Merge branch 'master' into 'main'

Master

See merge request sapme1/hexagonalsampling!6

ComputeMostHexagonalSampling.m

@@ -117,15 +117,12 @@ LArray = unique(sort([LArray L_CAIPI_B]));
 isBlippedCAIPI_A = ((ceil(LArray)==LArray) + (LArray<=nSlicesSimultaneously)) > 1;
 isBlippedCAIPI_B = ismember(LArray, L_CAIPI_B);
 
-colourCAIPI_A = [217, 83, 25]/255; % red
-colourCAIPI_B = [148, 0, 211]/255; % purple
-colourOptimum = [34, 139, 34]/255; % green
-
 howFar2Look = 10; % TODO: Find out what to put here!
 d_min = zeros(size(LArray));
 
 if doDebug
     figure('Name','Sampling grid and alps');
+    set(gcf, 'Position', [680   693   621   285])
     ah = subplot(1,2,1);
 end
 
@@ -144,19 +141,20 @@ for iL = 1:numel(LArray)
     if doDebug
         [kyArray, kzArray] = GetGridPoints(3*Lmax, deltak_inplane, sliceSpacing, LArray(iL));
         PlotGrid(kyArray, kzArray, sliceSpacing, ah);
-
+        title(sprintf('L = %.2f      %s = %.2f',LArray(iL), char(hex2dec('0394')), nSlicesSimultaneously/LArray(iL)));
+        
         subplot(1,2,2); hold on;
         plot(LArray(iL),packingDensityArray(iL),'.','Color','k');
 
         if isBlippedCAIPI_A(iL)
-            plot(LArray(iL),packingDensityArray(iL),'x','Color',colourCAIPI_A,'MarkerSize',10,'LineWidth',3);
+            plot(LArray(iL),packingDensityArray(iL),'x','Color',GetSamplingPatternColour(1),'MarkerSize',10,'LineWidth',3);
         elseif isBlippedCAIPI_B(iL)
-            plot(LArray(iL),packingDensityArray(iL),'x','Color',colourCAIPI_B,'MarkerSize',10,'LineWidth',3);
+            plot(LArray(iL),packingDensityArray(iL),'x','Color',GetSamplingPatternColour(2),'MarkerSize',10,'LineWidth',3);
         end
         
         xlabel('L'); ylabel('Packing density [%]');
-        xlim([Lmin Lmax]); ylim([min(packingDensityArray) 90.7]);
-        sgtitle(sprintf('L = %.2f',LArray(iL)));
+        xlim([Lmin Lmax]); ylim([0 90.7]);
+        axis square;
 
         %% Make GIF
         if ~isempty(gifName)
@@ -213,11 +211,11 @@ if doPlot
     plot(LArray, packingDensityArray, 'LineWidth', 3, 'Color', 'k', ...
         'DisplayName', 'All feasible sampling patterns');
     plot(L_CAIPI_A, packingDensityCAIPI_A, 'x', 'MarkerSize', 10, 'LineWidth', 3, ...
-        'Color', colourCAIPI_A, 'DisplayName', 'Blipped-CAIPIRINHA - A');
+        'Color', GetSamplingPatternColour(1), 'DisplayName', 'Blipped-CAIPIRINHA - A');
     plot(L_CAIPI_B, packingDensityCAIPI_B, 'x', 'MarkerSize', 10, 'LineWidth', 3, ...
-        'Color', colourCAIPI_B, 'DisplayName', 'Blipped-CAIPIRINHA - B');
+        'Color', GetSamplingPatternColour(2), 'DisplayName', 'Blipped-CAIPIRINHA - B');
     plot(L_optimum, packingDensity, 'x', 'MarkerSize', 10, 'LineWidth', 3, ...
-        'Color', colourOptimum, 'DisplayName', 'Optimum sampling');
+        'Color', GetSamplingPatternColour(0), 'DisplayName', 'Proposed method');
     legend;
     xlabel('L');
     ylabel('Packing density [%]');
@@ -244,6 +242,9 @@ scatter(ky, kz, 'MarkerEdgeColor', [0.5 0.5 0.5], 'MarkerFaceColor', [0.5 0.5 0.
 
 hold on;
 
+ind0 = find(ky==0);
+scatter(ky(ind0:ind0+1), kz(ind0:ind0+1), 'MarkerEdgeColor', [0 0 0], 'MarkerFaceColor', [0 0 0], 'LineWidth', 5);
+
 slabBorderColour = [100 149 237]/255; % light blue
 yline(0,'r','LineWidth',3, 'Color', slabBorderColour); 
 yline(2*pi/sliceSpacing, 'r', 'LineWidth', 3, 'Color', slabBorderColour);

GetSamplingPatternColour.m

+function colour = GetSamplingPatternColour(samplingPattern)
+% IN
+%   samplingPattern     0: optimum sampling (as hexagonal as possible)
+%                       1: blipped-CAIPIRINHA A (Setsompop et al. MRM 2012, Zahneisen et al. MRM 2014)
+%                       2: blipped-CAIPIRINHA B (Narsude et al. MRM 2016)
+% OUT
+%   colour              rgb triplet
+%
+% Author: Maria Engel
+% (c) Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, United Kingdom
+switch samplingPattern
+    case 0
+        colour = [34, 139, 34]/255; % green
+    case 1
+        colour = [217, 83, 25]/255; % red
+    case 2
+        colour = [153,50,204]/255; % purple
+end
\ No newline at end of file

MakeGridAndAlpGif.m

@@ -5,6 +5,8 @@ baseFolder = pwd;
 doSave = true;
 if doSave
     gifName = fullfile(baseFolder,'GridAndAlpsGif.gif');
+    dfws = get(0,'DefaultFigureWindowStyle');
+    set(0,'DefaultFigureWindowStyle','normal');
 else
     gifName = [];
 end
@@ -18,5 +20,6 @@ sliceSpacing = FOVinplane/2/Nsim;
 [packingDensity, L_optimum, isDegenerate, packingDensityCAIPItmp, L_CAIPItmp] = ...
     ComputeMostHexagonalSampling(R, FOVinplane, sliceSpacing, Nsim, [], [], [], [], true, gifName, 0.02);
 
-[packingDensityCAIPI, indCAIPI] = max(packingDensityCAIPItmp);
-L_CAIPI = L_CAIPItmp(indCAIPI);
+if doSave
+    set(0,'DefaultFigureWindowStyle',dfws);
+end

MakeOptDvsRPlot.m

@@ -51,17 +51,17 @@ for iNSim = 1:numel(NSimArray)
             name = sprintf(', N_{sim} = %i',Nsim);
         end
         nexttile;  hold on;
-        plot(RArray(1:numel(packingDensity))*Nsim, packingDensity,...
-            'DisplayName', ['As hexagonal as possible' name], 'LineWidth', 2, 'Color', [34, 139, 34]/255);
-        plot(RArray(1:numel(packingDensity))*Nsim, packingDensityCAIPI_A, 'Color', [217, 83, 25]/255,...
-            'DisplayName', ['Blipped-CAIPIRINHA - A' name], 'LineWidth', 2);
-        plot(RArray(1:min(numel(packingDensity),numel(packingDensityCAIPI_B)))*Nsim, packingDensityCAIPI_B, 'Color', [148, 0, 211]/255,...
-            'DisplayName', ['Blipped-CAIPIRINHA - B' name], 'LineWidth', 2);
+        plot(RArray(1:numel(packingDensity))*Nsim, packingDensity, 'LineWidth', 2,...
+            'DisplayName', ['Proposed method' name], 'Color', GetSamplingPatternColour(0));
+        plot(RArray(1:numel(packingDensity))*Nsim, packingDensityCAIPI_A, 'LineWidth', 2,...
+            'DisplayName', ['Blipped-CAIPIRINHA - A' name], 'Color', GetSamplingPatternColour(1));
+        plot(RArray(1:min(numel(packingDensity),numel(packingDensityCAIPI_B)))*Nsim, packingDensityCAIPI_B, 'LineWidth', 2,...
+            'DisplayName', ['Blipped-CAIPIRINHA - B' name], 'Color', GetSamplingPatternColour(2));
 
-        yline(pi/2/sqrt(3)*100, 'Color', [0.5 0.5 0.5], 'LineWidth', 2, 'DisplayName',...
-            'Maximum circle packing density, 90.7%');
+        yline(pi/2/sqrt(3)*100, 'Color', [0.5 0.5 0.5], 'LineWidth', 2,...
+            'DisplayName', 'Maximum circle packing density, 90.7%');
         xlim([Rtot_start Rtot_end]);
-        ylim([50 92]);
+        ylim([57 92]);
         if iNSim==numel(NSimArray) || doSave==false
             xlabel('R_{total}');
             legend;

README.md

@@ -13,4 +13,4 @@ MakeOptDvsRPlot.m (for Figure 3, this requires https://se.mathworks.com/matlabce
 
 and
 
-MakeExampleGridsPlot (for Figure 4, this requires export_fig code)
\ No newline at end of file
+MakeExampleGridsPlot.m (for Figure 4, this also requires export_fig code)
\ No newline at end of file