Masked array / package problem

[chiaradegeeter]

Hi,
I have been trying to get the py-eddy-tracker examples running, but keep getting 'NumbaTypeError: Unsupported array type: numpy.ma.MaskedArray.' errors. I encounter this problem for instance when running the https://github.com/AntSimi/py-eddy-tracker/blob/master/examples/02_eddy_identification/pet_eddy_detection_gulf_stream.py script for the g.add_uv("adt") line. I assume this is a package incompatibility issue, but I have been unable to find a solution.
I am running on windows with

Python: 3.10.20
numpy: 1.26.4
numba: 0.65.0
netCDF4: 1.7.4
pint: 0.24.4
py_eddy_tracker: v3.6.1

Any help would be greatly appreciated.

     56 update_axes(ax, m)
     58 # %%
     59 # Get geostrophic speed u,v
     60 # -------------------------
     61 # U/V are deduced from ADT, this algortihm is not ok near the equator (~+- 2°)
---> 62 g.add_uv("adt")
     64 # %%
     65 # Pre-processings
     66 # ---------------
     67 # Apply a high-pass filter to remove the large scale and highlight the mesoscale
     68 g.bessel_high_filter("adt", 700)

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\site-packages\py_eddy_tracker\dataset\grid.py:1872, in RegularGridDataset.add_uv(self, grid_height, uname, vname, stencil_halfwidth)
   1869 # Compute v
   1870 mode = "wrap" if self.is_circular() else "reflect"
   1871 self.vars[vname] = (
-> 1872     self.compute_stencil(data, mode=mode, stencil_halfwidth=stencil_halfwidth)
   1873     * gof
   1874 )
   1875 # Compute u
   1876 self.vars[uname] = (
   1877     -self.compute_stencil(
   1878         data, vertical=True, stencil_halfwidth=stencil_halfwidth
   1879     )
   1880     * gof
   1881 )

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\site-packages\py_eddy_tracker\dataset\grid.py:1754, in RegularGridDataset.compute_stencil(self, data, stencil_halfwidth, mode, vertical)
   1752 stencil_halfwidth = max(min(int(stencil_halfwidth), 4), 1)
   1753 logger.debug("Stencil half width apply : %d", stencil_halfwidth)
-> 1754 g, m = compute_stencil(
   1755     self.x_c,
   1756     self.y_c,
   1757     data.data,
   1758     self.get_mask(data),
   1759     self.EARTH_RADIUS,
   1760     vertical=vertical,
   1761     stencil_halfwidth=stencil_halfwidth,
   1762 )
   1763 return ma.array(g, mask=m)

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\site-packages\numba\core\dispatcher.py:687, in _DispatcherBase.typeof_pyval(self, val)
    681 """
    682 Resolve the Numba type of Python value *val*.
    683 This is called from numba._dispatcher as a fallback if the native code
    684 cannot decide the type.
    685 """
    686 try:
--> 687     tp = typeof(val, Purpose.argument)
    688 except (errors.NumbaValueError, ValueError):
    689     tp = types.pyobject

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\site-packages\numba\core\typing\typeof.py:33, in typeof(val, purpose)
     31 # Note the behaviour for Purpose.argument must match _typeof.c.
     32 c = _TypeofContext(purpose)
---> 33 ty = typeof_impl(val, c)
     34 if ty is None:
     35     msg = _termcolor.errmsg(
     36         f"Cannot determine Numba type of {type(val)}")

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\functools.py:889, in singledispatch.<locals>.wrapper(*args, **kw)
    885 if not args:
    886     raise TypeError(f'{funcname} requires at least '
    887                     '1 positional argument')
--> 889 return dispatch(args[0].__class__)(*args, **kw)

File ~\AppData\Local\miniconda3\envs\eddytracker\lib\site-packages\numba\core\typing\typeof.py:246, in _typeof_ndarray(val, c)
    244 if isinstance(val, np.ma.MaskedArray):
    245     msg = "Unsupported array type: numpy.ma.MaskedArray."
--> 246     raise errors.NumbaTypeError(msg)
    247 try:
    248     dtype = numpy_support.from_dtype(val.dtype)

NumbaTypeError: Unsupported array type: numpy.ma.MaskedArray.

[AntSimi]

Hi,
Take a look at issue #221
PyEddyTracker need evolution to work with recent version of numba.

[chiaradegeeter]

Hi,
Thanks a lot for your quick reply, and my apologies for overlooking issue 221. Indeed, I was able to make the environment work by downgrading numba and a couple of other packages.

conda create -n eddytracker_clean -c conda-forge python=3.10 numpy=1.22.4 numba=0.55.2 scipy=1.10.1 matplotlib=3.7.3 xarray=2023.1.0 netcdf4=1.5.8 setuptools spyder zarr opencv pint=0.18 pip -y
pip install py-eddy-tracker --no-deps
pip install polygon3

Thanks again for your help.