diff --git a/README.html b/README.html index e00af58..fecfc46 100644 --- a/README.html +++ b/README.html @@ -230,6 +230,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
  • @@ -526,6 +531,10 @@

    Running on Your Own Machine +
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    + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    + On this page +
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    +

    Animation

    +

    time stamp at 1:19

    +

    NCL_animate_1

    +

    Please note:

    +
      +
    • Executing this script will not display a gif, but you have the option to uncomment a line at the bottom that will save a gif in the same directory as this script.

    • +
    +

    GeoCAT-examples

    +
    +

    Import packages:

    +
    +
    +
    import cartopy.crs as ccrs
    +import matplotlib.animation as animation
    +import numpy as np
    +import xarray as xr
    +from matplotlib import pyplot as plt
    +
    +import geocat.datafiles as gdf
    +import geocat.viz as gv
    +
    +
    +
    +
    +
    Downloading file 'registry.txt' from 'https://github.com/NCAR/GeoCAT-datafiles/raw/main/registry.txt' to '/home/runner/.cache/geocat'.
    +
    +
    +
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    +
    +

    Read in data:

    +
    +
    +
    # Open a netCDF data file using xarray default engine and load the data into xarrays
    +# Disable time decoding due to missing necessary metadata
    +ds = xr.open_dataset(gdf.get("netcdf_files/meccatemp.cdf"), decode_times=False)
    +
    +tas = ds.t
    +tas
    +
    +
    +
    +
    +
    Downloading file 'netcdf_files/meccatemp.cdf' from 'https://github.com/NCAR/GeoCAT-datafiles/raw/main/netcdf_files/meccatemp.cdf' to '/home/runner/.cache/geocat'.
    +
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    +
    + + + + + + + + + + + + + + +
    <xarray.DataArray 't' (time: 31, lat: 40, lon: 49)>
    +[60760 values with dtype=float32]
    +Coordinates:
    +  * lat      (lat) int32 -86 -82 -77 -73 -68 -64 -59 ... 59 64 68 73 77 82 86
    +  * lon      (lon) int32 -180 -172 -165 -157 -150 -142 ... 150 157 165 172 180
    +  * time     (time) int32 1 2 3 4 5 6 7 8 9 10 ... 22 23 24 25 26 27 28 29 30 31
    +Attributes:
    +    units:    degrees
    +
    +
    +
    +

    Create animation:

    +
    +
    +
    # Set up Axes with Cartopy Projection
    +fig = plt.figure(figsize=(10, 8))
    +ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=150))
    +ax.coastlines(linewidths=0.5)
    +ax.set_extent([-180, 180, -90, 90], ccrs.PlateCarree())
    +
    +# Use geocat.viz.util convenience function to set axes limits & tick values
    +gv.set_axes_limits_and_ticks(ax,
    +                             xlim=(-180, 180),
    +                             ylim=(-90, 90),
    +                             xticks=np.linspace(-180, 180, 13),
    +                             yticks=np.linspace(-90, 90, 7))
    +
    +# Use geocat.viz.util convenience function to add minor and major tick lines
    +gv.add_major_minor_ticks(ax, labelsize=10)
    +
    +# Use geocat.viz.util convenience function to make latitude, longitude tick labels
    +gv.add_lat_lon_ticklabels(ax)
    +
    +# create initial plot that establishes a colorbar
    +tas[0, :, :].plot.contourf(ax=ax,
    +                           transform=ccrs.PlateCarree(),
    +                           vmin=195,
    +                           vmax=328,
    +                           levels=53,
    +                           cmap="inferno",
    +                           cbar_kwargs={
    +                               "extendrect": True,
    +                               "orientation": "horizontal",
    +                               "ticks": np.arange(195, 332, 9),
    +                               "label": "",
    +                               "shrink": 0.90
    +                           })
    +
    +
    +# animate function for matplotlib FuncAnimation
    +def animate(i):
    +    tas[i, :, :].plot.contourf(
    +        ax=ax,
    +        transform=ccrs.PlateCarree(),
    +        vmin=195,
    +        vmax=328,
    +        levels=53,
    +        cmap="inferno",
    +        add_colorbar=False,
    +    )
    +
    +    gv.set_titles_and_labels(
    +        ax,
    +        maintitle="January Global Surface Temperature (K) - Day  " +
    +        str(tas.coords['time'].values[i])[:13],
    +        xlabel="",
    +        ylabel="")
    +
    +
    +
    +
    +
    /usr/share/miniconda3/envs/cookbook-dev/lib/python3.10/site-packages/cartopy/io/__init__.py:241: DownloadWarning: Downloading: https://naturalearth.s3.amazonaws.com/110m_physical/ne_110m_coastline.zip
    +  warnings.warn(f'Downloading: {url}', DownloadWarning)
    +
    +
    +../_images/a8193169e72e8c4254ded28daa11b0c426f09c9b5a7713d0fe737ed0892eabb6.png +
    +
    +
    +
    +

    Run:

    +
    +
    +
    # runs the animation initiated with the frame from init and progressed with the animate function
    +anim = animation.FuncAnimation(fig, animate, frames=30, interval=200)
    +
    +
    +
    +
    +
    +
    +

    Save:

    +
    +
    +
    # Uncomment this line to save the created animation
    +anim.save('images/animate_1.gif', writer='pillow', fps=5);
    +
    +
    +
    +
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    + + + + +
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    + + + + + + \ No newline at end of file diff --git a/notebooks/comparison.html b/notebooks/comparison.html index 840b6f5..a8c01ab 100644 --- a/notebooks/comparison.html +++ b/notebooks/comparison.html @@ -231,6 +231,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
  • @@ -531,10 +536,6 @@

    Cartopy -
    /usr/share/miniconda3/envs/cookbook-dev/lib/python3.10/site-packages/cartopy/io/__init__.py:241: DownloadWarning: Downloading: https://naturalearth.s3.amazonaws.com/110m_physical/ne_110m_coastline.zip
    -  warnings.warn(f'Downloading: {url}', DownloadWarning)
    -
    -
    ../_images/a8678cc40ae48291a2c974b101b085777c0b09a7a64b408b3418d1861526dfbc.png @@ -636,9 +637,9 @@

    Plotly
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    MPAS with Datashader and Geoviews

    +
    +

    Interactively plotting unstructured grid MPAS data with Datashader and Geoviews

    +

    This example demonstrates several key points:

    +
      +
    1. Making use of the MPAS file’s connectivity information to render data on the native grid, and also +avoid costly Delaunay triangulation that is required if the MPAS connectivity information is not used.

    2. +
    3. Rendering data that is sampled on both the ‘primal’ and ‘dual’ MPAS mesh.

    4. +
    5. Using geoviews/holoviews for interactive plotting in a Jupyter Notebook. The plotting is interactive +in the sense that you can pan and zoom the data. Doing so will reveal greater and greater data fidelity.

    6. +
    7. Using Datashader to perform background rendering in place of Matplotlib. Unlike Matplotlib, Datashader +was designed for performance with large data sets.

    8. +
    +
    +
    +

    The data

    +

    The global data sets used in this example are from the same experiment, but run at several resolutions from +30km to 3.75km. Due to their size, the higher resolution data sets are only distributed with two variables +in them:

    +
      +
    • relhum_200hPa: Relative humidity vertically interpolated to 200 hPa

    • +
    • vorticity_200hPa: Relative vorticity vertically interpolated to 200 hPa

    • +
    +

    The relhum_200hPa is computed on the MPAS ‘primal’ mesh, while the vorticity_200hPa is computed on the MPAS +‘dual’ mesh. Note that data may also be sampled on the edges of the primal mesh. This example does not +include/cover edge-centered data.

    +

    These data are courtesy of NCAR’s Falko Judt, and were produced as part of the DYAMOND initiative: +http://dx.doi.org/10.1186/s40645-019-0304-z.

    +
    +
    +
    import cartopy.crs as ccrs
    +import numpy as np
    +import pandas as pd
    +
    +import math as math
    +
    +import geocat.datafiles as gdf  # Only for reading-in datasets
    +
    +from xarray import open_mfdataset
    +
    +from numba import jit
    +
    +import dask.dataframe as dd
    +
    +import holoviews as hv
    +from holoviews import opts
    +
    +from holoviews.operation.datashader import rasterize as hds_rasterize 
    +#import geoviews.feature as gf # only needed for coastlines
    +
    +hv.extension("bokeh","matplotlib")
    +
    +opts.defaults(
    +    opts.Image(frame_width=600, data_aspect=1),
    +    opts.RGB(frame_width=600, data_aspect=1))
    +
    +
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    Utility functions

    +
    +
    +
    # This funtion splits a global mesh along longitude
    +#
    +# Examine the X coordinates of each triangle in 'tris'. Return an array of 'tris' where only those triangles
    +# with legs whose length is less than 't' are returned. 
    +# 
    +def unzipMesh(x,tris,t):
    +    return tris[(np.abs((x[tris[:,0]])-(x[tris[:,1]])) < t) & (np.abs((x[tris[:,0]])-(x[tris[:,2]])) < t)]
    +
    +
    +
    +
    +
    +
    +
    # Compute the signed area of a triangle
    +#
    +def triArea(x,y,tris):
    +    return ((x[tris[:,1]]-x[tris[:,0]]) * (y[tris[:,2]]-y[tris[:,0]])) - ((x[tris[:,2]]-x[tris[:,0]]) * (y[tris[:,1]]-y[tris[:,0]]))
    +
    +
    +
    +
    +
    +
    +
    # Reorder triangles as necessary so they all have counter clockwise winding order. CCW is what Datashader and MPL
    +# require.
    +#
    +def orderCCW(x,y,tris):
    +    tris[triArea(x,y,tris)<0.0,:] = tris[triArea(x,y,tris)<0.0,::-1]
    +    return(tris)
    +
    +
    +
    +
    +
    +
    +
    # Create a Holoviews Triangle Mesh suitable for rendering with Datashader
    +#
    +# This function returns a Holoviews TriMesh that is created from a list of coordinates, 'x' and 'y',
    +# an array of triangle indices that addressess the coordinates in 'x' and 'y', and a data variable 'var'. The
    +# data variable's values will annotate the triangle vertices
    +#
    +
    +def createHVTriMesh(x,y,triangle_indices, var,n_workers=1):
    +    # Declare verts array
    +    verts = np.column_stack([x, y, var])
    +
    +
    +    # Convert to pandas
    +    verts_df  = pd.DataFrame(verts,  columns=['x', 'y', 'z'])
    +    tris_df   = pd.DataFrame(triangle_indices, columns=['v0', 'v1', 'v2'])
    +
    +    # Convert to dask
    +    verts_ddf = dd.from_pandas(verts_df, npartitions=n_workers)
    +    tris_ddf = dd.from_pandas(tris_df, npartitions=n_workers)
    +
    +    # Declare HoloViews element
    +    tri_nodes = hv.Nodes(verts_ddf, ['x', 'y', 'index'], ['z'])
    +    trimesh = hv.TriMesh((tris_ddf, tri_nodes))
    +    return(trimesh)
    +
    +
    +
    +
    +
    +
    +
    # Triangulate MPAS primary mesh:
    +#
    +# Triangulate each polygon in a heterogenous mesh of n-gons by connecting
    +# each internal polygon vertex to the first vertex. Uses the MPAS
    +# auxilliary variables verticesOnCell, and nEdgesOnCell.
    +#
    +# The function is decorated with Numba's just-in-time compiler so that it is translated into
    +# optimized machine code for better peformance
    +#
    +
    +@jit(nopython=True)
    +def triangulatePoly(verticesOnCell, nEdgesOnCell):
    +
    +    # Calculate the number of triangles. nEdgesOnCell gives the number of vertices for each cell (polygon)
    +    # The number of triangles per polygon is the number of vertices minus 2.
    +    #
    +    nTriangles = np.sum(nEdgesOnCell - 2)
    +
    +    triangles = np.ones((nTriangles, 3), dtype=np.int64)
    +    nCells = verticesOnCell.shape[0]
    +    triIndex = 0
    +    for j in range(nCells):
    +        for i in range(nEdgesOnCell[j]-2):
    +            triangles[triIndex][0] = verticesOnCell[j][0]
    +            triangles[triIndex][1] = verticesOnCell[j][i+1]
    +            triangles[triIndex][2] = verticesOnCell[j][i+2]
    +            triIndex += 1
    +
    +    return triangles
    +
    +
    +
    +
    +
    +
    +

    Load data and coordinates

    +

    The dyamond_1 data set is available in several resolutions, ranging from 30 km to 3.75 km.

    +

    Currently, the 30-km resolution dataset used in this example is available at geocat-datafiles. +However, the other resolutions of these data are stored on Glade because of their size.

    +
    +
    +

    Example 1 - Using MPAS’s cell connectivity array to plot primal mesh data

    +

    In this example we use the MPAS cellsOnVertex auxilliary variable, which defines mesh connectivity for the MPAS grid. +Specifically, this variable tells us the cell IDs for each cell that contains each vertex.

    +

    The benefits of this are twofold: 1. We’re using the actual mesh description from the MPAS output file; and 2. +For large grid this is much faster than synthesizing the connectivity information as is done +in the next example

    +
    +
    +

    Example 2 - Synthesizing triangles from points using Delaunay triangulation

    +

    In this second example we do not use the triangle connectivity information stored in the MPAS file. Instead we +use Delaunay triangulation to artifically create a triangle mesh. The benefit of this approach is that we do not +need the MPAS cellsOnVertex variable if it is not available. Also, since the triangulation algorithm is run on the +coordinates after they are projected to meters we do not have to worry about wraparound. The downside is that for +high-resolution data Delaunay triangulation is prohibitively expensive. The highest resolution data set included +in this notebook (3.75km) will not triangulate in a reasonable amount of time, if at all

    +
    +
    +

    Example 3 - Using MPAS’s cell connectivity array to plot dual mesh data

    +

    In this example we use the MPAS verticesOnCell and nEdgesOnCell auxilliary variables, which defines mesh connectivity for the +MPAS dual grid.

    +

    As with the first example using the MPAS primal grid, data on the dual grid could be plotted by first +triangulating them with, for example, Delaunay triangulation. But using grid’s native connectivity information +is faster.

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    + + \ No newline at end of file diff --git a/notebooks/notebook-template.html b/notebooks/notebook-template.html index b7679f4..d405efb 100644 --- a/notebooks/notebook-template.html +++ b/notebooks/notebook-template.html @@ -231,6 +231,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
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    of further and further
    header levels

    as well \(m = a * t / h\) text! Similarly, you have access to other \(\LaTeX\) equation functionality via MathJax (demo below from link),

    -
    -()\[\begin{align} +
    +()\[\begin{align} \dot{x} & = \sigma(y-x) \\ \dot{y} & = \rho x - y - xz \\ \dot{z} & = -\beta z + xy diff --git a/notebooks/plot-elements.html b/notebooks/plot-elements.html index fffafdd..25110fe 100644 --- a/notebooks/plot-elements.html +++ b/notebooks/plot-elements.html @@ -231,6 +231,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
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    Colorbars
    diff --git a/notebooks/skewt.html b/notebooks/skewt.html new file mode 100644 index 0000000..f2be0a6 --- /dev/null +++ b/notebooks/skewt.html @@ -0,0 +1,457 @@ + + + + + + + + Skew T Diagrams — Advanced Visualization Cookbook + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    +

    Skew T Diagrams

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    + + \ No newline at end of file diff --git a/notebooks/spagetti.html b/notebooks/spagetti.html index ebb12b9..84e55e3 100644 --- a/notebooks/spagetti.html +++ b/notebooks/spagetti.html @@ -54,7 +54,7 @@ - + @@ -230,6 +230,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
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    Prerequisites -
    Downloading file 'registry.txt' from 'https://github.com/NCAR/GeoCAT-datafiles/raw/main/registry.txt' to '/home/runner/.cache/geocat'.
    -
    -
    -

    - diff --git a/notebooks/taylor-diagrams.html b/notebooks/taylor-diagrams.html index 714c174..37503d3 100644 --- a/notebooks/taylor-diagrams.html +++ b/notebooks/taylor-diagrams.html @@ -54,7 +54,7 @@ - + @@ -231,6 +231,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
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    Resources and referencesPlot Elements

    - +

    next

    -

    Spagetti Plots

    +

    Skew T Diagrams

    diff --git a/objects.inv b/objects.inv index e4336ee..6c8a8df 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/search.html b/search.html index c4d98e2..b378ba6 100644 --- a/search.html +++ b/search.html @@ -235,6 +235,11 @@ Taylor Diagrams +
  • + + Skew T Diagrams + +
  • diff --git a/searchindex.js b/searchindex.js index fc7e8b3..6d352aa 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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