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StructureObj.m
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StructureObj.m
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classdef StructureObj < handle
%LOCATIONOBJ - Manages 3D information for one structurse
properties
%Locations used to draw this object
Structure = []
Verts = [];
Normals = [];
Faces = [];
FaceNormals = [];
MapIDToIndex = [];
%Name of the material used to render the object when creating .obj
%collada file
ColladaStructName = [];
ColladaMaterialName = [];
UseCommonSphere = 0;
%Name of the material used to render the object when creating .obj
%file
MaterialName = [];
%THe offset to use when writing faces to an obj file
ObjVertexOffset = 0;
Color = [.5 .5 .5];
Alpha = 1
Links = {}; %Links to valid locations, the second column is the offset of the vertex to create the faces to
BadLinks = {}; %Links to invalid locations
BadLocs = []; %Records whether a given location index is valid or not
LinkGraph = [];
%This counts the number of links to each location
%Locations with only one or fewer links get a sphere
LocLinkCount = [];
ModelTranslation = [0 0 0]; %The structure is translated to be centered on 0,0,0. This puts it in the proper position in the world.
ModelScale = [1 1 1];
WorldBoundingBox = zeros(2,3); %The bounding box in world coordinates
ModelBoundingBox = zeros(2,3); %The bounding box in local coordinates
ChildList = []; %StructureID of objects which are children of this structure
end
properties (SetAccess = protected )
StructureID;
TypeID;
ParentID;
Label;
HasParent;
NumLocs;
Locs;
HasValidLocs;
end
properties (Constant = true)
iID = 1;
iParentID = 2;
iX = 3;
iY = 4;
iZ = 5;
iRadius = 6;
%Indicies to the IDToIndex map
iLocID = 1;
iVertOffset = 2;
iVertCount = 3;
numCirclePts = 6;
%Standard circle verticies around unit cirle
CircleVerts = CirclePatch(StructureObj.numCirclePts, 1, [0 0 1]);
UnitHemisphere = SpherePatch(StructureObj.numCirclePts, 1, [0 0 1], true);
numHemisphereVerts = size(StructureObj.UnitHemisphere.Verts,1);
UnitSphere = SpherePatch(StructureObj.numCirclePts, 1, [0 0 1]);
numSphereVerts = size(StructureObj.UnitSphere.Verts,1);
GlobalScalar = 1; %This is here to make the meshes more usable in programs like blender
nmPerPixel = 1 * StructureObj.GlobalScalar;
nmPerSection = 1 * StructureObj.GlobalScalar;
end
methods
function obj = StructureObj( structure_data, color, alpha, MatName)
obj.Structure = structure_data;
obj.Color = color;
obj.Alpha = alpha;
obj.MaterialName = MatName;
obj.ColladaStructName = ['Struct-' num2str(obj.StructureID)];
obj.ColladaMaterialName = MatName; %[obj.ColladaStructName '-material'];
%Walk the array and create verticies for all Locs
numLocs = obj.NumLocs;
obj.Links = cell(numLocs, 1);
obj.BadLinks = cell(numLocs, 1);
obj.BadLocs = false(numLocs,1);
%Count the number of links to each location
obj.LocLinkCount = zeros(numLocs,1);
%Create the connectivity graph
obj.LinkGraph = sparse([],[],[],numLocs, numLocs, numLocs*4);
%This is a map containing two columns.
%Database ID Vertex Offset
%The index into the matrix corresponds to the index used for
%other datastructures with location information in this object
obj.MapIDToIndex = zeros(numLocs,3);
for iLoc = 1:numLocs
ID = obj.Locs.ID(iLoc);
obj.MapIDToIndex(iLoc,1) = ID;
end
end
function StructureID = get.StructureID(obj)
StructureID = obj.Structure.ID;
end
function TypeID = get.TypeID(obj)
TypeID = obj.Structure.TypeID;
end
function ParentID = get.ParentID(obj)
ParentID = obj.Structure.ParentID;
end
function Label = get.Label(obj)
Label = obj.Structure.Label;
end
function obj = set.Label(obj, value)
obj.Structure.Label = value;
end
function hasParent = get.HasParent(obj)
hasParent = ~isempty(obj.ParentID);
return;
end
function numLocs = get.NumLocs(obj)
numLocs = size(obj.Locs.ID,1);
return;
end
function hasValid = get.HasValidLocs(obj)
hasValid = obj.NumLocs ~= sum(obj.BadLocs);
return
end
function Locs = get.Locs(obj)
Locs = obj.Structure.Locations;
return;
end
function obj = set.Locs(obj, value)
obj.Structure.Locations = value;
return;
end
function obj = AddChildStructure(obj, ChildObj)
obj.ChildList = [obj.ChildList ChildObj.StructureID];
end
function [X,Y,Z] = GetPosition(obj, iLoc)
X = obj.Locs.X(iLoc) * obj.nmPerPixel;
Y = obj.Locs.Y(iLoc) * obj.nmPerPixel;
Z = obj.Locs.Z(iLoc) * obj.nmPerSection;
end
function [X,Y,Z,Radius] = GetPositionAndRadius(obj, iLoc)
[X,Y,Z] = obj.GetPosition(iLoc);
Radius = obj.Locs.Radius(iLoc) * obj.nmPerPixel;
end
function DisplayPosition(obj, iLoc)
disp(['X: ' num2str(obj.Locs.X(iLoc)) ' Y: ' num2str(obj.Locs.Y(iLoc)) ' Z: ' num2str(obj.Locs.Z(iLoc)) ' Radius: ' num2str(obj.Locs.Radius(iLoc))]);
end
%Create faces to render the link between location IDs A & B
function obj = AddLink(obj, A, B, AValid, BValid)
iA = find(obj.MapIDToIndex(:,obj.iID) == A);
iB = find(obj.MapIDToIndex(:,obj.iID) == B);
if(isempty(iA) || isempty(iB))
return;
end
%Increment the link count for those objects
if(BValid)
obj.LocLinkCount(iA) = obj.LocLinkCount(iA) + 1;
% obj.Links{iA} = sort([obj.Links{iA} iB]);
obj.Links{iA} = [obj.Links{iA}; iB 0];
else
obj.BadLocs(iB) = true;
% obj.BadLinks{iA} = sort([obj.BadLinks{iA} iB]);
obj.BadLinks{iA} = [obj.BadLinks{iA} iB];
end
if(AValid)
obj.LocLinkCount(iB) = obj.LocLinkCount(iB) + 1;
% obj.Links{iB} = sort([obj.Links{iB} iA]);
obj.Links{iB} = [obj.Links{iB}; iA 0];
else
obj.BadLocs(iA) = true;
% obj.BadLinks{iB} = sort([obj.BadLinks{iB} iA]);
obj.BadLinks{iB} = [obj.BadLinks{iB} iA];
end
end
%This must be called after the last link is added so they can be
%sorted. It resizes the Links field so it holds the offset to the
%vertex and the number of verticies for the link target
function obj = EndAddLinks(obj)
for i =1:length(obj.Links)
if(~isempty(obj.Links{i}))
obj.Links{i} = sort(obj.Links{i},1);
end
if(~isempty(obj.BadLinks{i}))
obj.BadLinks{i} = sort(obj.BadLinks{i});
end
%Remove duplicates
if(~isempty(obj.Links{i}))
uniqueLinks = unique(obj.Links{i}(:,1));
obj.Links{i} = cat(2,uniqueLinks,zeros(length(uniqueLinks),1));
end
%assert(length(unique(obj.Links{i}(:,1))) == length(obj.Links{i}(:,1)));
obj.Links{i} = cat(2, obj.Links{i}, zeros(size(obj.Links{i},1),1));
end
%Figure out how far apart linked locations are on average. If
%a link has a length more than four std deviations from the
%mean then print a message so users can check into it
obj = obj.BuildConnectionMap();
end
function obj = CullVeryLongLinks(obj)
numLocs = obj.NumLocs;
[numLinks,~] = size(obj.Links);
if(numLinks == 0)
return;
end
DistanceMatrix = sparse([],[],[],numLocs, numLocs, numLocs*3);
TotalLinks = 0;
for(iObj =1:numLinks)
if(isempty(obj.Links{iObj}))
continue;
end
objLinks = obj.Links{iObj};
iObjA = iObj;
iObjB = objLinks(:,1);
iObjB = iObjB( iObjB < iObjA); %Remove objects with an ID number less than ours, prevents duplicate measurement. Duplicates throw off std deviation.
if isempty(iObjB)
continue;
end
[XA, YA, ZA] = obj.GetPosition(iObjA);
[XB, YB, ZB] = obj.GetPosition(iObjB);
[numObjLinks,~] = size(iObjB);
DistanceMatrix(iObjA, iObjB) = pdist2([XA YA ZA], [XB YB ZB]);
%
% %TODO, this should not be in a for loop
% for(iLinkB = 1:numObjLinks)
% iObjB = objLinks(iLinkB,1);
%
% %Get the coordinates of the locations and calculate the
% %distance
% if(iObjB <= iObjA)
% continue;
% end
%
% DistanceMatrix(iObjA, iObjB) = pdist([XA YA ZA;
% XB YB ZB]);
% end
end
%%Determine median and standard deviation of link length
Distances = full(DistanceMatrix(DistanceMatrix > 0));
distStd = std(Distances);
distMedian = median(Distances);
iOutliers = abs( Distances - distMedian) > (distStd*3.5);
if(sum(iOutliers) > 0)
disp('*** Found extreme distance between two linked locations ***');
disp(['Std. Dev.: ' num2str(distStd)]);
disp(['Median : ' num2str(distMedian)]);
%disp(Distances(iOutliers > 0));
end
%TODO: Remove the outliers
end
function obj = BuildConnectionMap(obj)
% disp(['Building connection graph for ' num2str(obj.StructureID) ]);
LabelNumber = 1;
obj.LinkGraph = full(obj.LinkGraph);
for(iLoc = 1:obj.NumLocs)
%We won't have a connection to ourselves if we've never
%been checked
if(obj.LinkGraph(iLoc,iLoc) ~= 0)
continue;
end
connected = obj.AllConnections(iLoc);
%Add these connections to the map for all the connected
%locations
for(iConnection = 1:length(connected))
iConnectedLoc = connected(iConnection);
obj.LinkGraph(iConnectedLoc, connected) = LabelNumber;
obj.LinkGraph(connected, iConnectedLoc) = LabelNumber;
end
LabelNumber = LabelNumber+1;
end
obj.LinkGraph = sparse(obj.LinkGraph);
% if(LabelNumber > 2)
% disp(['Found ' num2str(LabelNumber-1) ' isolated graphs for structure ' num2str(obj.StructureID)]);
% end
end
%Return a list of all locations connected to the source
function connected = AllConnections(obj, iSource)
qToCheck = obj.Links{iSource}(:,1);
qChecked = [iSource];
% disp([num2str(iSource)]);
while(~isempty(qToCheck))
iTest = qToCheck(1);
qChecked = cat(1, qChecked, iTest);
UncheckedLinks = setdiff(obj.Links{iTest}(:,1), qChecked);
if ~isempty(UncheckedLinks)
qToCheck = cat(1, qToCheck, UncheckedLinks);
end
qToCheck(1) = [];
end
connected = qChecked;
return;
end
function connected = IsConnected(obj, iSource, iTarget)
qToCheck = obj.Links{iSource}(:,1);
qChecked = [iSource];
% disp([num2str(iSource) ' ' num2str(iTarget)]);
while(~isempty(qToCheck))
iTest = qToCheck(1);
if(iTest == iTarget)
connected = true;
return;
end
qChecked = cat(1, qChecked, iTest);
qToCheck = cat(1, qToCheck, setdiff(obj.Links{iTest}(:,1), qChecked));
qToCheck(1) = [];
end
connected = false;
return;
end
function obj = ApplyZLimits(obj, MinZ, MaxZ)
%Remove locations that are outside the Min/Max Z range
for(iLoc = obj.NumLocs:-1:1)
[~, ~, Z] = obj.GetPosition(iLoc);
if(~isnan(MinZ))
if(Z < MinZ)
obj.RemoveLocation(iLoc, false);
continue;
end
end
if(~isnan(MaxZ))
if(Z > MaxZ)
obj.RemoveLocation(iLoc, false);
continue;
end
end
end
end
function obj = CullOverlapping(obj, iObjs, iExclude)
%Remove locations with two links (part of a process) who
%overlap with adjacent locations. Do not remove endpoints or
%branch points.
for(i = 1:length(iObjs))
iLoc = iObjs(i);
if(isempty(obj.Links{iLoc}))
continue;
end
iLinked = obj.Links{iLoc}(:,1);
if(isempty(iLinked))
continue;
end
[X, Y, Z, Radius] = obj.GetPositionAndRadius(iLoc);
iIdenticalTest = intersect(iLinked, iExclude);
iLinked = setdiff(iLinked, iExclude);
%We only cull these if they are directly on top of the
%location
if(~isempty(iIdenticalTest))
for iLink = length(iIdenticalTest)
[AX,AY,AZ] = obj.GetPosition(iLink);
if(X == AX && Y == AY && Z == AZ)
%FindGoodLinks(obj, iLoc, iExcludeLocs, KnownGoodLinks, iSearched)
RemoveLocation(obj, iLink, true);
break;
end
end
end
%Do not bother checking locations we've already marked as bad, stop.
if(obj.BadLocs(iLoc))
continue;
end
LinkVerts = zeros(length(iLinked), 3);
minLinkDistance = 10^100;
for iLink = 1:length(iLinked)
iAdjacentLoc = iLinked(iLink);
[AX,AY,AZ, ARadius] = obj.GetPositionAndRadius(iAdjacentLoc);
LinkVerts(iLink,:) = [AX AY AZ];
%distance = pdist([X Y Z; AX AY AZ]);
SqDiff = [(X-AX)^2 (Y-AY)^2 (Z-AZ)^2];
sumSqDiff = sum(SqDiff);
Adistance = sqrt(sumSqDiff);
if(Adistance < minLinkDistance)
minLinkDistance = Adistance;
end
%Remove the link if the location is too close to the
%adjacent
if(Adistance < max(ARadius,Radius))
%Keep the larger of the two radii,
%TODO, linear interpolation of the radius...
%obj.Locs.Radius(iLoc) = mean([ARadius Radius]);
numLinksOnAdjacent = length(obj.Links{iAdjacentLoc}(:,1));
if numLinksOnAdjacent == 2
obj.RemoveLocation(iAdjacentLoc, true);
elseif (numLinksOnAdjacent == 1 || numLinksOnAdjacent > 2)
%We shouldn't remove terminals or endpoints. So
%remove ourselves
obj.RemoveLocation(iLoc, true);
break;
end
end
end
if(length(iLinked) == 2 && obj.BadLocs(iLoc) == false)
LinkDistance = pdist(LinkVerts);
%Remove the location if the linked locations are closer
%together than this location is to the linked point, this is
%my primitive outlier detector
if(min(LinkDistance) < minLinkDistance)
RemoveLocation(obj, iLoc, true);
%
% for iLinkUpdate = 1:length(iLinked)
% %FindGoodLinks(obj, iLoc, iExcludeLocs, KnownGoodLinks, iSearched)
% NewLinks = FindGoodLinks(obj, iLinked(iLinkUpdate), [iLinked(iLinkUpdate); iLoc], setdiff(iLinked, iLinked(iLinkUpdate)), []);
% obj.Links{iLinked(iLinkUpdate)} = NewLinks;
% obj.LocLinkCount(iLinked(iLinkUpdate)) = size(NewLinks,1);
% end
%
% % obj.Links{iLoc} = [];
% obj.BadLocs(iLoc) = true; %Skip this location
continue;
end
end
end
end
%Remove locations within the radius of adjacent sections
function obj = CullOverlappingLocations(obj)
% disp(['Cull overlapping locations for ' num2str(obj.StructureID) ]);
BadIndicies = find(obj.BadLocs == true);
obj = MendOverlappingTerminals(obj);
PairedLocations = find(obj.LocLinkCount(:,1) == 2);
PairedLocations = setdiff(PairedLocations, BadIndicies);
obj = CullOverlapping(obj, PairedLocations, []);
BadIndicies = find(obj.BadLocs == true);
DeadEndLocations = find(obj.LocLinkCount(:,1) == 1);
DeadEndLocations = setdiff(DeadEndLocations, BadIndicies);
BranchLocations = find(obj.LocLinkCount(:,1) > 2);
BranchLocations = setdiff(BranchLocations, BadIndicies);
%Leavnig this check in creates artifacts, for example cell
%bodies become long thin rods instead of circles
%obj = CullOverlapping(obj, DeadEndLocations, [DeadEndLocations;BranchLocations]);
end
function obj = MendOverlappingTerminals(obj)
%Remove the zeros from consideration
LinkedLocs = obj.LinkGraph > 0;
StructureNamePrinted = false;
numLabels = length(unique(obj.LinkGraph(LinkedLocs)));
for(Label = numLabels:-1:2)
%Figure out which locations are the closest between
%isolated graphs
iLocsLogicalIndex = obj.LinkGraph == Label;
[iLocRows, iLocCols] = find(obj.LinkGraph == Label);
iLocs = unique(iLocRows);
if(obj.NumLocs == 1)
if(~StructureNamePrinted)
StructureNamePrinted =true;
disp(['Mend required for structure #' num2str(obj.StructureID)]);
end
disp([' Ignoring orphan location #: ' num2str(obj.Locs.ID(iLocs))]);
end
NotLinkedToMe = obj.LinkGraph ~= Label;
TestLocs = and(LinkedLocs, NotLinkedToMe);
[TestLocs, Cols] = find(TestLocs > 0);
TestLocs = unique(TestLocs);
%Figure out the two locations which are closest to each
%other...
Pos = [obj.Locs.X(iLocs) obj.Locs.Y(iLocs) obj.Locs.Z(iLocs)];
TestPos = [obj.Locs.X(TestLocs) obj.Locs.Y(TestLocs) obj.Locs.Z(TestLocs)];
%Only test the 25% of nearest locations
%K = ceil(min([length(iLocs) length(TestLocs)]) / 4);
K = 5;
%[iClosest, Distances] = knnsearch(Pos,TestPos, 'K', K);
[D, I] = pdist2(Pos, TestPos, 'euclidean', 'Smallest', K );
%D isn't sorted, sort it and find the smallest distances
[SortedD, iSorted] = sort(D(1,:), 2);
%Apply the same sorting to the indicies
SortedD = D(:,iSorted);
SortedI = I(:,iSorted);
TestLocs = TestLocs(iSorted);
%OK, starting with the nearest location, try to look for
%overlap
numTestPos = length(TestLocs);
LinkFound = false;
for(iTest = 1:numTestPos)
iTestLoc = TestLocs(iTest);
TestRadius = obj.Locs.Radius(iTestLoc) * obj.nmPerPixel;
for(iIndexToLoc = 1:size(SortedI,1))
iLoc = iLocs(SortedI(iIndexToLoc,iTest));
Radius = obj.Locs.Radius(iLoc) * obj.nmPerPixel;
if(SortedD(iIndexToLoc, iTest) <= Radius + TestRadius)
obj.Links{iLoc} = [obj.Links{iLoc}; iTestLoc 0 0];
obj.Links{iTestLoc} = [obj.Links{iTestLoc}; iLoc 0 0];
obj.LocLinkCount(iLoc) = size(obj.Links{iLoc},1);
obj.LocLinkCount(iTestLoc) = size(obj.Links{iTestLoc},1);
if(~StructureNamePrinted)
StructureNamePrinted =true;
disp(['Mend required for structure #' num2str(obj.StructureID)]);
end
disp([' Jumped gap: ' num2str(iLoc) ' (' num2str(obj.Locs.ID(iLoc)) ') -> ' num2str(iTestLoc) ' (' num2str(obj.Locs.ID(iTestLoc)) ')']);
disp([' X: ' num2str(obj.Locs.UnscaledX(iLoc)) ...
' Y: ' num2str(obj.Locs.UnscaledY(iLoc)) ...
' Z: ' num2str(obj.Locs.UnscaledZ(iLoc)) ...
' DS: 4']);
newLabel = obj.LinkGraph(iTestLoc, iTestLoc);
obj.LinkGraph(iLocsLogicalIndex) = newLabel;
%Break the loop
LinkFound = true;
break;
end
end
if(LinkFound)
break;
end
end
%Just use closest location in this case
if(~LinkFound)
iTestLoc = TestLocs(1);
iLoc = iLocs(SortedI(1,1));
obj.Links{iLoc} = [obj.Links{iLoc}; iTestLoc 0 0];
obj.Links{iTestLoc} = [obj.Links{iTestLoc}; iLoc 0 0];
obj.LocLinkCount(iLoc) = size(obj.Links{iLoc},1);
obj.LocLinkCount(iTestLoc) = size(obj.Links{iTestLoc},1);
if(~StructureNamePrinted)
StructureNamePrinted =true;
disp(['Mend required for structure #' num2str(obj.StructureID)]);
end
disp([' Jumped gap: ' num2str(iLoc) ' (' num2str(obj.Locs.ID(iLoc)) ') -> ' num2str(iTestLoc) ' (' num2str(obj.Locs.ID(iTestLoc)) ')']);
newLabel = obj.LinkGraph(iTestLoc, iTestLoc);
obj.LinkGraph(iLocsLogicalIndex) = newLabel;
%Break the loop
LinkFound = true;
end
end
end
% function obj = MendOverlappingTerminals(obj)
% BadIndicies = find(obj.BadLocs == true);
% DeadEndIndicies = find(obj.LocLinkCount(:,1) == 1);
% DeadEndIndicies = setdiff(DeadEndIndicies, BadIndicies);
%
% for(i = 1:length(DeadEndIndicies))
% iLoc = DeadEndIndicies(i);
% iLinked = obj.Links{iLoc};
%
% if(~isempty(iLinked))
% iLinked = iLinked(:,1);
% end
%
% X = obj.Locs(iLoc, obj.iX) * obj.nmPerPixel;
% Y = obj.Locs(iLoc, obj.iY) * obj.nmPerPixel;
% Z = obj.Locs(iLoc, obj.iZ) * obj.nmPerSection;
% Radius = obj.Locs(iLoc, obj.iRadius) * obj.nmPerPixel;
%
% LinkVerts = zeros(length(iLinked), 3);
% minLinkDistance = 10^100;
% iBestLink = [];
% BestLinkRadius = 0;
% numLocs = size(obj.Locs,1);
% myLabel = obj.LinkGraph(iLoc,iLoc);
%
% LinkedLocs = obj.LinkGraph > 0;
% NotLinkedToMe = obj.LinkGraph ~= myLabel;
%
% TestLocs = and(LinkedLocs, NotLinkedToMe);
% [TestLocs, Cols] = find(TestLocs > 0);
% TestLocs = unique(TestLocs);
%
%
% for(iTestLoc = TestLocs')
% if(obj.BadLocs(iTestLoc))
% continue;
% end
%
% if(iLinked == iTestLoc)
% continue;
% end
%
% if(iLoc == iTestLoc)
% continue;
% end
%
% AX = obj.Locs(iTestLoc, obj.iX) * obj.nmPerPixel;
% AY = obj.Locs(iTestLoc, obj.iY) * obj.nmPerPixel;
% AZ = obj.Locs(iTestLoc, obj.iZ) * obj.nmPerSection;
% ARadius = obj.Locs(iTestLoc, obj.iRadius) * obj.nmPerPixel;
%
% % LinkVerts = [AX AY AZ];
% %distance = pdist([X Y Z; AX AY AZ]);
% SqDiff = [(X-AX)^2 (Y-AY)^2 (Z-AZ)^2];
% sumSqDiff = sum(SqDiff);
% Adistance = sqrt(sumSqDiff);
%
% if(Adistance < minLinkDistance)
% if(obj.LinkGraph(iTestLoc, iTestLoc) ~= myLabel)
% minLinkDistance = Adistance;
% iBestLink = iTestLoc;
% BestLinkRadius = ARadius;
% end
% end
% end
%
% if(minLinkDistance < BestLinkRadius + Radius)
% %Create a link if the location is too close to the
% %adjacent unlinked
%
%
% % disp(['Loc: ' num2str(iLoc)]);
% % disp(['Links: ' num2str(obj.Links{iLoc})]);
% obj.Links{iLoc} = [obj.Links{iLoc}; iBestLink 0 0];
% obj.Links{iBestLink} = [obj.Links{iBestLink}; iLoc 0 0];
% obj.LocLinkCount(iLoc) = size(obj.Links{iLoc},1);
% obj.LocLinkCount(iBestLink) = size(obj.Links{iBestLink},1);
%
% % NewLinks = FindGoodLinks(obj, iLinked(iLinkUpdate), [iLinked(iLinkUpdate); iLoc], setdiff(iLinked, iLinkUpdate), []);
% % obj.Links{iLinked(iLinkUpdate)} = NewLinks;
% % obj.LocLinkCount(iLinked(iLinkUpdate)) = size(NewLinks,1);
%
% disp(['Jumped gap: ' num2str(iLoc) ' -> ' num2str(iBestLink)]);
%
% end
%
%
% end
% end
function obj = CenterModel(obj)
%Put the center of the model at 0,0
%Calculate the bounding box using the valid locations
if(~obj.HasValidLocs)
return
end
GoodLocs = ~obj.BadLocs;
Centers = [obj.Locs.X(GoodLocs) obj.Locs.Y(GoodLocs), obj.Locs.Z(GoodLocs)];%(GoodLocs,[obj.iX obj.iY obj.iZ]);
%Adjust the model so we are centered on 0,0,0.
if(length(Centers(:,1)) == 1)
obj.ModelTranslation = Centers;
%Objects with one location are spheres, lets use a standard
%sphere model and scale it in COLLADA format
Radius = obj.Locs.Radius(GoodLocs);
obj.ModelScale = [Radius Radius Radius];
else
obj.ModelTranslation = median( Centers );
end
%NewLocs = obj.Locs;
obj.Locs.X = obj.Locs.X - obj.ModelTranslation(1);
obj.Locs.Y = obj.Locs.Y - obj.ModelTranslation(2);
obj.Locs.Z = obj.Locs.Z - obj.ModelTranslation(3);
%obj.Locs = NewLocs;
end
function obj = TranslateModel(obj, vector)
obj.Verts(:,obj.iX) = obj.Verts(:,obj.iX) + vector(1);
obj.Verts(:,obj.iY) = obj.Verts(:,obj.iY) + vector(2);
obj.Verts(:,obj.iZ) = obj.Verts(:,obj.iZ) + vector(3);
end
function obj = ScaleModel(obj, scalar)
%Calculate the bounding box using the valid locations
obj.Verts = obj.Verts * scalar;
% obj.Verts(:,obj.iY) = obj.Verts(:,obj.iY) * scalar;
%obj.Verts(:,obj.iZ) = obj.Verts(:,obj.iZ) * scalar;
end
function [obj] = CalculateBoundingBox(obj)
%Determine the bounding box of the model using the verticies
obj.ModelBoundingBox = BoundingBox(obj.Verts);
obj.WorldBoundingBox(1,:) = obj.ModelBoundingBox(1,:) + obj.ModelTranslation;
obj.WorldBoundingBox(2,:) = obj.ModelBoundingBox(2,:) + obj.ModelTranslation;
end
%Create faces for the two IDs
function Faces = CreateFaces(obj, iA, iB)
if(isempty(iA) || isempty(iB))
return;
end
%
% if(iB < iA)
% temp = iB;
% iB = iA;
% iA = temp;
% end
%
iAtoB = obj.Links{iA}(:,1) == iB;
iBtoA = obj.Links{iB}(:,1) == iA;
iVertStartB = obj.Links{iA}(iAtoB,2);
iVertStartA = obj.Links{iB}(iBtoA,2);
try
assert(iVertStartB > 0);
assert(iVertStartA > 0);
catch
disp(['CreateFaces error on ' num2str(obj.StructureID) ': ' num2str(iA) ' ' num2str(iB)]);
dbstop if true;
end
%iVertStartA = obj.MapIDToIndex(iA,obj.iVertOffset);
%iVertStartB = obj.MapIDToIndex(iB,obj.iVertOffset);
iVertsA = iVertStartA:iVertStartA + obj.numCirclePts-1;
iVertsB = iVertStartB:iVertStartB + obj.numCirclePts-1;
assert(length(iVertsA) == obj.numCirclePts);
assert(length(iVertsB) == obj.numCirclePts);
% iVertsA = ((iA-1)*obj.numCirclePts)+1:((iA-1)*obj.numCirclePts)+obj.numCirclePts;
% iVertsB = ((iB-1)*obj.numCirclePts)+1:((iB-1)*obj.numCirclePts)+obj.numCirclePts;
%
AX = obj.Locs.X(iA) * obj.nmPerPixel;
AY = obj.Locs.Y(iA) * obj.nmPerPixel;
AZ = obj.Locs.Z(iA) * obj.nmPerSection;
BX = obj.Locs.X(iB) * obj.nmPerPixel;
BY = obj.Locs.Y(iB) * obj.nmPerPixel;
BZ = obj.Locs.Z(iB) * obj.nmPerSection;
A = [AX AY AZ];
B = [BX BY BZ];
assert(length(A) == 3);
assert(length(B) == 3);
Faces = CylinderFacesOffset(obj.numCirclePts, iVertStartA-1, ...
iVertStartB-1, ...
A, B, ...
obj.Verts(iVertsA,:), ...
obj.Verts(iVertsB,:));
end
function Links = GetLocationLinks(obj, iLoc)
if isempty(obj.Links{iLoc})
Links = [];
else
Links = obj.Links{iLoc}(:,1);
end
end
%Walk the graph from a bad node and locate all good links that
%can be reached from it
function FoundLinks = FindGoodLinks(obj, iLoc, iExcludeLocs, KnownGoodLinks, iSearched)
FoundLinks = [KnownGoodLinks; obj.Links{iLoc}(:,1)];
%Remove links we don't want in the results
FoundLinks = setdiff(FoundLinks, iExcludeLocs);
RemoveBadLocs = ~obj.BadLocs(FoundLinks);
FoundLinks = FoundLinks(RemoveBadLocs);
%Remove duplicates
FoundLinks = unique(FoundLinks);
if(isempty(FoundLinks))
return
else
%Add a column for vertex offsets
FoundLinks = cat(2, FoundLinks, zeros(length(FoundLinks),2));
end
end
function obj = RemoveLocation(obj, iLoc, PreserveLinks)
%Removes a location from our structure. Mark the location as
%bad. Update location links to skip the removed location
% PreserveLinks - Set to true if links should be relocated
% to remaining locations. If false the links are removed.
%iLinked = obj.Links{iLoc}(:,1);
GoodLinks = GetLocationLinks(obj, iLoc);
%GoodLinks = obj.FindGoodLinks(iLoc, [iLoc], setdiff(iLinked, iLinked(iLink)), []);
%obj.Links{iLinked(iLink)} = GoodLinks;
%obj.LocLinkCount(iLinked(iLink)) = size(GoodLinks,1);
for(iLink = 1:length(GoodLinks))
iLocToUpdate = GoodLinks(iLink);
%FindGoodLinks(obj, iLoc, iExcludeLocs, KnownGoodLinks, iSearched)
LocToUpdateLinks = GetLocationLinks(obj, iLocToUpdate);
%Remove the location we are removing from the list
UpdatedLinks = [];
if(PreserveLinks)
UpdatedLinks = setdiff([LocToUpdateLinks;GoodLinks], [iLoc; iLocToUpdate]);
else
UpdatedLinks = setdiff([LocToUpdateLinks], [iLoc]);
end
%Add the locations linked by the location we are removing
%to the list
UpdatedLinks = unique(UpdatedLinks);
%Add columns for additional data
if(~isempty(UpdatedLinks))
UpdatedLinks = cat(2, UpdatedLinks, zeros(length(UpdatedLinks),2));
else
UpdatedLinks = [];
end
obj.Links{iLocToUpdate} = UpdatedLinks;
obj.LocLinkCount(iLocToUpdate) = size(UpdatedLinks,1);
end
obj.BadLocs(iLoc) = true; %Skip this location
obj.LocLinkCount(iLoc) = 0;
obj.Links{iLoc} = [];
end
%Attempts to repair bad sections by combining adjacent nodes on
%either side of the bad link
function obj = JumpBadLinks(obj)
for(iLoc = 1:length(obj.Links))
% disp(num2str(iLoc));
if( false == obj.BadLocs(iLoc))
BadLinksLocal = obj.BadLinks{iLoc};
%Add the known good links from each bad link, minus our
%own ID
for(iBadLink = 1:length(BadLinksLocal))
newLinks = obj.FindGoodLinks(BadLinksLocal(iBadLink), iLoc, [], []);
if(~isempty(newLinks) && ~isempty(obj.Links{iLoc}))
newLinkIDs = unique([newLinks(:,1); obj.Links{iLoc}(:,1)]);
obj.Links{iLoc} = cat(2,newLinkIDs,zeros(length(newLinkIDs)));
elseif(~isempty(newLinks))
obj.Links{iLoc} = newLinks;
end
end
obj.LocLinkCount(iLoc) = size(obj.Links{iLoc},1);
end
end
end
%We update the other objects vertex index, we expect them to update
%ours if they are created first
function obj = SetVertexForLink(obj, iSource, iTarget, VertexOffset, numVerticies)
LinksA = obj.Links{iTarget};
iLinkA = LinksA(:,1) == iSource;
LinksA(iLinkA,2) = VertexOffset;
LinksA(iLinkA,3) = numVerticies;
obj.Links{iTarget} = LinksA;
end
function obj = UpdateMesh(obj)
if(~obj.HasParent)
disp(['Build mesh for: ' num2str(obj.StructureID)]);
end
%Cylinder indicies and branches, branches use the first two
%links for rotation
BadIndicies = find(obj.BadLocs == true);