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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help in calculating planetary vorticity advection? #3227

tik619 Oct 14, 2023

Replies: 6 comments · 1 reply

winash12 Oct 15, 2023

tik619 Oct 15, 2023 Author

dopplershift Oct 17, 2023 Maintainer

tik619 Oct 18, 2023 Author

dopplershift Oct 18, 2023 Maintainer

tik619 Oct 19, 2023 Author

sgdecker Nov 29, 2023

tik619
Oct 14, 2023

Replies: 6 comments 1 reply

winash12
Oct 15, 2023

tik619
Oct 15, 2023
Author

dopplershift
Oct 17, 2023
Maintainer

tik619
Oct 18, 2023
Author

dopplershift Oct 18, 2023
Maintainer

tik619
Oct 19, 2023
Author

sgdecker
Nov 29, 2023