclusive'); + end + + if (~isempty(userParams.counts) && ~isempty(userParams.steps)) + error('Damkjer:MutExOpts', ... + '''steps'' and ''counts'' options are mutually exclusive'); + end + + % Default, if necessary. + if (userParams.neighbors <= 0 && ... + userParams.radius <= 0 && ... + isempty(userParams.counts) && ... + isempty(userParams.steps)) + userParams.radius = 1; + end +end Index: Damkjer/PointProcessing/Thinning_Dyn/thin_Dyn.m =================================================================== --- Damkjer/PointProcessing/Thinning_Dyn/thin_Dyn.m (revision 13) +++ Damkjer/PointProcessing/Thinning_Dyn/thin_Dyn.m (revision 13) @@ -0,0 +1,387 @@ +% Thin_Dyn Point Cloud Thinning (Dyn et al) +% +% File: thin_Dyn.m +% +% Description: +% Perform thinning according to Dyn 2004. +% +% Limitations: +% No known limitations. +% +% Synopsis: +% [results] = spanalyse(points, threshold, ...) +% +% Inputs: +% points - . +% threshold - must be positive. between 0-1, treated as percentage, > 1 +% points. +% +% Option strings may be provided as abbreviations as long as they resolve to +% a unique option. +% +% 'neighbors' - . +% 'radius' - . +% 'counts' - . +% 'steps' - . +% +% Outputs: +% results - Thinned point cloud. +% +% Toolbox requirements: +% None. +% +% Code requirements: +% None. +% +% Data requirements: +% None. +% +% References: +% Dyn reference. +% +% See Also: +% None. +% + +% Copyright (C) 2013 Kristian L. Damkjer. +% +% Software History: +% 2013-DEC-28 Initial coding. +% + +%****************************************************************************** +% thin_Dyn +%****************************************************************************** +function [ results ] = thin_Dyn( points, threshold, varargin ) + % Perform local feature attribution via eigenspace analysis. + % + % Parameters: + % points - . + % + % threshold - . + % + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % classes - Structure containing the spatial analysis classifications. + % + + userParams = parseInputs(varargin{:}); % Parse Inputs + + % Make sure we have unique points... we barf otherwise... + disp('Culling duplicate points...'); + tstart=tic; + points = unique(points.','rows').'; + disp(['...done in ' num2str(toc(tstart)) 's']); + + disp('Indexing points...'); + database = VpTree(points); + queries = points; + disp(['...done in ' num2str(toc(tstart)) 's']); + + database.excludeWithin(0.001); % Set mm precision on searches. + + % Sizing metrics + dimensions=size(queries, 1); + elements=size(queries, 2); + + % Pre-allocate classes +% norms=zeros(size(queries)); +% feats=zeros(size(queries)); +% biases=zeros(1,elements); +% ints=zeros(1,elements); + + + nbrs = cell(1,elements); + duals = cell(1,elements); + tests = cell(1,elements); + + sigs=zeros(1,elements); + + for elem=1:elements + tests{elem}=elem; + end + + %*** + % COMPUTE NEIGHBORHOODS + %*** + + % This process may take a while. Display time bar while processing. + msg='Computing Neigborhoods...'; + tstart=tic; + h = timebar(1, elements, msg, tstart); + + % Step through the queries in chunks. + step=1000; + + tic; + + for elem=1:step:elements + + % The last available element may be closer than elem + step. + last=min(elem+step-1,elements); + + % Get the nearest neighbors of elem + if (userParams.radius > 0 && userParams.neighbors <= 0) + % Perform a fixed radius search + nbrs(elem:last)=database.rnn(queries(:,elem:last),... + userParams.radius); + elseif (userParams.radius <= 0 && userParams.neighbors > 0) + % Search unconstrained neighbors + nbrs(elem:last)=database.knn(queries(:,elem:last),... + userParams.neighbors); + elseif (userParams.radius > 0 && userParams.neighbors > 0) + % Search constrained to radius + nbrs(elem:last)=database.knn(queries(:,elem:last),... + userParams.neighbors,... + 'lim',userParams.radius); + elseif (~isempty(userParams.counts) && userParams.radius <= 0) + % Search unconstrained neighbors + nbrs(elem:last)=database.knn(queries(:,elem:last),... + max(userParams.counts)); + elseif (~isempty(userParams.counts) && userParams.radius > 0) + % Search constrained to radius + nbrs(elem:last)=database.knn(queries(:,elem:last),... + max(userParams.counts),... + 'lim',userParams.radius); + elseif (~isempty(userParams.steps)) + % Perform a fixed radius search + [nbrs(elem:last),DISTS]=database.rnn(queries(:,elem:last),... + max(userParams.steps)); + end + + % Update the time bar. + if (toc > 1) + tic; + h = timebar(elem, elements, msg, tstart, h); + end + end + + % Close the time bar, if still open. + if (all(ishghandle(h, 'figure'))) + close(h); + end + + %*** + % COMPUTE SIGNIFICANCES (THIS IS SLOW AND SHOULD BE EASY TO PARALLELIZE) + %*** + + % This process may take a while. Display time bar while processing. + msg='Computing Significances...'; + tstart=tic; + h = timebar(1, elements, msg, tstart); + + % Step through the queries in chunks. + step=1000; + + tic; + + for elem=1:step:elements + + % The last available element may be closer than elem + step. + last=min(elem+step-1,elements); + + % Compute significance + sigs(elem:last)=sig_Dyn(points,tests(elem:last),nbrs(elem:last)); + + % Update the time bar. + if (toc > 1) + tic; + h = timebar(elem, elements, msg, tstart, h); + end + end + + % Close the time bar, if still open. + if (all(ishghandle(h, 'figure'))) + close(h); + end + + results = [points;sigs]; + +% %*** +% % COMPUTE DUAL NEIGHBORHOODS (THIS IS SLOW AND SHOULD BE EASY TO PARALLELIZE!) +% %*** +% +% % This process may take a while. Display time bar while processing. +% msg='Computing Dual Neigborhoods...'; +% tstart=tic; +% h = timebar(1, elements, msg, tstart); +% +% tic; +% +% for elem=1:elements +% % Build up dual set +% for nbr=1:length(nbrs{elem}) +% n = nbrs{elem}(nbr); +% duals{n}=[duals{n}(:); elem]; +% end +% +% % if rem(elem-1,100000)==0 +% % for insp=1:10 +% % disp(insp); +% % disp(duals{insp}'); +% % end +% % end +% +% % end +% +% % Update the time bar. +% if (toc > 1) +% tic; +% h = timebar(elem, elements, msg, tstart, h); +% end +% end +% +% % Close the time bar, if still open. +% if (all(ishghandle(h, 'figure'))) +% close(h); +% end +% +% results = points; +end + +%****************************************************************************** +% parseInputs +%****************************************************************************** +function [userParams] = parseInputs(varargin) + % Support function to parse inputs into userParams structure + % + % Parameters: + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % userParams - . + + userParams = struct('radius', 0, 'neighbors', 0, 'counts', [], 'steps', []); + + if isempty(varargin) + error('Damkjer:InvalidOptions', ... + ['A neighborhood size must be specified, either directly or '... + 'via optional parameters.']); + end + + if length(varargin) == 1 || ~isnumeric(varargin{2}) + value = varargin{1}; + + if (isscalar(value) && ... + isreal(value) && ... + value >= 5) + userParams.neighbors = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Number of Neighbors must be a real valued positive '... + 'integer greater or equal to 5: ' num2str(value)]); + end + + varargin(1) = []; + end + + % Parse the Property/Value pairs + if rem(length(varargin), 2) ~= 0 + error('Damkjer:PropertyValueNotPair', ... + ['Additional arguments must take the form of Property/Value '... + 'pairs']); + end + + propertyNames = {'neighbors', 'radius', 'counts', 'steps'}; + + while ~isempty(varargin) + property = varargin{1}; + value = varargin{2}; + + % If the property has been supplied in a shortened form, lengthen it + iProperty = find(strncmpi(property, propertyNames, length(property))); + + if isempty(iProperty) + error('Damkjer:InvalidProperty', 'Invalid Property'); + elseif length(iProperty) > 1 + error('Damkjer:AmbiguousProperty', ... + 'Supplied shortened property name is ambiguous'); + end + + property = propertyNames{iProperty}; + + switch property + case 'neighbors' + if (isscalar(value) && ... + isreal(value) && ... + value >= 5) + userParams.neighbors = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Number of Neighbors must be a real valued positive '... + 'integer greater or equal to 5']); + end + case 'radius' + if (isscalar(value) && ... + isnumeric(value) && ... + isreal(value) && ... + value > 0) + userParams.radius = value; + else + error('Damkjer:InvalidRadius', ... + 'Radius must be a real valued positive scalar'); + end + case 'counts' + if (isvector(value) && ... + isreal(value) && ... + issorted(value) && ... + all(value >= 5)) + userParams.counts = fix(value); + else + error('Damkjer:InvalidCount', ... + ['Counts must be a sorted vector of real valued positive '... + 'integers greater or equal to 5']); + end + case 'steps' + if (isvector(value) && ... + isreal(value) && ... + issorted(value) && ... + all(value > 0)) + userParams.steps = value; + else + error('Damkjer:InvalidSteps', ... + ['Steps must be a sorted vector of real valued positive '... + 'values']); + end + end + + varargin(1:2) = []; + end + + % Check for mutually exclusive options. + if (~isempty(userParams.counts) && userParams.neighbors >= 5) + error('Damkjer:MutExOpts', ... + '''neighbors'' and ''counts'' options are mutually exclusive'); + end + + if (~isempty(userParams.steps) && userParams.radius > 0) + error('Damkjer:MutExOpts', ... + '''steps'' and ''radius'' options are mutually exclusive'); + end + + if (~isempty(userParams.counts) && ~isempty(userParams.steps)) + error('Damkjer:MutExOpts', ... + '''steps'' and ''counts'' options are mutually exclusive'); + end + + % Default, if necessary. + if (userParams.neighbors <= 0 && ... + userParams.radius <= 0 && ... + isempty(userParams.counts) && ... + isempty(userParams.steps)) + userParams.radius = 1; + end +end Index: Damkjer/PointProcessing/sig_Dyn.m =================================================================== --- Damkjer/PointProcessing/sig_Dyn.m (revision 13) +++ Damkjer/PointProcessing/sig_Dyn.m (revision 13) @@ -0,0 +1,169 @@ +% Sig_Dyn Point Significance (Dyn et al) +% +% File: sig_Dyn.m +% +% Description: +% Compute point significance according to Dyn 2004. +% +% Limitations: +% No known limitations. +% +% Synopsis: +% [results] = sig_Dyn(points, test_sets, neighborhood_sets) +% +% Inputs: +% points - . +% test_sets - . +% neighborhood_sets - . +% +% +% Outputs: +% results - Thinned point cloud. +% +% Toolbox requirements: +% None. +% +% Code requirements: +% None. +% +% Data requirements: +% None. +% +% References: +% Dyn reference. +% +% See Also: +% None. +% + +% Copyright (C) 2013 Kristian L. Damkjer. +% +% Software History: +% 2013-DEC-28 Initial coding. +% + +%****************************************************************************** +% sig_Dyn +%****************************************************************************** +function [ sigs ] = sig_Dyn( points, tests, nbrs ) + % Perform local feature attribution via eigenspace analysis. + % + % Parameters: + % points - . + % + % threshold - . + % + % varargin - Variable-length input argument list. Option strings may be + % provided as abbreviations as long as they resolve to a + % unique option.Defined key-value pairs include the following: + % 'neighbors' - . + % 'radius' - . + % 'counts' - . + % 'steps' - . + % + % Returns: + % classes - Structure containing the spatial analysis classifications. + % + + % Sizing metrics + dimensions=size(points, 1); + elements=length(tests); + + % Pre-allocate classes + norms=zeros(dimensions, elements); + + + % Fit planes to the neighborhoods + cells=cell(1,elements); + + for elem=1:elements + cells{elem}=points(:,nbrs{elem}).'; % fastcov is expecting row-vectors + end + + [covs,~,~]=fastcov(cells); + + % Compute the neighborhood covariance eigenvalues. + [V,D]=par_eig(covs); + + sigs = zeros(1,elements); + + for elem=1:elements + + % skip underconstrained neighborhoods (possible with radius searches) + if (length(nbrs{elem})<5 || any(any(isnan(covs{elem})))) + continue; + end + + [~,index]=min(abs(D{elem})); + A=V{elem}; + aNorm=A(:,index); + + % Plane fit to the neighborhood is defined by the normal and the point. + norms(:,elem)=aNorm; + ys = points(:,tests{elem}); + x = ys(:,1).'; + + % Project neighborhood points to the fitted plane to establish local + % coordinate reference frame. + % + % NOTE: null-space method only works when treating norm as row-vector. + basis = null(aNorm.'); + coeffs = bsxfun(@minus, cells{elem}, x) * basis; + Z = bsxfun(@plus, coeffs * basis.', x); + + % Compute RBF function values for the neighborhood observations. + f=sqrt(sum(abs(cells{elem}-Z).^2,2)); + + % Compute RBF coefficients + + % Need R's established as |Zi-Zj| + % rM := radii Matrix + rM = min(1,pdist2(Z,Z)./1); + + % PhiM := A_{Phi,Z} = [Phi(z_{i},z_{j})] + % + % The equation used below is a Wendland compactly supported basis + % function in C2 to ensure curvature continuity. A C0 equivalent would be + % (1-r)^2 which would only ensure positional continuity. + PhiM = (1-rM).^4.*(4*rM+1); + + if rcond(PhiM) < 1e-12 + fmt=get(0, 'format'); + format('hex'); + disp(rM); + disp(Z); + disp(f); + disp(PhiM); + hold on + scatter3(cells{elem}(:,1),cells{elem}(:,2),cells{elem}(:,3), 5, 'blue', 'o'); + scatter3(Z(:,1),Z(:,2),Z(:,3), 5, 'green', 'o'); + scatter3(x(1),x(2),x(3), 5, 'red', 'x'); + hold off + set(0, 'format', fmt); + error('oops'); + end + + as = PhiM\f; + + % radii from x. + rawRx=sqrt(sum(abs(bsxfun(@minus, x, Z)).^2,2)); + rX = min(1,rawRx./1); + PhiX = (1-rX).^4.*(4*rX+1); + + sigs(elem)=abs(as.' * PhiX); + +% if (sigs(elem) == 0) +% hold on +% scatter3(cells{elem}(:,1),cells{elem}(:,2),cells{elem}(:,3), 5, 'blue', 'o'); +% scatter3(Z(:,1),Z(:,2),Z(:,3), 5, 'green', 'o'); +% scatter3(x(1),x(2),x(3), 5, 'red', 'x'); +% hold off +% +% disp(rawRx); +% error('oops'); +% end + end + +% disp(sigs); + +end Index: Damkjer/Top.dox =================================================================== --- Damkjer/Top.dox (revision 13) +++ Damkjer/Top.dox (revision 13) @@ -0,0 +1,21 @@ +//***************************************************************************** +// DIRECTORY: Util +//> General utilities. +//< +//***************************************************************************** + +//***************************************************************************** +// NAMESPACE: Damkjer +//> Kristian Damkjer's doctoral research code. Data structures and algorithms +// directly related to Kristian Damkjer's PhD research, implemented by +// Kristian Damkjer. +//< +//***************************************************************************** + +//***************************************************************************** +// NAMESPACE: MATLAB +//> MATLAB M-file documentation. M-files are transformed into a C++-like form +// using a PERL script. The resulting format is parsed by Doxygen to +// generate a semantic overview of the MATLAB code. +//< +//***************************************************************************** Index: Damkjer/Util.bib =================================================================== --- Damkjer/Util.bib (revision 13) +++ Damkjer/Util.bib (revision 13) @@ -0,0 +1,18 @@ +@inproceedings{Yianilos:1993, +crossref={SODA:1993}, +author={Peter N. Yianilos}, +title={Data Structures and Algorithms for Nearest Neighbor Search in General Metric Spaces}, +booktitle={Proceedings of the Fourth Annual ACM-SIAM Symposium on Discrete Algorithms}, +series={SODA '93}, +year={1993}, +pages={311--321}, +abstract={We consider the computational problem of finding nearest neighbors in general metric spaces. Of particular interest are spaces that may not be conveniently embedded or approximated in Euclidian space, or where the dimensionality of a Euclidian representation is very high.Also relevant are high-dimensional Euclidian settings in which the distribution of data is in some sense of lower dimension and embedded in the space.The \textit{vp-tree} (vantage point tree) is introduced in several forms, together with associated algorithms, as an improved method for these difficult search problems. Tree construction executes in \textit{O}(\textit{n}log(\textit{n}) time, and search is under certain circumstances and in the limit, \textit{O}(log(\textit{n})) expected time. The theoretical basis for this approach is developed and the results of several experiments are reported. In Euclidian cases, kd-tree performance is compared.}, +} +@proceedings{SODA:1993, +organization={Association for Computing Machinery and Society for Industrial and Applied Mathematics}, +title={Proceedings of the Fourth Annual ACM-SIAM Symposium on Discrete Algorithms}, +year={1993}, +publisher={Society for Industrial and Applied Mathematics}, +address={Philadelphia, PA, USA}, +isbn={9780898713138} +} Index: Damkjer/Util/Dictionaries/SplayTree.h =================================================================== --- Damkjer/Util/Dictionaries/SplayTree.h (revision 13) +++ Damkjer/Util/Dictionaries/SplayTree.h (revision 13) @@ -0,0 +1,164 @@ +//**************************************************************************** +// FILE: SplayTree.h +// +// Copyright (C) 2013 Kristian Damkjer. +// +// DESCRIPTION: +//> The interface definition for splay trees. +//< +// +// LIMITATIONS: +//> This class template file follows the template inclusion pattern. This +// header file should be the only file included by clients wishing to +// instantiate a VpTree specialization. +//< +// +// SOFTWARE HISTORY: +// +//> 2013-DEC-02 K. Damkjer +// Initial Coding. +//< +//**************************************************************************** +#ifndef Damkjer_SplayTree_HEADER +#define Damkjer_SplayTree_HEADER + +#include +#include + +namespace Damkjer +{ + +//***************************************************************************** +// CLASS: SplayTree +//> A splay tree data structure and related algorithms. +// +// @tparam MetricT The metric search space. +//< +//***************************************************************************** +template > +class SplayTree +{ +public: + class Node + { + public: + Node(const T& element = T()) + : theLBranch(0) + , theRBranch(0) + , theElement(element) + { + } + //> + //< + + ~Node() + { + std::deque q; + + q.push_back(this); + + while (q.size() > 0) + { + Node* node = q.front(); + q.pop_front(); + + if (node) + { + q.push_back(node->theLBranch); + q.push_back(node->theRBranch); + + node->theLBranch = 0; + node->theRBranch = 0; + + if (node != this) delete node; + } + } + } + //> + //< + + Node* theLBranch; + Node* theRBranch; + T theElement; + }; + //> A node interface for a splay tree. + //< + + SplayTree(); + //> Instantiate an empty tree. + //< + + virtual ~SplayTree(); + //> Destruct the tree and deallocate resources. + //< + + void insert(const T&); + //> Add a new element to the tree. + //< + + void erase(const T&); + //> Remove an element from the tree. + //< + + Node* find(const T&); + //> Find an element in the tree. + //< + + const T& head(); + //> Find the front (minimum) element in the tree. + //< + + const T& tail(); + //> Find the back (maximum) element in the tree. + //< + + bool empty() const { return theRoot == 0; } + //> Return true if and only if there are no elements in the tree. + //< + + const std::size_t& size() const { return theSize; } + //> Return the number of elements in the tree. + //< + +private: + + void splay(const T&); + //> Perform the splay operation. + //< + + Node* headFrom(Node*); + //> Calculate the head (minimum) of the subtree rooted at the given node. + //< + + Node* tailFrom(Node*); + //> Calculate the tail (maximum) of the subtree rooted at the given node. + //< + + ComparitorT theOrderIs; + //> Pairwise comparitor that returns true if and only if the argument + // order of elements is in-order according to the comparitor. + //< + + Node* theRoot; + //> The root is the starting point for all operations against the database + // represented by the SplayTree. + //< + + std::size_t theSize; + //> The total number of elements contained in the tree. + //< +}; + +} + +//***************************************************************************** +// External References +//***************************************************************************** +//#include "SplayTree_Node.h" + +//***************************************************************************** +// Template Inclusion +//***************************************************************************** +#include "SplayTree.hpp" // HASA SplayTree Template Implementation. + +#endif Index: Damkjer/Util/Dictionaries/SplayTree.hpp =================================================================== --- Damkjer/Util/Dictionaries/SplayTree.hpp (revision 13) +++ Damkjer/Util/Dictionaries/SplayTree.hpp (revision 13) @@ -0,0 +1,435 @@ +//**************************************************************************** +// FILE: SplayTree.hpp +// +// Copyright (C) 2013 Kristian Damkjer. +// +// DESCRIPTION: +//> The template implementation for splay trees. +//< +// +// LIMITATIONS: +//> This class template file follows the template inclusion pattern. This +// header file should be the only file included by clients wishing to +// instantiate a VpTree specialization. +//< +// +// SOFTWARE HISTORY: +// +//> 2013-DEC-02 K. Damkjer +// Initial Coding. +//< +//**************************************************************************** +#include "SplayTree.h" + +namespace Damkjer +{ + +//***************************************************************************** +// SplayTree::SplayTree() +//> Instantiate an empty tree. +// +// @tparam T The element type. +// @tparam ComparitorT The element comparitor type. +//< +//***************************************************************************** +template +SplayTree::SplayTree() + : theRoot(0) + , theSize(0) +{ +} + +//***************************************************************************** +// SplayTree::~SplayTree() +//> Destruct the tree and deallocate resources. +//< +//***************************************************************************** +template +SplayTree::~SplayTree() +{ + delete theRoot; + theRoot = 0; +} + +//***************************************************************************** +// SplayTree::insert(const T&) +//> Add a new element to the tree. +//< +//***************************************************************************** +template +void +SplayTree::insert(const T& element) +{ + Node* node = new Node(element); + + if (!theRoot) + { + theRoot = node; + ++theSize; + return; + } + + splay(element); + + if (theOrderIs(element, theRoot->theElement)) + { + node->theLBranch = theRoot->theLBranch; + node->theRBranch = theRoot; + theRoot->theLBranch = 0; + theRoot = node; + ++theSize; + } + else // if (theOrderIs(theRoot->theElement, element)) + { + node->theRBranch = theRoot->theRBranch; + node->theLBranch = theRoot; + theRoot->theRBranch = 0; + theRoot = node; + ++theSize; + } +// else +// { +// delete node; +// } + +#if USE_OBSOLETE + Node* current = theRoot; + Node* parent = 0; + + while (current) + { + parent = current; + + if (theOrderIs(current->theElement, element)) + { + current = current->theRBranch; + } + else + { + current = current->theLBranch; + } + } + + current = new Node(element); + current->theParent = parent; + + if (!parent) + { + theRoot = current; + } + else if (theOrderIs(parent->theElement, element)) + { + parent->theRBranch = current; + } + else + { + parent->theLBranch = current; + } + + splay(current); + + ++theSize; +#endif +} + +//***************************************************************************** +// SplayTree::erase(const T&) +//> Remove an element from the tree. +//< +//***************************************************************************** +template +void +SplayTree::erase(const T& element) +{ + Node* found = find(element); + + if (!found) return; + + if (!found->theLBranch) + { + theRoot = found->theRBranch; + } + else + { + theRoot = found->theLBranch; + splay(element); + theRoot->theRBranch = found->theRBranch; + } + + --theSize; + + found->theLBranch = 0; + found->theRBranch = 0; + delete found; + +#if USE_OBSOLETE + Node* found = find(element); + + if (!found) return; + + // No need to splay here... splay performed by find. + + if (!found->theLBranch) + { + replace(found, found->theRBranch); + } + else if (!found->theRBranch) + { + replace(found, found->theLBranch); + } + else + { + Node* newRoot = headFrom(found->theRBranch); + + // NOTE: by definition, newRoot has no left child + + if (newRoot->theParent != found) + { + replace(newRoot, newRoot->theRBranch); + newRoot->theRBranch = found->theRBranch; + newRoot->theRBranch->theParent = newRoot; + } + + replace(found, newRoot); + newRoot->theLBranch = found->theLBranch; + newRoot->theLBranch->theParent = newRoot; + } + + found->theLBranch = 0; + found->theRBranch = 0; + found->theParent = 0; + delete found; + --theSize; +#endif +} + +//***************************************************************************** +// SplayTree::find(const T&) +//> Find an element in the tree. +//< +//***************************************************************************** +template +typename SplayTree::Node* +SplayTree::find(const T& element) +{ + splay(element); + + if (theOrderIs(theRoot->theElement, element)) + { + return 0; + } + + if (theOrderIs(element, theRoot->theElement)) + { + return 0; + } + + return theRoot; + +#if USE_OBSOLETE + Node* previous = 0; + Node* current = theRoot; + + while (current) + { + if (theOrderIs(current->theElement, element)) + { + previous = current; + current = current->theRBranch; + } + else if (theOrderIs(element, current->theElement)) + { + previous = current; + current = current->theLBranch; + } + else + { + splay(current); + return current; + } + } + + if (previous) splay(previous); + + return 0; +#endif +} + +//***************************************************************************** +// SplayTree::head() +//> Find the minimum element in the tree. +//< +//***************************************************************************** +template +const T& +SplayTree::head() +{ + return headFrom(theRoot)->theElement; +} + +//***************************************************************************** +// SplayTree::tail() +//> Find the maximum element in the tree. +//< +//***************************************************************************** +template +const T& +SplayTree::tail() +{ + return tailFrom(theRoot)->theElement; +} + +//***************************************************************************** +// SplayTree::splay(Node* const) +//> Perform the splay operation. +//< +//***************************************************************************** +template +void +SplayTree::splay(const T& element) +{ + if (!theRoot) return; + + Node* node = theRoot; + Node* child = 0; + + Node temp; + Node* l = &temp; + Node* r = &temp; + + for(;;) + { + if (theOrderIs(element, node->theElement)) + { + if (!node->theLBranch) break; + + if (theOrderIs(element, node->theLBranch->theElement)) + { + child = node->theLBranch; + node->theLBranch = child->theRBranch; + child->theRBranch = node; + node = child; + + if (!node->theLBranch) break; + } + + r->theLBranch = node; + r = node; + node = node->theLBranch; + } + else if (theOrderIs(node->theElement, element)) + { + if (!node->theRBranch) break; + + if (theOrderIs(node->theRBranch->theElement, element)) + { + child = node->theRBranch; + node->theRBranch = child->theLBranch; + child->theLBranch = node; + node = child; + if (!node->theRBranch) break; + } + + l->theRBranch = node; + l = node; + node = node->theRBranch; + } + else + { + break; + } + } + + l->theRBranch = node->theLBranch; + r->theLBranch = node->theRBranch; + node->theLBranch = temp.theRBranch; + node->theRBranch = temp.theLBranch; + temp.theRBranch = 0; + temp.theLBranch = 0; + + theRoot = node; + +#if USE_OBSOLETE + while (bubble->theParent) + { + if (bubble->theParent->theLBranch == bubble) + { + // CASE: The bubble is a left-child + + if (!bubble->theParent->theParent) + { + // CASE: Zig Condition. + zig(bubble->theParent); + } + else if (bubble->theParent->theParent->theLBranch == bubble->theParent) + { + // CASE: Zig-Zig Condition + zig(bubble->theParent->theParent); + zig(bubble->theParent); + } + else + { + // CASE: Zig-Zag Condition + zig(bubble->theParent); + zag(bubble->theParent); + } + } + else + { + // CASE: The bubble is a right-child + + if (!bubble->theParent->theParent) + { + // CASE: Zag Condition. + zag(bubble->theParent); + } + else if (bubble->theParent->theParent->theRBranch == bubble->theParent) + { + // Zag-Zag Condition + zag(bubble->theParent->theParent); + zag(bubble->theParent); + } + else + { + // Zag-Zig Condition + zag(bubble->theParent); + zig(bubble->theParent); + } + } + } +#endif +} + +//***************************************************************************** +// SplayTree::headFrom(Node*) +//> Calculate the head (minimum) of the subtree rooted at the given node. +//< +//***************************************************************************** +template +typename SplayTree::Node* +SplayTree::headFrom(Node* current) +{ + if (!current) return 0; + + while (current->theLBranch) current = current->theLBranch; + + return current; +} + +//***************************************************************************** +// SplayTree::tailFrom(Node*) +//> Calculate the tail (maximum) of the subtree rooted at the given node. +//< +//***************************************************************************** +template +typename SplayTree::Node* +SplayTree::tailFrom(Node* current) +{ + if (!current) return 0; + + while (current->theRBranch) current = current->theRBranch; + + return current; +} + +} Index: Damkjer/Util/Dictionaries/test/TestSplayTree.cpp =================================================================== --- Damkjer/Util/Dictionaries/test/TestSplayTree.cpp (revision 13) +++ Damkjer/Util/Dictionaries/test/TestSplayTree.cpp (revision 13) @@ -0,0 +1,137 @@ +//***************************************************************************** +// FILE: TestSplayTree.cpp +// +// Copyright (C) 2013 Kristian Damkjer. +// +// DESCRIPTION: TestSplayTree +// +// See TestVpTree header for detailed description. +// +// LIMITATIONS: +// +// SOFTWARE HISTORY: +//> 2012-JUL-24 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#include +#include +#include +#include +#include +#include + +#include "TestSplayTree.h" +#include "Util/Exception/Exception.h" +#include "Util/Dictionaries/SplayTree.h" +#include "Util/Streams/BlockIndent.h" + +namespace Damkjer +{ + + +//***************************************************************************** +// FUNCTOR: testChebyshevRnn +//***************************************************************************** +class testSplayInsert : public TestCase::TestStep +{ +public: + testSplayInsert() + : TestCase::TestStep((std::string( + "insert into splay tree"))) + { + } + //> + //< + + bool operator()(TestCase& test) const + { + EXCEPTION_TRY("Damkjer::testSplayInsert::operator(TestCase&)"); + + // Create the spatially indexed database + typedef SplayTree SplayTreeT; + + SplayTreeT dictionary; + + dictionary.insert(5); + dictionary.insert(6); + dictionary.insert(4); + dictionary.insert(10); + dictionary.insert(12); + dictionary.insert(2); + dictionary.insert(1); + dictionary.insert(8); + + dictionary.erase(8); + dictionary.erase(1); + dictionary.erase(12); + + // Check the results + bool passedAll = true; + bool check; + + test.report() << "Check that dictionary size is five... "; + check = (dictionary.size() == 5); + passedAll &= check; + test.report() << ((check) ? "[OK]" : "[FAILED]") << "\n"; + +// for (unsigned int i = 0; i < 1024; ++i) +// { +// dictionary.insert((541 * i) & 1023); +// } + + { + + SplayTreeT dictionary2; + + for (unsigned int i = 0; i < 1048576; ++i) + { + dictionary2.insert((524309 * i) & 1048575); + if (i % 10486 == 0) test.report() << (100.*i/1048575) << "\n"; + } + + test.report() << "Check that dictionary size is 1048576... "; + check = (dictionary2.size() == 1048576); + passedAll &= check; + test.report() << ((check) ? "[OK]" : "[FAILED]") << "\n"; + + while (dictionary2.size() > 0) + { + dictionary2.erase(dictionary2.head()); + + if (dictionary2.size() % 10486 == 0) + { + test.report() << (100.*dictionary2.size()/1048575) << "\n"; + } + } + + } + + return passedAll; + + EXCEPTION_RETHROW; + } + //> The parentheses operator represents the body of the test step + // function. It will perform the necessary evaluation and return true if + // and only if the test passes. + //< +}; + +//***************************************************************************** +// CONSTRUCTOR: TestSplayTree::TestSplayTree(int, char**) +//***************************************************************************** +TestSplayTree::TestSplayTree(int argc, char** argv) + : TestCase(argc, argv, + "SplayTree: Splay Point Tree Test Suite", + "SplayTree_01", + "This test case tests the splay point tree data structure.") +{ + EXCEPTION_TRY("Damkjer::TestSplayTree::TestSplayTree(int, char**)"); + + registerStep(new testSplayInsert()); + + EXCEPTION_RETHROW; +} + +} Index: Damkjer/Util/Dictionaries/test/TestSplayTree.h =================================================================== --- Damkjer/Util/Dictionaries/test/TestSplayTree.h (revision 13) +++ Damkjer/Util/Dictionaries/test/TestSplayTree.h (revision 13) @@ -0,0 +1,38 @@ +//***************************************************************************** +// FILE: TestSplayTree.h +// +// Copyright (C) 2013 Kristian Damkjer. +// +// DESCRIPTION: +// +// LIMITATIONS: +// +// SOFTWARE HISTORY: +//> 2012-AUG-06 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#ifndef TestSplayTree_HEADER +#define TestSplayTree_HEADER + +#include "Util/UtilAPI.h" +#include "Util/UnitTest/TestCase.h" + +namespace Damkjer +{ + +class TestSplayTree : public TestCase +{ +public: + TestSplayTree(int, char**); + //> + //< +private: + TestSplayTree(const TestSplayTree&); + TestSplayTree& operator=(const TestSplayTree&); +}; + +} + +#endif Index: Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj =================================================================== --- Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj (revision 13) +++ Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj (revision 13) @@ -0,0 +1,437 @@ + + + + + DebugOMP + Win32 + + + DebugOMP + x64 + + + Debug + Win32 + + + Debug + x64 + + + OpenMP + Win32 + + + OpenMP + x64 + + + Release + Win32 + + + Release + x64 + + + + + + + + + + + + {20fe2624-c64f-d61a-bd8f-1725a8e68a42} + + + + Win32Proj + test_SplayTree + + + + Application + true + + + Application + true + + + Application + true + + + Application + true + + + Application + false + + + Application + false + + + Application + false + + + Application + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + call $(TargetPath) + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + call $(TargetPath) + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + call $(TargetPath) + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + call $(TargetPath) + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + $(SolutionDir)test-bin\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + + _USE_MATH_DEFINES;WIN32;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + MachineX86 + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + Console + + + + + + _USE_MATH_DEFINES;WIN32;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + + + MachineX86 + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + _USE_MATH_DEFINES;WIN64;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + Console + + + + + + _USE_MATH_DEFINES;WIN64;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + + + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + _USE_MATH_DEFINES;WIN32;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + MachineX86 + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + _USE_MATH_DEFINES;WIN32;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + + + MachineX86 + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + _USE_MATH_DEFINES;WIN64;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + _USE_MATH_DEFINES;WIN64;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + true + /wd4514 /wd4571 /wd4668 /wd4710 /wd4711 /wd4820 /wd4986 %(AdditionalOptions) + AnySuitable + true + Speed + + + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(SolutionDir)lib\$(Platform)\$(Configuration)\;$(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + Console + + + setlocal + +@rem Perform the unit test +echo Running Unit Test: $(ProjectName) +set PATH=%PATH%;$(SolutionDir)lib\$(Platform)\$(Configuration)\ +call $(TargetPath) > $(TargetDir)$(TargetName).txt 2>&1 + +@rem Check for success +if errorlevel 1 goto UnitTestFailed + +goto UnitTestPassed + +:UnitTestFailed +echo [FAILED] - Unit Test: $(ProjectName) +exit 1 + +:UnitTestPassed +echo [PASSED] - Unit Test: $(ProjectName) +exit 0 + +endlocal + + + + + + + + Index: Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj.filters =================================================================== --- Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj.filters (revision 13) +++ Damkjer/Util/Dictionaries/test/TestSplayTree.vcxproj.filters (revision 13) @@ -0,0 +1,26 @@ + + + + + {4010ed24-e68d-4e6e-97b0-8b8bb335aa86} + cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx + + + {0c039d31-de79-478b-9dc5-c3378145e52a} + h;hpp;hxx;hm;inl;inc;xsd + + + + + Source Files + + + Source Files + + + + + Header Files + + + Index: Damkjer/Util/Dictionaries/test/test_SplayTree.cpp =================================================================== --- Damkjer/Util/Dictionaries/test/test_SplayTree.cpp (revision 13) +++ Damkjer/Util/Dictionaries/test/test_SplayTree.cpp (revision 13) @@ -0,0 +1,33 @@ +//***************************************************************************** +// FILE: test_SplayTree.cpp +// +// Copyright (C) 2013 Kristian Damkjer. +// +// DESCRIPTION: +// +// LIMITATIONS: +// +// SOFTWARE HISTORY: +//> 2012-AUG-06 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#include "Util/Exception/Exception.h" +#include "TestSplayTree.h" + +using namespace Damkjer; + +//***************************************************************************** +// main +//***************************************************************************** +int main(int argc, char** argv) +{ + EXCEPTION_TRY("main(int, char**)"); + + TestSplayTree driver(argc, argv); + + return driver.execute(); + + EXCEPTION_CATCHALL; +} Index: Damkjer/Util/MATLAB/ClassHandle.h =================================================================== --- Damkjer/Util/MATLAB/ClassHandle.h (revision 12) +++ Damkjer/Util/MATLAB/ClassHandle.h (revision 13) @@ -75,5 +75,5 @@ //< - const ObjectT& object() const { return *thePointer; } + ObjectT& object() const { return *thePointer; } //> Return the object encapsulated by the ClassHandle. // @@ -90,5 +90,5 @@ //< - static const ObjectT& handleReference(const mxArray*); + static ObjectT& handleReference(const mxArray*); //> Reinterpret a MathWorks index as a C++ object reference. //< Index: Damkjer/Util/MATLAB/ClassHandle.hpp =================================================================== --- Damkjer/Util/MATLAB/ClassHandle.hpp (revision 12) +++ Damkjer/Util/MATLAB/ClassHandle.hpp (revision 13) @@ -67,5 +67,5 @@ //***************************************************************************** template -const ObjectT& +ObjectT& ClassHandle::handleReference(const mxArray* aMatrix) { Index: Damkjer/Util/MATLAB/SplayTree.m =================================================================== --- Damkjer/Util/MATLAB/SplayTree.m (revision 13) +++ Damkjer/Util/MATLAB/SplayTree.m (revision 13) @@ -0,0 +1,148 @@ +% SplayTree Splay Tree indexed search data structure +% +% File: SearchTree.m +% +% Description: +% This MATLAB class represents a splay tree data structure. The +% class is derived from the MATLAB handle class to provide automated object +% descruction on calls to "clear". +% +% Limitations: +% See SplayTree.h for complete description of limitations. +% +% Properties: +% None. +% +% Methods: +% [tree] = SplayTree(varargin) - VP Tree Constructor +% delete(tree) - Release this object and +% free memory. +% +% Toolbox requirements: +% None. +% +% Script requirements: +% None. +% +% Data requirements: +% SplayTreeAPI MEX library. +% +% References: +% Put the Splay Tree paper reference here. If the line wraps (which it +% probably will), then indent the subsequent lines. +% +% See Also: +% None. +% + +% Copyright (C) 2012 Kristian L. Damkjer. +% +% Software History: +% 2013-DEC-28 K. Damkjer +% Initial Coding. +% + +%****************************************************************************** +% CLASS: SplayTree +% Splay Tree indexed search data structure. The class is derived +% from the MATLAB handle class to provide automated object descruction on +% calls to "clear". +%****************************************************************************** +classdef (Sealed = true) SplayTree < handle + + properties (Hidden=true, Access = private) + % The C++ Splay-tree object owned by this handle class. + theTree + end + + methods + %************************************************************************ + % SplayTree/SplayTree + %************************************************************************ + function this = SplayTree(weights, elems) + % Build the index structure for the database. + % + % Parameters: + % varargin - Variable-length input argument list. Currently, only a + % single argument is permitted in the argument list. + % Specifically, a set of point observations that will be + % spatially indexed by the tree structure. + + if (nargin ~= 2) + error('SplayTree:InvalidArgumentList',... + 'SplayTree must be constructed with a set of indexes'); + end + + this.theTree = SplayTreeAPI('create', weights, uint64(elems)); + end + + %************************************************************************ + % SplayTree/delete + %************************************************************************ + function delete(this) + % This function frees memory on delete (clear) of the SplayTree. + SplayTreeAPI('destroy', this.theTree); + end + + %************************************************************************ + % VpTree/pop_head + %************************************************************************ + function [wgt,idx] = pop_head(this) + % Perform a k-nearest neighbor search on the database with the + % set of queries. + % + % Parameters: + % + % Returns: + % + + [wgt,idx] = SplayTreeAPI('pop_head', this.theTree); + end + + %************************************************************************ + % VpTree/head + %************************************************************************ + function [wgt,idx] = head(this) + % Perform a k-nearest neighbor search on the database with the + % set of queries. + % + % Parameters: + % + % Returns: + % + + [wgt,idx] = SplayTreeAPI('head', this.theTree); + end + + %************************************************************************ + % VpTree/insert + %************************************************************************ + function insert(this, weights, elems) + % Perform a k-nearest neighbor search on the database with the + % set of queries. + % + % Parameters: + % + % Returns: + % + + SplayTreeAPI('insert', this.theTree, weights, elems); + end + + %************************************************************************ + % VpTree/erase + %************************************************************************ + function erase(this, weights, elems) + % Perform a k-nearest neighbor search on the database with the + % set of queries. + % + % Parameters: + % + % Returns: + % + + SplayTreeAPI('erase', this.theTree, weights, elems); + end + end +end + Index: Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.cpp =================================================================== --- Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.cpp (revision 13) +++ Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.cpp (revision 13) @@ -0,0 +1,587 @@ +//***************************************************************************** +// FILE: SplayTreeAPI.cpp +// +// Copyright (C) 2012 Kristian Damkjer. +// +// DESCRIPTION: +//> The application interface for working with VP Trees in MATLAB. +//< +// +// LIMITATIONS: +//> All interfaces to the VP Tree objects from MATLAB must be routed through +// this gateway file. This interface is required until and unless MATLAB +// provides a mechanism for modifying locks on MEX files other than the +// current file. +//< +// +// SOFTWARE HISTORY: +//> 2013-DEC-13 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#if _OPENMP +#include +#endif + +#include "Util/MATLAB/ClassHandle.h" +#include "Util/Dictionaries/SplayTree.h" // USES + +#include +#include +#include +#include + +//*** +// Fix "wide char" definition for older versions of MATLAB. This must be placed +// after other includes and before the mex.h include. +//*** +#if (defined(MATLAB_MAJOR) && defined(MATLAB_MINOR)) + #if MATLAB_MAJOR <= 7 && MATLAB_MINOR <= 10 && defined(_CHAR16T) + #define CHAR16_T + #endif +#endif + +#include "mex.h" + +//***************************************************************************** +// NAMESPACE: +//> Splay Tree MEX API types, interfaces, and implementations. +//< +//***************************************************************************** +namespace +{ + +typedef double WeightT; + //> The MATLAB SplayTree weight (key) type. + +typedef std::deque WeightSetT; + //> The MATLAB SplayTree weight set type. + //< + +typedef std::pair WeightedPointT; + //> The MATLAB SplayTree weighted point type. + //< + +typedef std::deque WeightedPointSetT; + //> The MATLAB SplayTree weighted point set type. + //< + +typedef Damkjer::SplayTree TreeT; + //> The MATLAB SplayTree type. + //< + +typedef Damkjer::ClassHandle HandleT; + //> The SplayTree MATLAB Class Handle type. + //< + +//***************************************************************************** +// FUNCTION: splayTreeCreate +//> Create a SplayTree for use in MATLAB. +// +// New objects are wrapped by the ClassHandle template to ensure that locks +// are managed correctly to avoid double frees of memory managed by this +// class, to ensure objects have a life span separate from this function's +// scope, and to provide convenience methods for passing the pointer to the +// object between MATLAB and C++. +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +splayTreeCreate(int nlhs, mxArray** plhs, int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs < 3 || nrhs > 3) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeCreate:nargin", + "The splayTreeCreate function requires a two inputs."); + } + + if (nlhs > 1) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeCreate:nargout", + "The splayTreeCreate function requires a single output."); + } + + //*** + // The two inputs required by splayTreeErase is the collection of indices + // and the collection of weights. + //*** + const mxArray* weights=prhs[1]; + const mxArray* indices=prhs[2]; + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(indices) || + mxGetNumberOfDimensions(indices) != 2 || + mxIsComplex(indices) || + !mxIsNumeric(indices)) + { + std::stringstream msg; + msg << ((mxIsSparse(indices)) ? "" : "not ") << "sparse, " + << (mxGetNumberOfDimensions(indices)) << "-dimensions, " + << ((mxIsComplex(indices)) ? "" : "not ") << "complex, " + << ((mxIsNumeric(indices)) ? "" : "not ") << "numeric, " + << "Index input to splayTreeInsert must be a full vector " + "of real-valued data representing point indices."; + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + msg.str().c_str()); + } + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(weights) || + mxGetNumberOfDimensions(weights) != 2 || + mxIsComplex(weights) || + !mxIsNumeric(weights)) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + "Weight input to splayTreeInsert must be a full vector " + "of real-valued data representing point significance."); + } + + // Attempt to make the Splay Tree. + const mwSize iElems = mxGetN(indices); + const mwSize wElems = mxGetN(weights); + + // Check to make sure that weights are real-valued numerics + if (iElems != wElems) + { + std::stringstream msg; + msg << "Index elements : " << iElems << "\n" + << "Weight elements: " << wElems << "\n" + << "Must provide exactly one weight for each index."; + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + msg.str().c_str()); + } + + mwIndex* iData = (mwIndex*)mxGetData(indices); + double* wData = mxGetPr(weights); + + TreeT* returnTree = new TreeT(); + + for (mwSize elem = iElems; elem --> 0;) + { + returnTree->insert((WeightedPointT)std::make_pair(wData[elem], + iData[elem])); + } + + //*** + // Use the ClassHandle named constructor to provide a handle to the new + // Splay Tree object. + //*** + try + { + plhs[0] = HandleT::createHandle(returnTree); + } + catch (const std::exception& e) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeCreate:initError", e.what()); + } +} + +//***************************************************************************** +// FUNCTION: splayTreeDestroy +//> Destroy the SplayTree referenced by a ClassHandle object. +// +// Destroying objects through the ClassHandle wrapper ensures memory leaks +// are not introduced through this MEX function and allows the MEX library +// to be unlocked once all objects have been destroyed and their memory +// returned to the system. +// +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +inline +void +splayTreeDestroy(int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 2 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeDestroy:varargin", + "The splayTreeDestroy function requires a single " + "input."); + } + + // Free the Splay Tree through the ClassHandle named destructor. + HandleT::destroyHandle(prhs[1]); +} + +//***************************************************************************** +// FUNCTION: splayTreeHead +//> Find minumum element in splay tree. +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +splayTreeHead(int nlhs, mxArray** plhs, int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 2 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeHead:nargin", + "The splayTreeHead function requires a single input."); + } + + if (nlhs != 2) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeHead:nargout", + "The splayTreeHead function requires two outputs."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + const WeightedPointT& head=tree.head(); + + plhs[0]=mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL); + double* weight = (double*) mxGetData(plhs[0]); + weight[0] = head.first; + + plhs[1]=mxCreateNumericMatrix(1, 1, mxINDEX_CLASS, mxREAL); + mwSize* index = (mwSize*) mxGetData(plhs[1]); + index[0] = head.second; +} + +//***************************************************************************** +// FUNCTION: splayTreePopHead +//> Find minumum element in splay tree. +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +splayTreePopHead(int nlhs, mxArray** plhs, int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 2 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:splayTreePopHead:nargin", + "The splayTreePopHead function requires a single input."); + } + + if (nlhs != 2) + { + mexErrMsgIdAndTxt("Damkjer:splayTreePopHead:nargout", + "The splayTreePopHead function requires two outputs."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + const WeightedPointT& head=tree.head(); + + plhs[0]=mxCreateNumericMatrix(1, 1, mxDOUBLE_CLASS, mxREAL); + double* weight = (double*) mxGetData(plhs[0]); + weight[0] = head.first; + + plhs[1]=mxCreateNumericMatrix(1, 1, mxINDEX_CLASS, mxREAL); + std::size_t* index = (std::size_t*) mxGetData(plhs[1]); + index[0] = head.second; + + tree.erase(head); + + if (tree.find(head) != 0) + { + mexErrMsgIdAndTxt("Damkjer:splayTreePopHead:nargout", + "Pop failed."); + } +} + +//***************************************************************************** +// FUNCTION: splayTreeInsert +//> Find minumum element in splay tree. +// +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +splayTreeInsert(int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 4 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:nargin", + "The splayTreeInsert function requires three inputs."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + //*** + // The two inputs required by splayTreeErase is the collection of indices + // and the collection of weights. + //*** + const mxArray* weights=prhs[2]; + const mxArray* indices=prhs[3]; + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(indices) || + mxGetNumberOfDimensions(indices) != 2 || + mxIsComplex(indices) || + !mxIsNumeric(indices)) + { + std::stringstream msg; + msg << ((mxIsSparse(indices)) ? "" : "not ") << "sparse " + << (mxGetNumberOfDimensions(indices)) << " " + << ((mxIsComplex(indices)) ? "" : "not ") << "complex " + << ((mxIsNumeric(indices)) ? "" : "not ") << "numeric " + << "Index input to splayTreeInsert must be a full vector " + "of real-valued data representing point indices."; + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + msg.str().c_str()); + } + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(weights) || + mxGetNumberOfDimensions(weights) != 2 || + mxIsComplex(weights) || + !mxIsNumeric(weights)) + { + std::stringstream msg; + msg << ((mxIsSparse(weights)) ? "" : "not ") << "sparse " + << (mxGetNumberOfDimensions(weights)) << " " + << ((mxIsComplex(weights)) ? "" : "not ") << "complex " + << ((mxIsNumeric(weights)) ? "" : "not ") << "numeric " + << "Weight input to splayTreeInsert must be a full vector " + "of real-valued data representing point significance."; + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + msg.str().c_str()); + } + + // Attempt to make the Splay Tree. + const mwSize iElems = mxGetN(indices); + const mwSize wElems = mxGetN(weights); + + // Check to make sure that weights are real-valued numerics + if (iElems != wElems) + { + std::stringstream msg; + msg << "Index elements : " << mxGetM(indices) << "x" << iElems << "\n" + << "Weight elements: " << mxGetM(weights) << "x" << wElems << "\n" + << "Must provide exactly one weight for each index."; + mexErrMsgIdAndTxt("Damkjer:splayTreeInsert:prhs", + msg.str().c_str()); + } + + mwIndex* iData = (mwIndex*)mxGetData(indices); + double* wData = mxGetPr(weights); + + //*** + // Selection of data structure for the point database is not arbitrary. + // + // 1. Point coordinates are passed in as double-precision values. Preserve + // the data fidelity. + // 2. Individual points are often low-dimensional. Keep the coordinates for + // a single point in contiguous memory by using a std::vector container. + // 3. The point database can be quite large. Since VP Tree is an online data + // structure, allow references to points to occupy non-contiguous memory. + // This also speeds construction and destruction of the point database. + //*** +// WeightedPointSetT pointData(elems); + + for (mwSize elem = iElems; elem --> 0;) + { + tree.insert((WeightedPointT)std::make_pair(wData[elem], iData[elem])); + } +} + +//***************************************************************************** +// FUNCTION: splayTreeErase +//> Find minumum element in splay tree. +// +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +splayTreeErase(int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 4 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeErase:nargin", + "The splayTreeErase function requires three inputs."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + //*** + // The two inputs required by splayTreeErase is the collection of indices + // and the collection of weights. + //*** + const mxArray* weights=prhs[2]; + const mxArray* indices=prhs[3]; + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(indices) || + mxGetNumberOfDimensions(indices) != 2 || + mxIsComplex(indices) || + !mxIsNumeric(indices)) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeErase:prhs", + "Index input to splayTreeErase must be a full vector " + "of real-valued data representing point significance."); + } + + // Check to make sure that weights are real-valued numerics + if (mxIsSparse(weights) || + mxGetNumberOfDimensions(weights) != 2 || + mxIsComplex(weights) || + !mxIsNumeric(weights)) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeErase:prhs", + "Weight input to splayTreeErase must be a full vector " + "of real-valued data representing point significance."); + } + + // Attempt to make the Splay Tree. + const mwSize iElems = mxGetN(indices); + const mwSize wElems = mxGetN(weights); + + // Check to make sure that weights are real-valued numerics + if (iElems != wElems) + { + mexErrMsgIdAndTxt("Damkjer:splayTreeErase:prhs", + "Must provide exactly one weight for each index."); + } + + mwIndex* iData = (mwIndex*)mxGetData(indices); + double* wData = mxGetPr(weights); + + //*** + // Selection of data structure for the point database is not arbitrary. + // + // 1. Point coordinates are passed in as double-precision values. Preserve + // the data fidelity. + // 2. Individual points are often low-dimensional. Keep the coordinates for + // a single point in contiguous memory by using a std::vector container. + // 3. The point database can be quite large. Since VP Tree is an online data + // structure, allow references to points to occupy non-contiguous memory. + // This also speeds construction and destruction of the point database. + //*** +// WeightedPointSetT pointData(elems); + + for (mwSize elem = iElems; elem --> 0;) + { + tree.erase((WeightedPointT)std::make_pair(wData[elem], iData[elem])); + } +} + +} + +//***************************************************************************** +// FUNCTION: mexFunction +//> The MATLAB Executable Gateway Function. +// +// Provides the application interface for working with VP Trees in MATLAB. +// All functional interfaces are routed through this single function to +// ensure locks and memory management are handled properly by MATLAB. +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void +mexFunction(int nlhs, mxArray** plhs, int nrhs, const mxArray** prhs) +{ + //*** + // This MEX function should always have at least one input parameter to + // handle function dispatching through the MEX gateway. + //*** + if (nrhs < 1) + { + mexErrMsgIdAndTxt("Damkjer:SplayTreeAPI:nargin", + "SplayTreeAPI requires at least one input which " + "specifies the operation to be performed."); + } + + // The operation switch is simply a string. + char* operation = mxArrayToString(prhs[0]); + + if (!operation) + { + mexErrMsgIdAndTxt("Damkjer:SplayTreeAPI:InvalidOperation", + "Invalid mode supplied to SplayTreeAPI."); + return; // error should force return. + } + + // Dispatch to helper functions. Err if operation is not recognized. + if (!strcmp("create", operation)) + { + splayTreeCreate(nlhs, plhs, nrhs, prhs); + } + else if (!strcmp("destroy", operation)) + { + if (nlhs != 0) + { + mexErrMsgIdAndTxt("Damkjer:SplayTreeAPI:nargout", + "Nothing to return."); + } + + splayTreeDestroy(nrhs, prhs); + } + else if (!strcmp("head", operation)) + { + splayTreeHead(nlhs, plhs, nrhs, prhs); + } + else if (!strcmp("pop_head", operation)) + { + splayTreePopHead(nlhs, plhs, nrhs, prhs); + } + else if (!strcmp("insert", operation)) + { + splayTreeInsert(nrhs, prhs); + } + else if (!strcmp("erase", operation)) + { + splayTreeErase(nrhs, prhs); + } + else + { + mexErrMsgIdAndTxt("Damkjer:SplayTreeAPI:UnknownOperation", + "Unrecognized mode provided to SplayTreeAPI."); + } + + // Prevent a slow memory leak. + mxFree(operation); +} Index: Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj =================================================================== --- Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj (revision 13) +++ Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj (revision 13) @@ -0,0 +1,284 @@ + + + + + DebugOMP + Win32 + + + DebugOMP + x64 + + + Debug + Win32 + + + Debug + x64 + + + OpenMP + Win32 + + + OpenMP + x64 + + + Release + Win32 + + + Release + x64 + + + + + {20fe2624-c64f-d61a-bd8f-1725a8e68a42} + + + + + + + Win32Proj + SplayTreeAPI + + + + DynamicLibrary + true + + + DynamicLibrary + true + + + DynamicLibrary + true + + + DynamicLibrary + true + + + DynamicLibrary + false + + + DynamicLibrary + false + + + DynamicLibrary + false + + + DynamicLibrary + false + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .mexw32 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw32 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw64 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw64 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw32 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw32 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw64 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + .mexw64 + $(SolutionDir)lib\$(Platform)\$(Configuration)\ + $(SolutionDir)build\$(Platform)\$(Configuration)\$(ProjectName)\ + + + + _USE_MATH_DEFINES;WIN32;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + MachineX86 + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN32;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + + + MachineX86 + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN64;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN64;_DEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDebugDLL + Level4 + Disabled + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + + + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN32;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + MachineX86 + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN32;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + AnySuitable + true + Speed + + + MachineX86 + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN64;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + + + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + + + + + _USE_MATH_DEFINES;WIN64;NDEBUG;_WINDOWS;TEMPLATE_INCLUSION;%(PreprocessorDefinitions) + MultiThreadedDLL + Level4 + $(SolutionDir);$(MATLAB_R2012A)\extern\include;$(SolutionDir)\includes\eigen;%(AdditionalIncludeDirectories) + true + /wd4514 /wd4571 /wd4668 /wd4710 /wd4711 /wd4820 /wd4986 %(AdditionalOptions) + AnySuitable + true + Speed + + + true + true + true + libmx.lib;libmat.lib;libmex.lib;%(AdditionalDependencies) + $(MATLAB_R2012A)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + + + + + + Index: Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj.filters =================================================================== --- Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj.filters (revision 13) +++ Damkjer/Util/MATLAB/SplayTreeAPI/SplayTreeAPI.vcxproj.filters (revision 13) @@ -0,0 +1,18 @@ + + + + + {4010ed24-e68d-4e6e-97b0-8b8bb335aa86} + cpp;c;cc;cxx;def;odl;idl;hpj;bat;asm;asmx + + + {0c039d31-de79-478b-9dc5-c3378145e52a} + h;hpp;hxx;hm;inl;inc;xsd + + + + + Source Files + + + Index: Damkjer/Util/MATLAB/SplayTreeAPI/makeSplayTree.m =================================================================== --- Damkjer/Util/MATLAB/SplayTreeAPI/makeSplayTree.m (revision 13) +++ Damkjer/Util/MATLAB/SplayTreeAPI/makeSplayTree.m (revision 13) @@ -0,0 +1,126 @@ +% makeVpTree Build VpTree spatial indexing library MEX functions and classes. +% +% File: +% makeVpTree.m +% +% Description: +% This MATLAB function provides an simplified interface for building the +% VpTree C++ and MEX files. +% +% Limitations: +% Assumes mex -setup has been successfully run. +% +% Synopsis: +% makeVpTree(options...) +% +% Inputs: +% Option strings may be provided as abbreviations as long as they resolve to +% a unique option. +% +% 'debug' - Compile with debug flags and fully populated symbol table. +% 'parallel' - Enable OpenMP pragmas for multi-threaded computing. +% 'verbose' - Provide verbose output while compiling. +% 'warnings' - Provide compiler warning output for production-ready code. +% Implies 'verbose'. +% +% Outputs: +% None. +% +% Toolbox requirements: +% None. +% +% Code requirements: +% None. +% +% Data requirements: +% None. +% +% References: +% None. +% +% See Also: +% VpTree +% + +% Software History: +% 2012-AUG-29 K. Damkjer +% Initial Coding. +% 2013-JUN-17 K. Damkjer +% Additional Commenting. +% + +function makeSplayTree(varargin) + +command = 'mex -largeArrayDims -DTEMPLATE_INCLUSION'; + +matlab_ver = regexp(version, '[. ]', 'split'); +command = [command... + ' -DMATLAB_MAJOR=' matlab_ver{1}... + ' -DMATLAB_MINOR=' matlab_ver{2}... + ' -DMATLAB_REVIS=' matlab_ver{3}... + ' -DMATLAB_BUILD=' matlab_ver{4}... + ' -DMATLAB_REL=' matlab_ver{5}(2:end-1)]; + +flags = {'verbose', 'debug', 'warnings', 'parallel'}; +options = ''; + +isVerbose = 0; + +while ~isempty(varargin) + flag = varargin{1}; + + % If the property has been supplied in a shortened form, lengthen it + iFlag = find(strncmpi(flag, flags, length(flag))); + + if isempty(iFlag) + % Pass through any arguments we don't recognize + options = strcat(options, [' ' flag]); + + % Alternatively, escalate to an error. + %error('Damkjer:makeVpTree:InvalidFlag', ['Invalid Flag: ' flag]); + elseif length(iFlag) > 1 + error('Damkjer:makeSplayTree:AmbiguousFlag', ... + ['Supplied shortened flag is ambiguous: ' flag]); + else + flag = flags{iFlag}; + + switch flag + case 'verbose' + command = strcat(command, ' -v'); + isVerbose = 1; + case 'debug' + command = strcat(command, ' -g'); + case 'parallel' + if (ispc) + command = strcat(command, ' COMPFLAGS="$COMPFLAGS /openmp"'); + else + command = strcat(command, ' CFLAGS="\$CFLAGS -fopenmp"',... + ' CXXFLAGS="\$CXXFLAGS -fopenmp"',... + ' LDFLAGS="\$LDFLAGS -fopenmp"'); + end + case 'warnings' + if (ispc) + command = strcat(command, ' -v COMPFLAGS="$COMPFLAGS -W3"'); + else + command = strcat(command, ' -v',... + ' CFLAGS="\$CFLAGS -Wall -Wextra"',... + ' CXXFLAGS="\$CXXFLAGS -Wall -Wextra"'); + end + otherwise + error('Damkjer:makeVpTree:NotImplementedFlag', ... + ['Flag recognized, but not supported: ' flag]); + end + end + + varargin(1) = []; +end + +[path,~,~]=fileparts(mfilename('fullpath')); +command = [command options ' -I' fullfile(path,'..','..','..')... + ' -outdir ' path ' ' path '/']; + +disp([command 'SplayTreeAPI.cpp']); + +eval([command 'SplayTreeAPI.cpp']); + +end Index: Damkjer/Util/MATLAB/VpTree.m =================================================================== --- Damkjer/Util/MATLAB/VpTree.m (revision 12) +++ Damkjer/Util/MATLAB/VpTree.m (revision 13) @@ -95,4 +95,22 @@ %************************************************************************ + % VpTree/excludeWithin + %************************************************************************ + function excludeWithin(this, radius) + % This function establishes a closeness threshold for searches on the + % VpTree. + VpTreeAPI('exclude_within', this.theTree, radius); + end + + %************************************************************************ + % VpTree/includeAll + %************************************************************************ + function includeAll(this) + % This function clears closeness thresholds for searches on the + % VpTree. + VpTreeAPI('include_all', this.theTree); + end + + %************************************************************************ % VpTree/knn %************************************************************************ Index: Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp =================================================================== --- Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp (revision 12) +++ Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp (revision 13) @@ -33,6 +33,9 @@ #endif -#include "MATLAB/ClassHandle.h" +#include "Util/MATLAB/ClassHandle.h" #include "Util/SpatialIndexing/VpTree/VpTree.h" // USES + +#include +#include //*** @@ -206,4 +209,82 @@ // Free the VP Tree through the ClassHandle named destructor. HandleT::destroyHandle(prhs[1]); +} + +//***************************************************************************** +// FUNCTION: vpTreeExclude +//> Establish keep-out threshold for searches against the VpTree. +// +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +inline +void +vpTreeExclude(int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 3 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:vpTreeExclude:varargin", + "The vpTreeExclude function requires two " + "inputs."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + // The second parameter should be the threshold radius. + const mxArray* rData=prhs[2]; + + // Check to make sure that radius is a real-valued numeric scalar. + if (mxIsSparse(rData) || + mxGetNumberOfElements(rData) != 1 || + mxIsComplex(rData) || + !mxIsNumeric(rData)) + { + mexErrMsgIdAndTxt("Damkjer:vpTreeExclude:prhs", + "Second input parameter to vpTreeExclude must be a " + "real-valued scalar representing desired search " + "threshold radius limit."); + } + + // Get the desired neighborhood radius limit. + TreeT::DistT radius = (TreeT::DistT)(*(double*)mxGetData(rData)); + + tree.excludeWithin(radius); +} + +//***************************************************************************** +// FUNCTION: vpTreeInclude +//> Clear keep-out threshold for searches against the VpTree. +// +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +inline +void +vpTreeInclude(int nrhs, const mxArray** prhs) +{ + //*** + // Check parameters. Remember that we always have one "extra" input + // parameter to handle function dispatching through the MEX gateway. It + // always occupies the first input parameter position. + //*** + if (nrhs != 2 || !mxIsNumeric(prhs[1])) + { + mexErrMsgIdAndTxt("Damkjer:vpTreeInclude:varargin", + "The vpTreeDestroy function requires a single " + "input."); + } + + // Retrieve the tree object through the ClassHandle helper method. + TreeT& tree = HandleT::handleReference(prhs[1]); + + tree.includeAllMatches(); } @@ -771,4 +852,24 @@ vpTreeDestroy(nrhs, prhs); } + else if (!strcmp("exclude_within", operation)) + { + if (nlhs != 0) + { + mexErrMsgIdAndTxt("Damkjer:VpTreeAPI:nargout", + "Nothing to return."); + } + + vpTreeExclude(nrhs, prhs); + } + else if (!strcmp("include_all", operation)) + { + if (nlhs != 0) + { + mexErrMsgIdAndTxt("Damkjer:VpTreeAPI:nargout", + "Nothing to return."); + } + + vpTreeInclude(nrhs, prhs); + } else if (!strcmp("search_frann", operation)) { Index: Damkjer/Util/MATLAB/VpTreeAPI/makeVpTree.m =================================================================== --- Damkjer/Util/MATLAB/VpTreeAPI/makeVpTree.m (revision 12) +++ Damkjer/Util/MATLAB/VpTreeAPI/makeVpTree.m (revision 13) @@ -65,4 +65,6 @@ options = ''; +isVerbose = 0; + while ~isempty(varargin) flag = varargin{1}; @@ -73,5 +75,5 @@ if isempty(iFlag) % Pass through any arguments we don't recognize - options = strcat(options, ' ', flag); + options = strcat(options, [' ' flag]); % Alternatively, escalate to an error. @@ -86,4 +88,5 @@ case 'verbose' command = strcat(command, ' -v'); + isVerbose = 1; case 'debug' command = strcat(command, ' -g'); @@ -117,4 +120,6 @@ ' -outdir ' path ' ' path '/']; +disp([command 'VpTreeAPI.cpp']); + eval([command 'VpTreeAPI.cpp']); Index: Damkjer/Util/Math/fastsetdual.cpp =================================================================== --- Damkjer/Util/Math/fastsetdual.cpp (revision 13) +++ Damkjer/Util/Math/fastsetdual.cpp (revision 13) @@ -0,0 +1,163 @@ +//***************************************************************************** +// FILE: fastsetdual.cpp +// +// Copyright (C) 2014 Kristian Damkjer. +// +// DESCRIPTION: +//> @todo Describe this file +//< +// +// LIMITATIONS: +//> Does not work for cell-arrays of complex matrices. +//< +// +// SOFTWARE HISTORY: +//> 2014-JAN-13 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#ifdef _OPENMP +#include +#endif + +#include +#include +#include + +//*** +// Fix "wide char" definition for older versions of MATLAB. This must be placed +// after other includes and before the mex.h include. +//*** +#if (defined(MATLAB_MAJOR) && defined(MATLAB_MINOR)) + #if MATLAB_MAJOR <= 7 && MATLAB_MINOR <= 10 && defined(_CHAR16T) + #define CHAR16_T + #endif +#endif + +#include "mex.h" + +//***************************************************************************** +// FUNCTION: mexFunction +//> The MATLAB Executable Gateway Function. +// +// @todo Describe this MEX function +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void mexFunction( + int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + if (nrhs != 1 || !mxIsCell(prhs[0])) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargin", + "Missing or invalid input argument."); + } + + if (!(mxIsUint32(mxGetCell(prhs[0], 0)) || + mxIsUint64(mxGetCell(prhs[0], 0)))) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargin", + "Invalid input argument."); + } + + if (nlhs != 1) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargout", + "Fast set dual requires a single output."); + } + + mwSize cells = mxGetNumberOfElements (prhs[0]); + + std::vector nbrs(cells,0); + std::vector Ms(cells,0); + std::vector Ns(cells,0); + + mwSize maxElem = 0; + + // Note for future: Ms - neighbors, Ns - 1 + for (mwSize cell = 0; cell < cells; ++cell) + { + nbrs[cell]=(mwIndex*)(mxGetData(mxGetCell(prhs[0], cell))); + Ms[cell]=mxGetM(mxGetCell(prhs[0], cell)); + Ns[cell]=mxGetN(mxGetCell(prhs[0], cell)); + + for (mwSize n = Ns[cell]; n --> 0;) + { + for (mwSize m = Ms[cell]; m --> 0;) + { + mwSize idx = nbrs[cell][m + Ms[cell] * n]; + maxElem = (idx > maxElem) ? idx : maxElem; + } + } + } + + std::deque > duals(maxElem); + + for (mwSize cell = 0; cell < cells; ++cell) + { + for (mwSize n = Ns[cell]; n --> 0;) + { + for (mwSize m = Ms[cell]; m --> 0;) + { + mwIndex idx = nbrs[cell][m + Ms[cell] * n]; + duals[idx-1].push_back(cell + 1); + } + } + } + + plhs[0] = mxCreateCellMatrix(maxElem, 1); + + std::deque returns; + std::deque return_data; + + //*** + // Allocating memory for the results to be passed back to MATLAB must take + // place in a "critical section" since it involves exercising the MEX API. + //*** + for (std::size_t elem = 0; elem < maxElem; ++elem) + { + mwSize neighborhoods = duals[elem].size(); + + returns.push_back(mxCreateNumericMatrix(0, 0, mxINDEX_CLASS, mxREAL)); + mxSetM(returns[elem], neighborhoods); + mxSetN(returns[elem], 1); + mxSetData(returns[elem], mxMalloc(sizeof(mwIndex)*neighborhoods*1)); + + return_data.push_back((mwIndex*)mxGetData(returns[elem])); + } + + //*** + // Once memory has been allocated, the actual results can be populated in + // parallel. + //*** + #pragma omp parallel for + for (int elem = 0; elem < maxElem; ++elem) + { + std::size_t size_elem = static_cast(elem); + mwSize neighborhoods = duals[elem].size(); + + mwIndex* data = return_data[size_elem]; + + for (mwIndex idx = neighborhoods; idx --> 0;) + { + data[idx]=duals[elem][idx]; + } + } + + //*** + // Marking the data for return to MATLAB must take place in a "critical + // section" since it involves exercising the MEX API. This also changes + // ownership and memory management responsibilities to MATLAB. We will not + // free this data. + //*** + for (std::size_t elem = 0; elem < maxElem; ++elem) + { + mxSetCell(plhs[0], elem, returns[elem]); + } +} Index: Damkjer/Util/Math/fastsetunion.cpp =================================================================== --- Damkjer/Util/Math/fastsetunion.cpp (revision 13) +++ Damkjer/Util/Math/fastsetunion.cpp (revision 13) @@ -0,0 +1,131 @@ +//***************************************************************************** +// FILE: fastsetdual.cpp +// +// Copyright (C) 2014 Kristian Damkjer. +// +// DESCRIPTION: +//> @todo Describe this file +//< +// +// LIMITATIONS: +//> Does not work for cell-arrays of complex matrices. +//< +// +// SOFTWARE HISTORY: +//> 2014-JAN-13 K. Damkjer +// Initial Coding. +//< +//***************************************************************************** + +#ifdef _OPENMP +#include +#endif + +#include +#include +#include +#include + +//*** +// Fix "wide char" definition for older versions of MATLAB. This must be placed +// after other includes and before the mex.h include. +//*** +#if (defined(MATLAB_MAJOR) && defined(MATLAB_MINOR)) + #if MATLAB_MAJOR <= 7 && MATLAB_MINOR <= 10 && defined(_CHAR16T) + #define CHAR16_T + #endif +#endif + +#include "mex.h" + +//***************************************************************************** +// FUNCTION: mexFunction +//> The MATLAB Executable Gateway Function. +// +// @todo Describe this MEX function +// +// @param nlhs the number of left-hand side parameters. +// @param plhs the array of left-hand side parameters. +// @param nrhs the number of right-hand side parameters. +// @param prhs the array of right-hand side parameters. +//< +//***************************************************************************** +void mexFunction( + int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 1 || !mxIsCell(prhs[0])) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargin", + "Missing or invalid input argument."); + } + + if (!(mxIsUint32(mxGetCell(prhs[0], 0)) || + mxIsUint64(mxGetCell(prhs[0], 0)))) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargin", + "Invalid input argument."); + } + + if (nlhs > 1) + { + mexErrMsgIdAndTxt("Damkjer:fastsetdual:varargout", + "Fast set dual requires a single output."); + } + + mwSize cells = mxGetNumberOfElements (prhs[0]); + + std::vector nbrs(cells,0); + + std::set setUnion; + + // Note for future: Ms - neighbors, Ns - 1 + for (mwSize cell = 0; cell < cells; ++cell) + { + nbrs[cell]=(mwIndex*)(mxGetData(mxGetCell(prhs[0], cell))); + + mwSize Ms = mxGetM(mxGetCell(prhs[0], cell)); + + for (mwSize n = mxGetN(mxGetCell(prhs[0], cell)); n --> 0;) + { + for (mwSize m = Ms; m --> 0;) + { + setUnion.insert(nbrs[cell][m + Ms * n]); + } + } + } + + mwIndex* return_data; + + //*** + // Allocating memory for the results to be passed back to MATLAB must take + // place in a "critical section" since it involves exercising the MEX API. + //*** + mwSize neighbors = setUnion.size(); + + plhs[0] = mxCreateNumericMatrix(0, 0, mxINDEX_CLASS, mxREAL); + mxSetM(plhs[0], neighbors); + mxSetN(plhs[0], 1); + mxSetData(plhs[0], mxMalloc(sizeof(mwIndex)*neighbors*1)); + + return_data = (mwIndex*)mxGetData(plhs[0]); + + std::size_t nbr = 0; + + for (std::set::iterator itr = setUnion.begin(); + itr != setUnion.end(); + ++itr) + { + return_data[nbr] = *itr; + ++nbr; + } + +// //*** +// // Marking the data for return to MATLAB must take place in a "critical +// // section" since it involves exercising the MEX API. This also changes +// // ownership and memory management responsibilities to MATLAB. We will not +// // free this data. +// //*** +// +// mxSetCell(plhs[0], 0, returns); +} Index: Damkjer/Util/Math/makeMath.m =================================================================== --- Damkjer/Util/Math/makeMath.m (revision 7) +++ Damkjer/Util/Math/makeMath.m (revision 13) @@ -90,4 +90,6 @@ eval([command 'fastcenter.cpp']); eval([command 'par_eig.cpp']); +eval([command 'fastsetdual.cpp']); +eval([command 'fastsetunion.cpp']); end Index: Damkjer/Util/SpatialIndexing/VpTree/VpTree.h =================================================================== --- Damkjer/Util/SpatialIndexing/VpTree/VpTree.h (revision 12) +++ Damkjer/Util/SpatialIndexing/VpTree/VpTree.h (revision 13) @@ -128,5 +128,15 @@ //> Destruct the tree and deallocate resources. //< - + + void excludeWithin(const DistT&); + //> Exclude points from search results that fall within the specified + // distance. + //< + + void includeAllMatches(); + //> Include all matches in search results. Clears any previously set + // thresholds. + //< + SearchResultsT knn(const PointT&, const IndexT&, const DistT& limit=std::numeric_limits::max()) @@ -213,5 +223,13 @@ //> The distance metric used to construct and search this tree. //< - + + DistT theApproximateThreshold; + //> The distance threshold used to consider points equal to the query. + //< + + bool theApproximatesAreExcluded; + //> Exclude points that are approximately equal to the query point. + //< + friend class VpTree::Node; //> There is a defect in the C++03 standard that forces friendship of @@ -251,4 +269,6 @@ , theLeafCapacity((leafCapacity<1)?1:leafCapacity) , theMetric(metric) + , theApproximateThreshold(0) + , theApproximatesAreExcluded(false) { } @@ -275,4 +295,6 @@ , theLeafCapacity((leafCapacity<1)?1:leafCapacity) , theMetric(metric) + , theApproximateThreshold(0) + , theApproximatesAreExcluded(false) { #if _OPENMP @@ -310,4 +332,39 @@ } +//***************************************************************************** +// VpTree::excludeWithin(const DistT&) +//> Exclude Exclude points from search results that fall within the specified +// distance. +// +// @tparam MetricT The metric search space. +// @param threshold The distance threshold. +//< +//***************************************************************************** +template +inline +void +VpTree::excludeWithin(const DistT& threshold) +{ + theApproximateThreshold = threshold; + theApproximatesAreExcluded = true; +} + +//***************************************************************************** +// VpTree::includeAllMatches() +//> Include all matches in search results. Clears any previously set +// thresholds. +// +// @tparam MetricT The metric search space. +//< +//***************************************************************************** +template +inline +void +VpTree::includeAllMatches() +{ + theApproximateThreshold = 0; + theApproximatesAreExcluded = false; +} + } Index: Damkjer/Util/SpatialIndexing/VpTree/VpTree_Branch.hpp =================================================================== --- Damkjer/Util/SpatialIndexing/VpTree/VpTree_Branch.hpp (revision 12) +++ Damkjer/Util/SpatialIndexing/VpTree/VpTree_Branch.hpp (revision 13) @@ -61,5 +61,7 @@ query); - if (distance < kth_closest) + if (!(this->theTree->theApproximatesAreExcluded && + distance < this->theTree->theApproximateThreshold) && + distance < kth_closest) { if (candidates.size() == k) @@ -146,5 +148,7 @@ query); - if (distance <= range) + if (!(this->theTree->theApproximatesAreExcluded && + distance < this->theTree->theApproximateThreshold) && + distance <= range) { candidates.push(ResultsCandidate(theIndex, distance)); Index: Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp =================================================================== --- Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp (revision 12) +++ Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp (revision 13) @@ -65,5 +65,7 @@ query); - if (distance < kth_closest) + if (!(this->theTree->theApproximatesAreExcluded && + distance < this->theTree->theApproximateThreshold) && + distance < kth_closest) { if (candidates.size() == k) @@ -108,5 +110,7 @@ query); - if (distance <= range) + if (!(this->theTree->theApproximatesAreExcluded && + distance < this->theTree->theApproximateThreshold) && + distance <= range) { candidates.push(ResultsCandidate(item, distance)); Index: Damkjer/Util/Util.dox =================================================================== --- Damkjer/Util/Util.dox (revision 13) +++ Damkjer/Util/Util.dox (revision 13) @@ -0,0 +1,48 @@ +//***************************************************************************** +// DIRECTORY: Util/Exception +//> General exception classes. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/Math +//> General mathematics utilities. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/MATLAB +//> Inter-process communication code for interfacing MATLAB and C++. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/SpatialIndexing +//> Multi-dimensional search data structures and algorithms. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/SpatialIndexing/Metrics +//> Definitions of metric spaces fulfilling the requirement that distances +// between points are constrained by the triangle inequality. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/SpatialIndexing/VpTree +//> Vantage point tree spatial indexing data structure and search algorithms. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/Streams +//> General stream handlers. +//< +//***************************************************************************** + +//***************************************************************************** +// DIRECTORY: Util/UnitTest +//> Unit testing framework. +//< +//***************************************************************************** Index: Damkjer/Util/Util.vcxproj =================================================================== --- Damkjer/Util/Util.vcxproj (revision 12) +++ Damkjer/Util/Util.vcxproj (revision 13) @@ -36,4 +36,6 @@ + + Index: Damkjer/Util/Util.vcxproj.filters =================================================================== --- Damkjer/Util/Util.vcxproj.filters (revision 12) +++ Damkjer/Util/Util.vcxproj.filters (revision 13) @@ -82,4 +82,10 @@ Template Implementation Files + + Header Files + + + Template Implementation Files + Index: Damkjer/config/doxyfile.txt =================================================================== --- Damkjer/config/doxyfile.txt (revision 13) +++ Damkjer/config/doxyfile.txt (revision 13) @@ -0,0 +1,1948 @@ + # Doxyfile 1.8.4 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed +# in front of the TAG it is preceding . +# All text after a hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (" "). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# http://www.gnu.org/software/libiconv for the list of possible encodings. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or sequence of words) that should +# identify the project. Note that if you do not use Doxywizard you need +# to put quotes around the project name if it contains spaces. + +PROJECT_NAME = "Damkjer Research" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. +# This could be handy for archiving the generated documentation or +# if some version control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer +# a quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = "Kristian Damkjer's Doctoral Research Code" + +# With the PROJECT_LOGO tag one can specify an logo or icon that is +# included in the documentation. The maximum height of the logo should not +# exceed 55 pixels and the maximum width should not exceed 200 pixels. +# Doxygen will copy the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) +# base path where the generated documentation will be put. +# If a relative path is entered, it will be relative to the location +# where doxygen was started. If left blank the current directory will be used. + +OUTPUT_DIRECTORY = docs + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create +# 4096 sub-directories (in 2 levels) under the output directory of each output +# format and will distribute the generated files over these directories. +# Enabling this option can be useful when feeding doxygen a huge amount of +# source files, where putting all generated files in the same directory would +# otherwise cause performance problems for the file system. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# The default language is English, other supported languages are: +# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, +# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German, +# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English +# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian, +# Persian, Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, +# Slovak, Slovene, Spanish, Swedish, Ukrainian, and Vietnamese. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will +# include brief member descriptions after the members that are listed in +# the file and class documentation (similar to JavaDoc). +# Set to NO to disable this. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend +# the brief description of a member or function before the detailed description. +# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator +# that is used to form the text in various listings. Each string +# in this list, if found as the leading text of the brief description, will be +# stripped from the text and the result after processing the whole list, is +# used as the annotated text. Otherwise, the brief description is used as-is. +# If left blank, the following values are used ("$name" is automatically +# replaced with the name of the entity): "The $name class" "The $name widget" +# "The $name file" "is" "provides" "specifies" "contains" +# "represents" "a" "an" "the" + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. + +# Defaul NO +ALWAYS_DETAILED_SEC = YES + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full +# path before files name in the file list and in the header files. If set +# to NO the shortest path that makes the file name unique will be used. + +FULL_PATH_NAMES = YES + +# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag +# can be used to strip a user-defined part of the path. Stripping is +# only done if one of the specified strings matches the left-hand part of +# the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the +# path to strip. Note that you specify absolute paths here, but also +# relative paths, which will be relative from the directory where doxygen is +# started. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of +# the path mentioned in the documentation of a class, which tells +# the reader which header file to include in order to use a class. +# If left blank only the name of the header file containing the class +# definition is used. Otherwise one should specify the include paths that +# are normally passed to the compiler using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter +# (but less readable) file names. This can be useful if your file system +# doesn't support long names like on DOS, Mac, or CD-ROM. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen +# will interpret the first line (until the first dot) of a JavaDoc-style +# comment as the brief description. If set to NO, the JavaDoc +# comments will behave just like regular Qt-style comments +# (thus requiring an explicit @brief command for a brief description.) + +# Default NO +JAVADOC_AUTOBRIEF = YES + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will +# interpret the first line (until the first dot) of a Qt-style +# comment as the brief description. If set to NO, the comments +# will behave just like regular Qt-style comments (thus requiring +# an explicit \brief command for a brief description.) + +# Default NO +QT_AUTOBRIEF = YES + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen +# treat a multi-line C++ special comment block (i.e. a block of //! or /// +# comments) as a brief description. This used to be the default behaviour. +# The new default is to treat a multi-line C++ comment block as a detailed +# description. Set this tag to YES if you prefer the old behaviour instead. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented +# member inherits the documentation from any documented member that it +# re-implements. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce +# a new page for each member. If set to NO, the documentation of a member will +# be part of the file/class/namespace that contains it. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. +# Doxygen uses this value to replace tabs by spaces in code fragments. + +TAB_SIZE = 3 + +# This tag can be used to specify a number of aliases that acts +# as commands in the documentation. An alias has the form "name=value". +# For example adding "sideeffect=\par Side Effects:\n" will allow you to +# put the command \sideeffect (or @sideeffect) in the documentation, which +# will result in a user-defined paragraph with heading "Side Effects:". +# You can put \n's in the value part of an alias to insert newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding +# "class=itcl::class" will allow you to use the command class in the +# itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C +# sources only. Doxygen will then generate output that is more tailored for C. +# For instance, some of the names that are used will be different. The list +# of all members will be omitted, etc. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java +# sources only. Doxygen will then generate output that is more tailored for +# Java. For instance, namespaces will be presented as packages, qualified +# scopes will look different, etc. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources only. Doxygen will then generate output that is more tailored for +# Fortran. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for +# VHDL. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, +# and language is one of the parsers supported by doxygen: IDL, Java, +# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, +# C++. For instance to make doxygen treat .inc files as Fortran files (default +# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note +# that for custom extensions you also need to set FILE_PATTERNS otherwise the +# files are not read by doxygen. + +#EXTENSION_MAPPING = +EXTENSION_MAPPING = m=C++ + +# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all +# comments according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you +# can mix doxygen, HTML, and XML commands with Markdown formatting. +# Disable only in case of backward compatibilities issues. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by by putting a % sign in front of the word +# or globally by setting AUTOLINK_SUPPORT to NO. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should +# set this tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. +# func(std::string) {}). This also makes the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. + +# Default NO +BUILTIN_STL_SUPPORT = YES + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. +# Doxygen will parse them like normal C++ but will assume all classes use public +# instead of private inheritance when no explicit protection keyword is present. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES (the +# default) will make doxygen replace the get and set methods by a property in +# the documentation. This will only work if the methods are indeed getting or +# setting a simple type. If this is not the case, or you want to show the +# methods anyway, you should set this option to NO. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES (the default) to allow class member groups of +# the same type (for instance a group of public functions) to be put as a +# subgroup of that type (e.g. under the Public Functions section). Set it to +# NO to prevent subgrouping. Alternatively, this can be done per class using +# the \nosubgrouping command. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and +# unions are shown inside the group in which they are included (e.g. using +# @ingroup) instead of on a separate page (for HTML and Man pages) or +# section (for LaTeX and RTF). + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and +# unions with only public data fields or simple typedef fields will be shown +# inline in the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO (the default), structs, classes, and unions are shown on a separate +# page (for HTML and Man pages) or section (for LaTeX and RTF). + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum +# is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically +# be useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can +# be an expensive process and often the same symbol appear multiple times in +# the code, doxygen keeps a cache of pre-resolved symbols. If the cache is too +# small doxygen will become slower. If the cache is too large, memory is wasted. +# The cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid +# range is 0..9, the default is 0, corresponding to a cache size of 2^16 = 65536 +# symbols. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. +# Private class members and static file members will be hidden unless +# the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES + +# Default NO +EXTRACT_ALL = NO +#EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class +# will be included in the documentation. + +#EXTRACT_PRIVATE = NO +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal +# scope will be included in the documentation. + +#EXTRACT_PACKAGE = NO +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES all static members of a file +# will be included in the documentation. + +#EXTRACT_STATIC = NO +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) +# defined locally in source files will be included in the documentation. +# If set to NO only classes defined in header files are included. + +EXTRACT_LOCAL_CLASSES = YES +#EXTRACT_LOCAL_CLASSES = NO + +# This flag is only useful for Objective-C code. When set to YES local +# methods, which are defined in the implementation section but not in +# the interface are included in the documentation. +# If set to NO (the default) only methods in the interface are included. + +#EXTRACT_LOCAL_METHODS = NO +EXTRACT_LOCAL_METHODS = YES + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base +# name of the file that contains the anonymous namespace. By default +# anonymous namespaces are hidden. + +#EXTRACT_ANON_NSPACES = NO +EXTRACT_ANON_NSPACES = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members of documented classes, files or namespaces. +# If set to NO (the default) these members will be included in the +# various overviews, but no documentation section is generated. +# This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_MEMBERS = NO +#HIDE_UNDOC_MEMBERS = YES + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. +# If set to NO (the default) these classes will be included in the various +# overviews. This option has no effect if EXTRACT_ALL is enabled. + +HIDE_UNDOC_CLASSES = NO +#HIDE_UNDOC_CLASSES = YES + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all +# friend (class|struct|union) declarations. +# If set to NO (the default) these declarations will be included in the +# documentation. + +HIDE_FRIEND_COMPOUNDS = NO +#HIDE_FRIEND_COMPOUNDS = YES + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. +# If set to NO (the default) these blocks will be appended to the +# function's detailed documentation block. + +HIDE_IN_BODY_DOCS = NO +#HIDE_IN_BODY_DOCS = YES + +# The INTERNAL_DOCS tag determines if documentation +# that is typed after a \internal command is included. If the tag is set +# to NO (the default) then the documentation will be excluded. +# Set it to YES to include the internal documentation. + +#INTERNAL_DOCS = NO +INTERNAL_DOCS = YES + +# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate +# file names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen +# will show members with their full class and namespace scopes in the +# documentation. If set to YES the scope will be hidden. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen +# will put a list of the files that are included by a file in the documentation +# of that file. + +SHOW_INCLUDE_FILES = YES + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen +# will list include files with double quotes in the documentation +# rather than with sharp brackets. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] +# is inserted in the documentation for inline members. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen +# will sort the (detailed) documentation of file and class members +# alphabetically by member name. If set to NO the members will appear in +# declaration order. + +#SORT_MEMBER_DOCS = YES +SORT_MEMBER_DOCS = NO + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the +# brief documentation of file, namespace and class members alphabetically +# by member name. If set to NO (the default) the members will appear in +# declaration order. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen +# will sort the (brief and detailed) documentation of class members so that +# constructors and destructors are listed first. If set to NO (the default) +# the constructors will appear in the respective orders defined by +# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. +# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO +# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the +# hierarchy of group names into alphabetical order. If set to NO (the default) +# the group names will appear in their defined order. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be +# sorted by fully-qualified names, including namespaces. If set to +# NO (the default), the class list will be sorted only by class name, +# not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the +# alphabetical list. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to +# do proper type resolution of all parameters of a function it will reject a +# match between the prototype and the implementation of a member function even +# if there is only one candidate or it is obvious which candidate to choose +# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen +# will still accept a match between prototype and implementation in such cases. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or +# disable (NO) the todo list. This list is created by putting \todo +# commands in the documentation. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or +# disable (NO) the test list. This list is created by putting \test +# commands in the documentation. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or +# disable (NO) the bug list. This list is created by putting \bug +# commands in the documentation. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or +# disable (NO) the deprecated list. This list is created by putting +# \deprecated commands in the documentation. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional +# documentation sections, marked by \if section-label ... \endif +# and \cond section-label ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines +# the initial value of a variable or macro consists of for it to appear in +# the documentation. If the initializer consists of more lines than specified +# here it will be hidden. Use a value of 0 to hide initializers completely. +# The appearance of the initializer of individual variables and macros in the +# documentation can be controlled using \showinitializer or \hideinitializer +# command in the documentation regardless of this setting. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated +# at the bottom of the documentation of classes and structs. If set to YES the +# list will mention the files that were used to generate the documentation. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. +# This will remove the Files entry from the Quick Index and from the +# Folder Tree View (if specified). The default is YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the +# Namespaces page. +# This will remove the Namespaces entry from the Quick Index +# and from the Folder Tree View (if specified). The default is YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command , where is the value of +# the FILE_VERSION_FILTER tag, and is the name of an input file +# provided by doxygen. Whatever the program writes to standard output +# is used as the file version. See the manual for examples. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. +# You can optionally specify a file name after the option, if omitted +# DoxygenLayout.xml will be used as the name of the layout file. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files +# containing the references data. This must be a list of .bib files. The +# .bib extension is automatically appended if omitted. Using this command +# requires the bibtex tool to be installed. See also +# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style +# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this +# feature you need bibtex and perl available in the search path. Do not use +# file names with spaces, bibtex cannot handle them. + +CITE_BIB_FILES = Util.bib + +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated +# by doxygen. Possible values are YES and NO. If left blank NO is used. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated by doxygen. Possible values are YES and NO. If left blank +# NO is used. + +WARNINGS = YES + +# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings +# for undocumented members. If EXTRACT_ALL is set to YES then this flag will +# automatically be disabled. + +WARN_IF_UNDOCUMENTED = YES + +# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some +# parameters in a documented function, or documenting parameters that +# don't exist or using markup commands wrongly. + +WARN_IF_DOC_ERROR = YES + +# The WARN_NO_PARAMDOC option can be enabled to get warnings for +# functions that are documented, but have no documentation for their parameters +# or return value. If set to NO (the default) doxygen will only warn about +# wrong or incomplete parameter documentation, but not about the absence of +# documentation. + +#WARN_NO_PARAMDOC = NO +WARN_NO_PARAMDOC = YES + +# The WARN_FORMAT tag determines the format of the warning messages that +# doxygen can produce. The string should contain the $file, $line, and $text +# tags, which will be replaced by the file and line number from which the +# warning originated and the warning text. Optionally the format may contain +# $version, which will be replaced by the version of the file (if it could +# be obtained via FILE_VERSION_FILTER) + +# WARN_FORMAT = "$file:$line: $text" +WARN_FORMAT = "$file($line): $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning +# and error messages should be written. If left blank the output is written +# to stderr. + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag can be used to specify the files and/or directories that contain +# documented source files. You may enter file names like "myfile.cpp" or +# directories like "/usr/src/myproject". Separate the files or directories +# with spaces. + +INPUT = + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is +# also the default input encoding. Doxygen uses libiconv (or the iconv built +# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for +# the list of possible encodings. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank the following patterns are tested: +# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh +# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py +# *.f90 *.f *.for *.vhd *.vhdl + +FILE_PATTERNS = + +# The RECURSIVE tag can be used to turn specify whether or not subdirectories +# should be searched for input files as well. Possible values are YES and NO. +# If left blank NO is used. + +# Default NO +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = includes + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. Note that the wildcards are matched +# against the file with absolute path, so to exclude all test directories +# for example use the pattern */test/* + +# Default "" +# Add */test/* back into the space delimited list +#EXCLUDE_PATTERNS = */test/* *.m +EXCLUDE_PATTERNS = */test/* + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or +# directories that contain example code fragments that are included (see +# the \include command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp +# and *.h) to filter out the source-files in the directories. If left +# blank all files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude +# commands irrespective of the value of the RECURSIVE tag. +# Possible values are YES and NO. If left blank NO is used. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or +# directories that contain image that are included in the documentation (see +# the \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command , where +# is the value of the INPUT_FILTER tag, and is the name of an +# input file. Doxygen will then use the output that the filter program writes +# to standard output. +# If FILTER_PATTERNS is specified, this tag will be ignored. +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +#INPUT_FILTER = "" +INPUT_FILTER = "config\doxyfilter.pl" + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. +# Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. +# The filters are a list of the form: +# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further +# info on how filters are used. If FILTER_PATTERNS is empty or if +# non of the patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = *.m=config\m2cpp.pl + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will be used to filter the input files when producing source +# files to browse (i.e. when SOURCE_BROWSER is set to YES). + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) +# and it is also possible to disable source filtering for a specific pattern +# using *.ext= (so without naming a filter). This option only has effect when +# FILTER_SOURCE_FILES is enabled. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will +# be generated. Documented entities will be cross-referenced with these sources. +# Note: To get rid of all source code in the generated output, make sure also +# VERBATIM_HEADERS is set to NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body +# of functions and classes directly in the documentation. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct +# doxygen to hide any special comment blocks from generated source code +# fragments. Normal C, C++ and Fortran comments will always remain visible. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES +# then for each documented function all documented +# functions referencing it will be listed. + +# Default NO +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES +# then for each documented function all documented entities +# called/used by that function will be listed. + +# Default NO +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) +# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from +# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will +# link to the source code. +# Otherwise they will link to the documentation. + +REFERENCES_LINK_SOURCE = YES + +# If the USE_HTAGS tag is set to YES then the references to source code +# will point to the HTML generated by the htags(1) tool instead of doxygen +# built-in source browser. The htags tool is part of GNU's global source +# tagging system (see http://www.gnu.org/software/global/global.html). You +# will need version 4.8.6 or higher. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen +# will generate a verbatim copy of the header file for each class for +# which an include is specified. Set to NO to disable this. + +VERBATIM_HEADERS = YES + +# If CLANG_ASSISTED_PARSING is set to YES, then doxygen will use the clang parser +# for more acurate parsing at the cost of reduced performance. This can be +# particularly helpful with template rich C++ code for which doxygen's built-in +# parser lacks the necessairy type information. + +CLANG_ASSISTED_PARSING = NO + +# If clang assisted parsing is enabled you can provide the compiler with command +# line options that you would normally use when invoking the compiler. Note that +# the include paths will already be set by doxygen for the files and directories +# specified at INPUT and INCLUDE_PATH. + +CLANG_OPTIONS = + +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index +# of all compounds will be generated. Enable this if the project +# contains a lot of classes, structs, unions or interfaces. + +ALPHABETICAL_INDEX = YES + +# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then +# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns +# in which this list will be split (can be a number in the range [1..20]) + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all +# classes will be put under the same header in the alphabetical index. +# The IGNORE_PREFIX tag can be used to specify one or more prefixes that +# should be ignored while generating the index headers. + +#IGNORE_PREFIX = +IGNORE_PREFIX = sole the + +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES (the default) Doxygen will +# generate HTML output. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `html' will be used as the default path. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for +# each generated HTML page (for example: .htm,.php,.asp). If it is left blank +# doxygen will generate files with .html extension. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a personal HTML header for +# each generated HTML page. If it is left blank doxygen will generate a +# standard header. Note that when using a custom header you are responsible +# for the proper inclusion of any scripts and style sheets that doxygen +# needs, which is dependent on the configuration options used. +# It is advised to generate a default header using "doxygen -w html +# header.html footer.html stylesheet.css YourConfigFile" and then modify +# that header. Note that the header is subject to change so you typically +# have to redo this when upgrading to a newer version of doxygen or when +# changing the value of configuration settings such as GENERATE_TREEVIEW! + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a personal HTML footer for +# each generated HTML page. If it is left blank doxygen will generate a +# standard footer. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading +# style sheet that is used by each HTML page. It can be used to +# fine-tune the look of the HTML output. If left blank doxygen will +# generate a default style sheet. Note that it is recommended to use +# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this +# tag will in the future become obsolete. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional +# user-defined cascading style sheet that is included after the standard +# style sheets created by doxygen. Using this option one can overrule +# certain style aspects. This is preferred over using HTML_STYLESHEET +# since it does not replace the standard style sheet and is therefor more +# robust against future updates. Doxygen will copy the style sheet file to +# the output directory. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that +# the files will be copied as-is; there are no commands or markers available. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. +# Doxygen will adjust the colors in the style sheet and background images +# according to this color. Hue is specified as an angle on a colorwheel, +# see http://en.wikipedia.org/wiki/Hue for more information. +# For instance the value 0 represents red, 60 is yellow, 120 is green, +# 180 is cyan, 240 is blue, 300 purple, and 360 is red again. +# The allowed range is 0 to 359. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of +# the colors in the HTML output. For a value of 0 the output will use +# grayscales only. A value of 255 will produce the most vivid colors. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to +# the luminance component of the colors in the HTML output. Values below +# 100 gradually make the output lighter, whereas values above 100 make +# the output darker. The value divided by 100 is the actual gamma applied, +# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, +# and 100 does not change the gamma. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting +# this to NO can help when comparing the output of multiple runs. + +HTML_TIMESTAMP = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of +# entries shown in the various tree structured indices initially; the user +# can expand and collapse entries dynamically later on. Doxygen will expand +# the tree to such a level that at most the specified number of entries are +# visible (unless a fully collapsed tree already exceeds this amount). +# So setting the number of entries 1 will produce a full collapsed tree by +# default. 0 is a special value representing an infinite number of entries +# and will result in a full expanded tree by default. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files +# will be generated that can be used as input for Apple's Xcode 3 +# integrated development environment, introduced with OSX 10.5 (Leopard). +# To create a documentation set, doxygen will generate a Makefile in the +# HTML output directory. Running make will produce the docset in that +# directory and running "make install" will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find +# it at startup. +# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. + +GENERATE_DOCSET = NO + +# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the +# feed. A documentation feed provides an umbrella under which multiple +# documentation sets from a single provider (such as a company or product suite) +# can be grouped. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that +# should uniquely identify the documentation set bundle. This should be a +# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen +# will append .docset to the name. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely +# identify the documentation publisher. This should be a reverse domain-name +# style string, e.g. com.mycompany.MyDocSet.documentation. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES, additional index files +# will be generated that can be used as input for tools like the +# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) +# of the generated HTML documentation. + +GENERATE_HTMLHELP = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can +# be used to specify the file name of the resulting .chm file. You +# can add a path in front of the file if the result should not be +# written to the html output directory. + +CHM_FILE = + +# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can +# be used to specify the location (absolute path including file name) of +# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run +# the HTML help compiler on the generated index.hhp. + +HHC_LOCATION = + +# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag +# controls if a separate .chi index file is generated (YES) or that +# it should be included in the master .chm file (NO). + +GENERATE_CHI = NO + +# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING +# is used to encode HtmlHelp index (hhk), content (hhc) and project file +# content. + +CHM_INDEX_ENCODING = + +# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag +# controls whether a binary table of contents is generated (YES) or a +# normal table of contents (NO) in the .chm file. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members +# to the contents of the HTML help documentation and to the tree view. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated +# that can be used as input for Qt's qhelpgenerator to generate a +# Qt Compressed Help (.qch) of the generated HTML documentation. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can +# be used to specify the file name of the resulting .qch file. +# The path specified is relative to the HTML output folder. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#namespace + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating +# Qt Help Project output. For more information please see +# http://doc.trolltech.com/qthelpproject.html#virtual-folders + +QHP_VIRTUAL_FOLDER = doc + +# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to +# add. For more information please see +# http://doc.trolltech.com/qthelpproject.html#custom-filters + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see +# +# Qt Help Project / Custom Filters. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's +# filter section matches. +# +# Qt Help Project / Filter Attributes. + +QHP_SECT_FILTER_ATTRS = + +# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can +# be used to specify the location of Qt's qhelpgenerator. +# If non-empty doxygen will try to run qhelpgenerator on the generated +# .qhp file. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files +# will be generated, which together with the HTML files, form an Eclipse help +# plugin. To install this plugin and make it available under the help contents +# menu in Eclipse, the contents of the directory containing the HTML and XML +# files needs to be copied into the plugins directory of eclipse. The name of +# the directory within the plugins directory should be the same as +# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before +# the help appears. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have +# this name. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) +# at top of each HTML page. The value NO (the default) enables the index and +# the value YES disables it. Since the tabs have the same information as the +# navigation tree you can set this option to NO if you already set +# GENERATE_TREEVIEW to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. +# If the tag value is set to YES, a side panel will be generated +# containing a tree-like index structure (just like the one that +# is generated for HTML Help). For this to work a browser that supports +# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). +# Windows users are probably better off using the HTML help feature. +# Since the tree basically has the same information as the tab index you +# could consider to set DISABLE_INDEX to NO when enabling this option. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values +# (range [0,1..20]) that doxygen will group on one line in the generated HTML +# documentation. Note that a value of 0 will completely suppress the enum +# values from appearing in the overview section. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be +# used to set the initial width (in pixels) of the frame in which the tree +# is shown. + +TREEVIEW_WIDTH = 250 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open +# links to external symbols imported via tag files in a separate window. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of Latex formulas included +# as images in the HTML documentation. The default is 10. Note that +# when you change the font size after a successful doxygen run you need +# to manually remove any form_*.png images from the HTML output directory +# to force them to be regenerated. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are +# not supported properly for IE 6.0, but are supported on all modern browsers. +# Note that when changing this option you need to delete any form_*.png files +# in the HTML output before the changes have effect. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax +# (see http://www.mathjax.org) which uses client side Javascript for the +# rendering instead of using prerendered bitmaps. Use this if you do not +# have LaTeX installed or if you want to formulas look prettier in the HTML +# output. When enabled you may also need to install MathJax separately and +# configure the path to it using the MATHJAX_RELPATH option. + +#Default NO +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and +# SVG. The default value is HTML-CSS, which is slower, but has the best +# compatibility. + +# Default HTML-CSS +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the +# HTML output directory using the MATHJAX_RELPATH option. The destination +# directory should contain the MathJax.js script. For instance, if the mathjax +# directory is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to +# the MathJax Content Delivery Network so you can quickly see the result without +# installing MathJax. +# However, it is strongly recommended to install a local +# copy of MathJax from http://www.mathjax.org before deployment. + +# Default http://cdn.mathjax.org/mathjax/latest/ +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest/ + +# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension +# names that should be enabled during MathJax rendering. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript +# pieces of code that will be used on startup of the MathJax code. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box +# for the HTML output. The underlying search engine uses javascript +# and DHTML and should work on any modern browser. Note that when using +# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets +# (GENERATE_DOCSET) there is already a search function so this one should +# typically be disabled. For large projects the javascript based search engine +# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. + +SEARCHENGINE = YES + +# When the SERVER_BASED_SEARCH tag is enabled the search engine will be +# implemented using a web server instead of a web client using Javascript. +# There are two flavours of web server based search depending on the +# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for +# searching and an index file used by the script. When EXTERNAL_SEARCH is +# enabled the indexing and searching needs to be provided by external tools. +# See the manual for details. + +SERVER_BASED_SEARCH = NO + +# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP +# script for searching. Instead the search results are written to an XML file +# which needs to be processed by an external indexer. Doxygen will invoke an +# external search engine pointed to by the SEARCHENGINE_URL option to obtain +# the search results. Doxygen ships with an example indexer (doxyindexer) and +# search engine (doxysearch.cgi) which are based on the open source search +# engine library Xapian. See the manual for configuration details. + +EXTERNAL_SEARCH = NO + +# The SEARCHENGINE_URL should point to a search engine hosted by a web server +# which will returned the search results when EXTERNAL_SEARCH is enabled. +# Doxygen ships with an example search engine (doxysearch) which is based on +# the open source search engine library Xapian. See the manual for configuration +# details. + +SEARCHENGINE_URL = + +# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed +# search data is written to a file for indexing by an external tool. With the +# SEARCHDATA_FILE tag the name of this file can be specified. + +SEARCHDATA_FILE = searchdata.xml + +# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the +# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is +# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple +# projects and redirect the results back to the right project. + +EXTERNAL_SEARCH_ID = + +# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen +# projects other than the one defined by this configuration file, but that are +# all added to the same external search index. Each project needs to have a +# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id +# of to a relative location where the documentation can be found. +# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ... + +EXTRA_SEARCH_MAPPINGS = + +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- + +# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will +# generate Latex output. + +GENERATE_LATEX = NO + +# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `latex' will be used as the default path. + +LATEX_OUTPUT = latex + +# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be +# invoked. If left blank `latex' will be used as the default command name. +# Note that when enabling USE_PDFLATEX this option is only used for +# generating bitmaps for formulas in the HTML output, but not in the +# Makefile that is written to the output directory. + +LATEX_CMD_NAME = latex + +# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to +# generate index for LaTeX. If left blank `makeindex' will be used as the +# default command name. + +MAKEINDEX_CMD_NAME = makeindex + +# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact +# LaTeX documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_LATEX = NO + +# The PAPER_TYPE tag can be used to set the paper type that is used +# by the printer. Possible values are: a4, letter, legal and +# executive. If left blank a4 will be used. + +# Default a4 +PAPER_TYPE = letter + +# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX +# packages that should be included in the LaTeX output. + +EXTRA_PACKAGES = bm + +# The LATEX_HEADER tag can be used to specify a personal LaTeX header for +# the generated latex document. The header should contain everything until +# the first chapter. If it is left blank doxygen will generate a +# standard header. Notice: only use this tag if you know what you are doing! + +LATEX_HEADER = + +# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for +# the generated latex document. The footer should contain everything after +# the last chapter. If it is left blank doxygen will generate a +# standard footer. Notice: only use this tag if you know what you are doing! + +LATEX_FOOTER = + +# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images +# or other source files which should be copied to the LaTeX output directory. +# Note that the files will be copied as-is; there are no commands or markers +# available. + +LATEX_EXTRA_FILES = + +# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated +# is prepared for conversion to pdf (using ps2pdf). The pdf file will +# contain links (just like the HTML output) instead of page references +# This makes the output suitable for online browsing using a pdf viewer. + +PDF_HYPERLINKS = YES + +# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of +# plain latex in the generated Makefile. Set this option to YES to get a +# higher quality PDF documentation. + +USE_PDFLATEX = YES + +# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. +# command to the generated LaTeX files. This will instruct LaTeX to keep +# running if errors occur, instead of asking the user for help. +# This option is also used when generating formulas in HTML. + +LATEX_BATCHMODE = NO + +# If LATEX_HIDE_INDICES is set to YES then doxygen will not +# include the index chapters (such as File Index, Compound Index, etc.) +# in the output. + +LATEX_HIDE_INDICES = NO + +# If LATEX_SOURCE_CODE is set to YES then doxygen will include +# source code with syntax highlighting in the LaTeX output. +# Note that which sources are shown also depends on other settings +# such as SOURCE_BROWSER. + +LATEX_SOURCE_CODE = NO + +# The LATEX_BIB_STYLE tag can be used to specify the style to use for the +# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See +# http://en.wikipedia.org/wiki/BibTeX for more info. + +LATEX_BIB_STYLE = plain + +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- + +# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output +# The RTF output is optimized for Word 97 and may not look very pretty with +# other RTF readers or editors. + +GENERATE_RTF = NO + +# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `rtf' will be used as the default path. + +RTF_OUTPUT = rtf + +# If the COMPACT_RTF tag is set to YES Doxygen generates more compact +# RTF documents. This may be useful for small projects and may help to +# save some trees in general. + +COMPACT_RTF = NO + +# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated +# will contain hyperlink fields. The RTF file will +# contain links (just like the HTML output) instead of page references. +# This makes the output suitable for online browsing using WORD or other +# programs which support those fields. +# Note: wordpad (write) and others do not support links. + +RTF_HYPERLINKS = NO + +# Load style sheet definitions from file. Syntax is similar to doxygen's +# config file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. + +RTF_STYLESHEET_FILE = + +# Set optional variables used in the generation of an rtf document. +# Syntax is similar to doxygen's config file. + +RTF_EXTENSIONS_FILE = + +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- + +# If the GENERATE_MAN tag is set to YES (the default) Doxygen will +# generate man pages + +GENERATE_MAN = NO + +# The MAN_OUTPUT tag is used to specify where the man pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `man' will be used as the default path. + +MAN_OUTPUT = man + +# The MAN_EXTENSION tag determines the extension that is added to +# the generated man pages (default is the subroutine's section .3) + +MAN_EXTENSION = .3 + +# If the MAN_LINKS tag is set to YES and Doxygen generates man output, +# then it will generate one additional man file for each entity +# documented in the real man page(s). These additional files +# only source the real man page, but without them the man command +# would be unable to find the correct page. The default is NO. + +MAN_LINKS = NO + +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- + +# If the GENERATE_XML tag is set to YES Doxygen will +# generate an XML file that captures the structure of +# the code including all documentation. + +GENERATE_XML = NO + +# The XML_OUTPUT tag is used to specify where the XML pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be +# put in front of it. If left blank `xml' will be used as the default path. + +XML_OUTPUT = xml + +# The XML_SCHEMA tag can be used to specify an XML schema, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_SCHEMA = + +# The XML_DTD tag can be used to specify an XML DTD, +# which can be used by a validating XML parser to check the +# syntax of the XML files. + +XML_DTD = + +# If the XML_PROGRAMLISTING tag is set to YES Doxygen will +# dump the program listings (including syntax highlighting +# and cross-referencing information) to the XML output. Note that +# enabling this will significantly increase the size of the XML output. + +XML_PROGRAMLISTING = YES + +#--------------------------------------------------------------------------- +# configuration options related to the DOCBOOK output +#--------------------------------------------------------------------------- + +# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files +# that can be used to generate PDF. + +GENERATE_DOCBOOK = NO + +# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put. +# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in +# front of it. If left blank docbook will be used as the default path. + +DOCBOOK_OUTPUT = docbook + +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- + +# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will +# generate an AutoGen Definitions (see autogen.sf.net) file +# that captures the structure of the code including all +# documentation. Note that this feature is still experimental +# and incomplete at the moment. + +GENERATE_AUTOGEN_DEF = NO + +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- + +# If the GENERATE_PERLMOD tag is set to YES Doxygen will +# generate a Perl module file that captures the structure of +# the code including all documentation. Note that this +# feature is still experimental and incomplete at the +# moment. + +GENERATE_PERLMOD = NO + +# If the PERLMOD_LATEX tag is set to YES Doxygen will generate +# the necessary Makefile rules, Perl scripts and LaTeX code to be able +# to generate PDF and DVI output from the Perl module output. + +PERLMOD_LATEX = NO + +# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be +# nicely formatted so it can be parsed by a human reader. +# This is useful +# if you want to understand what is going on. +# On the other hand, if this +# tag is set to NO the size of the Perl module output will be much smaller +# and Perl will parse it just the same. + +PERLMOD_PRETTY = YES + +# The names of the make variables in the generated doxyrules.make file +# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. +# This is useful so different doxyrules.make files included by the same +# Makefile don't overwrite each other's variables. + +PERLMOD_MAKEVAR_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- + +# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will +# evaluate all C-preprocessor directives found in the sources and include +# files. + +ENABLE_PREPROCESSING = YES + +# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro +# names in the source code. If set to NO (the default) only conditional +# compilation will be performed. Macro expansion can be done in a controlled +# way by setting EXPAND_ONLY_PREDEF to YES. + +# MACRO_EXPANSION = NO +MACRO_EXPANSION = YES + +# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES +# then the macro expansion is limited to the macros specified with the +# PREDEFINED and EXPAND_AS_DEFINED tags. + +# EXPAND_ONLY_PREDEF = NO +EXPAND_ONLY_PREDEF = YES + +# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files +# pointed to by INCLUDE_PATH will be searched when a #include is found. + +SEARCH_INCLUDES = YES + +# The INCLUDE_PATH tag can be used to specify one or more directories that +# contain include files that are not input files but should be processed by +# the preprocessor. + +INCLUDE_PATH = + +# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard +# patterns (like *.h and *.hpp) to filter out the header-files in the +# directories. If left blank, the patterns specified with FILE_PATTERNS will +# be used. + +INCLUDE_FILE_PATTERNS = + +# The PREDEFINED tag can be used to specify one or more macro names that +# are defined before the preprocessor is started (similar to the -D option of +# gcc). The argument of the tag is a list of macros of the form: name +# or name=definition (no spaces). If the definition and the = are +# omitted =1 is assumed. To prevent a macro definition from being +# undefined via #undef or recursively expanded use the := operator +# instead of the = operator. + +PREDEFINED = __declspec(x)= \ + __attribute(x)__= \ + _WIN64 \ + +# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then +# this tag can be used to specify a list of macro names that should be expanded. +# The macro definition that is found in the sources will be used. +# Use the PREDEFINED tag if you want to use a different macro definition that +# overrules the definition found in the source code. + +EXPAND_AS_DEFINED = + +# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then +# doxygen's preprocessor will remove all references to function-like macros +# that are alone on a line, have an all uppercase name, and do not end with a +# semicolon, because these will confuse the parser if not removed. + +SKIP_FUNCTION_MACROS = YES + +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- + +# The TAGFILES option can be used to specify one or more tagfiles. For each +# tag file the location of the external documentation should be added. The +# format of a tag file without this location is as follows: +# +# TAGFILES = file1 file2 ... +# Adding location for the tag files is done as follows: +# +# TAGFILES = file1=loc1 "file2 = loc2" ... +# where "loc1" and "loc2" can be relative or absolute paths +# or URLs. Note that each tag file must have a unique name (where the name does +# NOT include the path). If a tag file is not located in the directory in which +# doxygen is run, you must also specify the path to the tagfile here. + +TAGFILES = + +# When a file name is specified after GENERATE_TAGFILE, doxygen will create +# a tag file that is based on the input files it reads. + +GENERATE_TAGFILE = + +# If the ALLEXTERNALS tag is set to YES all external classes will be listed +# in the class index. If set to NO only the inherited external classes +# will be listed. + +ALLEXTERNALS = NO + +# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will +# be listed. + +EXTERNAL_GROUPS = YES + +# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed +# in the related pages index. If set to NO, only the current project's +# pages will be listed. + +EXTERNAL_PAGES = YES + +# The PERL_PATH should be the absolute path and name of the perl script +# interpreter (i.e. the result of `which perl'). + +# PERL_PATH = /usr/bin/perl +PERL_PATH = "C:\Program Files\MATLAB\R2012a\sys\perl\win32\bin\perl" + +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- + +# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will +# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base +# or super classes. Setting the tag to NO turns the diagrams off. Note that +# this option also works with HAVE_DOT disabled, but it is recommended to +# install and use dot, since it yields more powerful graphs. + +CLASS_DIAGRAMS = YES + +# You can define message sequence charts within doxygen comments using the \msc +# command. Doxygen will then run the mscgen tool (see +# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the +# documentation. The MSCGEN_PATH tag allows you to specify the directory where +# the mscgen tool resides. If left empty the tool is assumed to be found in the +# default search path. + +MSCGEN_PATH = + +# If set to YES, the inheritance and collaboration graphs will hide +# inheritance and usage relations if the target is undocumented +# or is not a class. + +#HIDE_UNDOC_RELATIONS = YES +HIDE_UNDOC_RELATIONS = NO + +# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is +# available from the path. This tool is part of Graphviz, a graph visualization +# toolkit from AT&T and Lucent Bell Labs. The other options in this section +# have no effect if this option is set to NO (the default) + +# Default NO +HAVE_DOT = YES + +# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is +# allowed to run in parallel. When set to 0 (the default) doxygen will +# base this on the number of processors available in the system. You can set it +# explicitly to a value larger than 0 to get control over the balance +# between CPU load and processing speed. + +DOT_NUM_THREADS = 0 + +# By default doxygen will use the Helvetica font for all dot files that +# doxygen generates. When you want a differently looking font you can specify +# the font name using DOT_FONTNAME. You need to make sure dot is able to find +# the font, which can be done by putting it in a standard location or by setting +# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the +# directory containing the font. + +DOT_FONTNAME = Helvetica + +# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. +# The default size is 10pt. + +DOT_FONTSIZE = 10 + +# By default doxygen will tell dot to use the Helvetica font. +# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to +# set the path where dot can find it. + +DOT_FONTPATH = + +# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect inheritance relations. Setting this tag to YES will force the +# CLASS_DIAGRAMS tag to NO. + +CLASS_GRAPH = YES + +# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for each documented class showing the direct and +# indirect implementation dependencies (inheritance, containment, and +# class references variables) of the class with other documented classes. + +COLLABORATION_GRAPH = YES + +# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen +# will generate a graph for groups, showing the direct groups dependencies + +GROUP_GRAPHS = YES + +# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# collaboration diagrams in a style similar to the OMG's Unified Modeling +# Language. + +# Maybe set this to YES +UML_LOOK = NO + +# If the UML_LOOK tag is enabled, the fields and methods are shown inside +# the class node. If there are many fields or methods and many nodes the +# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS +# threshold limits the number of items for each type to make the size more +# manageable. Set this to 0 for no limit. Note that the threshold may be +# exceeded by 50% before the limit is enforced. + +UML_LIMIT_NUM_FIELDS = 10 + +# If set to YES, the inheritance and collaboration graphs will show the +# relations between templates and their instances. + +# Default NO +TEMPLATE_RELATIONS = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT +# tags are set to YES then doxygen will generate a graph for each documented +# file showing the direct and indirect include dependencies of the file with +# other documented files. + +INCLUDE_GRAPH = YES + +# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and +# HAVE_DOT tags are set to YES then doxygen will generate a graph for each +# documented header file showing the documented files that directly or +# indirectly include this file. + +INCLUDED_BY_GRAPH = YES + +# If the CALL_GRAPH and HAVE_DOT options are set to YES then +# doxygen will generate a call dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable call graphs +# for selected functions only using the \callgraph command. + +# Default NO +CALL_GRAPH = YES + +# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then +# doxygen will generate a caller dependency graph for every global function +# or class method. Note that enabling this option will significantly increase +# the time of a run. So in most cases it will be better to enable caller +# graphs for selected functions only using the \callergraph command. + +# Default NO +CALLER_GRAPH = YES + +# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen +# will generate a graphical hierarchy of all classes instead of a textual one. + +GRAPHICAL_HIERARCHY = YES + +# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES +# then doxygen will show the dependencies a directory has on other directories +# in a graphical way. The dependency relations are determined by the #include +# relations between the files in the directories. + +DIRECTORY_GRAPH = YES + +# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images +# generated by dot. Possible values are svg, png, jpg, or gif. +# If left blank png will be used. If you choose svg you need to set +# HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible in IE 9+ (other browsers do not have this requirement). + +DOT_IMAGE_FORMAT = png + +# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to +# enable generation of interactive SVG images that allow zooming and panning. +# Note that this requires a modern browser other than Internet Explorer. +# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you +# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files +# visible. Older versions of IE do not have SVG support. + +INTERACTIVE_SVG = NO + +# The tag DOT_PATH can be used to specify the path where the dot tool can be +# found. If left blank, it is assumed the dot tool can be found in the path. + +DOT_PATH = "C:\Program Files (x86)\Graphviz2.32\bin" + +# The DOTFILE_DIRS tag can be used to specify one or more directories that +# contain dot files that are included in the documentation (see the +# \dotfile command). + +DOTFILE_DIRS = + +# The MSCFILE_DIRS tag can be used to specify one or more directories that +# contain msc files that are included in the documentation (see the +# \mscfile command). + +MSCFILE_DIRS = + +# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of +# nodes that will be shown in the graph. If the number of nodes in a graph +# becomes larger than this value, doxygen will truncate the graph, which is +# visualized by representing a node as a red box. Note that doxygen if the +# number of direct children of the root node in a graph is already larger than +# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note +# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. + +DOT_GRAPH_MAX_NODES = 50 + +# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the +# graphs generated by dot. A depth value of 3 means that only nodes reachable +# from the root by following a path via at most 3 edges will be shown. Nodes +# that lay further from the root node will be omitted. Note that setting this +# option to 1 or 2 may greatly reduce the computation time needed for large +# code bases. Also note that the size of a graph can be further restricted by +# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. + +MAX_DOT_GRAPH_DEPTH = 0 + +# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent +# background. This is disabled by default, because dot on Windows does not +# seem to support this out of the box. Warning: Depending on the platform used, +# enabling this option may lead to badly anti-aliased labels on the edges of +# a graph (i.e. they become hard to read). + +DOT_TRANSPARENT = NO + +# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# files in one run (i.e. multiple -o and -T options on the command line). This +# makes dot run faster, but since only newer versions of dot (>1.8.10) +# support this, this feature is disabled by default. + +DOT_MULTI_TARGETS = NO + +# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will +# generate a legend page explaining the meaning of the various boxes and +# arrows in the dot generated graphs. + +GENERATE_LEGEND = YES + +# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will +# remove the intermediate dot files that are used to generate +# the various graphs. + +DOT_CLEANUP = YES Index: Damkjer/config/doxyfilter.pl =================================================================== --- Damkjer/config/doxyfilter.pl (revision 13) +++ Damkjer/config/doxyfilter.pl (revision 13) @@ -0,0 +1,145 @@ +############################################################################## +## FILE: doxygen-filter +## +## Copyright (C) 2006 Harris Corporation. All rights reserved. +## +## DESCRIPTION: Filters the input files to translate Origin style +## documentation into Doxygen style. +## +## LIMITATIONS: Only really works on one file at a time. +## +## SOFTWARE HISTORY: +## +## 19JAN06 932D PTR#06427-IPL S. Minster +## Initial delivery. +## 09APR07 932D PTR#07441-IPL S. Minster +## Use doxygen tags instead of HTML. +## 30JUN08 956F PTR#10111-IPL S. Minster +## Improved filter to better mark code sections. +############################################################################## + +$state = 0; +$swhist = 0; +$filehead = 0; +$isNote = 0; +$isBug = 0; +$isWarn = 0; +$isAttn = 0; +$isPre = 0; +$isInv = 0; +$isPost = 0; +$isFormula = 0; + +my $extraClassInfo = ""; +if (@ARGV) +{ + $ARGV[0] =~ s/\\/\//g; + my $fullpath = $ARGV[0]; + my ($path, $file) = ($fullpath =~ /Damkjer\/(.*\/([^\/]+))$/); + + if ($path and $file) + { + $extraClassInfo = "$file \"$path\""; + } +} + +while (<>) +{ + $swhist = 1 if (/SOFTWARE HISTORY/); + + if ($isFormula) + { + s|^\s*//||; + s|\\bm\{|\\boldsymbol\{|g; + $isFormula = 0 if ($isFormula && m|\\f\]|); + } + if ($filehead) + { + if (m|//\s+DESCRIPTION|) + { + $filehead = 0; + } + else + { + s|.+||; chomp; + } + } + if ($swhist && /^\/\/\>/) + { + $swhist = 0; + } + elsif ($state == 0) + { + if (s|^//\>\s*(\S+\|\n)|//\! $1|) + { + $state = 1; + } + elsif (s|//\>\s*(\S+\|\n)|//\!\< $1|) + { + $state = 1; + } + + s|//\s+CLASS:\s+(\S+)|//\! \\class $1 $extraClassInfo|; + s|//\s+FUNCTOR:\s+(\S+)|//\! \\class $1 $extraClassInfo|; + s|//\s+DIRECTORY:\s+(\S+)|//\! \\dir $1|; + s|//\s+ENUMERATION:\s+(\S+)|//\! \\enum $1|; + s|//\s+NAMESPACE:\s+(\S+)|//\! \\namespace $1|; + + $filehead = 1 if (m|//\s+FILE:|); + s|//\s+FILE:\s+(\S+)|//\! \\file $1|; + s"//\s+DESCRIPTION:(.*|$)"//\! $1"; + $isNote = 1 if (s"//\s+LIMITATIONS:(.*|$)"//\! \\note $1"); + s|^\s*//.*Copyright.*$||; + s|^\s*//\s*$||; + } + elsif ($state == 1) + { + if (!s/^(\s*)\/\/( |$)/$1\/\/\!$2/) + { + # 
 seems to strip C++ comments from the output
+      # According to bug 315006, this should be fixed, but I saw this error in 1.5.1:
+      # http://gcsd.harris.com/orgs/programs/origin/doxygen/3.11/html/d7/d22/classTimer.html#_details
+      # See the bug report for the potential workaround:
+      # http://bugzilla.gnome.org/show_bug.cgi?id=315006
+      $state = 2 if (s|^(\s*)//\-|$1//! \\code\n$1//!|);
+      $state = 0 if (s|\/\/<|\/\/\!|);
+
+      if (!$state)
+      {
+        $isNote = 0;
+        $isBug = 0;
+        $isWarn = 0;
+        $isAttn = 0;
+        $isPre = 0;
+        $isInv = 0;
+        $isPost = 0;
+      }
+    }
+    else
+    {
+      s|\s+->\s+| \&rarr\; |;
+      s|\s+<-\s+| \&larr\; |;
+      s|\s+<->\s+| \&harr\; |;
+
+      s|^\s*//\!\s*$|//\! \\note\n| if ($isNote);
+      s|^\s*//\!\s*$|//\! \\bug\n| if ($isBug);
+      s|^\s*//\!\s*$|//\! \\warning\n| if ($isWarn);
+      s|^\s*//\!\s*$|//\! \\attention\n| if ($isAttn);
+      s|^\s*//\!\s*$|//\! \\pre\n| if ($isPre);
+      s|^\s*//\!\s*$|//\! \\inv\n| if ($isInv);
+      s|^\s*//\!\s*$|//\! \\post\n| if ($isPost);
+    }
+  }
+  elsif ($state == 2)
+  {
+    if (!s|//\-|//!|)
+    {
+      $state = 1 if (s/(\s*)\/\/( |$)/$1\/\/\! \\endcode\n$1\/\/\!$2/);
+      $state = 0 if (s|//<|//\! \\endcode|);
+    }
+  }
+
+  $isFormula = 1 if (m|\\f\[| && !m|\\f\]|);
+
+  print;
+}
Index: Damkjer/config/m2cpp.pl
===================================================================
--- Damkjer/config/m2cpp.pl	(revision 13)
+++ Damkjer/config/m2cpp.pl	(revision 13)
@@ -0,0 +1,1054 @@
+##############################################################################
+## FILE:              m2cpp.pl
+##
+##    Copyright (C) 2013 Harris Corporation.  All rights reserved.
+##
+## DESCRIPTION:       
+##
+## LIMITATIONS:       Only really works on one file at a time.
+##
+## SOFTWARE HISTORY:
+##
+##############################################################################
+
+use strict;
+use warnings;
+
+use Cwd 'abs_path';
+
+sub tee;
+
+my $fullFile = undef; # The full file name passed to the script.
+my @fileList = ();    # Allow for classes defined in multiple files.
+my $output = "";      # Aggregate transformed text into $output.
+
+if ($#ARGV != 0)
+{
+   die "Argument must contain filename $#ARGV"
+}
+else
+{
+  $fullFile=abs_path($ARGV[0]);
+}
+
+# debug
+my $filtered = "$fullFile.flt";
+#my $out = "";
+open (my $out, '>', $filtered) or die "unable to open debug output file, $filtered: $!";
+
+# define MATLAB file grammar
+my $bolComment     = "^\\s*\[%\]+\\s*";
+my $identifier     = "[_a-zA-Z]\\w*";
+my $fqIdentifier   = "$identifier(?:\\.$identifier)*";
+my $fqMetaIdent    = "[?]$fqIdentifier";
+my $metaList       = "(?:$fqMetaIdent|\{(?:$fqMetaIdent\\s*(?:,\\s*$fqMetaIdent\\s*)*)?\})";
+my $superclassList = "$fqIdentifier(?:\\s*&\\s*$fqIdentifier)*";
+my $attrValue      = "[\\?\\w.]+";
+my $attrValueList  = "(?:$attrValue|\{\\s*(?:$attrValue\\s*(?:,\\s*$attrValue\\s*)*)?\\s*\})";
+my $attrItem       = "\\w+(?:\\s*=\\s*$attrValueList)?";
+my $attrList       = "\\(\\s*(?:$attrItem\\s*(?:,\\s*$attrItem\\s*)*)?\\s*\\)";
+my $argItem        = "(?:$identifier|~)";
+my $argList        = "\\(\\s*(?:$argItem\\s*(?:,\\s*$argItem\\s*)*)?\\s*\\)";
+my $returns        = "[\\[\\w,\\s\\]]+";
+
+#***
+# Determine if there is a special structure associated with the m file. MATLAB
+# provides two special folder constructs in the context of class definitions.
+#
+# 1. @-folders: allow for classes to be defined in multiple files. The @-folder
+#               is contained by a path folder, but is not on the path itself.
+#               The folder must contain a class definition file of the same
+#               name.
+# 2. +-folders: allow for package definition. Packages impose a namespace.
+#***
+
+my $packageStr = "";
+my @packages = ();
+my $inClassFolder = 0;
+
+if ($fullFile =~ /(?:[+]?([\w\-]+)[\/\\])+/)
+{
+   $packageStr = $fullFile;
+   $packageStr =~ s/(?:^|[\/\\])[^\/\\]*$//g;
+   $packageStr =~ s/(?:^|[\/\\])[^+\/\\][^\/\\]*//g;
+   $packageStr =~ s/[+]([^\/\\]+)/$1/g;
+   $packageStr =~ s/[\/\\]+/\//g;
+   $packageStr =~ s/^[\/]//;
+   @packages = split('/',$packageStr);
+}
+
+if ($fullFile =~ /^(.*)\@([\w\-]+)[\/\\](\2)\.m/)
+{
+   #***
+   # If we have a .m file inside a (@)-folder with the same name :
+   # we will read each file of this folder to acquire the complete class
+   # definition
+   #
+   # TODO: Make sure to associate the captured functions with the class.
+   #***
+   my $className = $2;
+   my $classFile = $className.".m";
+   my $pattern = $1."@".$className."/\*.m";
+   my @files = glob($pattern);
+
+   $fileList[0] = $fullFile;
+
+   my $i = 0;
+
+   my $classPattern = $classFile;
+   $classPattern =~ s/\./\\\./g;
+   $inClassFolder = 1;
+   
+   foreach my $testFile (@files)
+   {
+      if ($testFile !~ /$classPattern/)
+      {
+         $fileList[++$i] = $testFile;
+      }
+   }
+}
+elsif ($fullFile =~ /^(.*)\@([\w\-]+)[\/\\](.+)\.m/)
+{
+   # otherwise @-folder, but .m with a different name : ignore it
+}
+else
+{
+   # otherwise
+   $fileList[0] = $fullFile;
+}
+
+# track states
+my $className = "";
+my $inClass = 0;
+my $classIsHandle = 0;
+my $classIsSealed = 0;
+my $inProps = 0;
+my $propGet = "public:";
+my $propSet = "public:";
+my $propIsAbstract  = 0;
+my $propIsConstant  = 0;
+my $propIsDependent = 0;
+my $inMeths = 0;
+my $methAcc = "public:";
+my $methIsAbstract  = 0;
+my $methIsStatic  = 0;
+my $methIsSealed = 0;
+my $methDecl = "";
+my $methHead = "";
+my $inFunc = 0;
+my $inParams = 0;
+my $inReturns = 0;
+my $openControl = 0;
+my $startNext = 0;
+my $makeDoxyComments = 0;
+my $extraLines = 0;
+my $isLocalFunc = 0;
+my $funcsUseEnd = 1;
+my $blankComment = 0;
+my $inAnonNamespace = 0;
+
+my @blocks = ();
+
+my %propMeths;
+
+#***
+# First pass.
+#
+# 1. Look for overloaded getters and setters. Don't want to auto-gen them.
+# 2. TODO: Determine if functions use "end" or not
+# 3. and then?...
+#
+#***
+my $file;
+foreach $file (@fileList)
+{
+   open(my $in, $file) or die "unable to open input file: $file";
+
+   while (<$in>)
+   {
+      if (/^\s*(?:function)\s*(?:($returns)=)?\s*($fqIdentifier)/)
+      {
+         push(@blocks,"function");
+         
+         my $methName = $2 if defined($2);
+         
+         $propMeths{$methName} = 1 if ($methName =~ m/^[gs]et\./); 
+      }
+      elsif (/^\s*(?:classdef|properties|methods|events|enumeration|if|for|parfor|switch|try|while)/)
+      {
+         push(@blocks,"other");
+      }
+      
+      if (/^\s*\bend\b\s*/)
+      {
+         pop(@blocks) if (scalar @blocks > 0);
+      }
+   }
+   
+   $funcsUseEnd = 0 if (scalar(@blocks) > 0);
+
+   close($in);
+}
+
+@blocks = ();
+
+# Process each file.
+tee($out, "/** MATLAB files, packages, classes and functions. */");
+tee($out, "/** \@addtogroup MATLAB MATLAB Code */");
+tee($out, "/** \@{ */");
+tee($out, "namespace MATLAB {");
+tee($out, "/** \@addtogroup MATLAB*/");
+tee($out, "/** \@{ */ ");
+tee($out, "/** The MATLAB-defined Package: \"$_\". */namespace $_ { /** \@addtogroup MATLAB*//** \@{ */ ") foreach (@packages);
+
+my $funcNo = 0;
+foreach $file (@fileList)
+{
+   open(my $in, $file) or die "unable to open input file: $file";
+ 
+   $file =~ /[\/\\]([^\/\\]*)\.m$/;
+   my $baseName = $1;
+ 
+   # Process each line. We must not add or remove lines from the code.
+   while (<$in>)
+   {
+      chomp;
+      s/([^%]*)\.\.\./$1\%/;
+      
+      if (s/($bolComment)file\:/$1\@file /i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+      elsif (s/($bolComment)description\:/$1/i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+      elsif (s/($bolComment)limitations\:/$1\@note /i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+      elsif (s/($bolComment)class\:/$1\@class /i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+      elsif (s/($bolComment)todo\:/$1\@todo /i)
+      {
+      }
+      elsif (s/(?:$bolComment)parameters\:\s*$//i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 1;
+         $inReturns = 0;
+         $startNext = 1;
+         $extraLines = $extraLines + 1;
+      }
+      elsif (s/(?:$bolComment)returns\:\s*$//i)
+      {
+         $makeDoxyComments = 1;
+         $inParams = 0;
+         $inReturns = 1;
+         $startNext = 1;
+         $extraLines = $extraLines + 1;
+      }
+      elsif (!$inFunc && $blankComment && /(?:$bolComment)($identifier(\s+)?)+\:\s*$/i)
+      {
+         $makeDoxyComments = 0;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+      elsif (/(?:$bolComment)[*]{3,}/i)
+      {
+         $makeDoxyComments = 0;
+         $inParams = 0;
+         $inReturns = 0;
+      }
+
+      elsif (/($bolComment|^)\s*$/)
+      {
+         $blankComment = 1;
+      }
+      else
+      {
+         $blankComment = 0;
+      }
+      
+      if (/^\s*\bend\b\s*/)
+      {
+         my $closing = "";
+         $closing = pop(@blocks) if (scalar @blocks > 0);
+
+         if ($closing =~ /classdef/)
+         {
+            tee($out, "\};\n");
+            $inClass = 0;
+            $makeDoxyComments = 0;
+         }
+         elsif ($closing =~ /properties/)
+         {
+#            tee($out, "\n");
+            tee($out, "/**\@}*/\n");
+            $inProps = 0;
+            $makeDoxyComments = 0;
+         }
+         elsif ($closing =~ /methods/)
+         {
+            tee($out, "\n");
+            $inMeths = 0;
+            $makeDoxyComments = 0;
+         }
+         elsif ($closing =~ /function/)
+         {
+            tee($out, "}") if ($inAnonNamespace);
+            tee($out, "}\n");
+            $inFunc = 0;
+            $makeDoxyComments = 0;
+            $inAnonNamespace = 0;
+         }
+         elsif ($closing =~ /control/)
+         {
+#            tee($out, "}\n");
+            tee($out, "\n");
+         }
+         else
+         {
+            tee($out, "\n");
+         }
+         next;
+      }
+
+      if (/^\s*\bfunction\b\s*/ && $inFunc  && !$funcsUseEnd)
+      {
+         my $closing = "";
+         $closing = pop(@blocks) if (scalar @blocks > 0);
+
+         if ($closing =~ /function/)
+         {
+            tee($out, "}") if ($inAnonNamespace);
+            tee($out, "}\n");
+            $inFunc = 0;
+            $makeDoxyComments = 0;
+            $inAnonNamespace = 0;
+         }
+         else
+         {
+            push(@blocks, $closing) if ("$closing" ne "");
+            warn "Unexpected function structure";
+         }
+      }
+      
+      if ($inProps && (/^\s*($identifier)\s*(=\s*[\w\d\{\}\(\)'',\s\[\].]+)?\s*(?:%(.*))?/))
+      {
+         my $propName = $1;
+         my $propValue = "";
+         my $propComment = "";
+         
+         $propValue = $2 if defined($2);
+         $propComment = $3 if defined($3);
+         
+         $propValue =~ s/\([^\)]*(?:\))?//g;
+         $propValue =~ s/\{[^\}]*(?:\})?//g;
+         $propValue =~ s/\./::/g;
+
+         tee($out, "/** $propComment */") if ($propComment ne "");
+
+         unless ($propIsDependent)
+         {
+#            tee($out, "private: ");
+            tee($out, " const") if ($propIsConstant);
+            tee($out, " Property $propName$propValue;");
+
+            unless (exists $propMeths{"get.$propName"})
+            {
+#               tee($out, "/** Accessor for the property: $propName ");
+#               tee($out, "\@retval value The value stored in $propName");
+#               tee($out, "*/ ");
+#               tee($out, "$propGet ");
+#               tee($out, "virtual ") if ($propIsAbstract);
+#               tee($out, "Values $propName()");
+#               tee($out, "=0") if ($propIsAbstract);
+#               tee($out, "; ");
+            }
+
+            unless ($propIsConstant || exists $propMeths{"set.$propName"})
+            {
+#               tee($out, "/** Mutator for the property: $propName ");
+#               tee($out, "\@param value the value to set ");
+#               tee($out, "\@retval object The object with $propName updated to the argument value") unless ($classIsHandle);
+#               tee($out, "*/"); 
+#               tee($out, "$propSet ");
+#               tee($out, "virtual ") if ($propIsAbstract);
+               if ($classIsHandle)
+               {
+#                  tee($out, "void ");
+               }
+               else
+               {
+#                  tee($out, "MATLAB::$className ");
+               }
+#               tee($out, "$propName(Values value)");
+#               tee($out, "=0") if ($propIsAbstract);
+#               tee($out, "; ");
+            }
+         }
+
+         tee($out, "\n");
+         next;
+      }
+
+      if ($inParams && $startNext && s/^(\s*[%]+\s*)($identifier)\s*-/% \@param $2 /)
+      {
+         $startNext = 0;
+      }
+      
+      if ($inReturns && $startNext && s/^(\s*[%]+\s*)($identifier)\s*-/% \@retval $2 /)
+      {
+         $startNext = 0;
+      }
+      
+      if (($inParams || $inReturns) && /^(\s*[%]+\s*)$/)
+      {
+         $startNext = 1;
+      }
+      
+      if ($inFunc && $makeDoxyComments && /^\s*(?:[^%\s]|\n$)/)
+      {
+         $makeDoxyComments = 0;
+         tee($out, "/** Helper functions visible only to $baseName.m */ namespace {") if ($inAnonNamespace);
+         tee($out, "$methHead");
+         tee($out, "//\!\n" x $extraLines);
+         tee($out, "$methDecl");
+         $methHead = "";
+         $methDecl = "";
+         $extraLines = 0;
+      }
+      
+      if (!$inFunc && ($inMeths || !$inClass))
+      {
+         my $methRets = "";
+         my $methName = "";
+         my $methArgs = "()";
+         my $methComm = "";
+         
+         if (/^\s*(function)?\s*(?:($returns)=)?\s*($fqIdentifier)\s*($argList)?\s*(?:%(.*))?/ &&
+             (defined($1) || $inMeths))
+         {
+#            tee($out, "//$_\n");
+            
+            my $isDecl = ($inMeths && !defined($1));
+            
+            unless ($isDecl)
+            {
+               push(@blocks,"function");
+               $inFunc = 1;
+               $makeDoxyComments = 1;
+               ++$funcNo;
+            }
+            $methRets = $2 if defined($2);
+            $methName = $3 if defined($3);
+            $methArgs = $4 if defined($4);
+            $methComm = $5 if defined($5);
+
+            my $isClassFunc = 0;
+            
+            $isClassFunc = 1 if ($inMeths);
+            $isClassFunc = 1 if ($inClassFolder && !$inMeths && ("$baseName" eq "$methName"));
+
+#            tee($out, "//$methArgs\n");
+
+            my $tempSealed = 0;
+            my $methIsCtor = 0;
+
+            # Constructors are always sealed
+            if ($methName =~ /^$className$/)
+            {
+               $tempSealed = 1;
+               $methIsCtor = 1;
+            }
+
+            # So are accessors and mutators
+            if ($methName =~ s/^[gs]et\.//)
+            {
+               $tempSealed = 1;
+            }
+
+#            $methArgs =~ s/,/,MATLAB::Array /g;
+            $methArgs =~ s/^\s+//;
+            $methArgs =~ s/\s+$//;
+            $methArgs =~ s/,/,Value /g;
+            $methArgs =~ s/\b~\b/ignored/g;
+#            $methArgs =~ s/\(/\(MATLAB::Array /;
+            $methArgs =~ s/^([^\(])/Value $1/ unless ($methArgs =~ /^\s*$/);
+            $methArgs =~ s/\(/\(Value / unless ($methArgs =~ /^\(\s*\)$/);
+            $methArgs =~ s/^\(([^,)]+)(.*)/\($2/ unless (!$isClassFunc || $methIsCtor || $methIsStatic);
+            $methArgs =~ s/^\(,/\(/;
+               
+            $methArgs = "()" if ($methArgs =~ /^\(Value\s*\)$/);
+
+            if ($inMeths)
+            {
+               $methDecl .= "$methAcc ";
+
+               $methDecl .=  "virtual " unless ($tempSealed || $methIsSealed || $methIsStatic);
+
+               $methDecl .=  "static " if ($methIsStatic);
+            }
+
+            if(!$inClass && $funcNo > 1)
+            {
+               $inAnonNamespace = 1;
+            }
+
+            unless($methIsCtor)
+            {
+               if ($methRets =~ /^\s*$/)
+               {
+                  $methDecl .=  "void ";
+               }
+               else
+               {
+#                  $methArgs =~ s/^\s+//;
+#                  $methArgs =~ s/\s+$//;
+#                  $methRets =~ s/,/,Value /g;
+#                  $methRets =~ s/^([^\[])/Value $1/ unless ($methRets =~ /^\s*$/);
+#                  $methRets =~ s/^\[/\[Value / unless ($methRets =~ /^\[\s*\]$/);
+                  $methDecl .=  "Values ";
+#                  $methDecl .=  "Value ";
+#                  $methDecl .=  "$methRets ";
+               }
+#               $methDecl .=  "$methRets ";
+            }
+
+            if ($inClassFolder && !$inMeths && ("$baseName" eq "$methName"))
+            {
+               $methDecl .= "${className}::";
+            }
+            $methDecl .= "$methName ";
+            $methDecl .= "$methArgs";
+
+            if ($methIsAbstract)
+            {
+               $methDecl .=  "=0; ";
+            }
+            elsif ($isDecl)
+            {
+               $methDecl .=  "; ";
+            }
+            else
+            {
+               $methDecl .=  "\{ ";
+            }
+
+            $methDecl .=  "//\!< $methComm" unless ($methComm =~ /^\s*$/);
+            
+            $methDecl .= "\n";
+            
+            tee($out, "$methDecl") if ($isDecl);
+            $methDecl = "" if ($isDecl);
+         }
+      }
+      
+      {
+         no warnings 'uninitialized';
+         s/\'([^\']|\'\')*%([^\']|\'\')*\'/\'$1%$2\'/;
+
+         if ($makeDoxyComments)
+         {
+            if ($inFunc)
+            {
+               s|%|//\!|;
+            }
+            else
+            {
+               s|%|//\!|;
+            }
+         }
+         else
+         {
+            s|%|//|;
+         }
+         
+         s/\'([^\']|\'\')*%([^\']|\'\')*\'/\'$1%$2\'/;
+      }
+
+      if (m|(//\!.*)|)
+      {
+         $methHead .= "$1\n" if ($inFunc);
+         tee($out, "$1\n") unless ($inFunc);
+         next;
+      }
+
+      #***
+      # Class definition blocks
+      #
+      # classdef := classdef (\(\))?  (< )?
+      #***
+      if (/^\s*(?:classdef)\s+($attrList)?\s*($identifier)\s*(?:<\s*($superclassList))?/)
+      {
+         #tee($out, "===classdef===\n";
+         push(@blocks,"classdef");
+         $inClass = 1;
+         $makeDoxyComments = 0;
+         $classIsHandle = 0;
+         $classIsSealed = 0;
+
+         my $classAttrs   = "";
+         my $classParents = "";
+         my @classParents = ();
+         
+         $className    = $2;
+
+         # Attributes
+         my $classIsAbstract = 0;
+         my @baseFriends  = ();
+
+         $classAttrs   = $1 if defined($1);
+         $classParents = $3 if defined($3);
+ 
+         if ($classParents !~ /^\s*$/)
+         {
+            $classIsHandle = 1 if ($classParents =~ /\bhandle\b/);
+            $classParents =~ s/\s//g;
+            @classParents = split('&',$classParents);
+            $classParents =~ s/&/,public /g;
+            $classParents = "public MATLAB::$classParents";
+#            $classParents = "public $classParents";
+         }
+
+         #***
+         # Abstract
+         # 
+         # The C++ equivalent is a class with at least one pure virtual method.
+         #***
+         if ($classAttrs =~ /abstract\s*=\s*false/i)
+         {
+            # ignore "Abstract=false" settings.
+         }
+         elsif ($classAttrs =~ /abstract(?:\s*=\s*true)?/i)
+         {
+            $classIsAbstract = 1;
+         }
+
+         #***
+         # AllowedSubclasses
+         #
+         # The C++ equivalent is a "final" or "leaf" class with specific friend
+         # classes. There is no way to directly specify this restriction. It
+         # can be imposed through exploiting virtual inheritance.
+         #***
+         if ($classAttrs =~ /allowedsubclasses\s*=\s*($metaList)/i)
+         {
+            # AllowedSubclasses always implies Sealed=true.
+            $classIsSealed = 1;
+
+            my $allowed = $1;            
+            $allowed =~ s/[\{\}\?\s]//g;
+            $allowed =~ s/\./::/g;
+            @baseFriends = split(',',$allowed);
+            @baseFriends = ($className, @baseFriends);
+         }
+         
+         #***
+         # ConstructOnLoad
+         #
+         # The C++ equivalent would be to create a global instance immediately
+         # after defining the class.
+         #
+         # Not yet implemented.
+         #***
+
+         #***
+         # HandleCompatible
+         #
+         # No C++ equivalent. Ignore.
+         #***
+
+         #***
+         # Hidden
+         #
+         # No C++ equivalent. Ignore.
+         #***
+
+         #***         
+         # InferiorClasses
+         #
+         # No C++ equivalent. Ignore.
+         #***                  
+
+         #***
+         # Sealed
+         #
+         # The C++ equivalent is a "final" or "leaf" class. There is no way to
+         # directly specify this restriction. It can be imposed through
+         # exploiting virtual inheritance.
+         #
+         # Update: C++11 introduces the `final' keyword which performs the
+         #         desired modification. Doxygen understands the keyword.
+         #***
+         if ($classAttrs =~ /sealed\s*=\s*false/i)
+         {
+            # ignore "Sealed=false" settings.
+         }
+         elsif ($classAttrs =~ /sealed(?:\s*=\s*true)?/i)
+         {
+            $classIsSealed = 1;
+            @baseFriends = ($className, @baseFriends);
+            
+         }
+
+         if ($classIsSealed)
+         {
+            tee($out, "class $_;") foreach (@baseFriends);
+            tee($out, "/** Enforce the \"Sealed\" attribute for ${className}. ");
+            tee($out, "This class is automatically generated specifically to ");
+            tee($out, "illustrate the behavior of the \"Sealed\" class attribute.");
+            tee($out, "*/");
+            tee($out, "class ${className}Seal {");
+            tee($out, "/** Allowed subclass: $_ */ friend class $_;") foreach (@baseFriends);
+            tee($out, "/** Prevent public construction of the ${className} seal */");
+            tee($out, "private:${className}Seal()\{\}\};");
+            
+            $classParents = join(', ',("private virtual ${className}Seal",$classParents));
+         }
+
+         $classParents = ": $classParents";
+         tee($out, "/** \@nosubgrouping */class $className");
+         tee($out, " final") if ($classIsSealed);
+         tee($out, " $classParents\{\n");         
+      }
+      elsif (/^\s*(?:properties)\s*($attrList)?/)
+      {
+         #tee($out, "===properties===\n";
+         #***
+         # MATLAB properties are more like methods (class functions) than
+         # members. Non-dependant properties behave as though a member is
+         # backing them and all properties have default get/set methods.
+         #***
+         push(@blocks,"properties");
+         $inProps = 1;
+
+         my $getGrp = "Public";
+         my $setGrp = "Public";
+         
+         my $propAttrs = "";
+         $propAttrs = $1 if defined($1);
+         $propGet = "public:";
+         $propSet = "public:";
+         $propIsAbstract  = 0;
+         $propIsConstant  = 0;
+         $propIsDependent = 0;
+         
+         #***
+         # AbortSet
+         #
+         # No C++ equivalent. Ignore.
+         #***
+
+         #***
+         # Abstract
+         #
+         # Property get and set are pure virtual. Not yey implemented.
+         #***
+         if ($propAttrs =~ /abstract\s*=\s*false/i)
+         {
+            # Ignore Constant=false settings.
+         }
+         elsif ($propAttrs =~ /abstract\s*(?:=\s*true)?/i)
+         {
+            $propIsAbstract = 1;
+         }
+                  
+         #***
+         # Access
+         #
+         # Restrict access. C++ friendship is granted on a per-class basis, not
+         # a per-propery basis, so the friendship here will only be approximate.
+         #***
+         if ($propAttrs =~ /\baccess\b\s*=\s*private/i)
+         {
+            $propGet = "private:";
+            $propSet = "private:";
+            $getGrp = "Private";
+            $setGrp = "Private";
+         }
+         elsif ($propAttrs =~ /\baccess\b\s*=\s*$metaList/i)
+         {
+            $propGet = "private:";
+            $propSet = "private:";
+            $getGrp = "Restricted";
+            $setGrp = "Restricted";
+         }
+         elsif ($propAttrs =~ /\baccess\b\s*=\s*protected/i)
+         {
+            $propGet = "protected:";
+            $propSet = "protected:";
+            $getGrp = "Protected";
+            $setGrp = "Protected";
+         }
+         elsif ($propAttrs =~ /\baccess\b\s*=\s*public/i)
+         {
+            $propGet = "public:";
+            $propSet = "public:";
+            $getGrp = "Public";
+            $setGrp = "Public";
+         }
+
+         #***
+         # Constant
+         #
+         # Treat property as const.
+         #***
+         if ($propAttrs =~ /constant\s*=\s*false/i)
+         {
+            # Ignore Constant=false settings.
+         }
+         elsif ($propAttrs =~ /constant\s*(?:=\s*true)?/i)
+         {
+            $propIsConstant = 1;
+         }
+         
+         #***
+         # Dependent
+         #
+         # Treat property as non-member.
+         #***
+         if ($propAttrs =~ /dependent\s*=\s*false/i)
+         {
+            # Ignore Dependent=false settings.
+         }
+         elsif ($propAttrs =~ /dependent\s*(?:=\s*true)?/i)
+         {
+            $propIsDependent = 1;
+         }
+         
+         #***
+         # GetAccess
+         #
+         # Restrict access. C++ friendship is granted on a per-class basis, not
+         # a per-propery basis, so the friendship here will only be approximate.
+         #***
+         if ($propAttrs =~ /\bgetaccess\b\s*=\s*private/i)
+         {
+            $propGet = "private:";
+            $getGrp = "Private";
+         }
+         elsif ($propAttrs =~ /\bgetaccess\b\s*=\s*$metaList/i)
+         {
+            $propGet = "private:";
+            $getGrp = "Restricted";
+         }
+         elsif ($propAttrs =~ /\bgetaccess\b\s*=\s*protected/i)
+         {
+            $propGet = "protected:";
+            $getGrp = "Protected";
+         }
+         elsif ($propAttrs =~ /\bgetaccess\b\s*=\s*public/i)
+         {
+            $propGet = "public:";
+            $getGrp = "Public";
+         }
+
+         #***
+         # SetAccess
+         #
+         # Restrict access. C++ friendship is granted on a per-class basis, not
+         # a per-propery basis, so the friendship here will only be approximate.
+         #***
+         if ($propAttrs =~ /\bsetaccess\b\s*=\s*private/i)
+         {
+            $propSet = "private:";
+            $setGrp = "Private";
+         }
+         elsif ($propAttrs =~ /\bsetaccess\b\s*=\s*$metaList/i)
+         {
+            $propSet = "private:";
+            $setGrp = "Restricted";
+         }
+         elsif ($propAttrs =~ /\bsetaccess\b\s*=\s*protected/i)
+         {
+            $propSet = "protected:";
+            $setGrp = "Protected";
+         }
+         elsif ($propAttrs =~ /\bsetaccess\b\s*=\s*public/i)
+         {
+            $propSet = "public:";
+            $setGrp = "Public";
+         }
+         
+         $makeDoxyComments = 1 unless ($propIsDependent || $propIsAbstract);
+
+         tee($out, "public: /** \@name $getGrp Get Access, $setGrp Set Access Properties *//**\@{*/\n");
+#         tee($out, "\n");
+      }
+      elsif (/^\s*(?:methods)\s*($attrList)?/)
+      {
+#         tee($out, "//===methods===");
+         push(@blocks,"methods");
+         $inMeths = 1;
+         $makeDoxyComments = 0;
+
+         my $methAttrs = "";
+         $methAttrs = $1 if defined($1);
+         $methAcc = "public:";
+         $methIsAbstract  = 0;
+         $methIsStatic  = 0;
+         $methIsSealed = 0;
+         
+         #***
+         # Abstract
+         #
+         # Property get and set are pure virtual. Not yey implemented.
+         #***
+         if ($methAttrs =~ /abstract\s*=\s*false/i)
+         {
+            # Ignore Constant=false settings.
+         }
+         elsif ($methAttrs =~ /abstract\s*(?:=\s*true)?/i)
+         {
+            $methIsAbstract = 1;
+            $makeDoxyComments = 1;
+         }
+          
+         #***
+         # Access
+         #
+         # Restrict access. C++ friendship is granted on a per-class basis, not
+         # a per-propery basis, so the friendship here will only be approximate.
+         #***
+         if ($methAttrs =~ /\baccess\b\s*=\s*private/i)
+         {
+            $methAcc = "private:";
+         }
+         elsif ($methAttrs =~ /\baccess\b\s*=\s*$metaList/i)
+         {
+            $methAcc = "private:";
+         }
+         elsif ($methAttrs =~ /\baccess\b\s*=\s*protected/i)
+         {
+            $methAcc = "protected:";
+         }
+         elsif ($methAttrs =~ /\baccess\b\s*=\s*public/i)
+         {
+            $methAcc = "public:";
+         }
+
+         #***
+         # Hidden
+         #
+         # No C++ equivalent. Ignore.
+         #***
+         
+         #***
+         # Sealed
+         #
+         # Treat method as final.
+         #***
+         if ($methAttrs =~ /sealed\s*=\s*false/i)
+         {
+            # Ignore Sealed=false settings.
+         }
+         elsif ($methAttrs =~ /sealed\s*(?:=\s*true)?/i)
+         {
+            $methIsSealed = 1;
+         }
+         
+         #***
+         # Static
+         #
+         # Class method.
+         #***
+         if ($methAttrs =~ /static\s*=\s*false/i)
+         {
+            # Ignore Static=false settings.
+         }
+         elsif ($methAttrs =~ /static\s*(?:=\s*true)?/i)
+         {
+            $methIsStatic = 1;
+         }
+
+         tee($out, "\n");
+      }
+      elsif (/^\s*(if|for|parfor|switch|try|while)(.*)/)
+      {
+#         tee($out, "//===control===");
+         push(@blocks,"control");
+#         my $ctrl = $1;
+#         my $stmt = $2;
+#         $stmt =~ s/~/\!/g;
+#         $stmt =~ s/:/,/g;
+#         $stmt =~ s/($identifier)\.($identifier)/$1::$2/g;
+#         $stmt =~ s/\[$identifier(?:,$identifier)*\]/MATLAB::Array/g;
+#         $stmt =~ s/[\[]/\(/g;
+#         $stmt =~ s/[\)]/\)/g;
+#         $stmt =~ s/($identifier)\{(.*)\}/$1\[$2\]/g;
+#         $stmt =~ s/''/\"/g;
+#         $stmt =~ s/\'/\"/g;
+#         tee($out, "$ctrl$stmt";
+#         
+#         if ($_ !~ /[^%]*\.\.\./)
+#         {
+#            tee($out, "{";
+#         }
+#         else
+#         {
+#            $openControl = 1;
+#         }
+         
+         tee($out, "\n");
+      }
+      else
+      {
+         #tee($out, "===other===\n");
+#         s/~/\!/g;
+#         s/:/,/g;
+#         s/($identifier)\.($identifier)/$1::$2/g;
+#         s/\[$identifier(?:,$identifier)*\]/MATLAB::Array/g;
+#         s/[\[]/\(/g;
+#         s/[\]]/\)/g;
+#         s/($identifier)\{(.*)\}/$1\[$2\]/g;
+#         s/''/\"/g;
+#         s/\'/\"/g;
+#         
+#         unless ($inFunc && $makeDoxyComments)
+#         {
+#            if ($openControl && $_ !~ /[^%]*\.\.\./)
+#            {
+#               $openControl = 0;
+#               tee($out, "$_\{");
+#            }
+#            else
+#            {
+#               s|([^%]*)\.\.\.|$1//|;
+#               tee($out, "$_");
+#            }
+#         }
+
+         tee($out, "\n") unless ($inFunc && $makeDoxyComments);
+      }
+      
+
+   }
+
+   close $in;
+}
+
+tee($out, "}") if ($inFunc);
+
+tee($out, "/**\@}*/}" x scalar(@packages));
+tee($out, "/**\@}*/}/**\@}*/\n");
+
+close $out;
+
+sub tee (@)
+{
+   my $handle = shift;
+   print $handle @_;
+   print @_;
+}