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Commit effebd90 authored by Sebastien Herbert's avatar Sebastien Herbert
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Adapt for previous changes

parent cfd62f5a
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......@@ -46,7 +46,7 @@ if nargin == 0
% Define axial step size (in um)
PARAMS.imSettings.axPixSize = 0.5; % axial voxel size (in um)
PARAMS.imSettings.latPixSize = 0.2076; % lateral voxel size (in um)
PARAMS.imSettings.latPixSize = 0.183; % lateral voxel size (in um)
PARAMS.maxTiffImSize = 40000; % Limit the input image size when using an elevation map (in pix)
PARAMS.maxFaces = 300; % If need be, reduce the maximum number of faces for the mesh
......@@ -190,7 +190,7 @@ dataCells = checkCoverage(dataCells, dataCurv, dataSeg, PARAMS);
dataCells = cell2ellipse(dataCells, dataCurv, PARAMS);
%% Create a table output
[tableOutputDeproj, tableOutputBell] = formatTableOuputSurfaceCombine(dataCells, dataSeg);
tableOutputDeproj = formatTableOuputSurfaceCombine(dataCells, dataSeg);
%% Saving output
save([PARAMS.outputFolder filesep 'deprojectedData.mat'],...
......@@ -629,19 +629,21 @@ for bioCell = 1:numel(dataCells.cellIdx)
end
dataCells.cellContour3D = dataCells.cellContour3D';
% And the 2D sides on the mesh
dataCells.VERTICES.XYZs = zeros(size(dataSeg.VERTICES.XYs,1),3);
dataCells.VERTICES.XYZs = dataSeg.VERTICES.XYs;
for vertex = 1:length(dataCells.VERTICES.vertexOnFace)
if dataCells.VERTICES.vertexOnFace(vertex)==0
% when the vertex is not under the mesh, keep its z position at 0
continue
if PARAMS.deployJunctNet
% And the 2D sides on the mesh
dataCells.VERTICES.XYZs = zeros(size(dataSeg.VERTICES.XYs,1),3);
dataCells.VERTICES.XYZs = dataSeg.VERTICES.XYs;
for vertex = 1:length(dataCells.VERTICES.vertexOnFace)
if dataCells.VERTICES.vertexOnFace(vertex)==0
% when the vertex is not under the mesh, keep its z position at 0
continue
end
dataCells.VERTICES.XYZs(vertex,3) = horzcat(dataCells.VERTICES.XYZs(vertex,1:2),ones(1)) * ...
dataCurv.planeCoefPerFace(dataCells.VERTICES.vertexOnFace(vertex),:)';
end
dataCells.VERTICES.XYZs(vertex,3) = horzcat(dataCells.VERTICES.XYZs(vertex,1:2),ones(1)) * ...
dataCurv.planeCoefPerFace(dataCells.VERTICES.vertexOnFace(vertex),:)';
end
displayDeprojected(PARAMS,dataCurv,dataCells)
displayDeprojected(PARAMS,dataCurv,dataCells)
end
end
......
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