Updates output table

MainScripts/formatTableOuputSurfaceCombine.m

 
 
-function [tableOutputDeproj, tableOutputBell] = formatTableOuputSurfaceCombine(dataCells,dataSeg)
+function tableOutputDeproj = formatTableOuputSurfaceCombine(dataCells,dataSeg)
 % Format the important variables into a table output for simpler handling
 
 tableOutputDeproj = table;
-tableOutputBell = table;
+% tableOutputBell = table;
 
 %% Cell numbering
-tableOutputDeproj.Numbers = dataCells.numbers;
-tableOutputBell.Numbers = dataSeg.CELLS.numbers(dataCells.numbers);
+tableOutputDeproj.cellIdx = dataCells.cellIdx';
+% tableOutputBell.Numbers = dataSeg.CELLS.numbers(dataCells.cellIdx);
 
 %% Cell center (ellipse real)
-for bioCell = 1:numel(dataCells.numbers)
+for bioCell = 1:numel(dataCells.cellIdx)
     EllipseRealCenter(bioCell,:) = dataCells.cellContour3D{bioCell}.ellipseReal.center;
 end
 tableOutputDeproj.EllipseRealCenter = EllipseRealCenter;
 
 %% Cell areas
-for bioCell = 1:numel(dataCells.numbers)
+for bioCell = 1:numel(dataCells.cellIdx)
     areaEllReal(bioCell) = dataCells.cellContour3D{bioCell}.ellipseRotViaOri.areaEllipse;
     areaEllProj(bioCell) = dataCells.cellContour2D{bioCell}.ellipseProj.areaEllipse;
 end
@@ -25,26 +25,26 @@ tableOutputDeproj.AreaReal = cell2mat(dataCells.area.areaRealTot);
 tableOutputDeproj.AreaProj = cell2mat(dataCells.area.areaProjTot);
 tableOutputDeproj.AreaEllReal = areaEllReal';
 tableOutputDeproj.AreaEllProj = areaEllProj';
-tableOutputBell.AreaBell = dataSeg.CELLS.areas(dataCells.numbers);
+% tableOutputBell.AreaBell = dataSeg.CELLS.areas(dataCells.cellIdx);
 
 %% Cell neighbours
-tableOutputDeproj.nbrNeighbours = dataSeg.CELLS.n_neighbors(dataCells.numbers);
-tableOutputBell.nbrNeighbours = dataSeg.CELLS.n_neighbors(dataCells.numbers);
+% tableOutputDeproj.nbrNeighbours = dataSeg.CELLS.n_neighbors(dataCells.cellIdx);
+% tableOutputBell.nbrNeighbours = dataSeg.CELLS.n_neighbors(dataCells.cellIdx);
 
 %% Cell anisotropy (Bellaiche style) % Change for precalculated values !
-for bioCell = 1:numel(dataCells.numbers)
+for bioCell = 1:numel(dataCells.cellIdx)
     elongationReal(bioCell) = dataCells.cellContour3D{bioCell}.ellipseRotViaOri.semiMajAx / ...
         dataCells.cellContour3D{bioCell}.ellipseRotViaOri.semiMinAx;
     elongationProj(bioCell) = dataCells.cellContour2D{bioCell}.ellipseProj.semiMajAx / ...
         dataCells.cellContour2D{bioCell}.ellipseProj.semiMinAx;
-    elongationBell(bioCell) = dataSeg.CELLS.anisotropies(dataCells.numbers(bioCell));
+%     elongationBell(bioCell) = dataSeg.CELLS.anisotropies(dataCells.cellIdx(bioCell));
 end
 tableOutputDeproj.anisostropyReal = 1-1./elongationReal';
 tableOutputDeproj.anisotropyProj = 1-1./elongationProj';
-tableOutputBell.anisotropyBell = elongationBell';
+% tableOutputBell.anisotropyBell = elongationBell';
 
 %% Cell longer axis
-for bioCell = 1:numel(dataCells.numbers)
+for bioCell = 1:numel(dataCells.cellIdx)
     semiMajorAxisReal(bioCell) = dataCells.cellContour3D{bioCell}.ellipseRotViaOri.semiMajAx;
     semiMajorAxisProj(bioCell) = dataCells.cellContour2D{bioCell}.ellipseProj.semiMajAx;
 end
@@ -52,19 +52,19 @@ tableOutputDeproj.semiMajAxisReal = semiMajorAxisReal';
 tableOutputDeproj.semiMajAxisProj = semiMajorAxisProj';
 
 %% Cell angle (Projected only)
-for bioCell = 1:length(dataCells.numbers)
+for bioCell = 1:length(dataCells.cellIdx)
     %     angleReal(bioCell) =
     %     dataCells.cellContour3D{bioCell}.ellipseRotViaOri.alpha; => Not
     %     calculated yet
     angleProj(bioCell) = dataCells.cellContour2D{bioCell}.ellipseProj.alpha;
-    angleBell(bioCell) = dataSeg.CELLS.orientations(dataCells.numbers(bioCell));
+%     angleBell(bioCell) = dataSeg.CELLS.orientations(dataCells.cellIdx(bioCell));
 end
 % tableOutputDeproj.angleReal = angleReal';
 tableOutputDeproj.angleProj = angleProj';
-tableOutputBell.angleBell = angleBell';
+% tableOutputBell.angleBell = angleBell';
 
 %% Cell orientation real
-for bioCell = 1:numel(dataCells.numbers) % Only keep the end point of the vector. The beginning is the ellipse center
+for bioCell = 1:numel(dataCells.cellIdx) % Only keep the end point of the vector. The beginning is the ellipse center
     if isnan(dataCells.cellContour3D{bioCell}.ellipseReal.normOrientation(1,1))
         EllipseRealOrient(bioCell,:) = dataCells.cellContour3D{bioCell}.ellipseReal.normOrientation(1,1);
     else
@@ -75,7 +75,7 @@ end
 tableOutputDeproj.EllipseRealOrient = EllipseRealOrient;
 
 %% Cell perimeters
-for bioCell = 1:length(dataCells.numbers)
+for bioCell = 1:length(dataCells.cellIdx)
     perimeterReal(bioCell) = dataCells.cellContour3D{bioCell}.perimeterReal;
     perimeterProj(bioCell) = dataCells.cellContour2D{bioCell}.perimeterProj;
     perimeterEllipseReal(bioCell) = dataCells.cellContour3D{bioCell}.ellipseRotViaOri.perimeterEllipse;
@@ -83,13 +83,13 @@ end
 tableOutputDeproj.perimeterReal = perimeterReal';
 tableOutputDeproj.perimeterProj = perimeterProj';
 tableOutputDeproj.perimeterEllipseReal = perimeterEllipseReal';
-tableOutputBell.perimeterBell = dataSeg.CELLS.perimeters(dataCells.numbers);
+% tableOutputBell.perimeterBell = dataSeg.CELLS.perimeters(dataCells.cellIdx);
 
 %% Field naming
 tableOutputDeproj.Properties.VariableNames = {'cellID' 'centerEllipseReal' 'AreaReal' 'AreaProj' 'AreaEllipseReal' 'AreaEllipseProj'...
-    'NbrNeighbours' 'AnisotropyReal' 'AnisotropyProj' 'semiMajAxReal' 'semiMajAxProj' 'AngleProj' 'OrientationEllipseReal'...
+    'AnisotropyReal' 'AnisotropyProj' 'semiMajAxReal' 'semiMajAxProj' 'AngleProj' 'OrientationEllipseReal'...
     'PerimeterReal' 'PerimeterProj' 'PerimeterEllipseReal'};
-tableOutputBell.Properties.VariableNames = {'cellID' 'AreaBell' 'NbrNeighbours' 'AnisotropyBell' 'AngleBell'...
-    'PerimeterBell'};
+% tableOutputBell.Properties.VariableNames = {'cellID' 'AreaBell' 'NbrNeighbours' 'AnisotropyBell' 'AngleBell'...
+%     'PerimeterBell'};
 
 end