New function for Slice plotting added. Bug fixing in iso lines plotter. #818
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There was a problem hiding this comment. Looks nice. I guess by calling matRad_plotSlice from the old matRad_plotSliceWrapper you also cover most of the file with tests now due to the examples. You would just need to add a few tests for, e.g., leaving out certain arguments. |
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| Original file line number | Diff line number | Diff line change |
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| 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. | ||
| % | ||
| % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
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| defaultDose = []; | ||
|
There was a problem hiding this comment. Maybe leave a comment here before the argument handling. |
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| 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; | ||
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| 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); | ||
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| p = inputParser; | ||
| p.KeepUnmatched = true; | ||
| addRequired(p, 'ct') | ||
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| 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) | ||
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| parse(p, ct, varargin{:}); | ||
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| %% 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, []); | ||
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| %% Plot ct slice | ||
| matRad_cfg = MatRad_Config.instance(); | ||
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| % 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; | ||
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| %% 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 | ||
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| [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); | ||
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| %% 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 | ||
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| %% 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 | ||
|
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| 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{:}); | ||
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| 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 | ||
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| %% Adjust axes | ||
| axis(p.Results.axesHandle,'tight'); | ||
| set(p.Results.axesHandle,'xtick',[],'ytick',[]); | ||
| colormap(p.Results.axesHandle,p.Results.doseColorMap); | ||
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| 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 | ||
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| % Set axis ratio. | ||
| ratios = [1/p.Results.ct.resolution.x 1/p.Results.ct.resolution.y 1/p.Results.ct.resolution.z]; | ||
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| 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 | ||
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| %% Set text properties | ||
| if ~isempty(textVarargin) | ||
| set(p.Results.axesHandle, textVarargin{:}) | ||
| set(p.Results.axesHandle.Title, textVarargin{:}) | ||
| end | ||
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| end | ||
|
There was a problem hiding this comment. You can remove the commented code. We don't need it anymore. |
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