diff --git a/createTestData/createSimulatedSpectra.m b/createTestData/createSimulatedSpectra.m
index ebe45b688e560a4e1eadfcf558cd05ee9ba8a191..5e2a1dc4270c636b2285a401dcca01c61ea6fbc1 100644
--- a/createTestData/createSimulatedSpectra.m
+++ b/createTestData/createSimulatedSpectra.m
@@ -14,7 +14,7 @@ T2_std = [ 12, 10, 16, 35, 20, 25, 10,
TE = 24 * 1e-3;
numMetabolites = length(metabolites);
-saveData = true;
+saveData = false;
saveFigures = true;
saveRandNumbers = false; %should generally be kept false to have the same random numbers consistently
@@ -471,7 +471,7 @@ xlabel('\delta (ppm)')
ylabel('Signal (arb. u.)')
set(gca,'xDir','reverse')
set(gca,'ytick',[]);
-title(['Spectra with ', titleStr, ' simulations'], 'Interpreter','latex');
+title(['Spectra with ', titleStr, ' variations'], 'Interpreter','latex');
set(gca,'fontsize',FontSize);
set(gca,'FontWeight','bold');
h = findobj(gca,'Type','line');
diff --git a/createTestData/evaluateProFitFittingParameters.m b/createTestData/evaluateProFitFittingParameters.m
index cba0a1e0de45c4ae66717290f08b78710643c4d4..663aa23f462b35cb41738f30643b955fdd2142b4 100644
--- a/createTestData/evaluateProFitFittingParameters.m
+++ b/createTestData/evaluateProFitFittingParameters.m
@@ -4,8 +4,8 @@ folderName = 'final_simulations';
exportFolder = {'11 Simulations'};
pathNameExport = 'ProFit test data';
pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolder);
-% pathBaseExportFiles = pathBaseExportFiles(1:end-1);
-% pathBaseExportFiles = [pathBaseExportFiles ' - Weighted Cost Fun R3 0.25scale m_15 trunc\'];
+pathBaseExportFiles = pathBaseExportFiles(1:end-1);
+pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
dataExportPathBase = strcat(pathBaseExportFiles, exportFolder{1}, '\');
truncSuffix = '_truncOn';
folderFigures = [pathBaseExportFiles 'Output\' folderName, truncSuffix, '\'];
@@ -24,9 +24,11 @@ legendLabels = {'\varphi_0 :\hspace{3em}', '\varphi_1 :\hspace{3.em}', '\nu_g :\
parameters = {'pc0', 'pc12', 'gm', 'df2', ...
'em', 'conc', 'T2'};
titleLabels = {'\Delta\varphi_0', '\Delta\varphi_1', '\Delta\nu_g', '${\boldmath$\overline{\mid\Delta\omega\mid}$}$', ...
- '${\boldmath$\overline{\mid\Delta\nu_{e}\mid}$}$', '${\boldmath$\overline{\mid\Delta conc\mid}$}$', '${\boldmath$\overline{\mid\Delta T_{2}\mid}$}$'};
+ '${\boldmath$\overline{\mid\Delta\nu_{e}\mid}$}$', '${\boldmath$\overline{\mid\Delta c\mid}$}$', '${\boldmath$\overline{\mid\Delta T_{2}\mid}$}$'};
units = { ' (degrees)', ' (degrees/ppm)', ' (Hz)', ' (Hz)',...
' (Hz)', ' (mmol/kg)', ' (ms)'};
+titleOffset = {'\quad variations:\quad\quad','\quad variations:\quad', '\quad variations:\quad\quad\quad', '\quad variations:\quad\quad',...
+ '\quad variations:\quad\quad', '\quad variations:\quad', '\quad variations:\quad\quad'};
% parameters = {'conc'};
useSubPlots = true;
@@ -52,8 +54,8 @@ for iParam = 1: numParam
diff_mean = mean(mean(abs(diff_mat), 'omitnan'));
diff_std = std(mean(abs(diff_mat), 'omitnan'));
- numberOfNaNs = sum(sum(isnan(diff_mat)))
- numberOfNaNsV = sum((isnan(diff_mat)),2)'
+% numberOfNaNs = sum(sum(isnan(diff_mat)))
+% numberOfNaNsV = sum((isnan(diff_mat)),2)'
if useSubPlots
subplot(3,2,iParam)
@@ -69,8 +71,9 @@ for iParam = 1: numParam
end
title(['$$', titleLabels{iParam}, '$$'],'Interpreter','latex');
legendLabels_{iFolder}= ['$$' legendLabels{iFolder}, num2str(diff_mean,'%.2f'), ' \pm ', num2str(diff_std,'%.2f'), '$$'];
- lgd = legend(legendLabels_,'Interpreter','latex','Location','best');
- title(lgd,['$$Simulation: ', unitLabel,'$$']);
+ lgd = legend(legendLabels_,'Interpreter','latex','Location','northwest');
+
+ title(lgd,{'$$Spectra\,\,with\,\,induced$$',['$$', titleOffset{iParam}, unitLabel,'$$']},'FontSize',8);
end
xlim([0, length(folders)+1]);
xticks(1:length(folders));
diff --git a/createTestData/plotSimulationResults.m b/createTestData/plotSimulationResults.m
index 1848403dcb6f1532a43eef666c728f6937d1c3fd..c23d2979ec5418443751325dc0efa87f40843e96 100644
--- a/createTestData/plotSimulationResults.m
+++ b/createTestData/plotSimulationResults.m
@@ -4,13 +4,8 @@ function plotSimulationResults()
exportFolder = {'11 Simulations'};
pathNameExport = 'ProFit test data';
pathBaseExportFiles = pathToDataFolder(pathNameExport, exportFolder);
-% pathBaseExportFiles = pathBaseExportFiles(1:end-1);
-% pathBaseExportFiles = [pathBaseExportFiles ' - gm_0_R3\'];
-% pathBaseExportFiles = [pathBaseExportFiles ' - Weighted Cost Fun R3 0.25scale m_15 trunc\'];
-% pathBaseExportFiles = [pathBaseExportFiles ' - Weighted Cost Fun R3 0.25scale m_15 sinebell\'];
-% pathBaseExportFiles = [pathBaseExportFiles ' - Weighted Cost Fun R3 0.25scale m_15 matched\'];
-% pathBaseExportFiles = [pathBaseExportFiles ' - R1 0.25scale m_15 trunc\'];
-% pathBaseExportFiles = [pathBaseExportFiles ' - R2 0.25scale m_15 trunc\'];
+pathBaseExportFiles = pathBaseExportFiles(1:end-1);
+pathBaseExportFiles = [pathBaseExportFiles ' - R3\'];
dataExportPathBase = strcat(pathBaseExportFiles, exportFolder{1}, '\');
truncSuffix = '_truncOn';
scalingOn = true;
@@ -429,7 +424,7 @@ function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetCon
ylim([-yLimValue,yLimValue]);
xlim([positionsTicks(1)-1, positionsTicks(end)+1])
set(gca, 'FontSize', 11)
- ylabel('Concentration change {\boldmath$c_{\%}$}$_{,k}$ (\%)', 'FontSize', 13, 'Interpreter', 'latex')
+ ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotLCModel(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
%%
@@ -443,7 +438,7 @@ function [allSimulMetConc, allLCModelMetConc, allProFitMetConc, allLCModelMetCon
title('ProFit')
ylim([-yLimValue,yLimValue]);
set(gca, 'FontSize', 11)
- ylabel('Concentration change {\boldmath$c_{\%}$}$_{,k}$ (\%)', 'FontSize', 13, 'Interpreter', 'latex')
+ ylabel('$Concentration\,\,change\,\,c^\%_{k}\,(\%)$', 'FontSize', 13, 'Interpreter', 'latex')
set(boxPlotProFit(:,:),'linewidth',1);
yline(0,':', 'Color',[0.5 0.5 0.5]);
end
diff --git a/createTestData/plot_all_test_data_profit.m b/createTestData/plot_all_test_data_profit.m
index c8f8f0844e52f708224140071c0c8f0cb40e2d96..d7b90a9e637d885162dc6476383a406d31c01005 100644
--- a/createTestData/plot_all_test_data_profit.m
+++ b/createTestData/plot_all_test_data_profit.m
@@ -271,23 +271,24 @@ for indexMet = 1: numberOfMet
rpc_table{indexMet+2,5} = rpc_LCModel_64_ave;
end
-rpc_values = cell2mat(rpc_table(3:end-2,2:5));
+rpc_values = cell2mat(rpc_table(3:end-3,2:5));
rpc_meanProFit_32ave_main = mean(rpc_values(indecesMainMet,1));
rpc_meanProFit_64ave_main = mean(rpc_values(indecesMainMet,2));
rpc_meanLCModel_32ave_main = mean(rpc_values(indecesMainMet,3));
rpc_meanLCModel_64ave_main = mean(rpc_values(indecesMainMet,4));
-rpc_table{end-1,2} = rpc_meanProFit_32ave_main;
-rpc_table{end-1,3} = rpc_meanProFit_64ave_main;
-rpc_table{end-1,4} = rpc_meanLCModel_32ave_main;
-rpc_table{end-1,5} = rpc_meanLCModel_64ave_main;
+rpc_table(3:end-3,2:5) = sprintfc('%.0f',rpc_values);
+rpc_table{end-1,2} = num2str(rpc_meanProFit_32ave_main, '%.0f');
+rpc_table{end-1,3} = num2str(rpc_meanProFit_64ave_main, '%.0f');
+rpc_table{end-1,4} = num2str(rpc_meanLCModel_32ave_main, '%.0f');
+rpc_table{end-1,5} = num2str(rpc_meanLCModel_64ave_main, '%.0f');
rpc_meanProFit_32ave = mean(rpc_values(:,1));
rpc_meanProFit_64ave = mean(rpc_values(:,2));
rpc_meanLCModel_32ave = mean(rpc_values(:,3));
rpc_meanLCModel_64ave = mean(rpc_values(:,4));
-rpc_table{end,2} = rpc_meanProFit_32ave;
-rpc_table{end,3} = rpc_meanProFit_64ave;
-rpc_table{end,4} = rpc_meanLCModel_32ave;
-rpc_table{end,5} = rpc_meanLCModel_64ave;
+rpc_table{end,2} = num2str(rpc_meanProFit_32ave, '%.0f');
+rpc_table{end,3} = num2str(rpc_meanProFit_64ave, '%.0f');
+rpc_table{end,4} = num2str(rpc_meanLCModel_32ave, '%.0f');
+rpc_table{end,5} = num2str(rpc_meanLCModel_64ave, '%.0f');
xlswrite([pathBaseExportFiles, 'InVivoResults_RPC.xlsx'], rpc_table)
%% code will break here. This used to be the old style plotting/results without Bland-Altman plots.