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error plotting with cartopy & matplotlib #6927

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4 tasks done
arfriedman opened this issue Aug 17, 2022 · 2 comments
Closed
4 tasks done

error plotting with cartopy & matplotlib #6927

arfriedman opened this issue Aug 17, 2022 · 2 comments
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@arfriedman
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What happened?

I am encountering an error while attempting to plot xarray fields using cartopy & matplotlib. [I'm posting here first but I'm not sure if the error is due to xarray, cartopy, or matplotlib].

What did you expect to happen?

Here is an example of the error using a plot from @rabernat's course: https://earth-env-data-science.github.io/lectures/mapping_cartopy.html#xarray-integration

Minimal Complete Verifiable Example

import cartopy.crs as ccrs
import matplotlib.pyplot as plt
import xarray as xr
url = 'http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/noaa.ersst.v5/sst.mnmean.nc'
ds = xr.open_dataset(url, drop_variables=['time_bnds'])
sst = ds.sst.sel(time='2000-01-01', method='nearest')
fig = plt.figure(figsize=(9,6))
ax = plt.axes(projection=ccrs.Robinson())
ax.coastlines()
ax.gridlines()
sst.plot(ax=ax, transform=ccrs.PlateCarree(),
         vmin=2, vmax=30)

MVCE confirmation

  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

TypeError                                 Traceback (most recent call last)
Input In [12], in <cell line: 11>()
      9 ax.coastlines()
     10 ax.gridlines()
---> 11 sst.plot(ax=ax, transform=ccrs.PlateCarree(),
     12          vmin=2, vmax=30)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/xarray/plot/plot.py:868, in _PlotMethods.__call__(self, **kwargs)
    867 def __call__(self, **kwargs):
--> 868     return plot(self._da, **kwargs)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/xarray/plot/plot.py:334, in plot(darray, row, col, col_wrap, ax, hue, rtol, subplot_kws, **kwargs)
    330     plotfunc = hist
    332 kwargs["ax"] = ax
--> 334 return plotfunc(darray, **kwargs)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/xarray/plot/plot.py:1212, in _plot2d.<locals>.newplotfunc(darray, x, y, figsize, size, aspect, ax, row, col, col_wrap, xincrease, yincrease, add_colorbar, add_labels, vmin, vmax, cmap, center, robust, extend, levels, infer_intervals, colors, subplot_kws, cbar_ax, cbar_kwargs, xscale, yscale, xticks, yticks, xlim, ylim, norm, **kwargs)
   1208     raise ValueError("plt.imshow's `aspect` kwarg is not available in xarray")
   1210 ax = get_axis(figsize, size, aspect, ax, **subplot_kws)
-> 1212 primitive = plotfunc(
   1213     xplt,
   1214     yplt,
   1215     zval,
   1216     ax=ax,
   1217     cmap=cmap_params["cmap"],
   1218     vmin=cmap_params["vmin"],
   1219     vmax=cmap_params["vmax"],
   1220     norm=cmap_params["norm"],
   1221     **kwargs,
   1222 )
   1224 # Label the plot with metadata
   1225 if add_labels:

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/xarray/plot/plot.py:1478, in pcolormesh(x, y, z, ax, xscale, yscale, infer_intervals, **kwargs)
   1475         y = _infer_interval_breaks(y, axis=1, scale=yscale)
   1476         y = _infer_interval_breaks(y, axis=0, scale=yscale)
-> 1478 primitive = ax.pcolormesh(x, y, z, **kwargs)
   1480 # by default, pcolormesh picks "round" values for bounds
   1481 # this results in ugly looking plots with lots of surrounding whitespace
   1482 if not hasattr(ax, "projection") and x.ndim == 1 and y.ndim == 1:
   1483     # not a cartopy geoaxis

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:318, in _add_transform.<locals>.wrapper(self, *args, **kwargs)
    313     raise ValueError(f'Invalid transform: Spherical {func.__name__} '
    314                      'is not supported - consider using '
    315                      'PlateCarree/RotatedPole.')
    317 kwargs['transform'] = transform
--> 318 return func(self, *args, **kwargs)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:1799, in GeoAxes.pcolormesh(self, *args, **kwargs)
   1797 result = matplotlib.axes.Axes.pcolormesh(self, *args, **kwargs)
   1798 # Wrap the quadrilaterals if necessary
-> 1799 result = self._wrap_quadmesh(result, **kwargs)
   1800 # Re-cast the QuadMesh as a GeoQuadMesh to enable future wrapping
   1801 # updates to the collection as well.
   1802 result.__class__ = cartopy.mpl.geocollection.GeoQuadMesh

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:1982, in GeoAxes._wrap_quadmesh(self, collection, **kwargs)
   1968 # Plot all of the wrapped cells.
   1969 # `pcolor` only draws polygons where the data is not
   1970 # masked, so this will only draw a limited subset of
   (...)
   1978 #       fill in the proper data later with set_array()
   1979 #       calls.
   1980 pcolor_data = np.ma.array(np.zeros(C.shape),
   1981                           mask=~mask)
-> 1982 pcolor_col = self.pcolor(coords[..., 0], coords[..., 1],
   1983                          pcolor_data, zorder=zorder,
   1984                          **kwargs)
   1985 # Now add back in the masked data if there was any
   1986 full_mask = ~mask if C_mask is None else ~mask | C_mask

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:318, in _add_transform.<locals>.wrapper(self, *args, **kwargs)
    313     raise ValueError(f'Invalid transform: Spherical {func.__name__} '
    314                      'is not supported - consider using '
    315                      'PlateCarree/RotatedPole.')
    317 kwargs['transform'] = transform
--> 318 return func(self, *args, **kwargs)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:2027, in GeoAxes.pcolor(self, *args, **kwargs)
   2024 result = matplotlib.axes.Axes.pcolor(self, *args, **kwargs)
   2026 # Update the datalim for this pcolor.
-> 2027 limits = result.get_datalim(self.transData)
   2028 self.update_datalim(limits)
   2030 self.autoscale_view()

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py:280, in Collection.get_datalim(self, transData)
    277     return transforms.Bbox.null()
    279 if not transform.is_affine:
--> 280     paths = [transform.transform_path_non_affine(p) for p in paths]
    281     # Don't convert transform to transform.get_affine() here because
    282     # we may have transform.contains_branch(transData) but not
    283     # transforms.get_affine().contains_branch(transData).  But later,
    284     # be careful to only apply the affine part that remains.
    286 if any(transform.contains_branch_seperately(transData)):

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py:280, in <listcomp>(.0)
    277     return transforms.Bbox.null()
    279 if not transform.is_affine:
--> 280     paths = [transform.transform_path_non_affine(p) for p in paths]
    281     # Don't convert transform to transform.get_affine() here because
    282     # we may have transform.contains_branch(transData) but not
    283     # transforms.get_affine().contains_branch(transData).  But later,
    284     # be careful to only apply the affine part that remains.
    286 if any(transform.contains_branch_seperately(transData)):

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/transforms.py:2436, in CompositeGenericTransform.transform_path_non_affine(self, path)
   2434     return path
   2435 elif not self._a.is_affine and self._b.is_affine:
-> 2436     return self._a.transform_path_non_affine(path)
   2437 else:
   2438     return self._b.transform_path_non_affine(
   2439                             self._a.transform_path(path))

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:190, in InterProjectionTransform.transform_path_non_affine(self, src_path)
    186 geoms = cpatch.path_to_geos(src_path,
    187                             getattr(self, 'force_path_ccw', False))
    189 for geom in geoms:
--> 190     proj_geom = self.target_projection.project_geometry(
    191         geom, self.source_projection)
    192     transformed_geoms.append(proj_geom)
    194 if not transformed_geoms:

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py:805, in Projection.project_geometry(self, geometry, src_crs)
    803 if not method_name:
    804     raise ValueError(f'Unsupported geometry type {geom_type!r}')
--> 805 return getattr(self, method_name)(geometry, src_crs)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py:948, in Projection._project_polygon(self, polygon, src_crs)
    946 multi_lines = []
    947 for src_ring in [polygon.exterior] + list(polygon.interiors):
--> 948     p_rings, p_mline = self._project_linear_ring(src_ring, src_crs)
    949     if p_rings:
    950         rings.extend(p_rings)

File ~/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py:824, in Projection._project_linear_ring(self, linear_ring, src_crs)
    819 debug = False
    820 # 1) Resolve the initial lines into projected segments
    821 # 1abc
    822 # def23ghi
    823 # jkl41
--> 824 multi_line_string = cartopy.trace.project_linear(linear_ring,
    825                                                  src_crs, self)
    827 # Threshold for whether a point is close enough to be the same
    828 # point as another.
    829 threshold = max(np.abs(self.x_limits + self.y_limits)) * 1e-5

File lib/cartopy/trace.pyx:628, in cartopy.trace.project_linear()

File lib/cartopy/trace.pyx:100, in cartopy.trace.geos_from_shapely()

TypeError: an integer is required

Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/tkinter/__init__.py", line 1921, in __call__
    return self.func(*args)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/tkinter/__init__.py", line 839, in callit
    func(*args)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/_backend_tk.py", line 252, in idle_draw
    self.draw()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/backend_tkagg.py", line 9, in draw
    super().draw()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 436, in draw
    self.figure.draw(self.renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 74, in draw_wrapper
    result = draw(artist, renderer, *args, **kwargs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/figure.py", line 2845, in draw
    mimage._draw_list_compositing_images(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 558, in draw
    return matplotlib.axes.Axes.draw(self, renderer=renderer, **kwargs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 3091, in draw
    mimage._draw_list_compositing_images(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 990, in draw
    super().draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 366, in draw
    transform, transOffset, offsets, paths = self._prepare_points()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 343, in _prepare_points
    paths = [transform.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 343, in <listcomp>
    paths = [transform.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/transforms.py", line 2436, in transform_path_non_affine
    return self._a.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 190, in transform_path_non_affine
    proj_geom = self.target_projection.project_geometry(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 805, in project_geometry
    return getattr(self, method_name)(geometry, src_crs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 948, in _project_polygon
    p_rings, p_mline = self._project_linear_ring(src_ring, src_crs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 824, in _project_linear_ring
    multi_line_string = cartopy.trace.project_linear(linear_ring,
  File "lib/cartopy/trace.pyx", line 628, in cartopy.trace.project_linear
  File "lib/cartopy/trace.pyx", line 100, in cartopy.trace.geos_from_shapely
TypeError: an integer is required
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/tkinter/__init__.py", line 1921, in __call__
    return self.func(*args)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/tkinter/__init__.py", line 839, in callit
    func(*args)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/_backend_tk.py", line 252, in idle_draw
    self.draw()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/backend_tkagg.py", line 9, in draw
    super().draw()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 436, in draw
    self.figure.draw(self.renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 74, in draw_wrapper
    result = draw(artist, renderer, *args, **kwargs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/figure.py", line 2845, in draw
    mimage._draw_list_compositing_images(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 558, in draw
    return matplotlib.axes.Axes.draw(self, renderer=renderer, **kwargs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 3091, in draw
    mimage._draw_list_compositing_images(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/image.py", line 132, in _draw_list_compositing_images
    a.draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 990, in draw
    super().draw(renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/artist.py", line 51, in draw_wrapper
    return draw(artist, renderer)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 366, in draw
    transform, transOffset, offsets, paths = self._prepare_points()
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 343, in _prepare_points
    paths = [transform.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/collections.py", line 343, in <listcomp>
    paths = [transform.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/matplotlib/transforms.py", line 2436, in transform_path_non_affine
    return self._a.transform_path_non_affine(path)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py", line 190, in transform_path_non_affine
    proj_geom = self.target_projection.project_geometry(
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 805, in project_geometry
    return getattr(self, method_name)(geometry, src_crs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 948, in _project_polygon
    p_rings, p_mline = self._project_linear_ring(src_ring, src_crs)
  File "/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/cartopy/crs.py", line 824, in _project_linear_ring
    multi_line_string = cartopy.trace.project_linear(linear_ring,
  File "lib/cartopy/trace.pyx", line 628, in cartopy.trace.project_linear
  File "lib/cartopy/trace.pyx", line 100, in cartopy.trace.geos_from_shapely
TypeError: an integer is required

Anything else we need to know?

No response

Environment

/home/andrew/miniconda3/envs/AQUATIC/lib/python3.10/site-packages/_distutils_hack/init.py:33: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")

INSTALLED VERSIONS

commit: None
python: 3.10.5 | packaged by conda-forge | (main, Jun 14 2022, 07:04:59) [GCC 10.3.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-122-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.8.1

xarray: 2022.6.0
pandas: 1.4.3
numpy: 1.23.2
scipy: 1.9.0
netCDF4: 1.6.0
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: 1.6.1
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2022.8.0
distributed: 2022.8.0
matplotlib: 3.5.3
cartopy: 0.20.3
seaborn: 0.11.2
numbagg: None
fsspec: 2022.7.1
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 65.0.2
pip: 22.2.2
conda: None
pytest: None
IPython: 8.4.0
sphinx: None
@arfriedman arfriedman added bug needs triage Issue that has not been reviewed by xarray team member labels Aug 17, 2022
@keewis
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keewis commented Aug 18, 2022 •
edited
Loading

this seems to be a compatibility issue between cartopy and shapely=1.8.3, see SciTools/cartopy#2067. Installing shapely!=1.8.3 should avoid the TypeError for now.

closing since we can't really do anything about this.

@keewis keewis closed this as completed Aug 18, 2022
@keewis keewis added upstream issue and removed needs triage Issue that has not been reviewed by xarray team member bug labels Aug 18, 2022
@arfriedman
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Thank you. It also now works with shapely 1.8.4.

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