diff --git a/createTestData/plotBaselines_and_fitted_spectra.m b/createTestData/plotBaselines_and_fitted_spectra.m
index 3d519c0652607eca535698b46254f40c1b20a026..100c6a07b480efbc714824961d9dca73feedd113 100644
--- a/createTestData/plotBaselines_and_fitted_spectra.m
+++ b/createTestData/plotBaselines_and_fitted_spectra.m
@@ -5,7 +5,7 @@ exportFolder = {'11 Simulations'};
pathNameExport = 'ProFit test data';
pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolder);
pathBaseExportFiles = pathBaseExportFiles(1:end-1);
-pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
+pathBaseExportFiles = [pathBaseExportFiles ' - R3_new\'];
dataExportPathBase = strcat(pathBaseExportFiles, exportFolder{1}, '\');
plotPath = [dataExportPathBase, 'Plots\BaselinePlots\'];
@@ -48,7 +48,8 @@ backgroundInlayColor = [0.8 0.8 0.8];
LineWidth = 1.5;
offsetBaseline = 7; % percent of max peak
-offsetResidual = 20; % percent of max peak
+offsetBaselineDiff = 18; % percent of max peak
+offsetResidual = 30; % percent of max peak
offsetPlots = 4; % percent of max peak
subplotGridX = 2;
subplotGridY = 2;
@@ -63,114 +64,125 @@ for indexParam = 1:length(baselines)
% figure;
figure('units','normalized','outerposition',[0.13,-0.014,0.85,0.99]); %Works on the Dell screen
end
- indexParamSorted = sortedFigure(indexParam);
- %% load data: Input data, LCModel fit, ProFit Fit
- % import the spectra but also the used concentrations and all parameters
- fileName = ['Simulated_', paramKeyword, '_', num2str(indexParamSorted) '_truncOff'];
- load([dataExportPath, fileName, '.mat'], 'summedFidWithNoise', 'current_em', 'currentConcentrationRm', ...
- 'current_pc0', 'current_pc1', 'current_df2', 'current_gm', 'current_em_std_factor', 'conc_std_factor', 'baselineScaled');
- if plot_dkntmn
- fileName = ['Simulated_', paramKeyword, '_', num2str(indexParamSorted) truncSuffix];
- [~, ~, phasedData_lcm_05, fitData_05, baselineData_lcm_05, residualData_05, ...
- ~, ~, ~, ~, ~, ~, ~, ~, ~, ~] = ...
- extractFits(dataExportPath_05,[fileName, '.coord']);
- [~, ~, phasedData_lcm_015, fitData_015, baselineData_lcm_015, residualData_015, ...
- ~, ~, ~, ~, ~, ~, ~, ~, ~, ~] = ...
- extractFits(dataExportPath_015,[fileName, '.coord']);
- end
- [nOfPoints, ppmVector_lcm, phasedData_lcm, fitData, baselineData_lcm, residualData, ...
- metaboliteNames, metaboliteData, tableConcentrations, ppmStart_lcm, ppmEnd_lcm, ...
- scanFrequency, frequencyShift, ppmGap, phase0_deg_lcm, phase1_deg_ppm_lcm] = ...
- extractFits(dataExportPath,[fileName, '.coord']);
-
- load(strcat(dataExportPath,fileName, '_profit.mat'),'fitresult', 'data');
-
- %% process input data
- nTimepoints = length(summedFidWithNoise);
- ppmVector = ppmVectorFunction(scanFrequency*1e6, bandwidth, nTimepoints, '1H');
+ indexParamSorted = sortedFigure(indexParam);
+ %% load data: Input data, LCModel fit, ProFit Fit
+ % import the spectra but also the used concentrations and all parameters
+ fileName = ['Simulated_', paramKeyword, '_', num2str(indexParamSorted) '_truncOff'];
+ load([dataExportPath, fileName, '.mat'], 'summedFidWithNoise', 'current_em', 'currentConcentrationRm', ...
+ 'current_pc0', 'current_pc1', 'current_df2', 'current_gm', 'current_em_std_factor', 'conc_std_factor', 'baselineScaled');
+ if plot_dkntmn
+ fileName = ['Simulated_', paramKeyword, '_', num2str(indexParamSorted) truncSuffix];
+ [~, ~, phasedData_lcm_05, fitData_05, baselineData_lcm_05, residualData_05, ...
+ ~, ~, ~, ~, ~, ~, ~, ~, ~, ~] = ...
+ extractFits(dataExportPath_05,[fileName, '.coord']);
+ [~, ~, phasedData_lcm_015, fitData_015, baselineData_lcm_015, residualData_015, ...
+ ~, ~, ~, ~, ~, ~, ~, ~, ~, ~] = ...
+ extractFits(dataExportPath_015,[fileName, '.coord']);
+ end
+ [nOfPoints, ppmVector_lcm, phasedData_lcm, fitData, baselineData_lcm, residualData, ...
+ metaboliteNames, metaboliteData, tableConcentrations, ppmStart_lcm, ppmEnd_lcm, ...
+ scanFrequency, frequencyShift, ppmGap, phase0_deg_lcm, phase1_deg_ppm_lcm] = ...
+ extractFits(dataExportPath,[fileName, '.coord']);
- spectrum = fftshift(fft(summedFidWithNoise));
- baselineSpectrum = fftshift(fft(baselineScaled));
-
- indexEnd = find(ppmVector > ppmEnd_lcm, 1);
- spectrumInputOffset = real(spectrum(indexEnd));
- baselineInputOffset = real(baselineSpectrum(indexEnd));
-
- %% process ProFit data
- currentFitresult = fitresult{1,iteration};
- ppm_profit = currentFitresult.common_data.data.fitroi.ppm2;
- %phasedData
- pData_profit = currentFitresult.processed_spec;
- %residual
- rData_profit = currentFitresult.residual_spec;
- %spline baseline
- if ~isempty(currentFitresult.splines_baseline)
- spBB = currentFitresult.splines_baseline.basis_matrix;
- concSpline = currentFitresult.splines_baseline.coeff;
- bData_profit = (spBB * concSpline(1:size(spBB,2)))';
- splines_lambda = currentFitresult.splines_lambda;
- splines_ed_vec = currentFitresult.splines_ed_vec;
- splines_optim_model_vec = currentFitresult.splines_optim_model_vec;
- splines_optim_idx = currentFitresult.splines_optim_idx;
- else
- bData_profit = zeros(size(currentFitresult.residual_spec));
- splines_lambda = 0;
- splines_ed_vec = [];
- splines_optim_model_vec = [];
- splines_optim_idx = 0;
- end
+ load(strcat(dataExportPath,fileName, '_profit.mat'),'fitresult', 'data');
+
+ %% process input data
+ nTimepoints = length(summedFidWithNoise);
+ ppmVector = ppmVectorFunction(scanFrequency*1e6, bandwidth, nTimepoints, '1H');
+
+ spectrum = fftshift(fft(summedFidWithNoise));
+ baselineSpectrum = fftshift(fft(baselineScaled));
+
+ indexEnd = find(ppmVector > ppmEnd_lcm, 1);
+ spectrumInputOffset = real(spectrum(indexEnd));
+ baselineInputOffset = real(baselineSpectrum(indexEnd));
+
+ %% process ProFit data
+ currentFitresult = fitresult{1,iteration};
+ ppm_profit = currentFitresult.common_data.data.fitroi.ppm2;
+ %phasedData
+ pData_profit = currentFitresult.processed_spec;
+ %residual
+ rData_profit = currentFitresult.residual_spec;
+ %spline baseline
+ if ~isempty(currentFitresult.splines_baseline)
+ spBB = currentFitresult.splines_baseline.basis_matrix;
+ concSpline = currentFitresult.splines_baseline.coeff;
+ bData_profit = (spBB * concSpline(1:size(spBB,2)))';
+ splines_lambda = currentFitresult.splines_lambda;
+ splines_ed_vec = currentFitresult.splines_ed_vec;
+ splines_optim_model_vec = currentFitresult.splines_optim_model_vec;
+ splines_optim_idx = currentFitresult.splines_optim_idx;
+ else
+ bData_profit = zeros(size(currentFitresult.residual_spec));
+ splines_lambda = 0;
+ splines_ed_vec = [];
+ splines_optim_model_vec = [];
+ splines_optim_idx = 0;
+ end
+
+ %% Scale for plotting
+ % calculate scaling. Maximum has to be from the same fitted range as in LCModel/ProFit
+ ppmMask = (ppmVector < ppmStart_lcm) & (ppmVector > ppmEnd_lcm);
+ maxSpectrum = max(real(spectrum(ppmMask)));
+ maxSpectrum_lcm = max(phasedData_lcm);
+ maxSpectrum_profit = max(real(pData_profit));
+ scalingFactor_lcm = maxSpectrum ./ maxSpectrum_lcm;
+ scalingFactor_profit = maxSpectrum ./ maxSpectrum_profit;
+
+ minBaseline = min(real(baselineSpectrum(ppmMask)));
+
+ %scale the offsets
+ offsetBaselineScaled = offsetBaseline * maxSpectrum / 100;
+ offsetBaselineDiffScaled = offsetBaselineDiff * maxSpectrum / 100 - minBaseline;
+ offsetResidualScaled = offsetResidual * maxSpectrum / 100 - minBaseline;
+ offsetPlotsScaled = offsetPlots * maxSpectrum / 100;
+
+ %% create the figure
+ indexSubplot = mod(indexParam-1, nGrid)+1;
+ hs = subplot(subplotGridX,subplotGridY,indexSubplot);
+ coordinates = hs.Position;
+
+ hold on; %if not alligned, mind that the ppmVector has to be defined with the water resonance at 4.7 ppm
+ plot(ppmVector,real(spectrum),'LineWidth', LineWidth, 'Color', colorSpectrum);
+ % plot(ppmVector_lcm,real(phasedData_lcm)*scalingFactor_lcm,'LineWidth', LineWidth, 'Color', colorLCModel);
+ % plot(ppm_profit,real(pData_profit)*scalingFactor_profit,'LineWidth', LineWidth, 'Color', colorProFit);
+
+ if plot_dkntmn
+ offsetBaselineScaled = offsetBaselineScaled + offsetPlotsScaled;
+ plot(ppmVector_lcm,real(baselineData_lcm_05)*scalingFactor_lcm-offsetBaselineScaled+2.4*offsetPlotsScaled,':','LineWidth', LineWidth, 'Color', colorLCModel_05);
+ plot(ppmVector_lcm,real(baselineData_lcm)*scalingFactor_lcm-offsetBaselineScaled+1.6*offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorLCModel);
+ plot(ppmVector_lcm,real(baselineData_lcm_015)*scalingFactor_lcm-offsetBaselineDiffScaled*2+0.8*offsetPlotsScaled,':','LineWidth', LineWidth, 'Color', colorLCModel);
+ else
+ plot(ppmVector_lcm,real(baselineData_lcm)*scalingFactor_lcm-offsetBaselineScaled+offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorLCModel);
+ end
+ plot(ppmVector,real(baselineSpectrum)-offsetBaselineScaled,'-.','LineWidth', LineWidth, 'Color', colorOriginal);
+ plot(ppm_profit,real(bData_profit)*scalingFactor_profit-offsetBaselineScaled-offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorProFit);
+
+ fitBaselineLCM = fit(ppmVector_lcm, real(baselineData_lcm)*scalingFactor_lcm, 'linearinterp');
+ fitBaselineSpectrum = fit(ppmVector', real(baselineSpectrum)', 'linearinterp');
+ fitBaselineProFit = fit(ppm_profit', real(bData_profit)'*scalingFactor_profit, 'linearinterp');
+ plot(ppmVector_lcm, fitBaselineLCM(ppmVector_lcm)-fitBaselineSpectrum(ppmVector_lcm)-offsetBaselineDiffScaled,':','LineWidth', LineWidth, 'Color', colorLCModel)
+ plot(ppm_profit,fitBaselineProFit(ppm_profit)-fitBaselineSpectrum(ppm_profit)-offsetBaselineDiffScaled-offsetPlotsScaled,':','LineWidth', LineWidth, 'Color', colorProFit);
+
+ plot(ppmVector_lcm,real(residualData)*scalingFactor_lcm-offsetResidualScaled,'LineWidth', LineWidth, 'Color', colorLCModel);
+ plot(ppm_profit,real(rData_profit)*scalingFactor_profit-offsetResidualScaled-offsetPlotsScaled,'LineWidth', LineWidth, 'Color', colorProFit);
+ set(gca,'xdir','reverse');
+ xlim([ppmEnd_lcm, ppmStart_lcm]);
+ ylim([-offsetResidualScaled-3*offsetPlotsScaled maxSpectrum+5*offsetPlotsScaled])
+ xlabel('\delta (ppm)');
+ ylabel('Signal (arb. u.)');
+ set(gca,'ytick',[]);
- %% Scale for plotting
- % calculate scaling. Maximum has to be from the same fitted range as in LCModel/ProFit
- ppmMask = (ppmVector < ppmStart_lcm) & (ppmVector > ppmEnd_lcm);
- maxSpectrum = max(real(spectrum(ppmMask)));
- maxSpectrum_lcm = max(phasedData_lcm);
- maxSpectrum_profit = max(real(pData_profit));
- scalingFactor_lcm = maxSpectrum ./ maxSpectrum_lcm;
- scalingFactor_profit = maxSpectrum ./ maxSpectrum_profit;
-
- minBaseline = min(real(baselineSpectrum(ppmMask)));
-
- %scale the offsets
- offsetBaselineScaled = offsetBaseline * maxSpectrum / 100;
- offsetResidualScaled = offsetResidual * maxSpectrum / 100 - minBaseline;
- offsetPlotsScaled = offsetPlots * maxSpectrum / 100;
-
- %% create the figure
- indexSubplot = mod(indexParam-1, nGrid)+1;
- hs = subplot(subplotGridX,subplotGridY,indexSubplot);
- coordinates = hs.Position;
-
- hold on; %if not alligned, mind that the ppmVector has to be defined with the water resonance at 4.7 ppm
- plot(ppmVector,real(spectrum),'LineWidth', LineWidth, 'Color', colorSpectrum);
-% plot(ppmVector_lcm,real(phasedData_lcm)*scalingFactor_lcm,'LineWidth', LineWidth, 'Color', colorLCModel);
-% plot(ppm_profit,real(pData_profit)*scalingFactor_profit,'LineWidth', LineWidth, 'Color', colorProFit);
-
- if plot_dkntmn
- offsetBaselineScaled = offsetBaselineScaled + offsetPlotsScaled;
- plot(ppmVector_lcm,real(baselineData_lcm_05)*scalingFactor_lcm-offsetBaselineScaled+2.4*offsetPlotsScaled,':','LineWidth', LineWidth, 'Color', colorLCModel_05);
- plot(ppmVector_lcm,real(baselineData_lcm)*scalingFactor_lcm-offsetBaselineScaled+1.6*offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorLCModel);
- plot(ppmVector_lcm,real(baselineData_lcm_015)*scalingFactor_lcm-offsetBaselineScaled+0.8*offsetPlotsScaled,':','LineWidth', LineWidth, 'Color', colorLCModel_015);
- else
- plot(ppmVector_lcm,real(baselineData_lcm)*scalingFactor_lcm-offsetBaselineScaled+offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorLCModel);
- end
- plot(ppmVector,real(baselineSpectrum)-offsetBaselineScaled,'-.','LineWidth', LineWidth, 'Color', colorOriginal);
- plot(ppm_profit,real(bData_profit)*scalingFactor_profit-offsetBaselineScaled-offsetPlotsScaled,'-.','LineWidth', LineWidth, 'Color', colorProFit);
-
- plot(ppmVector_lcm,real(residualData)*scalingFactor_lcm-offsetResidualScaled,'LineWidth', LineWidth, 'Color', colorLCModel);
- plot(ppm_profit,real(rData_profit)*scalingFactor_profit-offsetResidualScaled-offsetPlotsScaled,'LineWidth', LineWidth, 'Color', colorProFit);
- set(gca,'xdir','reverse');
- xlim([ppmEnd_lcm, ppmStart_lcm]);
- ylim([-offsetResidualScaled-3*offsetPlotsScaled maxSpectrum+5*offsetPlotsScaled])
- xlabel('\delta (ppm)');
- ylabel('Signal (arb. u.)');
- set(gca,'ytick',[]);
-
if plot_dkntmn
legend('Spectrum',sprintf('LCModel baseline\ndkntmn=0.5'),sprintf('LCModel baseline\ndkntmn=0.25'),sprintf('LCModel baseline\ndkntmn=0.15'),'Input baseline','ProFit baseline','LCModel residual','ProFit residual')
else
- legend('Spectrum','LCModel baseline','Input baseline','ProFit baseline','LCModel residual','ProFit residual')
+% legend('Spectrum','LCModel baseline','Input baseline','ProFit baseline','LCModel residual','ProFit residual')
+ if mod(indexParam,nGrid)==2
+ handle_legend = legend('Spectrum','LCModel baseline','Input baseline','ProFit-1D baseline',['LCModel ' char(8211) ' Input baseline'],['ProFit-1D ' char(8211) ' Input baseline'], 'LCModel residual','ProFit-1D residual','FontSize',12);
+ title(handle_legend,'Legend');
+ end
end
%arrows residual
@@ -188,7 +200,13 @@ for indexParam = 1:length(baselines)
%arrows Input baseline - ProFit
yUpper = baselineInputOffset-offsetBaselineScaled+offsetPlotsScaled;
yLower = baselineInputOffset-offsetBaselineScaled;
- xa = [ppmEnd_lcm ppmEnd_lcm]-0.1;
+ xa = [ppmEnd_lcm ppmEnd_lcm]-0.12;
+ doublePointedArrowInside(xa,yUpper,yLower, arrowsColor);
+
+ %arrows Baseline differences ProFit & LCModel
+ yUpper = baselineInputOffset-offsetBaselineDiffScaled;
+ yLower = baselineInputOffset-offsetBaselineDiffScaled-offsetPlotsScaled;
+ xa = [ppmEnd_lcm ppmEnd_lcm]-0.12;
doublePointedArrowInside(xa,yUpper,yLower, arrowsColor);
% text box with label "Plot offsets"
@@ -197,12 +215,13 @@ for indexParam = 1:length(baselines)
[xaf,yaf] = axescoord2figurecoord(xa,ya);
str = {'Plot','offsets'};
annotation('textbox',[xaf(1) yaf(1)-0.02 0.1 0.1],'String',str,'FitBoxToText','On', ...
- 'EdgeColor','none', 'FontWeight','bold','Color',arrowsColor);
+ 'EdgeColor','none', 'FontWeight','bold','Color',arrowsColor,'FontSize',13);
set(gcf,'Color','w')
+ set(gca,'FontSize',13)
- annotation('rectangle',[coordinates(1)+coordinates(3)*0.02 coordinates(2)+coordinates(4)*0.62 ...
- .35./subplotGridX .4./subplotGridY],'FaceColor', 'w', 'FaceAlpha',0, 'Color',[0 0.4 0.1])
+% annotation('rectangle',[coordinates(1)+coordinates(3)*0.02 coordinates(2)+coordinates(4)*0.62 ...
+% .35./subplotGridX .4./subplotGridY],'FaceColor', 'w', 'FaceAlpha',0, 'Color',[0 0.4 0.1])
axes('Position',[coordinates(1)+coordinates(3)*0.15 coordinates(2)+coordinates(4)*0.81 ...
.2./subplotGridX .2./subplotGridY])
@@ -210,20 +229,28 @@ for indexParam = 1:length(baselines)
plot(splines_ed_vec, splines_optim_model_vec,'Color',[0. 0.5 0.2]);
hold on
if ~isempty(splines_ed_vec(splines_optim_idx))
- xl = xline(splines_ed_vec(splines_optim_idx),'-.', {['ED: ' sprintf('%.f',splines_ed_vec(splines_optim_idx))],...
- ['mAIC: ', sprintf('%.1f',splines_optim_model_vec(splines_optim_idx))]}, ...
+% xl = xline(splines_ed_vec(splines_optim_idx),'-.', {['ED: ' sprintf('%.f',splines_ed_vec(splines_optim_idx))],...
+% ['mAIC: ', sprintf('%.1f',splines_optim_model_vec(splines_optim_idx))]}, ...
+% 'HandleVisibility','off', 'LineWidth', 2);
+% xl.LabelVerticalAlignment = 'top';
+% xl.LabelHorizontalAlignment = 'center';
+% xl.FontSize = 9;
+ xl = xline(splines_ed_vec(splines_optim_idx),'-.',...
'HandleVisibility','off', 'LineWidth', 2);
- xl.LabelVerticalAlignment = 'top';
- xl.LabelHorizontalAlignment = 'center';
- xl.FontSize = 9;
end
- set(gca,'FontSize',10)
+ set(gca,'FontSize',12)
set(gca,'Xscale','log');
% set(gca,'Color',backgroundInlayColor)
xlabel('Baseline ED / ppm');
ylabel('mAIC');
ylim([min(splines_optim_model_vec)*0.99 max(splines_optim_model_vec)*1.01])
- title('ProFit Baseline Smoothness');
+ % title('ProFit Baseline Smoothness');
+ if isempty(splines_ed_vec(splines_optim_idx))
+ title('ProFit Baseline Smoothness');
+ else
+ title(['ED: ' sprintf('%.f',splines_ed_vec(splines_optim_idx)),...
+ ' mAIC: ', sprintf('%.1f',splines_optim_model_vec(splines_optim_idx))]);
+ end
annotation('textbox',[coordinates(1)+coordinates(3)*0.02-0.03 coordinates(2)+coordinates(4)*0.62 ...
.35./subplotGridX .4./subplotGridY],'String',subplotNames{indexSubplot},'FontSize', 16, 'FontWeight', 'bold','LineStyle','none')
@@ -233,26 +260,3 @@ for indexParam = 1:length(baselines)
end
end
end
-
-function doublePointedArrowInside(xa,yUpper,yLower, arrowsColor)
- set(gcf,'Units','normalized');
- yaDown = [yUpper+1e-8 yUpper];
- yaLine = [yLower yUpper];
- yaUp = [yLower-1e-8 yLower];
- [xaf,yafLine] = axescoord2figurecoord(xa,yaLine);
- line = annotation('line',xaf,yafLine);
- [xaf,yafDown] = axescoord2figurecoord(xa,yaDown);
- arDown = annotation('arrow',xaf,yafDown);
- [xaf,yafUp] = axescoord2figurecoord(xa,yaUp);
- arUp = annotation('arrow',xaf,yafUp);
- %styling
- line.Color = arrowsColor;
- arDown.HeadStyle = 'vback2';
- arDown.HeadLength = 5;
- arDown.HeadWidth = 7;
- arDown.Color = arrowsColor;
- arUp.HeadStyle = 'vback2';
- arUp.HeadLength = 5;
- arUp.HeadWidth = 7;
- arUp.Color = arrowsColor;
-end