PyGMT is too strict when checking for irregular grids #1468
Description
Description of the problem
Since GMT only supports regular grids, PyGMT has a check to make sure all point spacings are the same (here):
coord = grid.coords[dim].values
coord_incs = coord[1:] - coord[0:-1]
coord_inc = coord_incs[0]
if not np.allclose(coord_incs, coord_inc):
raise GMTInvalidInput(
"Grid appears to have irregular spacing in the '{}' dimension.".format(
dim
)
)The problem is that the np.allclose function has variable precision arguments to determine whether it fails or passes. So the degree to which we check for uniform spacing depends on coordinate units. This is not ideal as this check can fail in cases where the grid is evenly spaced within an acceptable accuracy for coordinates but maybe not for allclose.
I'm not sure there is a good solution here since:
- This will vary with units so it's hard to generalize.
- This part of the code is deep in the internals so getting the
rtolandatolarguments from the user into this part of the code will be awkward and bug prone. - Should this really be an exception if GMT may be OK with the coordinates?
I would propose turning this into a warning instead and let GMT fail if it really thinks it can't handle the grid. What do others think? I'm not sure that would solve the problem or if GMT will be equally strict.
Full code that generated the error
grid = xr.open_dataarray("topography-earth-10arcmin.nc")
fig = pygmt.Figure()
fig.grdimage(grid)
fig.show()Using this grid file: topography-earth-10arcmin.nc.zip (GitHub required a zip archive for this)
For context, this grid is coming from the ICGEM calculation service. I tracked down the error to them using the equivalent of np.arange to generate the grid coordinates instead of np.linspace (which is the correct way to do it).
Full error message
Details
---------------------------------------------------------------------------
GMTInvalidInput Traceback (most recent call last)
/tmp/ipykernel_207888/3701624484.py in <module>
1 fig = pygmt.Figure()
----> 2 fig.grdimage(grid)
3 fig.show()
~/bin/conda/envs/rockhound-data/lib/python3.9/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
580 )
581 warnings.warn(msg, category=SyntaxWarning, stacklevel=2)
--> 582 return module_func(*args, **kwargs)
583
584 new_module.aliases = aliases
~/bin/conda/envs/rockhound-data/lib/python3.9/site-packages/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
723 kwargs[arg] = separators[fmt].join(f"{item}" for item in value)
724 # Execute the original function and return its output
--> 725 return module_func(*args, **kwargs)
726
727 return new_module
~/bin/conda/envs/rockhound-data/lib/python3.9/site-packages/pygmt/src/grdimage.py in grdimage(self, grid, **kwargs)
171 kwargs["I"] = stack.enter_context(shading_context)
172
--> 173 fname = stack.enter_context(file_context)
174 arg_str = " ".join([fname, build_arg_string(kwargs)])
175 lib.call_module("grdimage", arg_str)
~/bin/conda/envs/rockhound-data/lib/python3.9/contextlib.py in enter_context(self, cm)
427 _cm_type = type(cm)
428 _exit = _cm_type.__exit__
--> 429 result = _cm_type.__enter__(cm)
430 self._push_cm_exit(cm, _exit)
431 return result
~/bin/conda/envs/rockhound-data/lib/python3.9/contextlib.py in __enter__(self)
115 del self.args, self.kwds, self.func
116 try:
--> 117 return next(self.gen)
118 except StopIteration:
119 raise RuntimeError("generator didn't yield") from None
~/bin/conda/envs/rockhound-data/lib/python3.9/site-packages/pygmt/clib/session.py in virtualfile_from_grid(self, grid)
1344 # guarantees that the copy will be around until the virtual file is
1345 # closed. The conversion is implicit in dataarray_to_matrix.
-> 1346 matrix, region, inc = dataarray_to_matrix(grid)
1347
1348 family = "GMT_IS_GRID|GMT_VIA_MATRIX"
~/bin/conda/envs/rockhound-data/lib/python3.9/site-packages/pygmt/clib/conversion.py in dataarray_to_matrix(grid)
96 coord_inc = coord_incs[0]
97 if not np.allclose(coord_incs, coord_inc):
---> 98 raise GMTInvalidInput(
99 "Grid appears to have irregular spacing in the '{}' dimension.".format(
100 dim
GMTInvalidInput: Grid appears to have irregular spacing in the 'longitude' dimension.
System information
Please paste the output of python -c "import pygmt; pygmt.show_versions()":
PyGMT information:
version: v0.4.1
System information:
python: 3.9.0 | packaged by conda-forge | (default, Nov 26 2020, 07:57:39) [GCC 9.3.0]
executable: /home/leo/bin/conda/envs/rockhound-data/bin/python
machine: Linux-5.13.11-1-MANJARO-x86_64-with-glibc2.33
Dependency information:
numpy: 1.21.2
pandas: 1.3.2
xarray: 0.19.0
netCDF4: 1.5.7
packaging: 21.0
ghostscript: 9.54.0
gmt: 6.2.0
GMT library information:
binary dir: /home/leo/bin/conda/envs/rockhound-data/bin
cores: 8
grid layout: rows
library path: /home/leo/bin/conda/envs/rockhound-data/lib/libgmt.so
padding: 2
plugin dir: /home/leo/bin/conda/envs/rockhound-data/lib/gmt/plugins
share dir: /home/leo/bin/conda/envs/rockhound-data/share/gmt
version: 6.2.0