[optional bug] fix MNI summary plots

Fix errors for tissue-specific heating spec; save combined files in simulation-specific in root of subdirectory; cleanup temp; properly deal with skipping missing files

Author: jkosciessa

functions/combine_plots_by_suffix.m

@@ -7,33 +7,28 @@ function combine_plots_by_suffix(suffix, outputs_path, subject_list, parameters,
 
         options.font_size = 64
     end
-    if ~exist(sprintf('%stmp/', outputs_path),'dir')
-        mkdir(sprintf('%stmp/', outputs_path));
+    if ~exist(sprintf('%s/tmp/', outputs_path),'dir')
+        mkdir(sprintf('%s/tmp/', outputs_path));
     end
-    system(sprintf('cd "%stmp/"; rm *.png', outputs_path));
-    if parameters.subject_subfolder
-        orig_imsize = size(imread(fullfile(outputs_path, sprintf('sub-%03i/sub-%03i_%s.png', subject_list(1),subject_list(1), suffix))));
-%        imarray = uint8(zeros(size(imread(fullfile(outputs_path, sprintf('sub-%03i/sub-%03i_%s.png', subject_list(end), subject_list(end), suffix))))));
-    else
-        orig_imsize = size(imread(fullfile(outputs_path, sprintf('sub-%03i_%s.png', subject_list(1),  suffix))));
-%        imarray = uint8(zeros(size(imread(fullfile(outputs_path, sprintf('sub-%03i_%s.png', subject_list(end), suffix))))));
-    end
-
-%    imarray = repmat(imarray, 1, 1, 1, length(subject_list));
+    
     for subject_i = 1:length(subject_list)
         if parameters.subject_subfolder
-            old_name = fullfile(outputs_path, sprintf('sub-%03i/sub-%03i_%s.png', subject_list(subject_i), subject_list(subject_i), suffix));
+            sub_path = fullfile(outputs_path, sprintf('sub-%03i', subject_list(subject_i)));
         else
-            old_name = fullfile(outputs_path, sprintf('sub-%03i_%s.png', subject_list(subject_i), suffix));
+            sub_path = fullfile(outputs_path);
         end
+        old_name = fullfile(sub_path, sprintf('sub-%03i_%s.png', subject_list(subject_i), suffix));
+        orig_imsize = size(imread(old_name));
         I = imread(old_name);
         I = padarray(I, max([0 0 0; orig_imsize-size(I)],[], 1), I(1), 'pre');
-
         I = insertText(I,[0 5],sprintf('P%02i',subject_list(subject_i)),'FontSize', options.font_size, 'BoxOpacity',0,'TextColor','white');
-        %imarray(1:size(I, 1), 1:size(I, 2), 1:size(I, 3), subject_i) = I;
-        new_name = sprintf('%stmp/%i.png', outputs_path, subject_list(subject_i));
+        new_name = sprintf('%s/tmp/%i.png', outputs_path, subject_list(subject_i));
         imwrite(I, new_name);
     end
 
-    system(sprintf('cd "%stmp/"; montage -background black -gravity south  -mode concatenate $(ls -1 *.png | sort -g)  ../all_%s.png', convertCharsToStrings(outputs_path), suffix));
+    system(sprintf('cd "%s/tmp/"; montage -background black -gravity south  -mode concatenate $(ls -1 *.png | sort -g)  ../all_%s.png', convertCharsToStrings(outputs_path), suffix));
+
+    % remove temporary directory
+    system(sprintf('cd "%s/tmp/"; rm *.png', outputs_path));
+    rmdir(sprintf('%s/tmp/', outputs_path));
 end

functions/create_group_MNI_plots.m

@@ -20,11 +20,17 @@ function create_group_MNI_plots(subject_list, parameters, options)
 assert(xor(options.plot_max_intensity,options.slice_to_plot), "You should indicate either the slice number to plot ('slice_to_plot') or ask for a max intensity plot ('plot_max_intensity')")
 slice_labels = {'x','y','z'};
 
-
 outputs_path = parameters.temp_output_dir;
 bg_range_to_use = [];
 isppa_range_to_use = [5, 6];
-temp_range_to_use = [parameters.thermal.temp_0, parameters.thermal.temp_0 + 0.5];    
+% Note: with tissue-specific heating values, the plotting may not work as intended?
+if isstruct(parameters.thermal.temp_0)
+    temp_range_to_use = [parameters.thermal.temp_0.skin, parameters.thermal.temp_0.water + 0.5];
+    temp_0_min = parameters.thermal.temp_0.skin;
+else
+    temp_range_to_use = [parameters.thermal.temp_0, parameters.thermal.temp_0 + 0.5];
+    temp_0_min = parameters.thermal.temp_0;
+end
 
 full_subject_list = subject_list;
 % first pass: get background intensity at the target slice & isppa range
@@ -65,7 +71,7 @@ function create_group_MNI_plots(subject_list, parameters, options)
         if ~exist(filename{:}, 'file')
             if options.skip_missing
                 sprintf('File does not exist: %s; skipping this subject', filename{:})
-                subject_list(subject_i) = [];
+                subject_list(subject_i) = NaN;
                 all_files_exist = 0;
 
                 break;
@@ -136,7 +142,7 @@ function create_group_MNI_plots(subject_list, parameters, options)
         new_water_ind = zeros(1, length(water_ind));
         heating_mask = logical(changem_vectorized(segmented_image_mni, new_water_ind, water_ind));
         maxT_mni = maxT_mni.*heating_mask;
-        maxT_mni(maxT_mni==0) = parameters.thermal.temp_0;
+        maxT_mni(maxT_mni==0) = temp_0_min;
 
         maxT_slice = get_slice_by_label(maxT_mni, options.slice_label, slice_n);
 
@@ -148,6 +154,8 @@ function create_group_MNI_plots(subject_list, parameters, options)
     end
 end
 
+% remove unavailable subjects
+subject_list(isnan(subject_list)) = [];
 
 % second pass, doing the actual images
 for subject_i = 1:length(subject_list)
@@ -221,7 +229,7 @@ function create_group_MNI_plots(subject_list, parameters, options)
         new_water_ind = zeros(1, length(water_ind));
         heating_mask = logical(changem_vectorized(segmented_image_mni, new_water_ind, water_ind));
         maxT_mni = maxT_mni.*heating_mask;
-        maxT_mni(maxT_mni==0) = parameters.thermal.temp_0;
+        maxT_mni(maxT_mni==0) = temp_0_min;
     end
 
     if options.slice_to_plot