Fixing RiverForcing.plot_locations() With MATLAB Grids

Dec 1, 2025 by Alex Johnson 55 views

Fixing RiverForcing.plot_locations() Failure with MATLAB-Generated Grids

Have you ever encountered an error when using RiverForcing.plot_locations() with ROMS grids generated by MATLAB? If so, you're not alone! This article dives deep into the issue, explaining why it occurs and, more importantly, how to fix it. We'll break down the technical details in a friendly, conversational way, ensuring you understand the problem and can confidently resolve it. Our goal is to provide you with high-quality information, making your experience with ROMS tools smoother and more efficient. Let's get started!

Understanding the `RiverForcing.plot_locations()` Error

When working with the Regional Ocean Modeling System (ROMS), visualizing river forcing locations is crucial for understanding how freshwater inputs affect ocean dynamics. The RiverForcing.plot_locations() function within the roms-tools library is designed to help with this task. However, a common issue arises when using grids generated by MATLAB: the function throws an error. This error typically manifests because of a missing units attribute on the mask_rho variable within the grid file. Let's dissect this further.

The core of the problem lies in how roms-tools handles grid files. The function attempts to read the units attribute of mask_rho to ensure proper handling of the data. Specifically, the problematic line of code can be found here: https://github.com/CWorthy-ocean/roms-tools/blob/8a9f5fae29e1c2ce8aa6a61fd127f6b00745d40a/roms_tools/plot.py#L657. This line expects mask_rho to have a units attribute, which is standard for grids created using Python-based tools. However, MATLAB-generated grids often lack this attribute. When roms-tools tries to access a non-existent attribute, it throws an error, halting the plotting process. This discrepancy highlights the subtle differences in how MATLAB and Python handle metadata within grid files. While both tools can generate valid ROMS grids, the way they store auxiliary information like units can vary, leading to compatibility issues with certain functions.

To put it simply, the RiverForcing.plot_locations() function relies on the presence of a 'units' attribute for the mask_rho variable. MATLAB-generated grids, by default, do not include this attribute. This mismatch causes the function to fail, preventing you from visualizing your river forcing locations. Understanding this fundamental difference is the first step in resolving the issue and ensuring your workflow remains smooth.

Why MATLAB Grids Lack the Units Attribute

To effectively address the RiverForcing.plot_locations() error, it's essential to understand why MATLAB-generated grids often lack the units attribute for mask_rho. The reason is rooted in the way MATLAB handles metadata compared to Python's NetCDF library, which is commonly used in the oceanographic community and by roms-tools. MATLAB, while powerful for numerical computation, doesn't enforce the same standards for storing metadata as NetCDF. This can lead to inconsistencies when interoperating between systems.

When creating ROMS grids in MATLAB, the process often involves defining the grid's spatial characteristics (like latitude and longitude) and the land-sea mask (mask_rho). While MATLAB allows you to save this information to a NetCDF file (the standard format for ROMS grids), it doesn't automatically attach units attributes to all variables. This contrasts with Python's NetCDF library, which often encourages or even requires specifying units for variables during creation. Consequently, when a grid is generated in MATLAB, the mask_rho variable might be saved without the crucial units attribute. This is not necessarily a flaw in MATLAB itself, but rather a difference in conventions and default behaviors.

Think of it like this: MATLAB is a versatile tool that gives you a lot of control over how you save your data. It's up to the user to explicitly add the units attribute if needed. On the other hand, Python's NetCDF library, as used in roms-tools, assumes that certain attributes like units are present for certain variables. When these assumptions are not met, as in the case of MATLAB-generated grids, errors can occur. The absence of the units attribute doesn't invalidate the grid itself; the spatial data and land-sea mask are still correctly represented. However, it does create a hurdle for functions like RiverForcing.plot_locations(), which rely on this metadata for their operation. Therefore, the solution lies in either modifying the grid file to include the missing units attribute or adapting the roms-tools function to handle grids without this attribute.

Solutions and Workarounds

Now that we understand the root cause of the RiverForcing.plot_locations() failure with MATLAB grids, let's explore some practical solutions and workarounds. There are primarily two approaches you can take: modifying the grid file to include the missing units attribute or adapting the roms-tools function to be more flexible in handling grids without this attribute. Both methods have their pros and cons, and the best choice depends on your specific needs and workflow.

1. Modifying the Grid File

One straightforward solution is to add the units attribute to the mask_rho variable directly within the grid file. This can be achieved using various tools, including Python's netCDF4 library or MATLAB's NetCDF functions. Here's how you can do it using Python:

import netCDF4

grid_file = 'your_grid_file.nc'  # Replace with your grid file name

with netCDF4.Dataset(grid_file, 'a') as ncfile:
    if 'mask_rho' in ncfile.variables:
        if 'units' not in ncfile.variables['mask_rho'].ncattrs():
            ncfile.variables['mask_rho'].units = '1'  # '1' is a common convention for dimensionless masks
            print("Added units attribute to mask_rho")
        else:
            print("mask_rho already has a units attribute")
    else:
        print("mask_rho variable not found in the grid file")

This script opens the NetCDF grid file in append mode ('a'), checks if the mask_rho variable exists and if it already has a units attribute. If the attribute is missing, it adds it with a value of '1', which is a common convention for dimensionless masks (since the mask is either 0 or 1). After running this script, the grid file will be modified to include the units attribute, and RiverForcing.plot_locations() should work without errors.

Alternatively, you can achieve the same result using MATLAB. The following code snippet demonstrates how to add the units attribute:

grid_file = 'your_grid_file.nc'; % Replace with your grid file name

ncwriteatt(grid_file, 'mask_rho', 'units', '1');
disp('Added units attribute to mask_rho');

This MATLAB code uses the ncwriteatt function to add the 'units' attribute to the mask_rho variable. Like the Python script, it sets the value to '1' for a dimensionless mask.

Pros of Modifying the Grid File:

Permanent Fix: Once the units attribute is added, it's permanently stored in the grid file, ensuring that RiverForcing.plot_locations() and other functions that rely on this attribute will work consistently.
Standard Compliant: Adding the units attribute makes the grid file more compliant with NetCDF conventions, which can improve interoperability with other tools and libraries.

Cons of Modifying the Grid File:

Requires Write Access: You need write access to the grid file, which might not always be possible, especially if you're working with shared or read-only data.
Manual Step: It's an extra step in your workflow that you need to remember to perform for each new MATLAB-generated grid.

2. Adapting the `roms-tools` Function

Another approach is to modify the RiverForcing.plot_locations() function to handle cases where the units attribute is missing. This can be achieved by adding a check within the function to see if the attribute exists and, if not, proceed with a default assumption. This approach requires modifying the roms-tools library itself, which might not be desirable for everyone, but it can be a more robust solution in the long run.

To implement this, you would need to edit the plot.py file within the roms-tools library. Locate the line of code mentioned earlier (https://github.com/CWorthy-ocean/roms-tools/blob/8a9f5fae29e1c2ce8aa6a61fd127f6b00745d40a/roms_tools/plot.py#L657) and add a conditional check. Here's an example of how you might modify the code:

try:
    units = nc.variables['mask_rho'].units
except AttributeError:
    units = '1'  # Default to '1' if units attribute is missing

This modification uses a try-except block to catch the AttributeError that occurs when the units attribute is missing. If the error is caught, it sets the units variable to a default value of '1'. This ensures that the function can proceed even if the units attribute is not present.

Pros of Adapting the Function:

Handles All Grids: Once the function is modified, it will work with both grids that have the units attribute and those that don't, making it a more universal solution.
No Need to Modify Grid Files: You don't need to modify the grid files themselves, which can be convenient if you're working with a large number of grids or if you don't have write access.

Cons of Adapting the Function:

Requires Modifying Library Code: You need to modify the roms-tools library itself, which might make it harder to update the library in the future.
Potentially Overlooks Other Issues: While this fix addresses the specific issue with MATLAB grids, it might mask other potential issues related to missing metadata.

Choosing the Right Solution

The best solution for you depends on your specific circumstances. If you only encounter this issue occasionally and have write access to your grid files, modifying the grid file might be the simplest approach. If you frequently work with MATLAB-generated grids and want a more permanent solution, adapting the roms-tools function might be more suitable. Ultimately, understanding the problem and the available solutions allows you to make an informed decision and keep your workflow running smoothly.

Conclusion

The RiverForcing.plot_locations() failure when used with MATLAB-generated grids is a common issue stemming from the absence of the units attribute for the mask_rho variable. By understanding why this occurs, you can choose the best solution for your needs. Whether you opt to modify the grid file or adapt the roms-tools function, the key is to ensure that the necessary metadata is available for the function to operate correctly. This article has provided you with the knowledge and tools to tackle this problem head-on, allowing you to visualize your river forcing locations with confidence.

For more information about ROMS and related tools, you can explore resources like the ROMS official website. This external link provides comprehensive documentation, tutorials, and community forums where you can find further assistance and insights.