help in calculating planetary vorticity advection? #3227

tik619 · 2023-10-14T07:31:52Z

tik619
Oct 14, 2023

Hi, I am trying to calculate the advection of planetary vorticity, but encountering an error. Can anyone say how to reslove this or hoe advection of planetary vorticity can be done. Below I am posting my code, along with the error.

import xarray as xr
import metpy.calc as mpcalc
import numpy as np
#################################
data = xr.open_dataset('/mnt/h/MPAS/HICS/VAR/ERA/AMPHAN.variables.nc')
##################################
data["lev"].attrs["units"] = "hPa"
#################################
# Calcualte dx and dy for calculations
dx, dy = mpcalc.lat_lon_grid_deltas(data.lon, data.lat)
f = mpcalc.coriolis_parameter(np.deg2rad(data.lat.values)).to('1/s')
vo_adv = mpcalc.advection(data.vorticity, data.uReconstructZonal, data.uReconstructMeridional )
planetary_vorticity_advection = mpcalc.advection(f[:,None,None,None], data.uReconstructZonal, data.uReconstructMeridional)

And the error:

Traceback (most recent call last):

  Input In [2] in <cell line: 1>
    planetary_vorticity_advection = mpcalc.advection(f[:,None,None,None], data.uReconstructZonal, data.uReconstructMeridional)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/kinematics.py:455 in advection
    gradient_vector = geospatial_gradient(scalar, dx=dx, dy=dy, x_dim=x_dim, y_dim=y_dim,

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1671 in geospatial_gradient
    derivatives[component] = first_derivative(f, delta=delta, axis=dim)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:951 in wrapper
    return preprocess_and_wrap()(func)(f, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1238 in first_derivative
    n, axis, delta = _process_deriv_args(f, axis, x, delta)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1731 in _process_deriv_args
    raise ValueError('f must have at least 3 point along the desired axis.')

ValueError: f must have at least 3 point along the desired axis.

winash12 · 2023-10-15T02:57:41Z

winash12
Oct 15, 2023

Can you share some sample data somewhere so that someone else can reproduce this issue ?

0 replies

tik619 · 2023-10-15T08:14:09Z

tik619
Oct 15, 2023
Author

please find the attached link for the sample data. data

0 replies

dopplershift · 2023-10-17T17:28:59Z

dopplershift
Oct 17, 2023
Maintainer

This line looks wrong:

planetary_vorticity_advection = mpcalc.advection(f[:,None,None,None], data.uReconstructZonal, data.uReconstructMeridional)

This tries to expand to 4-dims, but it puts latitude as the first dimension, followed by a bunch of size-1 dimensions.
You're trying to calculate advection across longitude, but the array only has a size of 1 along that dimension, that's why it raises an error.

Try this, which only calculates the advection across latitudes:

planetary_vorticity_advection = mpcalc.advection(f[..., :, None], v=data.uReconstructZonal)

0 replies

tik619 · 2023-10-18T07:11:11Z

tik619
Oct 18, 2023
Author

I tried by the way as suggested:

planetary_vorticity_advection = mpcalc.advection(f[..., :, None], data.uReconstructZonal, data.uReconstructMeridional)

But again I got an error:

Traceback (most recent call last):

  Input In [7] in <cell line: 1>
    planetary_vorticity_advection = mpcalc.advection(f[..., :, None], data.uReconstructZonal, data.uReconstructMeridional)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/kinematics.py:455 in advection
    gradient_vector = geospatial_gradient(scalar, dx=dx, dy=dy, x_dim=x_dim, y_dim=y_dim,

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1671 in geospatial_gradient
    derivatives[component] = first_derivative(f, delta=delta, axis=dim)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:951 in wrapper
    return preprocess_and_wrap()(func)(f, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1238 in first_derivative
    n, axis, delta = _process_deriv_args(f, axis, x, delta)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1728 in _process_deriv_args
    axis = normalize_axis_index(axis if axis is not None else 0, n)

AxisError: axis 3 is out of bounds for array of dimension 2

1 reply

dopplershift Oct 18, 2023
Maintainer

What you wrote:

planetary_vorticity_advection = mpcalc.advection(f[..., :, None], data.uReconstructZonal, data.uReconstructMeridional)

isn't what I suggested. I suggested only calculating 1-D advection, since the f array doesn't have any variation (or even the needed multiple data points) except along the latitude direction. Looks like I got the original wrong, since the the advection needs to be calculated in the meridional direction, so this should do it:

planetary_vorticity_advection = mpcalc.advection(f[..., :, None], v=data.uReconstructMeridional)

tik619 · 2023-10-19T06:06:20Z

tik619
Oct 19, 2023
Author

I am still getting this error:

Traceback (most recent call last):

  Input In [3] in <cell line: 1>
    planetary_vorticity_advection = mpcalc.advection(f[..., :, None], v=data.uReconstructMeridional)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/kinematics.py:455 in advection
    gradient_vector = geospatial_gradient(scalar, dx=dx, dy=dy, x_dim=x_dim, y_dim=y_dim,

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1178 in wrapper
    return func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/units.py:325 in wrapper
    return func(*args, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1671 in geospatial_gradient
    derivatives[component] = first_derivative(f, delta=delta, axis=dim)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:951 in wrapper
    return preprocess_and_wrap()(func)(f, **kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/xarray.py:1328 in wrapper
    result = func(*bound_args.args, **bound_args.kwargs)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1238 in first_derivative
    n, axis, delta = _process_deriv_args(f, axis, x, delta)

  File ~/miniconda3/lib/python3.8/site-packages/metpy/calc/tools.py:1728 in _process_deriv_args
    axis = normalize_axis_index(axis if axis is not None else 0, n)

AxisError: axis 2 is out of bounds for array of dimension 2.

0 replies

sgdecker · 2023-11-29T20:50:25Z

sgdecker
Nov 29, 2023

Since latitude is the third axis in this dataset, I think you want this:

planetary_vorticity_advection = mpcalc.advection(f[None, None, :, None], v=data.uReconstructMeridional)

I can't guarantee that the result of this computation is what is intended, but at least it doesn't crash.

0 replies

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Oct 15, 2023

tik619
Oct 15, 2023
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dopplershift
Oct 17, 2023
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tik619
Oct 18, 2023
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dopplershift Oct 18, 2023
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tik619
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sgdecker
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