Visualization

Plotting Ocean Transects

The function mpas_tools.ocean.viz.transect.plot_transect() is used to plot transects of various MPAS-Ocean variables. This function provide high-level plotting capabilities for visualizing transects of MPAS-Ocean data. It can create transect plots useful for visualizing test cases or analyzing global simulation output and comparing with observations.

The function mpas_tools.ocean.viz.transect.plot_feature_transects() and the associated plot_ocean_transects command-line tool can be used to plot transects of various MPAS-Ocean variables. The arguments to the command-line tool are:

$ plot_ocean_transects --help
usage: plot_ocean_transects [-h] -g GEOJSON_FILENAME [-m MESH_FILENAME] -f
                            FILENAME [-v VARIABLE_LIST [VARIABLE_LIST ...]]
                            [-c COLORMAP] [--flip]

options:
  -h, --help            show this help message and exit
  -g GEOJSON_FILENAME, --geojson GEOJSON_FILENAME
                        A geojson file with transects to plot
  -m MESH_FILENAME, --mesh MESH_FILENAME
                        An MPAS-Ocean mesh file.  If not specified, the MPAS-Ocean data file must contain the mesh.
  -f FILENAME, --file FILENAME
                        An MPAS-Ocean data file
  -v VARIABLE_LIST [VARIABLE_LIST ...], --variable_list VARIABLE_LIST [VARIABLE_LIST ...]
                        List of variables to plot.  All variables on cells in the data file is the default.
  -c COLORMAP, --colormap COLORMAP
                        A colormap to use for the plots, default depends on the field name.
  --flip                Flip the x axis for all transects
  --write_netcdf        Whether to write a NetCDF file for the transect in addition to the image
  --method METHOD       The type of interpolation to use in plots. Options are "flat" and "bilinear"

See transects from geometric_features for a examples of what a geojson transect might look like:

{
    "type": "FeatureCollection",
    "features": [
        {
            "type": "Feature",
            "properties": {
                "name": "Drake Passage",
                "object": "transect",
                "component": "ocean",
                "author": "Mark Petersen, Xylar Asay-Davis, Milena Veneziani",
            },
            "geometry": {
                "type": "LineString",
                "coordinates": [
                    [
                        -63.02,
                        -65.46
                    ],
                    [
                        -63.81,
                        -63.8
                    ],
                    [
                        -64.42,
                        -62.02
                    ],
                    [
                        -65.04,
                        -60.25
                    ],
                    [
                        -65.74,
                        -58.28
                    ],
                    [
                        -66.37,
                        -56.39
                    ],
                    [
                        -67.02,
                        -54.44
                    ]
                ]
            }
        }
    ]
}

Add more features to the features list to plot multiple transects at the same time.

The MPAS-Ocean mesh file must including not just the horizontal mesh variables but also the vertical mesh variables (minLevelCell, maxLevelCell, layerThickness, etc.)

If you don’t specify the list of variables to plot, all variables with dimensions nCells and nVertLevels will be plotted.

One way of customizing these visualizaitons is to make your own copy of transects.py and change _plot_transect() to suite your needs, (changing figure size, dpi, colorbar, etc.)

Ocean Transect Interpolation

The mpas_tools.ocean.viz.transect.vert module provides functions for interpolating MPAS-Ocean data onto a vertical transect. This is useful for visualizing data along a specific path through the ocean, showing the vertical structure of ocean properties. These functions allow you to create cross-sectional plots of temperature, salinity, and other variables.

The following functions are available:

The function mpas_tools.ocean.viz.transect.compute_transect() builds a sequence of quads showing the transect intersecting MPAS cells. This function takes horizontal and vertical mesh information and constructs a set of quadrilaterals that represent the transect’s path through the MPAS-Ocean mesh. The resulting quads can then be used for plotting or further analysis.

The remaining functions and those in Horizontal Transect Interpolation are lower level functions that are used by compute_transect() and are not typically called directly.

The function mpas_tools.ocean.viz.transect.find_transect_levels_and_weights() constructs a vertical coordinate for a transect and computes interpolation weights that can be used in interp_mpas_to_transect_nodes() to performed linear interpolation.

The function mpas_tools.ocean.viz.transect.interp_mpas_to_transect_cells() interpolates an MPAS-Ocean DataArray to transect cells, keeping constant values over each MPAS-Ocean cell. This function uses the indices computed by find_transect_levels_and_weights() to map data from the MPAS-Ocean mesh onto the transect. The result is an xarray.DataArray with values sampled to transect cells.

The function mpas_tools.ocean.viz.transect.interp_mpas_to_transect_nodes() interpolates an MPAS-Ocean DataArray to transect nodes, linearly interpolating fields between the closest neighboring cells. This function uses the interpolation weights computed by find_transect_levels_and_weights() to map data from the MPAS-Ocean mesh onto the transect. The result is an xarray.DataArray with values interpolated to the transect’s nodes.

The function mpas_tools.ocean.viz.transect.interp_transect_grid_to_transect_nodes() interpolates a 2D grid of data to transect nodes, linearly interpolating fields between the closest neighboring cells. This requires that the z_transect parameter has been passed into function find_transect_levels_and_weights() (or compute_transect()) uses weights generated in find_transect_levels_and_weights() to interpolate data from the MPAS-Ocean mesh to transect nodes the transect, resulting an xarray.DataArray with values.