Improve T1 tran plot + bug fix missing input param setup_grid_source_sensor

- Adapt percentage of dt_stability limit to 90%, because 1% will result in very long simulations.

Author: MaCuinea

functions/preprocess_brain.m

@@ -71,18 +71,17 @@
 
     % Creates and exports an unprocessed T1 slice that is oriented 
     % along the transducer's axis
-    [t1_with_trans_img, ~] = plot_t1_with_transducer(...
-        t1_image, round(t1_header.PixelDimensions(1),2), trans_pos_grid, focus_pos_grid, parameters);
-    
     h = figure;
-    imshow(rot90(t1_with_trans_img));
+    imshowpair(plot_t1_with_transducer(t1_image, t1_header.PixelDimensions(1), trans_pos_grid, focus_pos_grid, parameters), ...
+        plot_t1_with_transducer(t1_image, t1_header.PixelDimensions(1), trans_pos_grid, focus_pos_grid, parameters, 'slice_dim', 1),'montage');
+   
     title('T1 with transducer');
     output_plot_filename = fullfile(parameters.debug_dir, ...
         sprintf('sub-%03d_t1_with_transducer_before_smoothing_and_cropping%s.png', ...
         subject_id, parameters.results_filename_affix));
     saveas(h, output_plot_filename, 'png')
-    close(h); clear t1_with_trans_img;
-    
+    close(h);
+
     %% SEGMENTATION using SimNIBS
 
     disp('Starting segmentation...')
@@ -111,7 +110,7 @@
             focus_pos_final = [];
             final_transformation_matrix = [];
             inv_final_transformation_matrix = [];
-            return;
+			return;
         end
     else
         disp('Skipping, the file already exists, loading it instead.')

functions/setup_grid_source_sensor.m

@@ -1,4 +1,4 @@
-function [kgrid, source, sensor, source_labels] = setup_grid_source_sensor(parameters, max_sound_speed, trans_pos_final, focus_pos_final)
+function [kgrid, source, sensor, source_labels] = setup_grid_source_sensor(parameters, max_sound_speed, trans_pos_final, focus_pos_final, grid_time_step)
 
     % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % %
     %                  Set up the transducer and sensor                 %
@@ -21,6 +21,10 @@
     wave_period   = 1 / parameters.transducer.source_freq_hz;                                                       % period [s]
 
     % Check the number of input arguments
+    % As a default the time step is based on the default CFL number of 0.3.
+    % If grid_time_step is given, it means that the transducer and sensor
+    % has to be set up again with a smaller time step due to simulation
+    % instability.
     if nargin < 5
         % Calculate the time step using an integer number of points per period
         points_per_wavelength = max_sound_speed / (parameters.transducer.source_freq_hz * parameters.grid_step_m);      % points per wavelength

single_subject_pipeline.m

@@ -246,10 +246,17 @@
         max_sound_speed = max(kwave_medium.sound_speed(:));
         [kgrid, source, sensor, source_labels] = setup_grid_source_sensor(parameters, max_sound_speed, trans_pos_final, focus_pos_final);
         % check stability
+        % If estimated time step is smaller than the time step based on
+        % default CFL, the estimated time step is used to redefine
+        % transducer and sensor. Note: the estimated time step doesn't 
+        % guarantee a stable simulation. If Nan numbers are acquired as
+        % a result, you may want to try a time step smaller than the
+        % estimated time step.	  
         disp('Check stability...')
         dt_stability_limit = checkStability(kgrid, kwave_medium);
         if ~isinf(dt_stability_limit) && kgrid.dt > dt_stability_limit
-            grid_time_step = dt_stability_limit/100; % use a 1% of the limit (which are only aan approximation in the heterogenous medium case: http://www.k-wave.org/documentation/checkStability.php)
+			disp('Adapt time step for simulation stability...')
+            grid_time_step = dt_stability_limit*0.90; % use 90% of the limit (which are only an approximation in the heterogenous medium case: http://www.k-wave.org/documentation/checkStability.php)
             [kgrid, source, sensor, source_labels] = setup_grid_source_sensor(parameters, max_sound_speed, trans_pos_final, focus_pos_final, grid_time_step);
         end
     end