-JEPSG:4326 not writing CRS to netcdf in surface

Description of the problem

Using a Spanish government gravity dataset converted to epsg:4326. Run blockmedian and surface seems to work fine. If I put a proj string in it seems to write that projection to the netcdf file.

However, -JEPSG:4326 (or -Jepsg:4326 or 4326) do

es not.

I made a script version and put a debug print in the utils library generating the run arguments and that gives this:

RUNARGS -I65.15s -R-9.34335092522/3.46340435922/35.8532670285/43.8612236053 RUNARGS -GD:\Spain\GMTtext15.nc -I65.15s -J4326 -R-9.34335092522/3.46340435922/35.8532670285/43.8612236053 -Vc

Full code that generated the error

#!/usr/bin/env python
# coding: utf-8

# In[1]:


import pygmt
import pandas as pd
import geopandas as gpd
import numpy as np
#import rasterio


#import pyvista as pv

from mpl_toolkits.mplot3d import Axes3D  # noqa: F401 unused import

import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
from matplotlib.patches import Rectangle

import verde as vd
#import cartopy.crs as ccrs
import dask
import pyproj
import pooch
import xarray as xr
import os

spain = gpd.read_file(r'D:\Spain\Gravimetria.shp')

# In[60]:

spain.head()

# In[3]:

Z = spain['VALU_BOU26'].values
lat =  spain.geometry.y.values
lon =  spain.geometry.x.values

# In[4]:

xmin = spain.total_bounds[0]
xmax = spain.total_bounds[2]
ymin = spain.total_bounds[1]
ymax = spain.total_bounds[3]
region = [xmin, xmax, ymin, ymax]

# In[5]:

datatable = pd.DataFrame()
datatable['longitude'] = lon.tolist()
datatable['latitude'] = lat.tolist()
datatable['bouguer_anomaly'] = Z.tolist()

# In[61]:

region2=[-9.31, 3.430053434000058, 35.92, 43.77780739100007]
region3="-9.34335092522/3.46340435922/35.8532670285/43.8612236053"

datatable_blockmedian = pygmt.blockmedian(table=datatable, spacing="65.15s", region=region3)  #e is metres
#grid_s = pygmt.surface(datatable_blockmedian['longitude'],datatable_blockmedian['latitude'],datatable_blockmedian['bouguer_anomaly'],spacing="65.15s",region=region3,J="epsg:4326",V="c",outfile=r'D:\Spain\GMTtext15.nc')
grid_s = pygmt.surface(datatable_blockmedian['longitude'],datatable_blockmedian['latitude'],datatable_blockmedian['bouguer_anomaly'],spacing="65.15s",region=region3,J="4326",V="c",outfile=r'D:\Spain\GMTtext15.nc')

 #+proj=longlat+ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0

# In[62]:

get_ipython().system('gdalinfo "D:\\Spain\\GMTText15.nc"')

# In[ ]:

Full error message

From gdalinfo
Driver: netCDF/Network Common Data Format

Warning 1: Recode from UTF-8 to CP_ACP failed with the error: "Invalid argument".
Warning 1: dimension #1 (x) is not a Longitude/X dimension.
Warning 1: dimension #0 (y) is not a Latitude/Y dimension.
C:\Users\rscott\AppData\Local\Continuum\anaconda3\envs\pygmt\lib\threading.py:874: ResourceWarning: unclosed file <_io.BufferedWriter name=4>
  del self._target, self._args, self._kwargs
ResourceWarning: Enable tracemalloc to get the object allocation traceback
C:\Users\rscott\AppData\Local\Continuum\anaconda3\envs\pygmt\lib\threading.py:874: ResourceWarning: unclosed file <_io.BufferedReader name=5>
  del self._target, self._args, self._kwargs
ResourceWarning: Enable tracemalloc to get the object allocation traceback
C:\Users\rscott\AppData\Local\Continuum\anaconda3\envs\pygmt\lib\threading.py:874: ResourceWarning: unclosed file <_io.BufferedReader name=6>
  del self._target, self._args, self._kwargs
ResourceWarning: Enable tracemalloc to get the object allocation traceback


Files: D:\Spain\GMTText15.nc
Size is 709, 443
Origin = (-9.352395243923700,43.870282379708144)
Pixel Size = (0.018088637407401,-0.018117548816290)
Metadata:
  NC_GLOBAL#Conventions=CF-1.7
  NC_GLOBAL#GMT_version=6.1.1 [64-bit]
  NC_GLOBAL#history=surface @GMTAPI@-S-I-D-V-T-N-000000 -GD:\Spain\GMTtext15.nc -I65.15s -J+4326 -R-9.34335092522/3.46340435922/35.8532670285/43.8612236053 -Vc
  NC_GLOBAL#title=Data gridded with continuous surface splines in tension
  x#actual_range={-9.343350925219999,3.46340435922}
  x#long_name=x
  y#actual_range={35.8532670285,43.8612236053}
  y#long_name=y
  z#actual_range={-143.2124328613281,312.9815673828125}
  z#long_name=z
  z#_FillValue=-nan(ind)
Corner Coordinates:
Upper Left  (  -9.3523952,  43.8702824) 
Lower Left  (  -9.3523952,  35.8442083) 
Upper Right (   3.4724487,  43.8702824) 
Lower Right (   3.4724487,  35.8442083) 
Center      (  -2.9399733,  39.8572453) 
Band 1 Block=709x1 Type=Float32, ColorInterp=Undefined
  NoData Value=nan
  Metadata:
    actual_range={-143.2124328613281,312.9815673828125}
    long_name=z
    NETCDF_VARNAME=z
    _FillValue=-nan(ind)
In [ ]:

System information

Please paste the output of python -c "import pygmt; pygmt.show_versions()":

PyGMT information:
  version: v0.2.0
System information:
  python: 3.8.6 | packaged by conda-forge | (default, Oct  7 2020, 18:22:52) [MSC v.1916 64 bit (AMD64)]
  executable: C:\Users\rscott\AppData\Local\Continuum\anaconda3\envs\pygmt\python.exe
  machine: Windows-10-10.0.18362-SP0
Dependency information:
  numpy: 1.19.2
  pandas: 1.1.3
  xarray: 0.16.1
  netCDF4: 1.5.3
  packaging: 20.4
  ghostscript: 9.53.3
  gmt: 6.1.1
GMT library information:
  binary dir: C:/Users/rscott/AppData/Local/Continuum/anaconda3/envs/pygmt
  cores: 12
  grid layout: rows
  library path: C:/Users/rscott/AppData/Local/Continuum/anaconda3/envs/pygmt/Library/bin/gmt.dll
  padding: 2
  plugin dir: C:/Users/rscott/AppData/Local/Continuum/anaconda3/envs/pygmt/Library/bin/gmt_plugins
  share dir: C:/Users/rscott/AppData/Local/Continuum/anaconda3/envs/pygmt/Library/share/gmt
  version: 6.1.1

[weiji14]

There’s different versions of WKT?!! Great 😂 Looking at https://gdal.org/programs/gdalsrsinfo.html#cmdoption-gdalsrsinfo-o, there’s wkt1, wkt2_2015, wkt2_2018, and so on. Now my question is: “How can we tell GMT which wkt version to use?”. And why isn’t the current default “wkt: Latest WKT version supported, currently wkt2_2018”, but wkt1?

[joa-quim]

The conversions are done via calls to GDAL functions, but there are several versions of WKT. I don’t remember to select anyone in particular but it looks you are getting wkt1, e.g.

$ gdalsrsinfo EPSG:3031 -o wkt1

PROJCS["WGS 84 / Antarctic Polar Stereographic",
    GEOGCS["WGS 84",
        DATUM["WGS_1984",
            SPHEROID["WGS 84",6378137,298.257223563,
                AUTHORITY["EPSG","7030"]],
            AUTHORITY["EPSG","6326"]],
        PRIMEM["Greenwich",0,
            AUTHORITY["EPSG","8901"]],
        UNIT["degree",0.0174532925199433,
            AUTHORITY["EPSG","9122"]],
        AUTHORITY["EPSG","4326"]],
    PROJECTION["Polar_Stereographic"],
    PARAMETER["latitude_of_origin",-71],
    PARAMETER["central_meridian",0],
    PARAMETER["false_easting",0],
    PARAMETER["false_northing",0],
    UNIT["metre",1,
        AUTHORITY["EPSG","9001"]],
    AXIS["Easting",NORTH],
    AXIS["Northing",NORTH],
    AUTHORITY["EPSG","3031"]]