New function for Slice plotting added. Bug fixing in iso lines plotter.

matRad/plotting/matRad_plotIsoDoseLines.m

@@ -58,11 +58,11 @@
 %fly
 if isempty(isoContours)
     if plane == 1
-        C = contourc(doseCube(slice,:,:),isoLevels);
+        C = contourc(squeeze(doseCube(slice,:,:)),isoLevels);
     elseif plane == 2
-        C = contourc(doseCube(:,slice,:),isoLevels);
+        C = contourc(squeeze(doseCube(:,slice,:)),isoLevels);
     elseif plane == 3
-        C = contourc(doseCube(:,:,slice),isoLevels);
+        C = contourc(squeeze(doseCube(:,:,slice)),isoLevels);
     end    
     isoContours{slice,plane} = C;
 end

matRad/util/matRad_plotSlice.m

@@ -0,0 +1,215 @@
+function [hCMap,hDose,hCt,hContour,hIsoDose] = matRad_plotSlice(ct, varargin)
+% matRad tool function to directly plot a complete slice of a ct with dose
+% optionally including contours and isolines
+%
+% call
+% [] = matRad_plotSlice(ct, dose, varargin)
+%
+% input (required)
+%   ct              matRad ct struct
+%   dose            dose cube
+%
+% input (optional/empty) to be called as Name-value pair arguments:
+%   axesHandle      handle to axes the slice should be displayed in
+%   cst             matRad cst struct
+%   cubeIdx         Index of the desired cube in the ct struct
+%   plane           plane view (coronal=1,sagittal=2,axial=3)
+%   slice           slice in the selected plane of the 3D cube
+%   thresh          threshold for display of dose values
+%   alpha           alpha value for the dose overlay
+%   contourColorMap colormap for the VOI contours
+%   doseColorMap    colormap for the dose
+%   doseWindow      dose value window
+%   doseIsoLevels   levels defining the isodose contours
+%   voiSelection    logicals defining the current selection of contours
+%                   that should be plotted. Can be set to [] to plot
+%                   all non-ignored contours.
+%   colorBarLabel   string defining the yLabel of the colorBar
+%   boolPlotLegend  boolean if legend should be plottet or not
+%   varargin        Additional MATLAB Line or Text Properties (e.g. 'LineWidth', 'FontSize', etc.)
+%
+%
+% 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/LICENSE.md. 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.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+defaultDose             = [];
+defaultCst              = [];
+defaultSlice            = floor(min(ct.cubeDim)./2);
+defaultAxesHandle       = gca;
+defaultCubeIdx          = 1;
+defaultPlane            = 1;
+defaultDoseWindow       = [];
+defaultThresh           = [];
+defaultAlpha            = [];
+defaultDoseColorMap     = jet;
+defaultDoseIsoLevels    = [];
+defaultVOIselection     = [];
+defaultContourColorMap  = [];
+defaultBoolPlotLegend   = false;
+defaultColorBarLabel    = [];
+defaultShowCt           = true;
+
+isDose              = @(x) isnumeric(x) && all(size(x) == ct.cubeDim);
+isSlice             = @(x) x>=1 && x<=max(ct.cubeDim) && floor(x)==x;
+isAxes              = @(x) strcmp(get(gca, 'type'), 'axes');
+isCubeIdx           = @(x) isscalar(x);
+isPlane             = @(x) isscalar(x) && (sum(x==[1, 2, 3])==1);
+isDoseWindow        = @(x) (length(x) == 2 && isvector(x));
+isThresh            = @(x) (isscalar(x) && (x>=0) && (x<=1)) || isempty(x);
+isAlpha             = @(x) isscalar(x) && (x>=0) && (x<=1) || isempty(x);
+isDoseColorMap      = @(x) isnumeric(x) && (size(x, 2)==3) &&  all(x(:) >= 0) && all(x(:) <= 1);
+isDoseIsoLevels     = @(x) isnumeric(x) && isvector(x)|| isempty(x);
+isVOIselection      = @(x) isnumeric(x) || isempty(x); %all(x(:)==1 | x(:)==0) || isempty(x);
+isContourColorMap   = @(x) isnumeric(x) && (size(x, 2)==3) && size(x, 1)>=2 && all(x(:) >= 0) && all(x(:) <= 1);
+isBoolPlotLegend    = @(x) x==0 || x ==1;
+isColorBarLabel     = @(x) isstring(x) || ischar(x) || isempty(x);
+isShowCt            = @(x) isscalar(x) && (x==0) || (x==1);
+
+p = inputParser;
+p.KeepUnmatched = true;
+addRequired(p, 'ct')
+
+addParameter(p, 'dose', defaultDose, isDose)
+addParameter(p, 'cst', defaultCst)
+addParameter(p, 'slice', defaultSlice, isSlice)
+addParameter(p, 'axesHandle', defaultAxesHandle, isAxes)
+addParameter(p, 'cubeIdx', defaultCubeIdx, isCubeIdx)
+addParameter(p, 'plane', defaultPlane, isPlane)
+addParameter(p, 'doseWindow', defaultDoseWindow, isDoseWindow)
+addParameter(p, 'thresh', defaultThresh, isThresh)
+addParameter(p, 'alpha', defaultAlpha, isAlpha)
+addParameter(p, 'doseColorMap', defaultDoseColorMap, isDoseColorMap)
+addParameter(p, 'doseIsoLevels', defaultDoseIsoLevels, isDoseIsoLevels)
+addParameter(p, 'voiSelection', defaultVOIselection, isVOIselection)
+addParameter(p, 'contourColorMap', defaultContourColorMap, isContourColorMap)
+addParameter(p, 'boolPlotLegend', defaultBoolPlotLegend, isBoolPlotLegend)
+addParameter(p, 'colorBarLabel', defaultColorBarLabel, isColorBarLabel)
+addParameter(p, 'showCt', defaultShowCt, isShowCt)
+
+parse(p, ct, varargin{:});
+
+%% Unmatched properties
+% General properties
+lineFieldNames = fieldnames(set(line));
+textFieldNames = fieldnames(set(text));
+% Filter line properties from Unmatched
+unmParamNames = fieldnames(p.Unmatched);
+lineFields = unmParamNames(ismember(unmParamNames, lineFieldNames));
+lineValues = struct2cell(p.Unmatched);
+lineValues = lineValues(ismember(unmParamNames, lineFieldNames));
+lineVarargin = reshape([lineFields, lineValues]', 1, []);
+% Filter text properites from Unmatched
+textFields = unmParamNames(ismember(unmParamNames, textFieldNames));
+textValues = struct2cell(p.Unmatched);
+textValues = textValues(ismember(unmParamNames, textFieldNames));
+textVarargin = reshape([textFields, textValues]', 1, []);
+
+%% Plot ct slice
+matRad_cfg = MatRad_Config.instance();
+
+% Flip axes direction
+set(p.Results.axesHandle,'YDir','Reverse');
+% plot ct slice
+if p.Results.showCt
+    hCt = matRad_plotCtSlice(p.Results.axesHandle,p.Results.ct.cubeHU,p.Results.cubeIdx,p.Results.plane,p.Results.slice, [], []);
+else
+    %figure()
+end
+hold on;
+
+%% Plot dose
+if ~isempty(p.Results.dose)
+    if ~isempty(p.Results.doseWindow) && p.Results.doseWindow(2) - p.Results.doseWindow(1) <= 0
+        p.Results.doseWindow = [0 2];
+    end
+
+    [hDose,doseColorMap,doseWindow] = matRad_plotDoseSlice(p.Results.axesHandle, p.Results.dose, p.Results.plane, p.Results.slice, p.Results.thresh, p.Results.alpha, p.Results.doseColorMap, p.Results.doseWindow);
+
+    %% Plot iso dose lines
+    if ~isempty(p.Results.doseIsoLevels)
+        hIsoDose = matRad_plotIsoDoseLines(p.Results.axesHandle,p.Results.dose,[],p.Results.doseIsoLevels,false,p.Results.plane,p.Results.slice,p.Results.doseColorMap,p.Results.doseWindow, lineVarargin{:});
+        hold on;
+    else
+        hIsoDose = [];
+    end
+
+    %% Set Colorbar
+    hCMap = matRad_plotColorbar(p.Results.axesHandle,doseColorMap,doseWindow,'Location','EastOutside');
+    set(hCMap,'Color',matRad_cfg.gui.textColor);
+    if ~isempty(p.Results.colorBarLabel)
+        set(get(hCMap,'YLabel'),'String', p.Results.colorBarLabel,'FontSize',matRad_cfg.gui.fontSize);
+    end
+    set(get(hCMap,'YLabel'),'String', p.Results.colorBarLabel, textVarargin{:});
+end
+%% Plot VOI contours & Legend
+
+if  ~isempty(p.Results.cst)
+    [hContour,~] = matRad_plotVoiContourSlice(p.Results.axesHandle, p.Results.cst, p.Results.ct, p.Results.cubeIdx, p.Results.voiSelection, p.Results.plane, p.Results.slice, p.Results.contourColorMap, lineVarargin{:});
+
+    if p.Results.boolPlotLegend
+        visibleOnSlice = (~cellfun(@isempty,hContour));
+        ixLegend = find(p.Results.voiSelection);
+        hContourTmp    = cellfun(@(X) X(1),hContour(visibleOnSlice),'UniformOutput',false);
+        if ~isempty(p.Results.voiSelection)
+            hLegend        =  legend(p.Results.axesHandle,[hContourTmp{:}],[p.Results.cst(ixLegend(visibleOnSlice),2)],'AutoUpdate','off','TextColor',matRad_cfg.gui.textColor);
+        else
+            hLegend        =  legend(p.Results.axesHandle,[hContourTmp{:}],[p.Results.cst(visibleOnSlice,2)],'AutoUpdate','off','TextColor',matRad_cfg.gui.textColor);
+        end
+        set(hLegend,'Box','On');
+        set(hLegend,'TextColor',matRad_cfg.gui.textColor);
+        if ~isempty(textVarargin)
+            set(hLegend, textVarargin{:});
+        else
+            set(hLegend,'FontSize',matRad_cfg.gui.fontSize);
+        end
+    end
+else
+    hContour = [];
+end
+
+%% Adjust axes
+axis(p.Results.axesHandle,'tight');
+set(p.Results.axesHandle,'xtick',[],'ytick',[]);
+colormap(p.Results.axesHandle,p.Results.doseColorMap);
+
+if isfield(p.Unmatched, 'FontSize')
+    matRad_plotAxisLabels(p.Results.axesHandle,p.Results.ct,p.Results.plane,p.Results.slice, p.Unmatched.FontSize, [])
+else
+    matRad_plotAxisLabels(p.Results.axesHandle,p.Results.ct,p.Results.plane,p.Results.slice, [], [])
+end
+
+% Set axis ratio.
+ratios = [1/p.Results.ct.resolution.x 1/p.Results.ct.resolution.y 1/p.Results.ct.resolution.z];
+
+set(p.Results.axesHandle,'DataAspectRatioMode','manual');
+if p.Results.plane == 1
+    res = [ratios(3) ratios(2)]./max([ratios(3) ratios(2)]);
+    set(p.Results.axesHandle,'DataAspectRatio',[res 1])
+elseif p.Results.plane == 2 % sagittal plane
+    res = [ratios(3) ratios(1)]./max([ratios(3) ratios(1)]);
+    set(p.Results.axesHandle,'DataAspectRatio',[res 1])
+elseif  p.Results.plane == 3 % Axial plane
+    res = [ratios(2) ratios(1)]./max([ratios(2) ratios(1)]);
+    set(p.Results.axesHandle,'DataAspectRatio',[res 1])
+end
+
+%% Set text properties
+if ~isempty(textVarargin)
+    set(p.Results.axesHandle, textVarargin{:})
+    set(p.Results.axesHandle.Title, textVarargin{:})
+end
+
+end

matRad/util/matRad_plotSliceWrapper.m

@@ -63,6 +63,8 @@
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+warning('Deprecation warning: matRad_plotSliceWrapper is deprecated. Using matRad_plot_Slice instead');
+
 % Handle the argument list
 if ~exist('thresh','var') || isempty(thresh)
     thresh = [];
@@ -101,6 +103,11 @@
 
 matRad_cfg = MatRad_Config.instance();
 
+warning('Deprecation warning: matRad_plotSliceWrapper is deprecated. Using matRad_plot_Slice instead');
+
+[hCMap,hDose,hCt,hContour,hIsoDose] = matRad_plotSlice(ct, 'axesHandle', axesHandle, 'cst', cst, 'cubeIdx', cubeIdx, 'dose', dose, 'plane', plane, 'slice', slice,'thresh', thresh, 'alpha', alpha, 'contourColorMap', contourColorMap, 'doseColorMap', doseColorMap, 'doseWindow', doseWindow, 'doseIsoLevels', doseIsoLevels, 'voiSelection', voiSelection, 'colorBarLabel', colorBarLabel, 'boolPlotLegend', boolPlotLegend, 'others', varargin);
+
+%{
 set(axesHandle,'YDir','Reverse');
 % plot ct slice
 hCt = matRad_plotCtSlice(axesHandle,ct.cubeHU,cubeIdx,plane,slice); 
@@ -171,6 +178,6 @@
 if ~isempty(colorBarLabel)
     set(get(hCMap,'YLabel'),'String', colorBarLabel,'FontSize',matRad_cfg.gui.fontSize);
 end
-
+%}
 end