Closed
Description
Description of the problem
The surface gridding function doesn't allow passing in a python list to region (e.g. [245, 255, 20, 30]). This is actually an oversight on my part since I wrapped the function in #245 😨.
Full code that generated the error adapted from tests_surface.py
import pygmt
from pygmt.datasets import load_sample_bathymetry
ship_data = load_sample_bathymetry()
data = ship_data.values # convert pandas.DataFrame to numpy.ndarray
pygmt.surface(data=data, spacing="5m", region=[245, 255, 20, 30])Full error message
-R<xmin>/<xmax>/<ymin>/<ymax>[/<zmin>/<zmax>]
Append r if giving lower left and upper right coordinates
-Rg or -Rd for global domain
-R<grdfile> to take the domain from a grid file
surface [ERROR]: Offending option -R245
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
-R<xmin>/<xmax>/<ymin>/<ymax>[/<zmin>/<zmax>]
Append r if giving lower left and upper right coordinates
-Rg or -Rd for global domain
-R<grdfile> to take the domain from a grid file
surface [ERROR]: Offending option -R255
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
-R<xmin>/<xmax>/<ymin>/<ymax>[/<zmin>/<zmax>]
Append r if giving lower left and upper right coordinates
-Rg or -Rd for global domain
-R<grdfile> to take the domain from a grid file
surface [ERROR]: Offending option -R20
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
-R<xmin>/<xmax>/<ymin>/<ymax>[/<zmin>/<zmax>]
Append r if giving lower left and upper right coordinates
-Rg or -Rd for global domain
-R<grdfile> to take the domain from a grid file
surface [ERROR]: Offending option -R30
---------------------------------------------------------------------------
GMTCLibError Traceback (most recent call last)
<ipython-input-6-918159e76c71> in <module>
----> 1 pygmt.surface(data=data, spacing="5m", region=[245, 255, 20, 30])
~/miniconda/envs/pygmt/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
181 if alias in kwargs:
182 kwargs[arg] = kwargs.pop(alias)
--> 183 return module_func(*args, **kwargs)
184
185 new_module.aliases = aliases
~/miniconda/envs/pygmt/pygmt/gridding.py in surface(x, y, z, data, **kwargs)
83 outfile = kwargs["G"]
84 arg_str = " ".join([infile, build_arg_string(kwargs)])
---> 85 lib.call_module(module="surface", args=arg_str)
86
87 if outfile == tmpfile.name: # if user did not set outfile, return DataArray
~/miniconda/envs/pygmt/pygmt/clib/session.py in call_module(self, module, args)
488 raise GMTCLibError(
489 "Module '{}' failed with status code {}:\n{}".format(
--> 490 module, status, self._error_message
491 )
492 )
GMTCLibError: Module 'surface' failed with status code 71:
surface [ERROR]: Syntax error -R option. Correct syntax:
surface [ERROR]: Offending option -R245
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
surface [ERROR]: Offending option -R255
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
surface [ERROR]: Offending option -R20
surface [ERROR]: Option -R given more than once
surface [ERROR]: Syntax error -R option. Correct syntax:
surface [ERROR]: Offending option -R30
Solution
This will be a relatively straightforward fix, and I'd be happy for someone new-ish wanting to contribute to PyGMT to submit a Pull Request (and learn from it). We can guide you through the process on how to add a Python decorator to fix the issue, and update the unit tests so that the problem won't surface 😉 again in the future.
Before you start, read up on our CONTRIBUTING.md. Also, please leave a comment below if you decide to start working on this!!
Anyhow, first part is to add a python decorator @kwargs_to_strings(R="sequence") after @use_alias and before def surface here:
Lines 18 to 20 in cdcdf70
Make sure that you add a line to import kwargs_to_string near the top of gridding.py file, or it won't work!
What the decorator does is to convert a list like [245, 255, 20, 30] into a slash separated string like "245/255/20/30", the code for it which is found at here.
Secondly, you'll need to edit the unit test file to capture this change at https://github.com/GenericMappingTools/pygmt/edit/master/pygmt/tests/test_surface.py. Change all the lines mentioning region="245/255/20/30" to region=[245, 255, 20, 30].
That should be the bulk of it! Feel free to ask for help in the comments below if you encounter any issues, and good luck!
System information
- Operating system: Linux
- Python installation (Anaconda, system, ETS): Miniconda
- Version of GMT: 6.0.0rc4
- Version of Python: 3.7
- Version of this package: cdcdf70
- If using conda, paste the output of
conda listbelow:
output of conda list
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