Index: Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m =================================================================== --- Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m (revision 14) +++ Damkjer/PointProcessing/Thinning_Damkjer/thin_Damkjer.m (revision 15) @@ -53,5 +53,5 @@ % thin_Dyn %****************************************************************************** -function [ results ] = thin_Damkjer( points, threshold, varargin ) +function [ results, removed_wgts, impact ] = thin_Damkjer( points, threshold, varargin ) % Perform local feature attribution via eigenspace analysis. % @@ -85,4 +85,7 @@ disp(['...done in ' num2str(toc(tstart)) 's']); +% size(check) +% size(points) +% if (any(size(check) ~= size(points))) error('Points must be unique. Try: unique(X.'',''rows'',''stable'').'''); @@ -194,10 +197,5 @@ natives = nbrspanalyze(points, nbrs, test, 'timebar'); -% natives = nbrspanalyze(points, nbrs, 'timebar'); - -% if (any(isnan(natives.entropy))) -% disp('Ugh... seriously?'); -% end -% + disp(['...done in ' num2str(toc(tstart)) 's']); @@ -210,8 +208,4 @@ feats = nbrspanalyze(points, nbrs, 'timebar'); -% if (any(isnan(feats.entropy))) -% disp('Ugh... seriously?'); -% end -% disp(['...done in ' num2str(toc(tstart)) 's']); @@ -244,23 +238,6 @@ close(h); end - -% if (any(isnan(sigs))) -% disp('Ugh... seriously?'); -% end -% + disp(['...done in ' num2str(toc(tstart)) 's']); - -% origFormat = get(0, 'format'); -% format('longG'); -% min(sigs) -% max(sigs) -% set(0, 'format', origFormat); - -% results = natives; -% end -% -% function cont -% error('Stop'); - %*** @@ -289,5 +266,5 @@ removed=zeros(1,elements-threshold); - dual_size=zeros(1,elements-threshold); +% dual_size=zeros(1,elements-threshold); current=1; @@ -308,6 +285,10 @@ n = length(sigs) - tau; removed_wgts=zeros(1,n); - -% msg=['Thin Dimension ' num2str(dim) '(' num2str(length(parts{dim})) ... + baseline=natives.entropy; + + impact=zeros(1,n+1); + impact(1) = mean(natives.entropy); + +% msg=['Thin Dimension ' num2str(dim) '(' num2str(length(parts{dim})) ... % '->' num2str(tau) ')...']; msg='Thin...'; @@ -318,50 +299,21 @@ tic; -% disp(nbrs{318935}) -% disp(test{318935}) -% disp(duals{318935}) -% -% disp(nbrs{458702}) -% disp(test{458702}) -% disp(duals{458702}) - + max_sig=0; + for x=1:n -% disp('Pop'); - -% heap_size = heap.size(); - % Locate the least significant point to remove [wgt, idx]=heap.pop_head(); - -% disp('Popped'); - -% if (heap.size() ~= (heap_size - 1)) -% disp(['...and there it is: ' num2str(heap_size) ' - 1 vs. ' num2str(heap.size())]); -% disp(idx); -% error('oops'); -% end - -% if (isempty(nbrs{idx}) || isempty(duals{idx})) -% disp(idx); -% end - -% if (isempty(nbrs{idx}) && isempty(duals{idx})) -% disp('uh oh'); -% disp(idx); -% end -% idx -% wgt - -% if (any(removed==idx)) -% disp('uh oh'); -% disp(['Index already removed ' num2str(idx)]); -% end % Mark the point as removed removed(current)=idx; % removed_wgts{dim}(x)=wgt; - removed_wgts(x)=wgt; - + max_sig=max(max_sig, wgt); +% removed_wgts(x)=wgt; + removed_wgts(x)=max_sig; + + impact(1 + x) = ((elements - x + 1) * impact(x) - natives.entropy(idx)) / ... + (elements - x); +% impact(1 + x) % Distribute the points in the test set to the neighbor's test sets. @@ -369,39 +321,16 @@ samples = test{idx}; -% neighbors -% samples - for samp=1:length(samples) % Find the closest -% [dsq,new_idx]=min(sum((bsxfun(@minus, points(:,neighbors), ... +% [dsq,new_idx]=min(sum((bsxfun(@minus, points(:,neighbors), ... % points(:,samples(samp)))).^2, 1)); - [dsq,new_idx]=min(sum((bsxfun(@minus, points(1:3,neighbors), ... + [dsq,new_idx]=min(sum((bsxfun(@minus, points(1:3,neighbors), ... points(1:3,samples(samp)))).^2, 1)); - -% samples(samp) -% points(1:3,neighbors) -% points(1:3,samples(samp)) -% dsq -% new_idx -% neighbors(new_idx) % Update the test set test{neighbors(new_idx)}(end + 1,1) = samples(samp); -% if (samples(samp) == 458702) -% disp(['relocating 458702 from test{' num2str(idx) '} to test{'... -% num2str(neighbors(new_idx)) '}']); -% -% disp(test{neighbors(new_idx)}); -% end -% -% if (neighbors(new_idx) == 458702) -% disp(['relocating ' num2str(samples(samp)) ' from test{' num2str(idx) '} to test{458702}']); -% -% disp(test{neighbors(new_idx)}); -% end - -% tdist(neighbors(new_idx)) = max(tdist(neighbors(new_idx)),... +% tdist(neighbors(new_idx)) = max(tdist(neighbors(new_idx)), ... % sqrt(dsq)); end @@ -410,19 +339,10 @@ % contains the neighbors. Update the neighbor duals appropriately. for nbr=1:length(neighbors) -% if (neighbors(nbr) == 458702) -% disp([num2str(idx) '''s neighborhood no longer contains 458702']); -% disp(duals{neighbors(nbr)}); -% end - duals{neighbors(nbr)}=duals{neighbors(nbr)}(duals{neighbors(nbr)}~=idx); - -% if (neighbors(nbr) == 458702) -% disp(duals{neighbors(nbr)}); -% end end % Find neighborhoods that contain removed element neighborhoods=duals{idx}; - dual_size(current)=length(neighborhoods); +% dual_size(current)=length(neighborhoods); neighborhoods=sort(neighborhoods(neighborhoods~=idx), 'ascend'); @@ -436,6 +356,4 @@ % Build up the list of potential new neighbors -% disp('building candidates...'); - nbr_pool=fastsetunion({nbrs{nbrs{neighborhoods(hood)}}}); non_nbrs=fastsetunion({nbrs{neighborhoods(hood)},idx,neighborhoods(hood)}); @@ -451,45 +369,10 @@ 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} -%% -% points(1:3,nbr_pool) -% points(1:3,neighborhoods(hood)) -% - [dsq,new_idx]=min(sum((bsxfun(@minus, points(1:3,nbr_pool), ... + [dsq,new_idx]=min(sum((bsxfun(@minus, points(1:3,nbr_pool), ... points(1:3,neighborhoods(hood)))).^2, 1)); -% points(1:3,nbr_pool) -% points(1:3,neighborhoods(hood)) -% bsxfun(@minus, points(1:3,nbr_pool), points(1:3,neighborhoods(hood))) -% (bsxfun(@minus, points(1:3,nbr_pool), points(1:3,neighborhoods(hood)))).^2 -% sum((bsxfun(@minus, points(1:3,nbr_pool), points(1:3,neighborhoods(hood)))).^2,1) -% [dsq,new_idx]=min(sum((bsxfun(@minus, points(1:3,nbr_pool), points(1:3,neighborhoods(hood)))).^2,1)) - % Update the neighborhood -% disp('updating neighborhood...'); - new_dist = sqrt(dsq); -% if (neighborhoods(hood) == 458702) -% disp(['replace ' num2str(idx) ' in 458702''s neighborhood']); -% disp('Pool...'); -% disp(nbr_pool(new_idx)); -% disp('Before...'); -% disp(nbrs{neighborhoods(hood)}); -% end -% -% if (nbr_pool(new_idx) == 458702) -% disp(['458702 is replacing ' idx ' in ' neighborhoods(hood) '''s neighborhood']); -% disp(nbrs{neighborhoods(hood)}); -% end -% % Maintain a partially sorted list of indices by max distance. if (new_dist > dists{neighborhoods(hood)}(end)) @@ -514,31 +397,7 @@ disp(neighborhoods(hood)); end -% nbrs{neighborhoods(hood)} -% dists{neighborhoods(hood)} % Update the dual -% disp('updating dual...'); - - -% duals{nbr_pool(new_idx)} duals{nbr_pool(new_idx)}(end + 1,1) = neighborhoods(hood); -% duals{nbr_pool(new_idx)} -% disp(nbrs{neighborhoods(hood)}); -% disp(duals{nbr_pool(new_idx)}); - -% error('stop'); -% if (neighborhoods(hood) == 458702) -% disp('After...'); -% disp(nbrs{neighborhoods(hood)}); -% disp([num2str(nbr_pool(new_idx)) ' is now in 458702''s neighborhood']); -% disp(duals{nbr_pool(new_idx)}); -% end -% -% if (nbr_pool(new_idx) == 458702) -% disp(nbrs{neighborhoods(hood)}); -% disp(['458702 is now in ' num2str(nbr_pool(new_idx)) '''s neighborhood']); -% disp(duals{nbr_pool(new_idx)}); -% end - end @@ -548,35 +407,13 @@ % Update analysis for elements -% disp('updating analysis...'); - -% if (isempty(neighborhoods)) -% warning('Damkjer:strange','empty neighborhoods'); -% end -% -% if (isempty(neighbors)) -% warning('Damkjer:stranger','empty neighbors'); -% end -% if (isempty(neighborhoods)) neighborhoods=neighbors; end -% if (~isempty(neighborhoods) && ~isempty(neighbors)) neighborhoods=fastsetunion({neighborhoods, neighbors}); -% elseif (isempty(neighborhoods) && ~isempty(neighbors)) -% neighborhoods=neighbors; -% end - -% nbrs{neighborhoods} -% test{neighborhoods} - -% error('Stop'); if (~isempty(neighborhoods)) locfeats = nbrspanalyze(points, ... nbrs(neighborhoods)); -% locfeats = nbrspanalyze(points, ... -% nbrs(neighborhoods), ... -% test(neighborhoods)); locsigs=zeros(1,length(neighborhoods)); @@ -592,25 +429,4 @@ sig_upd=locsigs; -% for pt=1:length(updates) -% if (any(removed==updates(pt))) -% disp('uh oh'); -% disp(['Index already removed ' num2str(updates(pt))]); -% end -% end - - -% heap_size = heap.size(); -% -% heap.erase(sigs(updates),updates); -% -% if (heap.size() ~= (heap_size - length(updates))) -% disp(['...and there it is: ' num2str(heap_size) ' - ' num2str(length(updates)) ' vs. ' num2str(heap.size())]); -% disp(sigs(updates)); -% disp(updates); -% error('oops'); -% end -% -% heap.insert(sig_upd,updates); - heap.update(sig_upd,updates); sigs(neighborhoods)=locsigs; @@ -631,5 +447,5 @@ end - disp(['...done in ' num2str(toc(tstart)) 's']); + disp(['...done in ' num2str(toc(tstart)) 's']); % end @@ -647,6 +463,6 @@ figure, plot(1:x_max,y); - figure, plot(1:length(dual_size),dual_size); - + figure, plot(1:length(impact),impact); + % results = points(:,~ismember(1:size(points,2),removed)); results = removed; @@ -675,6 +491,6 @@ if isempty(varargin) - error('Damkjer:InvalidOptions', ... - ['A neighborhood size must be specified, either directly or '... + error('Damkjer:InvalidOptions', ... + ['A neighborhood size must be specified, either directly or ' ... 'via optional parameters.']); end @@ -683,11 +499,11 @@ value = varargin{1}; - if (isscalar(value) && ... - isreal(value) && ... + if (isscalar(value) && ... + isreal(value) && ... value >= 5) userParams.neighbors = fix(value); else - error('Damkjer:InvalidCount', ... - ['Number of Neighbors must be a real valued positive '... + error('Damkjer:InvalidCount', ... + ['Number of Neighbors must be a real valued positive ' ... 'integer greater or equal to 5: ' num2str(value)]); end @@ -698,6 +514,6 @@ % Parse the Property/Value pairs if rem(length(varargin), 2) ~= 0 - error('Damkjer:PropertyValueNotPair', ... - ['Additional arguments must take the form of Property/Value '... + error('Damkjer:PropertyValueNotPair', ... + ['Additional arguments must take the form of Property/Value ' ... 'pairs']); end @@ -715,5 +531,5 @@ error('Damkjer:InvalidProperty', 'Invalid Property'); elseif length(iProperty) > 1 - error('Damkjer:AmbiguousProperty', ... + error('Damkjer:AmbiguousProperty', ... 'Supplied shortened property name is ambiguous'); end @@ -723,43 +539,43 @@ switch property case 'neighbors' - if (isscalar(value) && ... - isreal(value) && ... + if (isscalar(value) && ... + isreal(value) && ... value >= 5) userParams.neighbors = fix(value); else - error('Damkjer:InvalidCount', ... - ['Number of Neighbors must be a real valued positive '... + 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) && ... + if (isscalar(value) && ... + isnumeric(value) && ... + isreal(value) && ... value > 0) userParams.radius = value; else - error('Damkjer:InvalidRadius', ... + error('Damkjer:InvalidRadius', ... 'Radius must be a real valued positive scalar'); end case 'counts' - if (isvector(value) && ... - isreal(value) && ... - issorted(value) && ... + if (isvector(value) && ... + isreal(value) && ... + issorted(value) && ... all(value >= 5)) userParams.counts = fix(value); else - error('Damkjer:InvalidCount', ... + 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) && ... + 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 '... + error('Damkjer:InvalidSteps', ... + ['Steps must be a sorted vector of real valued positive ' ... 'values']); end @@ -771,22 +587,22 @@ % Check for mutually exclusive options. if (~isempty(userParams.counts) && userParams.neighbors >= 5) - error('Damkjer:MutExOpts', ... + error('Damkjer:MutExOpts', ... '''neighbors'' and ''counts'' options are mutually exclusive'); end if (~isempty(userParams.steps) && userParams.radius > 0) - error('Damkjer:MutExOpts', ... + error('Damkjer:MutExOpts', ... '''steps'' and ''radius'' options are mutually exclusive'); end if (~isempty(userParams.counts) && ~isempty(userParams.steps)) - error('Damkjer:MutExOpts', ... + error('Damkjer:MutExOpts', ... '''steps'' and ''counts'' options are mutually exclusive'); end % Default, if necessary. - if (userParams.neighbors <= 0 && ... - userParams.radius <= 0 && ... - isempty(userParams.counts) && ... + if (userParams.neighbors <= 0 && ... + userParams.radius <= 0 && ... + isempty(userParams.counts) && ... isempty(userParams.steps)) userParams.radius = 1; Index: Damkjer/Util/FileIO/LasFile/LasFile.m =================================================================== --- Damkjer/Util/FileIO/LasFile/LasFile.m (revision 12) +++ Damkjer/Util/FileIO/LasFile/LasFile.m (revision 15) @@ -294,5 +294,5 @@ pointData = lasFile.pPoints; end - + %************************************************************************ % LasFile/get.gpsTime Index: Damkjer/Util/FileIO/LasFile/LasPublicHeader.m =================================================================== --- Damkjer/Util/FileIO/LasFile/LasPublicHeader.m (revision 12) +++ Damkjer/Util/FileIO/LasFile/LasPublicHeader.m (revision 15) @@ -264,5 +264,5 @@ % % The scale factor fields contain a double floating point value - % that is uysed to scale the corresponding X, Y, and Z long values + % that is used to scale the corresponding X, Y, and Z long values % within the point records. The corresponding X, Y, and Z scale % factor must be multiplied by the X, Y, or Z point record value to @@ -275,5 +275,5 @@ % % The scale factor fields contain a double floating point value - % that is uysed to scale the corresponding X, Y, and Z long values + % that is used to scale the corresponding X, Y, and Z long values % within the point records. The corresponding X, Y, and Z scale % factor must be multiplied by the X, Y, or Z point record value to @@ -286,5 +286,5 @@ % % The scale factor fields contain a double floating point value - % that is uysed to scale the corresponding X, Y, and Z long values + % that is used to scale the corresponding X, Y, and Z long values % within the point records. The corresponding X, Y, and Z scale % factor must be multiplied by the X, Y, or Z point record value to Index: Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp =================================================================== --- Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp (revision 14) +++ Damkjer/Util/MATLAB/VpTreeAPI/VpTreeAPI.cpp (revision 15) @@ -427,5 +427,5 @@ // superior results. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { @@ -458,5 +458,5 @@ // parallel. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { @@ -510,5 +510,5 @@ // parallel. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { @@ -687,5 +687,5 @@ // superior results. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { @@ -717,5 +717,5 @@ // parallel. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { @@ -769,5 +769,5 @@ // parallel. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int q = 0; q < queryData.size(); ++q) { Index: Damkjer/Util/Math/fastcenter.cpp =================================================================== --- Damkjer/Util/Math/fastcenter.cpp (revision 12) +++ Damkjer/Util/Math/fastcenter.cpp (revision 15) @@ -93,5 +93,5 @@ #endif - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int cellp = 0; cellp < cells; ++cellp) { Index: Damkjer/Util/Math/fastcoeffvar.cpp =================================================================== --- Damkjer/Util/Math/fastcoeffvar.cpp (revision 12) +++ Damkjer/Util/Math/fastcoeffvar.cpp (revision 15) @@ -94,5 +94,5 @@ #endif - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int cellp = 0; cellp < cells; ++cellp) { Index: Damkjer/Util/Math/fastcov.cpp =================================================================== --- Damkjer/Util/Math/fastcov.cpp (revision 14) +++ Damkjer/Util/Math/fastcov.cpp (revision 15) @@ -131,5 +131,5 @@ #endif - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int cellp = 0; cellp < cells; ++cellp) { Index: Damkjer/Util/Math/fastsetdual.cpp =================================================================== --- Damkjer/Util/Math/fastsetdual.cpp (revision 13) +++ Damkjer/Util/Math/fastsetdual.cpp (revision 15) @@ -137,5 +137,5 @@ // parallel. //*** - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int elem = 0; elem < maxElem; ++elem) { Index: Damkjer/Util/Math/par_eig.cpp =================================================================== --- Damkjer/Util/Math/par_eig.cpp (revision 12) +++ Damkjer/Util/Math/par_eig.cpp (revision 15) @@ -111,5 +111,5 @@ #endif - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int cellp = 0; cellp < cells; ++cellp) { @@ -150,5 +150,5 @@ #endif - #pragma omp parallel for + #pragma omp parallel for schedule(guided) for (int cellp = 0; cellp < cells; ++cellp) { Index: Damkjer/Util/SpatialIndexing/VpTree/VpTree.hpp =================================================================== --- Damkjer/Util/SpatialIndexing/VpTree/VpTree.hpp (revision 12) +++ Damkjer/Util/SpatialIndexing/VpTree/VpTree.hpp (revision 15) @@ -201,5 +201,5 @@ ++threads; - #pragma omp parallel + #pragma omp parallel num_threads(2) { #pragma omp sections nowait Index: Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp =================================================================== --- Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp (revision 13) +++ Damkjer/Util/SpatialIndexing/VpTree/VpTree_Leaf.hpp (revision 15) Index: Damkjer/Util/Util.vcxproj =================================================================== --- Damkjer/Util/Util.vcxproj (revision 13) +++ Damkjer/Util/Util.vcxproj (revision 15) @@ -39,4 +39,5 @@ + @@ -63,4 +64,5 @@ + Index: Damkjer/Util/Util.vcxproj.filters =================================================================== --- Damkjer/Util/Util.vcxproj.filters (revision 13) +++ Damkjer/Util/Util.vcxproj.filters (revision 15) @@ -88,4 +88,7 @@ Template Implementation Files + + Header Files + @@ -102,4 +105,7 @@ Source Files + + Source Files +