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SciTools / cartopy

Cartopy - a cartographic python library with matplotlib support
https://scitools.org.uk/cartopy/docs/latest
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TypeError: 'GeometryCollection' object is not subscriptable (cartopy calling shapely) #2176

Open durack1 opened 1 year ago

durack1 commented 1 year ago

Description

I have hit a repeatable, but confusing error with ~20 timesteps in a long ~1800 timestep global array. The error appears to be sensitive to the levels specified in the optional levels argument, and is reproduced below. It triggers a GeometryCollection error in the shapely library call (see traceback below).

I have included a working example below, which loops through two timesteps, the first works great plotting cleanly, and the second bombs, triggering the GeometryCollection bug. The error continues on subsequent timesteps, after ~20 or so, it starts to work again.

I would appreciate any pointers to resolving this issue, or tips at identifying a workaround to get me plotting through the problem ~20 timesteps.

Code to reproduce

# %% imports
import cartopy.crs as ccrs
import matplotlib.pyplot as plt
import numpy as np
from xarray import open_dataset

# %% load dataset
f = "cartopyLevelBugTwoTimesteps.nc"  # (file will be dropped below)
ds = open_dataset(f)
da = ds.siconc

# %% setup plot
levs1 = list(np.arange(-20, 121, 10))  # siconc
centralLon = 202

# %% step through working and failing timesteps
for time in np.arange(0, 2):
    print("Step:", time)
    ar = da.isel(time=time)
    fig = plt.figure(figsize=(10, 15))

    # Start subplots
    ax1 = fig.add_subplot(3, 1, 1,
                          projection=ccrs.Robinson(
                              central_longitude=centralLon,
                              globe=None,
                              false_easting=None,
                              false_northing=None,
                          ),
                          )
    cs1 = ax1.contourf(da.lon.data, da.lat.data, ar.data,
                       levs1,
                       transform=ccrs.PlateCarree(),
                       cmap="RdBu_r"
                       )
    plt.show()
    # time = 1; Should bomb with "TypeError: 'GeometryCollection' object is not subscriptable"

Data to reproduce

cartopyLevelBugTwoTimesteps.nc.gz

Traceback

Traceback (most recent call last):
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/spyder_kernels/py3compat.py:356 in compat_exec
    exec(code, globals, locals)
  File ~/git/amipbcs/cartopyBug.py:41
    cs1 = ax1.contourf(da.lon.data, da.lat.data, ar.data,
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:318 in wrapper
    return func(self, *args, **kwargs)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:362 in wrapper
    return func(self, *args, **kwargs)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:1665 in contourf
    bboxes = [col.get_datalim(self.transData)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:1665 in <listcomp>
    bboxes = [col.get_datalim(self.transData)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/matplotlib/collections.py:266 in get_datalim
    paths = [transform.transform_path_non_affine(p) for p in paths]
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/matplotlib/collections.py:266 in <listcomp>
    paths = [transform.transform_path_non_affine(p) for p in paths]
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/matplotlib/transforms.py:2431 in transform_path_non_affine
    return self._a.transform_path_non_affine(path)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/mpl/geoaxes.py:190 in transform_path_non_affine
    proj_geom = self.target_projection.project_geometry(
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/crs.py:808 in project_geometry
    return getattr(self, method_name)(geometry, src_crs)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/crs.py:963 in _project_polygon
    return self._rings_to_multi_polygon(rings, is_ccw)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/crs.py:1224 in _rings_to_multi_polygon
    multi_poly = sgeom.MultiPolygon(polygon_bits)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/shapely/geometry/multipolygon.py:79 in __new__
    shell = ob[0]
TypeError: 'GeometryCollection' object is not subscriptable
Full environment definition ### Operating system ``` RHEL7.9 (xcd050xes071spy543mat371car0211ipy8132) bash-4.2$ uname -a Linux detect 3.10.0-1160.76.1.el7.x86_64 #1 SMP Tue Jul 26 14:15:37 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux ``` ### Cartopy version ``` cartopy.__version__** '0.21.1' ``` ### conda list ``` (xcd050xes071spy543mat371car0211ipy8132) bash-4.2$ conda list # packages in environment at ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alabaster 0.7.13 pyhd8ed1ab_0 conda-forge alsa-lib 1.2.8 h166bdaf_0 conda-forge anyio 3.6.2 pyhd8ed1ab_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge arrow 1.2.3 pyhd8ed1ab_0 conda-forge arrow-cpp 11.0.0 ha770c72_16_cpu conda-forge astroid 2.15.4 py310hff52083_0 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge atomicwrites 1.4.1 pyhd8ed1ab_0 conda-forge attr 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pyha2e5f31_6 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-lsp-black 1.2.1 pyhd8ed1ab_0 conda-forge python-lsp-jsonrpc 1.0.0 pyhd8ed1ab_0 conda-forge python-lsp-server 1.7.2 pyhd8ed1ab_0 conda-forge python-lsp-server-base 1.7.2 pyhd8ed1ab_0 conda-forge python-slugify 8.0.1 pyhd8ed1ab_1 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytoolconfig 1.2.5 pyhd8ed1ab_0 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyxdg 0.28 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge pyzmq 25.0.2 py310h059b190_0 conda-forge qdarkstyle 3.1 pyhd8ed1ab_0 conda-forge qstylizer 0.2.2 pyhd8ed1ab_0 conda-forge qt-main 5.15.8 h5c52f38_10 conda-forge qt-webengine 5.15.8 h77d6d84_0 conda-forge qtawesome 1.2.3 pyhd8ed1ab_0 conda-forge qtconsole 5.4.3 pyhd8ed1ab_0 conda-forge qtconsole-base 5.4.3 pyha770c72_0 conda-forge qtpy 2.3.1 pyhd8ed1ab_0 conda-forge re2 2023.02.02 hcb278e6_0 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.29.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rope 1.8.0 pyhd8ed1ab_0 conda-forge rtree 1.0.1 py310hbdcdc62_1 conda-forge s2n 1.3.42 h3358134_0 conda-forge scipy 1.10.1 py310h8deb116_1 conda-forge secretstorage 3.3.3 py310hff52083_1 conda-forge send2trash 1.8.2 pyh41d4057_0 conda-forge setuptools 67.7.2 pyhd8ed1ab_0 conda-forge shapely 2.0.1 py310h056c13c_1 conda-forge sip 6.7.9 py310hc6cd4ac_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sparse 0.14.0 pyhd8ed1ab_0 conda-forge sphinx 7.0.0 pyhd8ed1ab_0 conda-forge sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge spyder 5.4.3 py310hff52083_0 conda-forge spyder-kernels 2.4.3 unix_pyhd8ed1ab_0 conda-forge sqlite 3.40.0 h4ff8645_1 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge tblib 1.7.0 pyhd8ed1ab_0 conda-forge terminado 0.17.1 pyh41d4057_0 conda-forge text-unidecode 1.3 py_0 conda-forge textdistance 4.5.0 pyhd8ed1ab_0 conda-forge three-merge 0.1.1 pyh9f0ad1d_0 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tomlkit 0.11.8 pyha770c72_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.3 py310h1fa729e_0 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ucx 1.14.0 h3484d09_2 conda-forge ujson 5.7.0 py310heca2aa9_0 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge unidecode 1.3.6 pyhd8ed1ab_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge watchdog 3.0.0 py310hff52083_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge whatthepatch 1.0.5 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py310h1fa729e_0 conda-forge wurlitzer 3.0.3 pyhd8ed1ab_0 conda-forge xarray 2023.4.2 pyhd8ed1ab_0 conda-forge xcb-util 0.4.0 h516909a_0 conda-forge xcb-util-image 0.4.0 h166bdaf_0 conda-forge xcb-util-keysyms 0.4.0 h516909a_0 conda-forge xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge xcb-util-wm 0.4.1 h516909a_0 conda-forge xcdat 0.5.0 pyhd8ed1ab_0 conda-forge xesmf 0.7.1 pyhd8ed1ab_0 conda-forge xkeyboard-config 2.38 h0b41bf4_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xyzservices 2023.2.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yapf 0.32.0 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge ``` ### pip list ``` nil ```
greglucas commented 1 year ago

This is likely some bad projection going on when transforming the geometries near a boundary. As a workaround, you can use the transform_first keyword which should avoid that path. https://scitools.org.uk/cartopy/docs/latest/gallery/scalar_data/contour_transforms.html#sphx-glr-gallery-scalar-data-contour-transforms-py

durack1 commented 1 year ago

Thanks @greglucas! This tweak gets me back up and running again, great.

Should I close this issue, or leave this open for a more permanent diagnosis and fix? Apologies, I became confused as to what was going on, so without guidance you will not be getting a PR from me.

greglucas commented 1 year ago

I think we should leave it open and hope for a better solution rather than a workaround.

If you're interested in tackling this that would be great! It may not be too difficult, but it is sometimes hard to tell how deep into the code you'll have to get. If you want some guidance, I'd suggest isolating the failure geometry from the contour call. Adding some print or to_wkt() statements into the geometry transform region of the code should help get the one right before the failure.

  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/crs.py:963 in _project_polygon
    return self._rings_to_multi_polygon(rings, is_ccw)
  File ~/mambaforge/envs/xcd050xes071spy543mat371car0211ipy8132/lib/python3.10/site-packages/cartopy/crs.py:1224 in _rings_to_multi_polygon
    multi_poly = sgeom.MultiPolygon(polygon_bits)

Then find out why that input geometry gets transformed into an output GeometryCollection and what geometries are in that GeometryCollection, maybe it is as simple as removing any extraneous point geometries after cutting/stitching.

david-shu commented 12 months ago

I encountered the same problem. Trace to cartopy.crs.Projection Rings To Multi Polygon method. When boundary_poly. intersection (polygon), a GeoCollection object is obtained instead of a Polygon object, resulting in Exception thrown when sgeom.MultiPolygon(polygon_bits).

from shapely.geometry.collection import GeometryCollection
import shapely.geometry as sgeom
from shapely.prepared import prep

def _rings_to_multi_polygon(self, rings, is_ccw):
    exterior_rings = []
    interior_rings = []
    for ring in rings:
        if ring.is_ccw != is_ccw:
            interior_rings.append(ring)
        else:
            exterior_rings.append(ring)

    polygon_bits = []

    # Turn all the exterior rings into polygon definitions,
    # "slurping up" any interior rings they contain.
    for exterior_ring in exterior_rings:
        polygon = sgeom.Polygon(exterior_ring)
        prep_polygon = prep(polygon)
        holes = []
        for interior_ring in interior_rings[:]:
            if prep_polygon.contains(interior_ring):
                holes.append(interior_ring)
                interior_rings.remove(interior_ring)
            elif polygon.crosses(interior_ring):
                # Likely that we have an invalid geometry such as
                # that from #509 or #537.
                holes.append(interior_ring)
                interior_rings.remove(interior_ring)
        polygon_bits.append((exterior_ring.coords,
                             [ring.coords for ring in holes]))

    # Any left over "interior" rings need "inverting" with respect
    # to the boundary.
    if interior_rings:
        boundary_poly = self.domain
        x3, y3, x4, y4 = boundary_poly.bounds
        bx = (x4 - x3) * 0.1
        by = (y4 - y3) * 0.1
        x3 -= bx
        y3 -= by
        x4 += bx
        y4 += by
        for ring in interior_rings:
            # Use shapely buffer in an attempt to fix invalid geometries
            polygon = sgeom.Polygon(ring).buffer(0)
            if not polygon.is_empty and polygon.is_valid:
                x1, y1, x2, y2 = polygon.bounds
                bx = (x2 - x1) * 0.1
                by = (y2 - y1) * 0.1
                x1 -= bx
                y1 -= by
                x2 += bx
                y2 += by
                box = sgeom.box(min(x1, x3), min(y1, y3),
                                max(x2, x4), max(y2, y4))

                # Invert the polygon
                polygon = box.difference(polygon)

                # Intersect the inverted polygon with the boundary
                polygon = boundary_poly.intersection(polygon)
                if not polygon.is_empty:
                    polygon_bits.append(polygon)

    if polygon_bits:
        ##### added by david.shu ###################################
        polygon_bits2 = []
        for polygon in polygon_bits:
            if isinstance( polygon, GeometryCollection ):
                for g in polygon.geoms:
                    if isinstance( g, sgeom.Polygon ):
                        polygon_bits2.append( g )
                    else:
                        print( f'{type(g)} found. but Polygon required.' )
            else:
                polygon_bits2.append( polygon )
        polygon_bits = polygon_bits2 
        #######################################################

        multi_poly = sgeom.MultiPolygon(polygon_bits)
    else:
        multi_poly = sgeom.MultiPolygon()
    return multi_poly        

ccrs.Projection._rings_to_multi_polygon = _rings_to_multi_polygon
kafitzgerald commented 6 months ago

I'm also seeing this error with cartopy (version 0.22.0) and shapely version 2 and above (dropping down to version 1.8.x allows things to work properly).

In this particular case it's coming from Xarray DataArray.plot which uses pcolormesh and pcolor

I can try to dig into this a bit more and/or put together a MRE, but wanted to at least log this here in case it helps other users or devs.

``` --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[7], line 13 10 tas_present = test.sel(time="2014-07").squeeze() 12 # plot the model data ---> 13 (tas_present - 273.15).plot( 14 ax=ax_present, 15 x="lon", 16 y="lat", 17 transform=ccrs.PlateCarree(), 18 vmin=-10, 19 vmax=30, 20 cmap="magma" 21 #robust=True 22 ) 23 ax_present.coastlines() 24 ax_present.set_title("July 2014") File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/xarray/plot/accessor.py:48, in DataArrayPlotAccessor.__call__(self, **kwargs) 46 @functools.wraps(dataarray_plot.plot, assigned=("__doc__", "__annotations__")) 47 def __call__(self, **kwargs) -> Any: ---> 48 return dataarray_plot.plot(self._da, **kwargs) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/xarray/plot/dataarray_plot.py:309, in plot(darray, row, col, col_wrap, ax, hue, subplot_kws, **kwargs) 305 plotfunc = hist 307 kwargs["ax"] = ax --> 309 return plotfunc(darray, **kwargs) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/xarray/plot/dataarray_plot.py:1601, in _plot2d..newplotfunc(***failed resolving arguments***) 1597 raise ValueError("plt.imshow's `aspect` kwarg is not available in xarray") 1599 ax = get_axis(figsize, size, aspect, ax, **subplot_kws) -> 1601 primitive = plotfunc( 1602 xplt, 1603 yplt, 1604 zval, 1605 ax=ax, 1606 cmap=cmap_params["cmap"], 1607 vmin=cmap_params["vmin"], 1608 vmax=cmap_params["vmax"], 1609 norm=cmap_params["norm"], 1610 **kwargs, 1611 ) 1613 # Label the plot with metadata 1614 if add_labels: File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/xarray/plot/dataarray_plot.py:2309, in pcolormesh(x, y, z, ax, xscale, yscale, infer_intervals, **kwargs) 2306 y = _infer_interval_breaks(y, axis=0, scale=yscale) 2308 ax.grid(False) -> 2309 primitive = ax.pcolormesh(x, y, z, **kwargs) 2311 # by default, pcolormesh picks "round" values for bounds 2312 # this results in ugly looking plots with lots of surrounding whitespace 2313 if not hasattr(ax, "projection") and x.ndim == 1 and y.ndim == 1: 2314 # not a cartopy geoaxis File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:315, in _add_transform..wrapper(self, *args, **kwargs) 310 raise ValueError(f'Invalid transform: Spherical {func.__name__} ' 311 'is not supported - consider using ' 312 'PlateCarree/RotatedPole.') 314 kwargs['transform'] = transform --> 315 return func(self, *args, **kwargs) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:1783, in GeoAxes.pcolormesh(self, *args, **kwargs) 1781 result = super().pcolormesh(*args, **kwargs) 1782 # Wrap the quadrilaterals if necessary -> 1783 result = self._wrap_quadmesh(result, **kwargs) 1784 # Re-cast the QuadMesh as a GeoQuadMesh to enable future wrapping 1785 # updates to the collection as well. 1786 result.__class__ = cartopy.mpl.geocollection.GeoQuadMesh File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:1965, in GeoAxes._wrap_quadmesh(self, collection, **kwargs) 1955 if _MPL_VERSION.release[:2] < (3, 8): 1956 # We will add the original data mask in later to 1957 # make sure that set_array can work in future (...) 1962 # fill in the proper data later with set_array() 1963 # calls. 1964 pcolor_zeros = np.ma.array(np.zeros(C.shape), mask=pcolor_mask) -> 1965 pcolor_col = self.pcolor(coords[..., 0], coords[..., 1], 1966 pcolor_zeros, zorder=zorder, 1967 **kwargs) 1969 # The pcolor_col is now possibly shorter than the 1970 # actual collection, so grab the masked cells 1971 pcolor_col.set_array(pcolor_data[mask].ravel()) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:315, in _add_transform..wrapper(self, *args, **kwargs) 310 raise ValueError(f'Invalid transform: Spherical {func.__name__} ' 311 'is not supported - consider using ' 312 'PlateCarree/RotatedPole.') 314 kwargs['transform'] = transform --> 315 return func(self, *args, **kwargs) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:2012, in GeoAxes.pcolor(self, *args, **kwargs) 2009 result = super().pcolor(*args, **kwargs) 2011 # Update the datalim for this pcolor. -> 2012 limits = result.get_datalim(self.transData) 2013 self.update_datalim(limits) 2015 self.autoscale_view() File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/matplotlib/collections.py:266, in Collection.get_datalim(self, transData) 263 return transforms.Bbox.null() 265 if not transform.is_affine: --> 266 paths = [transform.transform_path_non_affine(p) for p in paths] 267 # Don't convert transform to transform.get_affine() here because 268 # we may have transform.contains_branch(transData) but not 269 # transforms.get_affine().contains_branch(transData). But later, 270 # be careful to only apply the affine part that remains. 272 if any(transform.contains_branch_seperately(transData)): 273 # collections that are just in data units (like quiver) 274 # can properly have the axes limits set by their shape + 275 # offset. LineCollections that have no offsets can 276 # also use this algorithm (like streamplot). File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/matplotlib/collections.py:266, in (.0) 263 return transforms.Bbox.null() 265 if not transform.is_affine: --> 266 paths = [transform.transform_path_non_affine(p) for p in paths] 267 # Don't convert transform to transform.get_affine() here because 268 # we may have transform.contains_branch(transData) but not 269 # transforms.get_affine().contains_branch(transData). But later, 270 # be careful to only apply the affine part that remains. 272 if any(transform.contains_branch_seperately(transData)): 273 # collections that are just in data units (like quiver) 274 # can properly have the axes limits set by their shape + 275 # offset. LineCollections that have no offsets can 276 # also use this algorithm (like streamplot). File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/matplotlib/transforms.py:2439, in CompositeGenericTransform.transform_path_non_affine(self, path) 2437 return path 2438 elif not self._a.is_affine and self._b.is_affine: -> 2439 return self._a.transform_path_non_affine(path) 2440 else: 2441 return self._b.transform_path_non_affine( 2442 self._a.transform_path(path)) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/mpl/geoaxes.py:186, in InterProjectionTransform.transform_path_non_affine(self, src_path) 182 geoms = cpatch.path_to_geos(src_path, 183 getattr(self, 'force_path_ccw', False)) 185 for geom in geoms: --> 186 proj_geom = self.target_projection.project_geometry( 187 geom, self.source_projection) 188 transformed_geoms.append(proj_geom) 190 if not transformed_geoms: File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/crs.py:817, in Projection.project_geometry(self, geometry, src_crs) 815 if not method_name: 816 raise ValueError(f'Unsupported geometry type {geom_type!r}') --> 817 return getattr(self, method_name)(geometry, src_crs) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/crs.py:972, in Projection._project_polygon(self, polygon, src_crs) 968 rings.extend(self._attach_lines_to_boundary(multi_lines, is_ccw)) 970 # Resolve all the inside vs. outside rings, and convert to the 971 # final MultiPolygon. --> 972 return self._rings_to_multi_polygon(rings, is_ccw) File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/cartopy/crs.py:1233, in Projection._rings_to_multi_polygon(self, rings, is_ccw) 1230 polygon_bits.append(polygon) 1232 if polygon_bits: -> 1233 multi_poly = sgeom.MultiPolygon(polygon_bits) 1234 else: 1235 multi_poly = sgeom.MultiPolygon() File ~/miniconda3/envs/geocat-examples/lib/python3.11/site-packages/shapely/geometry/multipolygon.py:79, in MultiPolygon.__new__(self, polygons) 77 ob = polygons[i] 78 if not isinstance(ob, polygon.Polygon): ---> 79 shell = ob[0] 80 if len(ob) > 1: 81 holes = ob[1] TypeError: 'GeometryCollection' object is not subscriptable ```
guidoca commented 1 day ago

We are getting the same issue. Somehow a GeometryCollection appears. Modifying rings_to_multipolygon to skip any GeometryCollections fixes the issue.

It's probably the result of a weird geometry in the underlying contours, but impossible to tell exactly what when working with very big datasets.

I would suggest adding a mechanism to skip GeometrieCollection if present within polygon_bits and throw a warning, or recursively call rings_to_multipolygon with the GeometryCollection parts ?