home / github / issues

Menu
  • Search all tables
  • GraphQL API

issues: 1368027148

This data as json

id node_id number title user state locked assignee milestone comments created_at updated_at closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1368027148 I_kwDOAMm_X85RinAM 7014 xarray imshow and pcolormesh behave badly when the array does not contain values larger the BoundaryNorm vmax 19285200 closed 0     10 2022-09-09T15:59:31Z 2023-03-28T09:18:02Z 2023-03-28T09:18:02Z NONE      

What happened?

If cmap.set_over is specified, the array color mapping and the colorbar behave badly if the array does not contain values above the norm.vmax.

Let's take an array and apply a colormap and norm (see code below) Now, if in the array I change the array values larger than the norm.vmax (the 2 bottom right pixels) with other values inside the norm: - Using matplotlib I get the expected results - Using xarray I get this weird behavior.

What did you expect to happen?

The colorbar should not "shift" and the array should be colormapped correctly This is possibily related also to https://github.com/pydata/xarray/issues/4061

Minimal Complete Verifiable Example

```Python import matplotlib.colors import numpy as np import xarray as xr import matplotlib as mpl import matplotlib.pyplot as plt

Define DataArray

arr = np.array([[0, 10, 15, 20], [ np.nan, 40, 50, 100], [150, 158, 160, 161], ]) lon = np.arange(arr.shape[1]) lat = np.arange(arr.shape[0])[::-1] lons, lats = np.meshgrid(lon, lat) da = xr.DataArray(arr, dims=["y", "x"], coords={"lon": (("y","x"), lons), "lat": (("y","x"), lats), } ) da

Define colormap

color_list = ["#9c7e94", "#640064", "#009696", "#C8FF00", "#FF7D00"] levels = [0.05, 1, 10, 20, 150, 160] cmap = mpl.colors.LinearSegmentedColormap.from_list("cmap", color_list, len(levels) - 1) norm = mpl.colors.BoundaryNorm(levels, cmap.N) cmap.set_over("darkred") # color for above 160 cmap.set_under("none") # color for below 0.05 cmap.set_bad("gray", 0.2) # color for nan

Define colorbar settings

ticks = levels cbar_kwargs = {
'extend': "max",

}

Correct plot

p = da.plot.pcolormesh(x="lon", y="lat", cmap=cmap, norm=norm, cbar_kwargs=cbar_kwargs) plt.show()

Remove values larger than the norm.vmax level

da1 = da.copy() da1.data[da1.data>=norm.vmax] = norm.vmax - 1 # could be replaced with any value inside the norm

With matplotlib.pcolormesh [OK]

p = plt.pcolormesh(da1["lon"].data, da1["lat"], da1.data, cmap=cmap, norm=norm) plt.colorbar(p, **cbar_kwargs) plt.show()

With matplotlib.imshow [OK]

p = plt.imshow(da1.data, cmap=cmap, norm=norm) plt.colorbar(p, **cbar_kwargs) plt.show()

With xarray.pcolormesh [BUG]

--> The colorbar shift !!!

da1.plot.pcolormesh(x="lon", y="lat", cmap=cmap, norm=norm, cbar_kwargs=cbar_kwargs) plt.show()

With xarray.imshow [BUG]

--> The colorbar shift !!!

da1.plot.imshow(cmap=cmap, norm=norm, cbar_kwargs=cbar_kwargs, origin="upper") ```

MVCE confirmation

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

Relevant log output

No response

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21) [GCC 10.3.0] python-bits: 64 OS: Linux OS-release: 5.4.0-124-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.1 libnetcdf: 4.8.1 xarray: 2022.6.0 pandas: 1.4.3 numpy: 1.22.4 scipy: 1.9.0 netCDF4: 1.6.0 pydap: None h5netcdf: 1.0.2 h5py: 3.7.0 Nio: None zarr: 2.12.0 cftime: 1.6.1 nc_time_axis: None PseudoNetCDF: None rasterio: 1.3.0 cfgrib: None iris: None bottleneck: 1.3.5 dask: 2022.7.1 distributed: 2022.7.1 matplotlib: 3.5.2 cartopy: 0.20.3 seaborn: 0.11.2 numbagg: None fsspec: 2022.7.1 cupy: None pint: 0.19.2 sparse: None flox: None numpy_groupies: None setuptools: 63.3.0 pip: 22.2.2 conda: None pytest: None IPython: 7.33.0 sphinx: 5.1.1 /home/ghiggi/anaconda3/envs/gpm_geo/lib/python3.9/site-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils. warnings.warn("Setuptools is replacing distutils.")
{
    "url": "https://api.github.com/repos/pydata/xarray/issues/7014/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
  completed 13221727 issue

Links from other tables

  • 2 rows from issues_id in issues_labels
  • 10 rows from issue in issue_comments
Powered by Datasette · Queries took 0.744ms · About: xarray-datasette