Dev rc/v3 bug fix (#785)

* Minor bug, update cube dimension in writeMHD to make dimension permeutation effective

* Minor bug fix, misisng matRad_cfg

* Modify use of cube permutation and transformation matrix

* Add permutation to vtk writer

---------

Co-authored-by: Niklas Wahl <[email protected]>

matRad/IO/matRad_readMHD.m

@@ -68,9 +68,15 @@
 T = zeros(3);
 T(:) = cell2mat(tmp);
 
+if ~isequal(T, diag(ones(1,numel(dimensions))))
+    matRad_cfg.dispWarning('Non identity transformation matrix detected in the loaded cube. This might lead to reconstruction inconsistency.')
+end
+
 % Apply Matlab permutation
+% This ensures that the cube is reverted back to the matLab standard
+% indexing
 Tmatlab = [0 1 0; 1 0 0; 0 0 1];
-%T = T * [0 1 0; 1 0 0; 0 0 1];
+T = T*Tmatlab;
 
 % get data type
 idx = find(~cellfun(@isempty,strfind(s{1}, 'ElementType')),1,'first');
@@ -84,20 +90,18 @@
     fseek(headerFileHandle,-S.bytes*prod(dimensions),'eof');
     cube = fread(headerFileHandle,prod(dimensions),type,endian);
     cube = reshape(cube,dimensions);
-    cube = permute(cube,[2 1 3]);
-    %matRad_cfg.dispError('MHA not implemented!');
+    cube = permute(cube,abs([1 2 3]*T));
 else
     %% read data
     [filepath,~,~] = fileparts(filename);
     dataFileHandle = fopen(fullfile(filepath,dataFilename),'r');
     cube = reshape(fread(dataFileHandle,inf,type,endian),dimensions);
-    cube = permute(cube,[2 1 3]);
-    %cube = flip(cube,1);
+    cube = permute(cube,abs([1 2 3]*T));
     fclose(dataFileHandle);
 end
 fclose(headerFileHandle);
 metadata.resolution = resolution;
-metadata.cubeDim = dimensions * Tmatlab;
+metadata.cubeDim = dimensions * T;
 
 end
 

matRad/IO/matRad_writeMHA.m

@@ -48,15 +48,28 @@ function matRad_writeMHA(filepath,cube,metadata)
 %cleaner = onCleanup(@() fclose(fid));
 
 %We perform the permutation
-if isfield(metadata,'axisPermutation')
-    cube = permute(cube,metadata.axisPermutation);
+if ~isfield(metadata, 'axisPermutation')
+    % This reverts the matRlab conventianl indexing
+    axisPermutation = [2,1,3];
+elseif ~isequal(metadata.axisPermutation, [2,1,3])
+    matRad_cfg.dispWarning('Unconventianal permutation of patient indexing, this might cause inconsistency');
+    axisPermutation = metadata.axisPermutation;
 end
 
-%Set up Transform Matrix
-T=zeros(4);
-ixOnes = sub2ind([4 4],metadata.axisPermutation,[1 2 3]);
-T(ixOnes) = 1;
-T(4,4) = 1;
+% Force the permutation here according to the axis permutation
+cube = permute(cube, axisPermutation);
+
+% Need to permute the dimensions as well
+dimensions = size(cube);
+
+% Note in the cube permutation:
+% Permutation of the cube is enforced here to standdard indexing so that
+% reconstruction of the cube for further use does not rely on the use of 
+% a transformation matrix, which is now only the identity matrix.
+
+%The transformation matrix is now the unit matrix
+transformMatrix = diag(ones(1,numel(dimensions)));
+tmString = sprintf(' %d',transformMatrix(:));
 
 %Correct for coordinate system
 switch metadata.coordinateSystem
@@ -68,12 +81,6 @@ function matRad_writeMHA(filepath,cube,metadata)
         matRad_cfg.dispError('Only LPS currently supported for export!');
 end
 
-%Now add Translation
-%The transformation matrix is now the unit matrix
-%transformMatrix = diag(ones(1,numel(dimensions)));
-%tmString = sprintf(' %d',transformMatrix(:));
-
-tmString = sprintf(' %d',T(1:3,1:3));
 
 %Determine the endian
 [~,~,endian] = computer;

matRad/IO/matRad_writeMHD.m

@@ -47,9 +47,25 @@ function matRad_writeMHD(filepath,cube,metadata)
 end
 
 %We perform the permutation
-if isfield(metadata,'axisPermutation')
-    cube = permute(cube,metadata.axisPermutation);
+if ~isfield(metadata, 'axisPermutation')
+    % This reverts the matRlab conventianl indexing
+    axisPermutation = [2,1,3];
+elseif ~isequal(metadata.axisPermutation, [2,1,3])
+    matRad_cfg.dispWarning('Unconventianal permutation of patient indexing, this might cause inconsistency');
+    axisPermutation = metadata.axisPermutation;
 end
+
+% Force the permutation here according to the axis permutation
+cube = permute(cube, axisPermutation);
+
+% Need to permute the dimensions as well
+dimensions = size(cube);
+
+% Note in the cube permutation:
+% Permutation of the cube is enforced here to standdard indexing so that
+% reconstruction of the cube for further use does not rely on the use of 
+% a transformation matrix, which is now only the identity matrix.
+
 %The transformation matrix is now the unit matrix
 transformMatrix = diag(ones(1,numel(dimensions)));
 tmString = sprintf(' %d',transformMatrix(:));

matRad/IO/matRad_writeVTK.m

@@ -44,11 +44,20 @@ function matRad_writeVTK(filepath,cube,metadata)
 end
 cleaner = onCleanup(@() fclose(fid));
 
-%We perform 
-if isfield(metadata,'axisPermutation')
-    cube = permute(cube,metadata.axisPermutation);
+%We perform the permutation
+if ~isfield(metadata, 'axisPermutation')
+    % This reverts the matRlab conventianl indexing
+    axisPermutation = [2,1,3];
+elseif ~isequal(metadata.axisPermutation, [2,1,3])
+    matRad_cfg.dispWarning('Unconventianal permutation of patient indexing, this might cause inconsistency');
+    axisPermutation = metadata.axisPermutation;
 end
 
+% Force the permutation here according to the axis permutation
+cube = permute(cube, axisPermutation);
+
+% Need to permute the dimensions as well
+dimensions = size(cube);
 
 fprintf(fid, '# vtk DataFile Version 3.0\n');
 fprintf(fid, 'vtk output\n');

matRad/steering/matRad_StfGeneratorBase.m

@@ -227,7 +227,7 @@ function assignPropertiesFromPln(this,pln,warnWhenPropertyChanged)
     methods (Access = protected)
         function initialize(this)
             %Do nothing
-
+            matRad_cfg = MatRad_Config.instance();
             % get machine
             if ~isstruct(this.machine)
                 try