matRad function that plots isolines in 3D, by precomputed contourc data
computed by matRad_computeIsoDoseContours or manually by calling
contourslice itself
call
isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice)
isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap)
isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,window)
isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap,window)
isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap,window, ...)
input
axesHandle handle to axes the slice should be displayed in
ct matRad ct struct which contains resolution
doseCube 3D array of the corresponding dose cube
isoContours precomputed isodose contours in a cell array {maxDim,3}
if the parameter is empty, contours will be plotted the
slow way with MATLABs contour function
isoLevels the levels of the isodose (same units as doseCube)
plane plane view (coronal=1,sagittal=2,axial=3)
slice slice in the selected plane of the 3D cube
cMap optional argument defining the colormap, default is jet
if you want to use the default map with the window argument
you can use an empty array []
window optional argument defining the displayed range. default is
[min(doseCube(:)) max(doseCube(:))]
varargin Additional Matlab Line-Property/value pairs
output
isoLineHandles: handle to the plotted isolines
References
-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Copyright 2015 the matRad development team.
This file is part of the matRad project. It is subject to the license
terms in the LICENSE file found in the top-level directory of this
distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
of the matRad project, including this file, may be copied, modified,
propagated, or distributed except according to the terms contained in the
LICENSE file.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%0001 function isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap,window,varargin) 0002 % matRad function that plots isolines in 3D, by precomputed contourc data 0003 % computed by matRad_computeIsoDoseContours or manually by calling 0004 % contourslice itself 0005 % 0006 % call 0007 % isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice) 0008 % isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap) 0009 % isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,window) 0010 % isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap,window) 0011 % isoLineHandles = matRad_plotIsoDoseLines3D(axesHandle,ct,doseCube,isoContours,isoLevels,plane,slice,cMap,window, ...) 0012 % 0013 % input 0014 % axesHandle handle to axes the slice should be displayed in 0015 % ct matRad ct struct which contains resolution 0016 % doseCube 3D array of the corresponding dose cube 0017 % isoContours precomputed isodose contours in a cell array {maxDim,3} 0018 % if the parameter is empty, contours will be plotted the 0019 % slow way with MATLABs contour function 0020 % isoLevels the levels of the isodose (same units as doseCube) 0021 % plane plane view (coronal=1,sagittal=2,axial=3) 0022 % slice slice in the selected plane of the 3D cube 0023 % cMap optional argument defining the colormap, default is jet 0024 % if you want to use the default map with the window argument 0025 % you can use an empty array [] 0026 % window optional argument defining the displayed range. default is 0027 % [min(doseCube(:)) max(doseCube(:))] 0028 % varargin Additional Matlab Line-Property/value pairs 0029 % 0030 % output 0031 % isoLineHandles: handle to the plotted isolines 0032 % 0033 % References 0034 % - 0035 % 0036 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0037 % 0038 % Copyright 2015 the matRad development team. 0039 % 0040 % This file is part of the matRad project. It is subject to the license 0041 % terms in the LICENSE file found in the top-level directory of this 0042 % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part 0043 % of the matRad project, including this file, may be copied, modified, 0044 % propagated, or distributed except according to the terms contained in the 0045 % LICENSE file. 0046 % 0047 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0048 0049 matRad_cfg = MatRad_Config.instance(); 0050 0051 %% manage optional arguments 0052 %Use default colormap? 0053 if nargin < 7 || isempty(cMap) 0054 cMap = jet(64); 0055 end 0056 if nargin < 8 || isempty(window) 0057 window = [min(doseCube(:)) max(doseCube(:))]; 0058 end 0059 0060 cMapScale = size(cMap,1) - 1; 0061 isoColorLevel = uint8(cMapScale*(isoLevels - window(1))./(window(2)-window(1))); 0062 0063 %This circumenvents a bug in Octave when the index in the image hase the maximum value of uint8 0064 if matRad_cfg.isOctave 0065 isoColorLevel(isoColorLevel == 255) = 254; 0066 isoLineHandles = []; 0067 elseif matRad_cfg.isMatlab 0068 isoLineHandles = gobjects(0); 0069 end 0070 0071 colors = squeeze(ind2rgb(isoColorLevel,cMap)); 0072 0073 slices = {[],[],[]}; 0074 0075 coords{1} = ct.resolution.x * double(1:ct.cubeDim(2)); 0076 coords{2} = ct.resolution.y * double(1:ct.cubeDim(1)); 0077 coords{3} = ct.resolution.z * double(1:ct.cubeDim(3)); 0078 0079 %slice spacing 0080 spacing = 5; 0081 sliceIndices = [1:spacing:ct.cubeDim(plane)]; 0082 if isempty(sliceIndices(sliceIndices==slice)) 0083 sliceIndices(end+1) = slice; 0084 sort(sliceIndices); 0085 end 0086 slices{plane} = coords{plane}(sliceIndices); 0087 0088 %% Plotting 0089 %Check if precomputed contours where passed, if not, calculate it on the 0090 %fly 0091 if isempty(isoContours) 0092 0093 [xMesh,yMesh,zMesh] = meshgrid(coords{1},coords{2},coords{3}); 0094 isoLineHandles = contourslice(axesHandle,xMesh,yMesh,zMesh,doseCube,slices{[1 2 3]},isoLevels); 0095 else 0096 axes(axesHandle); 0097 hold on; 0098 0099 for s = 1:numel(sliceIndices) 0100 currSlice = sliceIndices(s); 0101 currSlicePlaneCoords = slices{plane}(s); 0102 0103 %opacity of the isolines. Will be fully opaque if we are on the 0104 %requested (and shown) slice 0105 if currSlice == slice 0106 opacity = 1; 0107 else 0108 opacity = 0.4; 0109 end 0110 0111 %Check if there is a contour in the plane 0112 if any(isoContours{currSlice,plane}(:)) 0113 % plot precalculated contourc data 0114 lower = 1; % lower marks the beginning of a section 0115 while lower-1 ~= size(isoContours{currSlice,plane},2) 0116 steps = isoContours{currSlice,plane}(2,lower); % number of elements of current line section 0117 if numel(unique(isoLevels)) > 1 0118 color = colors(isoLevels(:) == isoContours{currSlice,plane}(1,lower),:); 0119 else 0120 color = unique(colors,'rows'); 0121 end 0122 0123 % Align 2D Contours in3D 0124 isoLine2Dx = isoContours{currSlice,plane}(1,lower+1:lower+steps); 0125 isoLine2Dy = isoContours{currSlice,plane}(2,lower+1:lower+steps); 0126 if plane == 2 0127 isoLine3Dx = currSlicePlaneCoords*ones(1,numel(isoLine2Dx)); 0128 isoLine3Dz = interp1(double(1:ct.cubeDim(3)),coords{3},isoLine2Dx); 0129 isoLine3Dy = interp1(double(1:ct.cubeDim(1)),coords{1},isoLine2Dy); 0130 elseif plane == 1 0131 isoLine3Dy = currSlicePlaneCoords*ones(1,numel(isoLine2Dx)); 0132 isoLine3Dx = interp1(double(1:ct.cubeDim(2)),coords{2},isoLine2Dy); 0133 isoLine3Dz = interp1(double(1:ct.cubeDim(3)),coords{3},isoLine2Dx); 0134 elseif plane == 3 0135 isoLine3Dz = currSlicePlaneCoords*ones(1,numel(isoLine2Dx)); 0136 isoLine3Dx = interp1(double(1:ct.cubeDim(2)),coords{2},isoLine2Dx); 0137 isoLine3Dy = interp1(double(1:ct.cubeDim(1)),coords{1},isoLine2Dy); 0138 else 0139 continue; 0140 end 0141 0142 %We render the isodose lines transparent by adding a fourth color value (undocumented) 0143 if verLessThan('matlab','8.5') 0144 isoLineHandles(end+1) = line(isoLine3Dx,isoLine3Dy,isoLine3Dz,'Color',[color ],'Parent',axesHandle,varargin{:}); 0145 else 0146 isoLineHandles(end+1) = line(isoLine3Dx,isoLine3Dy,isoLine3Dz,'Color',[color opacity],'Parent',axesHandle,varargin{:}); 0147 end 0148 %We do not plot labels 0149 %{ 0150 if plotLabels 0151 text(isoLine3Dx,isoLine3Dy,isoLine3Dz,num2str(isoContours{currSlice,plane}(1,lower)),'Parent',axesHandle); 0152 end 0153 %} 0154 lower = lower+steps+1; 0155 0156 end 0157 end 0158 end 0159 0160 hold off; 0161 end 0162 0163 end