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ndarray take method doesn't work with slice #2237

Closed Xunius closed 5 years ago

Xunius commented 5 years ago

I installed cdat using this conda command:

conda create -n cdat81 -c cdat/label/v81 -c conda-forge python=3.6 cdat

Running some scripts that used to work in older versions (I was using py2 previously) now breaks. I got this error:

Traceback (most recent call last):
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/pdb.py", line 1667, in main
    pdb._runscript(mainpyfile)
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/pdb.py", line 1548, in _runscript
    self.run(statement)
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/bdb.py", line 434, in run
    exec(cmd, globals, locals)
  File "<string>", line 1, in <module>
  File "/home/guangzhi/scripts/project_ar/river_tracker1.py", line 57, in <module>
    '''
  File "/home/guangzhi/scripts/project_ar/computerecano.py", line 191, in reProjectMap
    im2,lonscyc=addcyclic(im,lons)
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/site-packages/mpl_toolkits/basemap/__init__.py", line 5111, in addcyclic
    return list(map(_addcyclic,arr[:-1])) + [_addcyclic_lon(arr[-1])]
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/site-packages/mpl_toolkits/basemap/__init__.py", line 5096, in _addcyclic
    return npsel.concatenate((a,a[slicer]),axis=axis)
  File "/home/guangzhi/anaconda3/envs/cdat3/lib/python3.6/site-packages/cdms2/avariable.py", line 1749, in __getitem__
    return self.data.take(index)
TypeError: int() argument must be a string, a bytes-like object or a number, not 'slice'

where self.data is a 3d ndarray, index is [[slice(None, None, None), slice(None, None, None), slice(0, 1, None)]].

So the ndarray's take method is not working with slices any more. How do I fix this?

The entire outputs from conda list:

# Name Version Build Channel _libgcc_mutex 0.1 main alabaster 0.7.12 py_0 conda-forge asn1crypto 0.24.0 py36_1003 conda-forge astroid 2.2.5 py36_0 conda-forge attrs 19.1.0 py_0 conda-forge autopep8 1.4.4 py_0 conda-forge babel 2.7.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge basemap 1.2.0 py36hd759880_4 conda-forge blas 1.1 openblas conda-forge bleach 3.1.0 py_0 conda-forge bokeh 1.2.0 py36_0 conda-forge bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.5.15 0 cdat 8.1 1 cdat/label/v81 cdat_info 8.1.1 py_0 cdat/label/v81 cdms2 3.0.0 pypi_0 pypi cdp 1.4.2 py_1 cdat/label/v81 cdtime 3.1.2 py36h6091dcd_1 conda-forge cdutil 8.1 py_1 cdat/label/v81 certifi 2019.6.16 py36_0 cffi 1.12.3 py36h8022711_0 conda-forge chardet 3.0.4 py36_1003 conda-forge cibots 0.2 py_0 cdat/label/v81 click 7.0 py_0 conda-forge cloudpickle 1.2.1 py_0 conda-forge cryptography 2.7 py36h72c5cf5_0 conda-forge curl 7.65.3 hf8cf82a_0 conda-forge cycler 0.10.0 py_1 conda-forge cytoolz 0.10.0 py36h516909a_0 conda-forge dask 2.1.0 py_0 conda-forge dask-core 2.1.0 py_0 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.5.0 py_1 conda-forge distarray 2.12.2 py_1 conda-forge distributed 2.1.0 py_0 conda-forge docutils 0.14 py36_1001 conda-forge dv3d 8.1 py_0 cdat/label/v81 entrypoints 0.3 py36_1000 conda-forge eofs 1.4.0 py_0 conda-forge esmf 7.1.0 h9eb252b_1005 conda-forge esmpy 7.1.0 py36h24bf2e0_3 conda-forge expat 2.2.5 he1b5a44_1003 conda-forge ffmpeg 4.0.2 ha0c5888_2 conda-forge flake8 3.7.7 py36_0 conda-forge fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.0 he983fc9_0 conda-forge future 0.17.1 py36_1000 conda-forge g2clib 1.6.0 hf3f1b0b_9 conda-forge genutil 8.1.1 py36h3010b51_0 conda-forge geos 3.7.2 he1b5a44_1 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge ghostscript 9.22 hf484d3e_1001 conda-forge glib 2.58.3 h6f030ca_1002 conda-forge gmp 6.1.2 hf484d3e_1000 conda-forge gnutls 3.5.19 h2a4e5f8_1 conda-forge gst-plugins-base 1.14.5 h0935bb2_0 conda-forge gstreamer 1.14.5 h36ae1b5_0 conda-forge hdf4 4.2.13 h9a582f1_1002 conda-forge hdf5 1.10.4 nompi_h3c11f04_1106 conda-forge heapdict 1.0.0 py36_1000 conda-forge icu 58.2 hf484d3e_1000 conda-forge idna 2.8 py36_1000 conda-forge imageio 2.5.0 py36_0 imagesize 1.1.0 py_0 conda-forge ipykernel 5.1.1 py36h5ca1d4c_0 conda-forge ipython 7.6.1 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.0 py_0 conda-forge isort 4.3.21 py36_0 conda-forge jasper 1.900.1 h07fcdf6_1006 conda-forge jedi 0.14.1 py36_0 conda-forge jeepney 0.4 py_0 conda-forge jinja2 2.10.1 py_0 conda-forge jpeg 9c h14c3975_1001 conda-forge jsonschema 3.0.1 py36_0 conda-forge jupyter 1.0.0 py_2 conda-forge jupyter_client 5.3.1 py_0 conda-forge jupyter_console 6.0.0 py_0 conda-forge jupyter_core 4.4.0 py_0 conda-forge keyring 19.0.2 py36_0 conda-forge kiwisolver 1.1.0 py36hc9558a2_0 conda-forge krb5 1.16.3 h05b26f9_1001 conda-forge lazy-object-proxy 1.4.1 py36h516909a_0 conda-forge libcdms 3.1.2 hcbdc9ef_1000 cdat/label/v81 libcf 1.0.2 py36h6d95edf_1007 conda-forge libcurl 7.65.3 hda55be3_0 conda-forge libdrs 3.1.2 h8c6403c_2 conda-forge libdrs_f 3.1.2 h0ebed7e_2 conda-forge libedit 3.1.20170329 hf8c457e_1001 conda-forge libffi 3.2.1 he1b5a44_1006 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 libiconv 1.15 h516909a_1005 conda-forge libnetcdf 4.6.2 hbdf4f91_1001 conda-forge libopenblas 0.3.6 h5a2b251_1 libpng 1.6.37 hed695b0_0 conda-forge libsodium 1.0.17 h516909a_0 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.0.10 h57b8799_1003 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.9 h13577e0_2 conda-forge locket 0.2.0 py_2 conda-forge lz4-c 1.8.3 he1b5a44_1001 conda-forge markupsafe 1.1.1 py36h14c3975_0 conda-forge matplotlib 3.1.1 py36_0 conda-forge matplotlib-base 3.1.1 py36hfd891ef_0 conda-forge mccabe 0.6.1 py_1 conda-forge mistune 0.8.4 py36h14c3975_1000 conda-forge mpi 1.0 mpich conda-forge mpich 3.2.1 hc99cbb1_1013 conda-forge msgpack-python 0.6.1 py36h6bb024c_0 conda-forge nb_conda 2.2.1 py36_2 conda-forge nb_conda_kernels 2.2.2 py36_0 conda-forge nbconvert 5.5.0 py_0 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge netcdf-fortran 4.4.5 hea25ff8_1000 conda-forge nettle 3.3 0 conda-forge networkx 2.3 py_0 notebook 6.0.0 py36_0 conda-forge numpy 1.16.4 py36h99e49ec_0 numpy-base 1.16.4 py36h2f8d375_0 numpydoc 0.9.1 py_0 conda-forge olefile 0.46 py_0 conda-forge openblas 0.3.3 h9ac9557_1001 conda-forge openh264 1.8.0 hdbcaa40_1000 conda-forge openssl 1.1.1c h7b6447c_1 output_viewer 1.2.5 py36_0 cdat/label/v81 packaging 19.0 py_0 conda-forge pandas 0.25.0 py36hb3f55d8_0 conda-forge pandoc 2.7.3 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge parso 0.5.1 py_0 conda-forge partd 1.0.0 py_0 conda-forge pcre 8.41 hf484d3e_1003 conda-forge pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 6.0.0 py36he7afcd5_0 conda-forge pip 19.1.1 py36_0 conda-forge proj4 5.2.0 he1b5a44_1004 conda-forge prometheus_client 0.7.1 py_0 conda-forge prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h516909a_0 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge pycodestyle 2.5.0 py_0 conda-forge pycparser 2.19 py36_1 conda-forge pyflakes 2.1.1 py_0 conda-forge pygments 2.4.2 py_0 conda-forge pylint 2.3.1 py36_0 conda-forge pyopenssl 19.0.0 py36_0 conda-forge pyparsing 2.4.0 py_0 conda-forge pyproj 1.9.6 py36h516909a_1002 conda-forge pyqt 5.9.2 py36hcca6a23_0 conda-forge pyrsistent 0.15.3 py36h516909a_0 conda-forge pyshp 2.1.0 py_0 conda-forge pysocks 1.7.0 py36_0 conda-forge pyspharm 1.0.9 py36h6091dcd_1003 conda-forge python 3.6.7 h357f687_1005 conda-forge python-dateutil 2.8.0 py_0 conda-forge pytz 2019.1 py_0 conda-forge pywavelets 1.0.3 py36hdd07704_1 pyyaml 5.1.1 py36h516909a_0 conda-forge pyzmq 18.0.2 py36h1768529_2 conda-forge qt 5.9.7 h52cfd70_2 conda-forge qtawesome 0.5.7 pyh8a2030e_0 conda-forge qtconsole 4.5.1 py_0 conda-forge qtpy 1.8.0 py_0 conda-forge readline 8.0 hf8c457e_0 conda-forge regrid2 3.0.0 pypi_0 pypi requests 2.22.0 py36_1 conda-forge rope 0.14.0 py_0 conda-forge scikit-image 0.15.0 py36he6710b0_0 scipy 1.2.1 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge secretstorage 3.1.1 py36_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 41.0.1 py36_0 conda-forge sip 4.19.8 py36hf484d3e_1000 conda-forge six 1.12.0 py36_1000 conda-forge snowballstemmer 1.9.0 py_0 conda-forge sortedcontainers 2.1.0 py_0 conda-forge sphinx 2.1.2 py_0 conda-forge sphinxcontrib-applehelp 1.0.1 py_0 conda-forge sphinxcontrib-devhelp 1.0.1 py_0 conda-forge sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.2 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.1 py_0 conda-forge spyder 3.3.6 py36_0 conda-forge spyder-kernels 0.5.1 py36_0 conda-forge sqlite 3.29.0 hcee41ef_0 conda-forge tblib 1.4.0 py_0 conda-forge terminado 0.8.2 py36_0 conda-forge testpath 0.4.2 py_1001 conda-forge tk 8.6.9 hed695b0_1002 conda-forge toolchain3 1.1.1 0 conda-forge toolz 0.10.0 py_0 conda-forge tornado 6.0.3 py36h516909a_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge typed-ast 1.4.0 py36h516909a_0 conda-forge udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge urllib3 1.25.3 py36_0 conda-forge vcs 8.1 py_0 cdat/label/v81 vcsaddons 8.1 py36h14c3975_0 cdat/label/v81 vtk-cdat 8.2.0rc2.8.1 py36h413fb2d_0 cdat/label/v81 wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.33.4 py36_0 conda-forge widgetsnbextension 3.5.0 py36_0 conda-forge windspharm 1.7.0 py36_1000 conda-forge wk 8.1 py_0 cdat/label/v81 wrapt 1.11.2 py36h516909a_0 conda-forge wurlitzer 1.0.3 py36_0 conda-forge x264 1!152.20180806 h14c3975_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xz 5.2.4 h14c3975_1001 conda-forge yaml 0.1.7 h14c3975_1001 conda-forge zeromq 4.3.2 he1b5a44_2 conda-forge zict 1.0.0 py_0 conda-forge zlib 1.2.11 h516909a_1005 conda-forge zstd 1.4.0 h3b9ef0a_0 conda-forge <\details>
Xunius commented 5 years ago

Update myself:

It started from basemap.addcyclic(im, lons), where im is a TransientVariable. If I do basemap.addcyclic(np.array(im), lons) it works.

Inside addcyclic it is this line that triggers the error: npsel.concatenate((a,a[slicer]),axis=axis). a[slicer] works for ndarray but not for TransientVariable.