matRad function that generates a dose plot of a selected slice
The function can also be used in personal matlab figures by passing the
corresponding axes handle.
call
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,cMap)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,window)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,cMap)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,window)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,cMap,window)
[doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,cMap,window)
input
axesHandle handle to axes the slice should be displayed in
doseCube 3D array of the dose to select the slice from
plane plane view (coronal=1,sagittal=2,axial=3)
slice slice in the selected plane of the 3D cube
threshold threshold above which the dose shall be displayed
for negative values (i.e. difference maps), also the values
smaller than the negative threshold will be displayed
if empty, no threshold will be applied
alpha optional argument defining the alpha value, default is 0.6.
To use the default when providing a custom culormap, put in
an empty array by [].
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(:))]
output
doseHandle: handle of the plotted dose axes
cMap used colormap (same as input if set)
window used window (same as input if set)
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 [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle,doseCube,plane,slice,threshold,alpha,cMap,window) 0002 % matRad function that generates a dose plot of a selected slice 0003 % The function can also be used in personal matlab figures by passing the 0004 % corresponding axes handle. 0005 % 0006 % call 0007 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold) 0008 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha) 0009 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,cMap) 0010 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,window) 0011 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,cMap) 0012 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,window) 0013 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,cMap,window) 0014 % [doseHandle,cMap,window] = matRad_plotDoseSlice(axesHandle, doseCube,plane,slice,threshold,alpha,cMap,window) 0015 % 0016 % input 0017 % axesHandle handle to axes the slice should be displayed in 0018 % doseCube 3D array of the dose to select the slice from 0019 % plane plane view (coronal=1,sagittal=2,axial=3) 0020 % slice slice in the selected plane of the 3D cube 0021 % threshold threshold above which the dose shall be displayed 0022 % for negative values (i.e. difference maps), also the values 0023 % smaller than the negative threshold will be displayed 0024 % if empty, no threshold will be applied 0025 % alpha optional argument defining the alpha value, default is 0.6. 0026 % To use the default when providing a custom culormap, put in 0027 % an empty array by []. 0028 % cMap optional argument defining the colormap, default is jet 0029 % if you want to use the default map with the window argument 0030 % you can use an empty array [] 0031 % window optional argument defining the displayed range. default is 0032 % [min(doseCube(:)) max(doseCube(:))] 0033 % 0034 % output 0035 % doseHandle: handle of the plotted dose axes 0036 % cMap used colormap (same as input if set) 0037 % window used window (same as input if set) 0038 % 0039 % References 0040 % - 0041 % 0042 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0043 % 0044 % Copyright 2015 the matRad development team. 0045 % 0046 % This file is part of the matRad project. It is subject to the license 0047 % terms in the LICENSE file found in the top-level directory of this 0048 % distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part 0049 % of the matRad project, including this file, may be copied, modified, 0050 % propagated, or distributed except according to the terms contained in the 0051 % LICENSE file. 0052 % 0053 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0054 0055 matRad_cfg = MatRad_Config.instance(); 0056 0057 %Use default colormap? 0058 if nargin < 7 || isempty(cMap) 0059 cMap = jet(64); 0060 end 0061 if nargin < 6 || isempty(alpha) 0062 alpha = 0.6; 0063 end 0064 if nargin < 8 || isempty(window) 0065 window = [min(doseCube(:)) max(doseCube(:))]; 0066 end 0067 0068 maxDose = max(doseCube(:)); 0069 0070 cMapScale = size(cMap,1) - 1; 0071 0072 if plane == 1 % Coronal plane 0073 dose_slice = squeeze(doseCube(slice,:,:)); 0074 elseif plane == 2 % sagittal plane 0075 dose_slice = squeeze(doseCube(:,slice,:)); 0076 elseif plane == 3 % Axial plane 0077 dose_slice = squeeze(doseCube(:,:,slice)); 0078 else 0079 matRad_cfg.dispError('Invalid plane ''%d'' selected for visualization!',plane); 0080 end 0081 0082 if ~isempty(threshold) 0083 mask = alpha * (dose_slice < window(2) & dose_slice > window(1) & dose_slice > threshold*maxDose); 0084 else 0085 mask = alpha * (dose_slice < window(2) & dose_slice > window(1)); 0086 end 0087 0088 dose_slice = uint8(cMapScale*(dose_slice - window(1))/(window(2)-window(1))); 0089 0090 %This circumenvents a bug in Octave when the index in the image hase the maximum value of uint8 0091 if matRad_cfg.isOctave 0092 dose_slice(dose_slice == 255) = 254; 0093 end 0094 0095 dose_rgb = ind2rgb(dose_slice,cMap); 0096 0097 % plot dose distribution 0098 doseHandle = image('CData',dose_rgb,'Parent',axesHandle); 0099 0100 % alphadata for image objects is not yet implemented in Octave 0101 set(doseHandle,'AlphaData',mask); 0102 0103 end 0104 0105