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Support datetime data types as input
See original GitHub issueDescription of the problem I want to plot some datetime data on a map. However, gmt-python doesn’t accept string as input.
Full code that generated the error
import pygmt
x = ['2008-01-01', '2012-01-01']
y = [5, 5]
fig = pygmt.Figure()
fig.plot(x, y, J='X10c/5c', R='2005-01-01/2015-01-01/0/10', B=True, W='2p')
fig.show(method='external')
Full error message
Traceback (most recent call last):
File "test.py", line 7, in <module>
fig.plot(x, y, J='X10c/5c', R='2005-01-01/2015/01-01/0/10', B=True, W='2p')
File "/Users/seisman/Gits/gmt/gmt-python/gmt/helpers/decorators.py", line 199, in new_module
return module_func(*args, **kwargs)
File "/Users/seisman/Gits/gmt/gmt-python/gmt/helpers/decorators.py", line 294, in new_module
return module_func(*args, **kwargs)
File "/Users/seisman/Gits/gmt/gmt-python/gmt/base_plotting.py", line 344, in plot
with file_context as fname:
File "/Users/seisman/.anaconda/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/Users/seisman/Gits/gmt/gmt-python/gmt/clib/session.py", line 1067, in virtualfile_from_vectors
self.put_vector(dataset, column=col, vector=array)
File "/Users/seisman/Gits/gmt/gmt-python/gmt/clib/session.py", line 754, in put_vector
gmt_type = self._check_dtype_and_dim(vector, ndim=1)
File "/Users/seisman/Gits/gmt/gmt-python/gmt/clib/session.py", line 703, in _check_dtype_and_dim
"Unsupported numpy data type '{}'.".format(array.dtype.name)
gmt.exceptions.GMTInvalidInput: Unsupported numpy data type 'str320'.
System information
- Operating system: macOS 10.14
- Python installation (Anaconda, system, ETS): Anaconda
- Version of GMT: 6.0.0_15a9160
- Version of Python: 3.7.0
- Version of this package: latest
- If using conda, paste the output of
conda listbelow:
output of conda list
# packages in environment at /Users/seisman/.anaconda: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 alabaster 0.7.11 py37_0 anaconda 5.3.0 py37_0 anaconda-client 1.7.2 py37_0 anaconda-navigator 1.9.2 py37_0 anaconda-project 0.8.2 py37_0 appdirs 1.4.3 py37h28b3542_0 appnope 0.1.0 py37_0 appscript 1.0.1 py37h1de35cc_1 argh 0.26.2 <pip> asn1crypto 0.24.0 py37_0 astroid 2.0.4 py37_0 astropy 3.0.4 py37h1de35cc_0 atomicwrites 1.2.1 py37_0 attrs 18.2.0 py37h28b3542_0 automat 0.7.0 py37_0 babel 2.6.0 py37_0 backcall 0.1.0 py37_0 backports 1.0 py37_1 backports.shutil_get_terminal_size 1.0.0 py37_2 basemap 1.2.0 py37h0acbc05_0 beautifulsoup4 4.6.3 py37_0 bitarray 0.8.3 py37h1de35cc_0 bkcharts 0.2 py37_0 black 18.9b0 <pip> blas 1.0 mkl blaze 0.11.3 py37_0 bleach 2.1.4 py37_0 blosc 1.14.4 hd9629dc_0 bokeh 0.13.0 py37_0 boto 2.49.0 py37_0 bottleneck 1.2.1 py37h1d22016_1 bzip2 1.0.6 h1de35cc_5 ca-certificates 2018.03.07 0 cartopy 0.16.0 py37h9263bd1_0 certifi 2018.8.24 py37_1 cffi 1.11.5 py37h6174b99_1 cftime 1.0.0b1 py37h1d22016_0 chardet 3.0.4 py37_1 click 6.7 py37_0 cloud-sptheme 1.9.4 <pip> cloudpickle 0.5.5 py37_0 clyent 1.2.2 py37_1 cmarkgfm 0.4.2 <pip> colorama 0.3.9 py37_0 conda 4.5.11 py37_1000 conda-forge conda-build 3.15.1 py37_0 conda-env 2.6.0 1 constantly 15.1.0 py37h28b3542_0 contextlib2 0.5.5 py37_0 cryptography 2.3.1 py37hdbc3d79_0 curl 7.61.0 ha441bb4_0 cycler 0.10.0 py37_0 cython 0.28.5 py37h0a44026_0 cytoolz 0.9.0.1 py37h1de35cc_1 dask 0.19.1 py37_0 dask-core 0.19.1 py37_0 datashape 0.5.4 py37_1 dbus 1.13.2 h760590f_1 decorator 4.3.0 py37_0 defusedxml 0.5.0 py37_1 distributed 1.23.1 py37_0 docutils 0.14 py37_0 entrypoints 0.2.3 py37_2 et_xmlfile 1.0.1 py37_0 expat 2.2.6 h0a44026_0 fastcache 1.0.2 py37h1de35cc_2 filelock 3.0.8 py37_0 flask 1.0.2 py37_1 flask-cors 3.0.6 py37_0 freetype 2.9.1 hb4e5f40_0 future 0.16.0 <pip> future 0.17.0 py37_1000 conda-forge geographiclib 1.49 <pip> geos 3.6.2 h5470d99_2 get_terminal_size 1.0.0 h7520d66_0 gettext 0.19.8.1 h15daf44_3 gevent 1.3.6 py37h1de35cc_0 glib 2.56.2 hd9629dc_0 glob2 0.6 py37_0 gmp 6.1.2 hb37e062_1 gmpy2 2.0.8 py37h6ef4df4_2 gmt-python 0.1a3+126.g4617492.dirty <pip> greenlet 0.4.15 py37h1de35cc_0 guzzle-sphinx-theme 0.7.11 <pip> h5py 2.8.0 py37h878fce3_3 hdf4 4.2.13 h39711bb_2 hdf5 1.10.2 hfa1e0ec_1 heapdict 1.0.0 py37_2 html5lib 1.0.1 py37_0 hyperlink 18.0.0 py37_0 icu 58.2 h4b95b61_1 idna 2.7 py37_0 imageio 2.4.1 py37_0 imagesize 1.1.0 py37_0 incremental 17.5.0 py37_0 intel-openmp 2019.0 118 ipykernel 4.9.0 py37_1 ipython 6.5.0 py37_0 ipython_genutils 0.2.0 py37_0 ipywidgets 7.4.1 py37_0 isort 4.3.4 py37_0 itsdangerous 0.24 py37_1 jbig 2.1 h4d881f8_0 jdcal 1.4 py37_0 jedi 0.12.1 py37_0 jinja2 2.10 py37_0 jpeg 9b he5867d9_2 jsonschema 2.6.0 py37_0 jupyter 1.0.0 py37_7 jupyter_client 5.2.3 py37_0 jupyter_console 5.2.0 py37_1 jupyter_core 4.4.0 py37_0 jupyterlab 0.34.9 py37_0 jupyterlab_launcher 0.13.1 py37_0 keyring 13.2.1 py37_0 kiwisolver 1.0.1 py37h0a44026_0 lazy-object-proxy 1.3.1 py37h1de35cc_2 libcurl 7.61.0 hf30b1f0_0 libcxx 4.0.1 h579ed51_0 libcxxabi 4.0.1 hebd6815_0 libedit 3.1.20170329 hb402a30_2 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 h93005f0_2 libiconv 1.15 hdd342a3_7 libnetcdf 4.6.1 h4e6abe9_1 libpng 1.6.34 he12f830_0 libsodium 1.0.16 h3efe00b_0 libssh2 1.8.0 h322a93b_4 libtiff 4.0.9 hcb84e12_2 libxml2 2.9.8 hab757c2_1 libxslt 1.1.32 hb819dd2_0 livereload 2.5.2 <pip> llvmlite 0.24.0 py37hc454e04_0 locket 0.2.0 py37_1 lxml 4.2.5 py37hef8c89e_0 lzo 2.10 h362108e_2 markupsafe 1.0 py37h1de35cc_1 matplotlib 2.2.3 py37h54f8f79_0 mccabe 0.6.1 py37_1 mistune 0.8.3 py37h1de35cc_1 mkl 2019.0 118 mkl-service 1.1.2 py37h6b9c3cc_5 mkl_fft 1.0.4 py37h5d10147_1 mkl_random 1.0.1 py37h5d10147_1 more-itertools 4.3.0 py37_0 mpc 1.1.0 h6ef4df4_1 mpfr 4.0.1 h3018a27_3 mpmath 1.0.0 py37_2 msgpack-python 0.5.6 py37h04f5b5a_1 multipledispatch 0.6.0 py37_0 navigator-updater 0.2.1 py37_0 nbconvert 5.4.0 py37_1 nbformat 4.4.0 py37_0 ncurses 6.1 h0a44026_0 netcdf4 1.4.1 py37h08833f9_0 networkx 2.1 py37_0 nltk 3.3.0 py37_0 nose 1.3.7 py37_2 notebook 5.6.0 py37_0 numba 0.39.0 py37h6440ff4_0 numexpr 2.6.8 py37h1dc9127_0 numpy 1.15.1 py37h6a91979_0 numpy-base 1.15.1 py37h8a80b8c_0 numpydoc 0.8.0 py37_0 obspy 1.1.0 py37h39e3cac_2 conda-forge obspy 1.1.0 <pip> odo 0.5.1 py37_0 olefile 0.46 py37_0 openpyxl 2.5.6 py37_0 openssl 1.0.2p h1de35cc_0 owslib 0.17.0 py37_0 packaging 17.1 py37_0 pandas 0.23.4 py37h6440ff4_0 pandoc 1.19.2.1 ha5e8f32_1 pandocfilters 1.4.2 py37_1 parso 0.3.1 py37_0 partd 0.3.8 py37_0 path.py 11.1.0 py37_0 pathlib2 2.3.2 py37_0 pathtools 0.1.2 <pip> patsy 0.5.0 py37_0 pcre 8.42 h378b8a2_0 pep8 1.7.1 py37_0 pexpect 4.6.0 py37_0 pickleshare 0.7.4 py37_0 pillow 5.2.0 py37hb68e598_0 pip 10.0.1 py37_0 pkginfo 1.4.2 py37_1 pluggy 0.7.1 py37h28b3542_0 ply 3.11 py37_0 port-for 0.3.1 <pip> proj4 5.0.1 h1de35cc_0 prometheus_client 0.3.1 py37h28b3542_0 prompt_toolkit 1.0.15 py37_0 psutil 5.4.7 py37h1de35cc_0 ptyprocess 0.6.0 py37_0 py 1.6.0 py37_0 pyasn1 0.4.4 py37h28b3542_0 pyasn1-modules 0.2.2 py37_0 pycodestyle 2.4.0 py37_0 pycosat 0.6.3 py37h1de35cc_0 pycparser 2.18 py37_1 pycrypto 2.6.1 py37h1de35cc_9 pycurl 7.43.0.2 py37hdbc3d79_0 pyepsg 0.3.2 py37_0 pyflakes 2.0.0 py37_0 pygments 2.2.0 py37_0 pylint 2.1.1 py37_0 pyodbc 4.0.24 py37h0a44026_0 pyopenssl 18.0.0 py37_0 pyparsing 2.2.0 py37_1 pyproj 1.9.5.1 py37h833a5d7_1 pyqt 5.9.2 py37h655552a_2 pyshp 1.2.12 py37_0 pysocks 1.6.8 py37_0 pytables 3.4.4 py37h13cba08_0 pytest 3.8.0 py37_0 pytest-arraydiff 0.2 py37h39e3cac_0 pytest-astropy 0.4.0 py37_0 pytest-doctestplus 0.1.3 py37_0 pytest-mpl 0.10 <pip> pytest-openfiles 0.3.0 py37_0 pytest-remotedata 0.3.0 py37_0 python 3.7.0 hc167b69_0 python-dateutil 2.7.3 py37_0 python.app 2 py37_8 pytz 2018.5 py37_0 pywavelets 1.0.0 py37h1d22016_0 pyyaml 3.13 py37h1de35cc_0 pyzmq 17.1.2 py37h1de35cc_0 qt 5.9.6 h45cd832_2 qtawesome 0.4.4 py37_0 qtconsole 4.4.1 py37_0 qtpy 1.5.0 py37_0 readline 7.0 h1de35cc_5 readme-renderer 22.0 <pip> requests 2.19.1 py37_0 requests-toolbelt 0.8.0 <pip> rope 0.11.0 py37_0 ruamel_yaml 0.15.46 py37h1de35cc_0 scikit-image 0.14.0 py37h0a44026_1 scikit-learn 0.19.2 py37h4f467ca_0 scipy 1.1.0 py37h28f7352_1 seaborn 0.9.0 py37_0 send2trash 1.5.0 py37_0 service_identity 17.0.0 py37h28b3542_0 setuptools 40.2.0 py37_0 shapely 1.6.4 py37h20de77a_0 simplegeneric 0.8.1 py37_2 singledispatch 3.4.0.3 py37_0 sip 4.19.8 py37h0a44026_0 six 1.11.0 py37_1 snappy 1.1.7 he62c110_3 snowballstemmer 1.2.1 py37_0 sortedcollections 1.0.1 py37_0 sortedcontainers 2.0.5 py37_0 sphinx 1.7.9 py37_0 Sphinx 1.8.1 <pip> sphinx-autobuild 0.7.1 <pip> sphinx-cjkspace 0.1.2 <pip> sphinx-intl 0.9.11 <pip> sphinx-rtd-theme 0.4.1 <pip> sphinxcontrib 1.0 py37_1 sphinxcontrib-websupport 1.1.0 py37_1 spyder 3.3.1 py37_1 spyder-kernels 0.2.6 py37_0 sqlalchemy 1.2.11 py37h1de35cc_0 sqlite 3.24.0 ha441bb4_0 statsmodels 0.9.0 py37h1d22016_0 sympy 1.2 py37_0 tblib 1.3.2 py37_0 terminado 0.8.1 py37_1 testpath 0.3.1 py37_0 tk 8.6.8 ha441bb4_0 toml 0.10.0 <pip> toolz 0.9.0 py37_0 tornado 5.1 py37h1de35cc_0 tqdm 4.26.0 py37h28b3542_0 traitlets 4.3.2 py37_0 twine 1.12.1 <pip> twisted 18.7.0 py37h1de35cc_1 unicodecsv 0.14.1 py37_0 unixodbc 2.3.7 h1de35cc_0 urllib3 1.23 py37_0 watchdog 0.9.0 <pip> wcwidth 0.1.7 py37_0 webencodings 0.5.1 py37_1 werkzeug 0.14.1 py37_0 wheel 0.31.1 py37_0 widgetsnbextension 3.4.1 py37_0 wrapt 1.10.11 py37h1de35cc_2 xarray 0.10.8 py37_0 xlrd 1.1.0 py37_1 xlsxwriter 1.1.0 py37_0 xlwings 0.11.8 py37_0 xlwt 1.3.0 py37_0 xz 5.2.4 h1de35cc_4 yaml 0.1.7 hc338f04_2 zeromq 4.2.5 h0a44026_1 zhon 1.1.5 <pip> zict 0.1.3 py37_0 zlib 1.2.11 hf3cbc9b_2 zope 1.0 py37_1 zope.interface 4.5.0 py37h1de35cc_0
Issue Analytics
- State:
- Created 5 years ago
- Comments:22 (21 by maintainers)
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Any datetime types (raw strings, datetime, np.datetim64 and pandas.DatetimeIndex) are converted to strings (
char **in C) before passing to the GMT API.NaTis converted to the stringNaT. GMT can’t handle NaT, so it just gives an error and skips the NaT data points. (Perhaps it should be a warning instead of an error).NaT is basically like NaN, but for time. To be honest, I’m not sure why they don’t just use NaN, but yeah, it exists…
Yeah, a warning might be better here. Not sure if there is an ISO datetime for NaT.