Acoustic simulations with NaNs

[jkosciessa]

With the updated tissue attenuation, I run into sporadic acoustic simulations that are filled with NaNs. Those will eventually crash and are characterized by max ISPPA positions of 1 1 1:

Final transducer, expected focus, and max ISPPA positions

ans =

   175   175     1
   189   189     1
   363   194     1

The crash will happen at the attempt to plot, and will be of the format:

{Error using matlab.graphics.axis.Axes/set
Error setting property 'CLim' of class 'Axes':
Value must be a 1x2 vector of numeric type in which the second element is
greater than the first element or is Inf.

Error in clim (line 142)
        set(axHandle, 'CLim',  climits);

Error in plot_isppa_over_image (line 201)
        clim(options.isppa_color_range);

Error in single_subject_pipeline (line 379)
        [~,~,~,~,~,~,~,h]=plot_isppa_over_image(...

Error in tpb5b9b4be_c0ba_4372_a00e_bf852ef7b5b1 (line 1)
load /project/2424103.01/thalstim_simulations/thalstim_sim/data/tussim/CTX500-026-010_79.6mm_pCT_60W_debug/sub-007/batch_job_logs/tpc8e4bab0_f2a1_40a7_9c57_54ef6096e020.mat; cd /project/2424103.01/thalstim_simulations/thalstim_sim/tools/PRESTUS; single_subject_pipeline(subject_id, parameters); delete /project/2424103.01/thalstim_simulations/thalstim_sim/data/tussim/CTX500-026-010_79.6mm_pCT_60W_debug/sub-007/batch_job_logs/tpc8e4bab0_f2a1_40a7_9c57_54ef6096e020.mat; delete /project/2424103.01/thalstim_simulations/thalstim_sim/data/tussim/CTX500-026-010_79.6mm_pCT_60W_debug/sub-007/batch_job_logs/tpb5b9b4be_c0ba_4372_a00e_bf852ef7b5b1.m;
} 

[jkosciessa]

Debugging in the k-Wave function kSpaceFirstOrder suggests that this may arise from unreasonable tissue values somewhere. A major pressure line in this instance is estimated around the neck area after only a few executed time steps (far away from the transducer plane, suggesting a computational problem). I attached some plots of different time steps, that ultimately converge in NaNs. Note that this is from the pseudoCT implementation that uses continuous tissue property values.

[jkosciessa]

This seems fixed in commit 361c869e0bee9c688d96626abfef36a77f68847b after regularizing minimum pseudoCT-based bone density to the water estimate. As also discussed here this suggests that the conversion of pseudo-HU into tissue values may not be very sensible yet and should be double-checked.

I additionally increased the time step to 10% of the limit (from 1%) in commit d83e970ae456580f4a68052584014b13eae07e9f, but the former should be the relevant change.