Adjusted colorbar and a few other things

meica_component_displayer.m

@@ -17,6 +17,11 @@ function meica_component_displayer(tr, savedir)
 
 end
 
+% Custom color map
+[path,name,ext] = fileparts(which('meica_component_displayer'));
+custom_cmap_loc = fullfile(path,'custom_map.mat');
+load(custom_cmap_loc);
+
 
 %Prepare motion calc and loading.
 cfg.motionparam = 'dfile.r01.1D'; %output from MEICA, organized as: roll pitch yaw dS  dL  dP
@@ -111,7 +116,7 @@ function meica_component_displayer(tr, savedir)
 if Motion
 %%Making the motion plots, including framewise displacement
 
-figure('visible', 'off', 'windowstyle', 'normal');
+figure('visible', 'on', 'windowstyle', 'normal');
 grid on; grid minor;
 [fwd,~]=bramila_framewiseDisplacement(cfg); %calculate FD using script
 
@@ -151,10 +156,18 @@ function meica_component_displayer(tr, savedir)
 fprintf('Making component plots.\n');
 count = 0; %for displaying things every so often
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 
+n_colors = 256;
+colormaptype = 'parula';
+cmap_fh = str2func(colormaptype);
 
-for i = 1:comp_number;
+for i = 1:comp_number
+%    cmap = cmap_fh(n_colors);
+%     for v = 1:(n_colors/2)
+%         cmap(v,:) = [1 1 1];
+%     end
+    cmap = custom_map;
 
     if mod(count, 10) == 0
         fprintf('.'); %print progress every 10 components, less annoying.
@@ -197,16 +210,13 @@ function meica_component_displayer(tr, savedir)
     [sag_img, cor_img, hor_img] = three_cut_maker(current_image,num_cuts);
 
     subplot(12,5,16:25)
-    imshow(sag_img,[-bounds bounds])
-    colormap bone
+    imshow(sag_img,[-bounds bounds],'Colormap',cmap)
 
     subplot(12,5,26:35)
-    imshow(cor_img,[-bounds bounds])
-    colormap bone
+    imshow(cor_img,[-bounds bounds],'Colormap',cmap)
 
     subplot(12,5,36:45)
-    imshow(hor_img,[-bounds bounds])
-    colormap bone
+    imshow(hor_img,[-bounds bounds],'Colormap',cmap)
 
     %Now adding in the fourier transform.
     Fs = 1/tr;            % Sampling frequency
@@ -230,7 +240,7 @@ function meica_component_displayer(tr, savedir)
 %%
 fprintf('\nCollecting Explained Variance...');
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 
 BOLD_var = 0;
 REJ_var = 0;
@@ -282,7 +292,7 @@ function meica_component_displayer(tr, savedir)
 %%
 fprintf('\nShowing Elbow of Kappa, with Rho...');
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 plot(imported_ctab(:,2))
 hold on
 plot(imported_ctab(:,3))
@@ -296,7 +306,7 @@ function meica_component_displayer(tr, savedir)
 fprintf('\nScattering Kappa vs Rho ');
 
 k_r = horzcat(imported_ctab(:,2),imported_ctab(:,3));
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 scatter(k_r(:,1),k_r(:,2), imported_ctab(:,4)*100, color_table);
 title('Kappa vs Rho');
 ylabel('Rho');
@@ -336,7 +346,7 @@ function meica_component_displayer(tr, savedir)
 
 tsnr_range = tsnr_max_MEDN*0.8;
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 tsnr_range])
 title('TSNR of MEDN timeseries');
@@ -382,7 +392,7 @@ function meica_component_displayer(tr, savedir)
 
 [sag_img, cor_img, hor_img] = three_cut_maker(tsnr_tsoc,num_cuts);
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 tsnr_range])
 
@@ -418,7 +428,7 @@ function meica_component_displayer(tr, savedir)
 
 [sag_img, cor_img, hor_img] = three_cut_maker(tsnr_e2,num_cuts);
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 tsnr_range])
 title('TSNR of Second Echo');
@@ -451,7 +461,7 @@ function meica_component_displayer(tr, savedir)
 
 [sag_img, cor_img, hor_img] = three_cut_maker(tsnr_ratio,num_cuts);
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 5])
 title('TSNR Ratio, MEDN vs TSOC timeseries');
@@ -488,7 +498,7 @@ function meica_component_displayer(tr, savedir)
 
 [sag_img, cor_img, hor_img] = three_cut_maker(tsnr_ratio,num_cuts);
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 5])
 title('TSNR of TSOC vs 2nd Echo');
@@ -521,7 +531,7 @@ function meica_component_displayer(tr, savedir)
 
 [sag_img, cor_img, hor_img] = three_cut_maker(tsnr_ratio,num_cuts);
 
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 subplot(8,5,1:10)
 imshow(sag_img,[0 5])
 title('TSNR of MEDN vs 2nd Echo');
@@ -550,7 +560,7 @@ function meica_component_displayer(tr, savedir)
 
 %Creating a covariance matrix
 fprintf('\nPlotting correlations');
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 imagesc(corr_mat, [-1 1]);
 title('Correlation of Motion and ICA comps.');
 colorbar
@@ -560,7 +570,7 @@ function meica_component_displayer(tr, savedir)
 %%
 %Creating R^2 matrix
 fprintf('\nPlotting correlations...squared\n');
-figure('visible', 'off', 'windowstyle','normal');
+figure('visible', 'on', 'windowstyle','normal');
 imagesc((corr_mat.^2), [0 1]);
 title('Correlation Coefficient of Motion and ICA comps.');
 colorbar