Initial start to fix the PML offset issue. Committing to serve as a base.
last commit missed a semicolon and didn’t compile. Committing that change with verification everything compiles.
Adding changes that take into account the sensor.mask. Everything has been updated from the computation side, but needs extensive testing.
This is the starting point from which that testing should begging.
Committing latest changes. Still needs more testing.
The PML offset issue, along with what the sensor.mask saves has been fixed in this commit. Now, when data is written out disk in the OUTPUT h5 file, only the portion that is
enabled (i.e. sensor.mask = 1) is written to disk. This allows much less data to be saved. The following is in this commit

- Ability to save displacement, refractive index changes, etc to disk only using the ‘kWave_sim’ option.
- Ability to specify a small ROI to save data over based on sensor.mask = 1 (this is created in the matlab script the generates the INPUT h5 file).
- No longer need to offset into the medium (MC_sim) to take into account the PML.
        + NOTE:
        + The bounds that the MC_sim uses are specified by ‘makeGrid(Nx, dx, Ny, dy, Nz, dz)’ in the INPUT h5 file.
        + The overall sensor.mask defined in the INPUT h5 file should match the Nx, Ny, Nz region (e.g. sensor.mask = zeros(Nx, Ny, Nz))
            but to enable the recording of data, only turn on a portion of the medium (e.g. sensor.mask(offset:Nx-offset, offset:Ny-offset, offset:Nz-offset) = 1)
- This has been verified to work using the ‘kWave_sim’ option and save all data to disk correctly.
- This commit will be merged into the ‘developement’ branch for further testing.
Merge branch 'Fix_PML_offset' into developement
Adding in changes to dimension sizes for refractive_x, refractive_y, refractive_z
in the 'MatrixContainer.cpp' class.
Updated the printing of ultrasound statistics and removed the old version.
Small update to print ultrasound statics method.
Updated timing interval (i.e. -s and -e values specified on the commandline) so that
data is saved over the entire range specified.