//WIP just some changes to get a plot of current status

sEEG_Segmentation_Script.m

 % PCA
 CT_post = NiftiMod('Seeg_chinese_1_before_final.nii');
+%CT_post = NiftiMod('seeg_seg_bul_inside_binary.nii');
 
 %% CONSTANTS
 % for the contact region (from the paper)
 % contact region areas have defined interval of voxels, because they are the smallest parts in the data
 MINVOXELNUMBER_CONTACTS = 4; % at least 4 as minimum value
-MAXVOXELNUMBER_CONTACTS = 50;
+MAXVOXELNUMBER_CONTACTS = 150;
 
 % for head
 % bolt head areas have defined minimum of voxels, as they are bigger than contact regions
 % a maximum is also defined, as there are sometimes cable artifacts left in the data, so the heads are not the
 % biggest areas in the data
-MINVOXELNUMBER_HEAD = 51;
-MAXVOXELNUMBER_HEAD = 300;
+MINVOXELNUMBER_HEAD = 200;
+MAXVOXELNUMBER_HEAD = 2000;
 
 %% TODO: find some solution for electrodes, where the contacts regions are "melted" together and no seperate
 %% regions and head are defined
 
+%% TODO: find solution for thresholds of heads and contacts, because they're different for every data set
+
 
 %% get nifti img to binary img, so we can apply some functions
 maskedImg = CT_post.img;
@@ -73,11 +76,11 @@ for i = 1:(length(headCandidate))
     % vector of the centroid of the current head candidate
     for j = 1:(length(contactCandidate))
         centroidPositionContact = ccProps(componentIdxsContacts(j)).Centroid;
-        newContactPosition = coeff * centroidPositionContact' + centroidPositionHead';
+        %newContactPosition = coeff * centroidPositionContact' + centroidPositionHead';
         
-        disp(['new Contact Position at ' num2str(j) ' is: ' num2str(newContactPosition')]);
+        %disp(['new Contact Position at ' num2str(j) ' is: ' num2str(newContactPosition')]);
         
-        newPositionsContactCandidates(:,j) = newContactPosition;
+        newPositionsContactCandidates(:,j) = centroidPositionContact';
     end
     
     % just for plotting purposes
@@ -127,27 +130,27 @@ for i = 1:(length(headCandidate))
     % with the contact candidates
     baseline = @(t)(originOfLine + originToSecondPoint * t);
     
-    concreteCandidatesForElectrode = zeros(3,:);
+   % concreteCandidatesForElectrode = zeros(3,:);
     
     % 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))
-        
-        % max dist between contact candidate and baseline, to actually consider it for the electrode
-        maxAllowedDist = 5;
-        
-        % max length of electrode, cutting every eletrode beyond that
-        thresholdElecMaxValue = baseline(10);
-        xValueOfThreshold = thresholdElecMaxValue(1,:);
-        
-        % get a candidate from the contacts and the x-Value to compare it to the baseline
-        contactPoint = newPositionsContactCandidates(:,k);
-        xValueOfContactPoint = contactPoint(1,:);
-        
-        if(xValueOfContactPoint <= xValueOfThreshold)
-            concreteCandidatesForElectrode(:,k) = contactPoint;
-        end
+%     for k = 1:(length(contactCandidate))
+%         
+%         % max dist between contact candidate and baseline, to actually consider it for the electrode
+%         maxAllowedDist = 5;
+%         
+%         % max length of electrode, cutting every eletrode beyond that
+         thresholdElecMaxValue = baseline(50);
+%         xValueOfThreshold = thresholdElecMaxValue(1,:);
+%         
+%         % get a candidate from the contacts and the x-Value to compare it to the baseline
+%         contactPoint = newPositionsContactCandidates(:,k);
+%         xValueOfContactPoint = contactPoint(1,:);
+%         
+%         if(xValueOfContactPoint <= xValueOfThreshold)
+%             concreteCandidatesForElectrode(:,k) = contactPoint;
+%         end
         
         
         % wanted to compute distance between point and corresponding point
@@ -160,17 +163,22 @@ for i = 1:(length(headCandidate))
         %         if(dist < threshold)
         %             %add point to matrix
         %         end
-    end
+    %end
     %
     %
     %     figure
     %     plotv(baseline);
     
     figure
+    
+    
+    figure
+    axis([0 500 0 500 0 500])
+    axis equal
     scatterMatrix3(newPositionsContactCandidates);
     hold on
     scatterMatrix3(centroidOfAllContacts');
-    scatterMatrix3(thresholdElecMaxValue');
+    scatterMatrix3(thresholdElecMaxValue', {}, '*');
     scatterMatrix3(endOneOfBoltHead');
     scatterMatrix3(endTwoOfBoltHead');
     % hold off
@@ -193,7 +201,7 @@ for i = 1:(length(headCandidate))
     %     te=det(newcoeff);
 end
 
-scatterMatrix3(newHeadPositions);
+scatterMatrix3(newHeadPositions');
 hold off
 
 % figure
@@ -201,34 +209,4 @@ hold off
 % X = ccProps(componentIdxs(i)).PixelList .* repmat(CT_post.voxsize', length(ccProps(componentIdxs(i)).PixelList) ,1);
 % scatterMatrix3(X)
 % hold on
-% 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, '-');
+% end
\ No newline at end of file