Important: updated matlab scripts repository

[arango]

I updated the matlab repository and included several new scripts and improved others.

The new scripts are:

• 4dvar/c_observations.m: creates 4D-Var observation NetCDF file.

• 4dvar/d_observations.m: driver template to process 4D-Var observation NetCDF file.

• 4dvar/d_ssh_obs.m: driver template to extract SSH observations for AVISO, create and write observation file. Then, it computes super observations and creates and writes super observations NetCDF file.

• 4dvar/inside.m: checks if a point is strictly inside of the region defined by a polygon. This is an old Matlab function which is not longer supported. It is very useful to find outliers observations.

• 4dvar/load_ssh_data.m: extracts AVISO sea level anomaly for the period of interest and specified region from ROMS Grid file.

• 4dvar/plot_super.m: sample script to compute and plot super observations from specified 4D-Var observations NetCDF file.

• 4dvar/obs_ijpos.m: computes observations locations in ROMS fractional coordinates. It uses the inside deprecated Matlab function.

• 4dvar/obs_read.m: reads observation NetCDF file and load all data into a structure array.

• 4dvar/obs_write.m: writes all observation data in structure array into an existing NetCDF file.

• 4dvar/super_obs.m: checks the provided observation data (4D-Var NetCDF file or structure) and creates super observations if there is more than one datum of the same observation type per grid cell.

• boundary/c_boundary.m: creates ROMS open boundary conditions NetCDF file.

• boundary/d_mercator.m: driver template to extract open boundary conditions from Mercator dataset. It creates open boundary conditions NetCDF file, interpolates data to application grid, and writes out data.

• boundary/obc_mercator.m: interpolates requested variable open boundary conditions from Mercator to ROMS grid boundary edges.

• grid/c_grid.m: creates or modifies a ROMS grid NetCDF file.

• initial/c_biology.m: defines ROMS biology variables to an existing initial conditions or climatology NetCDF file.

• initial/mercator2roms.m: interpolates requested variable data from Mercator to ROMS grid.

• utility/roms_vectors: processes vector data for either the full grid for boundary edges. The strategy is to get any horizontal vector field at RHO-points for the event that a rotation to ROMS curvilinear grid is needed. Then, they are computed at the appropriate Arakawa C-grid location.

• utility/uv_barotropic: computes vertically integrated velocity components for ROMS full grid or boundaries.

I also updated various existing scripts. I highly recommend users to update this repository.

Notice that two new directories were added: boundary and grid. Therefore, the startup.m was also modified to include the path of these directories.