seisman
commented
3 years ago I have a similar issue when passing pandas columns to text().
Full code that generated the error
The script works with PyGMT v0.1.2, but fails with PyGMT v0.2.0 (and master). Here is the example input file used in the script: input.txt
import pandas as pd
import pygmt
data = pd.read_csv("input.txt", names=("id", "longitude", "latitude"), delim_whitespace=True)
fig = pygmt.Figure()
fig.basemap(region=[0, 100, 0, 100], projection='X10c', frame=True)
fig.plot(x=data.longitude, y=data.latitude, style='c0.2c', color='red')
fig.text(x=data.longitude, y=data.latitude, text=data.id, font='16p,red', offset='0.25c')
fig.show()Full error message
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
~/Gits/gmt/pygmt/pygmt/clib/session.py in _check_dtype_and_dim(self, array, ndim)
726 # Try to convert any unknown numpy data types to np.datetime64
--> 727 array = np.asarray(array, dtype=np.datetime64)
728 except ValueError as e:
~/.anaconda/lib/python3.8/site-packages/numpy/core/_asarray.py in asarray(a, dtype, order)
84 """
---> 85 return array(a, dtype, copy=False, order=order)
86
ValueError: Cannot create a NumPy datetime other than NaT with generic units
The above exception was the direct cause of the following exception:
GMTInvalidInput Traceback (most recent call last)
<ipython-input-7-b64e448be657> in <module>
6 fig.basemap(region=[0, 100, 0, 100], projection='X10c', frame=True)
7 fig.plot(x=data.longitude, y=data.latitude, style='c0.2c', color='red')
----> 8 fig.text(x=data.longitude, y=data.latitude, text=data.id, font='16p,red', offset='0.25c')
9 fig.show()
~/Gits/gmt/pygmt/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
268 if alias in kwargs:
269 kwargs[arg] = kwargs.pop(alias)
--> 270 return module_func(*args, **kwargs)
271
272 new_module.aliases = aliases
~/Gits/gmt/pygmt/pygmt/helpers/decorators.py in new_module(*args, **kwargs)
405 kwargs[arg] = separators[fmt].join(f"{item}" for item in value)
406 # Execute the original function and return its output
--> 407 return module_func(*args, **kwargs)
408
409 return new_module
~/Gits/gmt/pygmt/pygmt/base_plotting.py in text(self, textfiles, x, y, position, text, angle, font, justify, **kwargs)
1211 np.atleast_1d(x), np.atleast_1d(y), np.atleast_1d(text)
1212 )
-> 1213 with file_context as fname:
1214 arg_str = " ".join([fname, build_arg_string(kwargs)])
1215 lib.call_module("text", arg_str)
~/.anaconda/lib/python3.8/contextlib.py in __enter__(self)
111 del self.args, self.kwds, self.func
112 try:
--> 113 return next(self.gen)
114 except StopIteration:
115 raise RuntimeError("generator didn't yield") from None
~/Gits/gmt/pygmt/pygmt/clib/session.py in virtualfile_from_vectors(self, *vectors)
1171 # Use put_vector for columns with numerical type data
1172 for col, array in enumerate(arrays[:columns]):
-> 1173 self.put_vector(dataset, column=col, vector=array)
1174
1175 # Use put_strings for last column(s) with string type data
~/Gits/gmt/pygmt/pygmt/clib/session.py in put_vector(self, dataset, column, vector)
775 )
776
--> 777 gmt_type = self._check_dtype_and_dim(vector, ndim=1)
778 if gmt_type == self["GMT_DATETIME"]:
779 vector_pointer = (ctp.c_char_p * len(vector))()
~/Gits/gmt/pygmt/pygmt/clib/session.py in _check_dtype_and_dim(self, array, ndim)
727 array = np.asarray(array, dtype=np.datetime64)
728 except ValueError as e:
--> 729 raise GMTInvalidInput(
730 f"Unsupported numpy data type '{array.dtype.type}'."
731 ) from e
GMTInvalidInput: Unsupported numpy data type '<class 'numpy.object_'>'.
weiji14
Description of the problem
PR #480 mention that, x and y of the
text()function can accept int, float or str. It's true for PyGMT v0.1.2, but since PyGMT v0.2.0, it's no longer possible to pass string-type x or y.I haven't looked into the codes to check why it works for v0.1.2. The question is, do we want to accept string-type x and y coordinates?
Full code that generated the error
Full error message
System information
Please paste the output of
python -c "import pygmt; pygmt.show_versions()":