//WIP added computing of electrode direction and baseline

also tried to implement computing distance between contact points and baseline, doesn't work correctly yet

sEEG_Segmentation_Script.m

@@ -51,7 +51,7 @@ componentIdxsHeads = idxs(areas >= MINVOXELNUMBER_HEAD & areas <= MAXVOXELNUMBER
 %% PCA to get biggest eigenvalue from latent and principle direction from coeff matrix
 % TODO:
 
-A = [];
+newPositionsContactCandidates = zeros(3,length(contactCandidate));
 
 % this should be the same as length of componentIdxs?
 numCandidates = length(contactCandidate)+length(headCandidate);
@@ -69,19 +69,97 @@ for i = 1:(length(headCandidate))
     
     disp(['centroid at ' num2str(i) ' is: ' num2str(centroidPositionHead)]);
     
-    shiftcoord = global2localcoord([0;0;0], 'rr', centroidPositionHead');
+    % shiftcoord = global2localcoord([0;0;0], 'rr', centroidPositionHead');
     
+    % get the centroids of the contactCandidates and shift them by the
+    % vector of the centroid of the current head candidate
     for j = 1:(length(contactCandidate))
-        
         centroidPositionContact = ccProps(componentIdxsContacts(j)).Centroid;
-        
         newContactPosition = coeff * centroidPositionContact' + centroidPositionHead';
+   
+        disp(['new Contact Position at ' num2str(j) ' is: ' num2str(newContactPosition')]);
         
+        newPositionsContactCandidates(:,j) = newContactPosition;
+    end
+    
+    % compute the centroid of all contact points together to later get the
+    % direction in which we define our estimated electrode
+    centroidOfAllContacts = mean(newPositionsContactCandidates, 2);
+
+    % new origin is centroid point of head and new (local) coordinate
+    % system is coeff from the pca
+    
+    % compute vector between the two points
+    vectorBetweenHeadCentroidCentroidOfAll = centroidOfAllContacts - centroidPositionHead';
+    
+    % compute both "end points" on the bolt head, were the x-axis of our
+    % new coordinate system is going through
+    % then we can use them to determine, to which end the mean is nearer
+    % and therefore we now on which side of the bolt head the contact
+    % candidates lie
+    endOneOfBoltHead = coeff(:,1) * latent(1,:) + centroidPositionHead';
+    endTwoOfBoltHead = coeff(:,1) * latent(1,:) * (-1.0) + centroidPositionHead';
+    
+    % compute the lengths of the vectors between both endpoints and the
+    % centroid point of the contact candidates
+    distMeanToEndOne = norm(centroidOfAllContacts - endOneOfBoltHead);
+    distMeanToEndTwo = norm(centroidOfAllContacts - endTwoOfBoltHead);
+    
+    % we set the origin of our future line to the end which is furthest
+    % away from the centroid point and go with it in the direction of the
+    % other endpoint, because now we know, there are all the contact
+    % candidates
+    if(distMeanToEndOne < distMeanToEndTwo) 
+        originOfLine = endTwoOfBoltHead;
+        secondPointOnLine = endOneOfBoltHead;
         
-        
+    else
+        originOfLine = endOneOfBoltHead;
+        secondPointOnLine = endTwoOfBoltHead;
     end
     
+    % can this be 3-dimensional
+    % baseline = polyfit(originOfLine, secondPointOnLine, 1);
+    
+    % vector pointing from origin point of line to second one
+    originToSecondPoint = secondPointOnLine - originOfLine;
+    lengthBetweenPoints = norm(originToSecondPoint);
+    % get unit vector along the line
+    originToSecondPoint = originToSecondPoint / lengthBetweenPoints;
+    % compute y = a * x + b to get the line, where a is 0 < a <
+    % lengthBetweenPoints
+    %baseline = originOfLine + (lengthBetweenPoints/2) * originToSecondPoint;
+    % description of our baseline going out from one end of the bolt
+    % through the other end into the head space with the contact candidates
+    baseline = @(t)(originOfLine + originToSecondPoint * t);
+    
+    % iterate through all contact candidates to find all of them, that have
+    % a smaller distance to the baseline than some defined threshold
+    % TODO: sort out possible problems with voxels/mm between line and
+    % point
+    for k = 1:(length(contactCandidate))
+        contactPoint = newPositionsContactCandidates(:,k);
+        xValueOfContactPoint = contactPoint(1,:);
+        % wanted to compute distance between point and corresponding point
+        % on the baseline, but there may be conflicts with position of
+        % point and baseline measurement in mm
+        dist = norm(componentIdxsContacts(k) - baseline(k));
         
+        if(dist < threshold)
+            %add point to matrix
+        end
+    end
+    
+    
+    figure
+    plotv(baseline);
+    
+    figure
+    scatterMatrix3(newPositionsContactCandidates);
+    hold on
+    scatterMatrix3(centroidOfAllContacts');
+    hold off
+%     
 %     de=det(coeff);
 %     
 %     newcoeff = [coeff(:,2), -coeff(:,3), coeff(:,1)];
@@ -109,31 +187,31 @@ end
 % end
 
 
-
-x=coeff(:,1);
-y=coeff(:,2);
-z=coeff(:,3);
-
-inter = intersect(intersect(x,y),z);
-
-plot(x);
-plot(y);
-plot(z);
-
-t=det(coeff);
-
-plot3(x,y,z);
-
-%coeff(:,1)
-
-
-M = [0,0,1;0,0,-1;0,1,0];
-
-a = M(:,1);
-b = M(:,2);
-c = M(:,3);
-
-vec_inter = intersect(intersect(a,b), c);
-
-figure;
-plotv(M, '-');
+% 
+% x=coeff(:,1);
+% y=coeff(:,2);
+% z=coeff(:,3);
+% 
+% inter = intersect(intersect(x,y),z);
+% 
+% plot(x);
+% plot(y);
+% plot(z);
+% 
+% t=det(coeff);
+% 
+% plot3(x,y,z);
+% 
+% %coeff(:,1)
+% 
+% 
+% M = [0,0,1;0,0,-1;0,1,0];
+% 
+% a = M(:,1);
+% b = M(:,2);
+% c = M(:,3);
+% 
+% vec_inter = intersect(intersect(a,b), c);
+% 
+% figure;
+% plotv(M, '-');