import pyhdf.HDF, ImportError: No module named '_hdfext'

Question

import pyhdf.HDF, ImportError: No module named '_hdfext'

fzhu2e opened this issue 10 years ago · comments

Hi there,

My system is OSX and Python version is Python3.
I installed hdf4 library by homebrew, and I set the environment as:

export INCLUDE_DIRS=/usr/local//include
export LIBRARY_DIRS=/usr/local/lib

since homebrew installs files under /usr/local.
Also, I can successfully install pyhdf by:

$ python3 setup.py install
running install
running bdist_egg
running egg_info
running build_src
build_src
building extension "pyhdf._hdfext" sources
build_src: building npy-pkg config files
writing python_hdf4.egg-info/PKG-INFO
writing dependency_links to python_hdf4.egg-info/dependency_links.txt
writing top-level names to python_hdf4.egg-info/top_level.txt
reading manifest file 'python_hdf4.egg-info/SOURCES.txt'
writing manifest file 'python_hdf4.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.5-x86_64/egg
running install_lib
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
creating build/bdist.macosx-10.5-x86_64/egg
creating build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/__init__.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/_hdfext.so -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/error.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/HC.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/HDF.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/hdfext.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/SD.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/six.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/test_SD.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/V.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
copying build/lib.macosx-10.5-x86_64-3.4/pyhdf/VS.py -> build/bdist.macosx-10.5-x86_64/egg/pyhdf
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/__init__.py to __init__.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/error.py to error.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/HC.py to HC.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/HDF.py to HDF.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/hdfext.py to hdfext.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/SD.py to SD.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/six.py to six.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/test_SD.py to test_SD.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/V.py to V.cpython-34.pyc
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/VS.py to VS.cpython-34.pyc
creating stub loader for pyhdf/_hdfext.so
byte-compiling build/bdist.macosx-10.5-x86_64/egg/pyhdf/_hdfext.py to _hdfext.cpython-34.pyc
creating build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
copying python_hdf4.egg-info/PKG-INFO -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
copying python_hdf4.egg-info/SOURCES.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
copying python_hdf4.egg-info/dependency_links.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
copying python_hdf4.egg-info/top_level.txt -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
copying python_hdf4.egg-info/zip-safe -> build/bdist.macosx-10.5-x86_64/egg/EGG-INFO
writing build/bdist.macosx-10.5-x86_64/egg/EGG-INFO/native_libs.txt
creating 'dist/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg' and adding 'build/bdist.macosx-10.5-x86_64/egg' to it
removing 'build/bdist.macosx-10.5-x86_64/egg' (and everything under it)
Processing python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg
Removing /Users/Lyric/Tools/Python3/lib/python3.4/site-packages/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg
Copying python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg to /Users/Lyric/Tools/Python3/lib/python3.4/site-packages
python-hdf4 0.9 is already the active version in easy-install.pth

Installed /Users/Lyric/Tools/Python3/lib/python3.4/site-packages/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg
Processing dependencies for python-hdf4==0.9
Finished processing dependencies for python-hdf4==0.9

I can import pyhdf. However, when I import pyhdf.HDF, it raises error:

import pyhdf.HDF
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-c2e4930f14c5> in <module>()
----> 1 import pyhdf.HDF

/Users/Lyric/Tools/Python3/lib/python3.4/site-packages/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg/pyhdf/HDF.py in <module>()
     72 import os, sys, types
     73
---> 74 from . import hdfext as _C
     75 from .six.moves import xrange
     76 from .HC import HC

/Users/Lyric/Tools/Python3/lib/python3.4/site-packages/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg/pyhdf/hdfext.py in <module>()
     26                 fp.close()
     27             return _mod
---> 28     _hdfext = swig_import_helper()
     29     del swig_import_helper
     30 else:

/Users/Lyric/Tools/Python3/lib/python3.4/site-packages/python_hdf4-0.9-py3.4-macosx-10.5-x86_64.egg/pyhdf/hdfext.py in swig_import_helper()
     18             fp, pathname, description = imp.find_module('_hdfext', [dirname(__file__)])
     19         except ImportError:
---> 20             import _hdfext
     21             return _hdfext
     22         if fp is not None:

ImportError: No module named '_hdfext'

Should I need to compile all the libraries (zlib, libjpeg, hdf4) by myself?

Fazlul Shahriar · Answer 1 · Sat Jan 17 2015 03:38:21 GMT+0800 (China Standard Time)

Should I need to compile all the libraries (zlib, libjpeg, hdf4) by myself?

No, you don't need to compile them.

You should look inside /Users/Lyric/Tools/Python3/lib/python3.4/site-packages/ and check _hdfext.so is linked against all the required libraries. You can use something equivalent to Linux ldd command (otool -L ?) to check. I don't have an OS X system, so it's hard for me to reproduce this problem.

Feng Zhu · Answer 2 · Sat Jan 17 2015 03:51:49 GMT+0800 (China Standard Time)

Thanks. I copied the _hdfext.so file to the site-packages directory manually and it works now. So it turns out that the .so file was not copied to the directory automatically.

Thank you!

Juan Saenz · Answer 3 · Thu Mar 23 2017 23:19:58 GMT+0800 (China Standard Time)

I had a similar issue. I used ldd as suggested above (thank you!) and found that libjpeg.so.8 was not present. I then checked the version of jpeg, and the version that had been installed was version 9, so libjpeg.so.9 was present. So I uninstalled jpeg, which removes hdf4 and python-hdf4. Then I ran 'conda install jpeg=8', and then conda install -c hcc python-hdf4. This way the links were correctly set and my problem was solved.

So it seems like running conda install -c hcc python-hdf4 does not correctly check and/or install the correct version of jpeg.

Daradorn · Answer 4 · Sat Oct 07 2017 18:59:15 GMT+0800 (China Standard Time)

error: Command "gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/Daradorn/.local/include -fPIC -I/home/appl/usr/local/lib/python2.7/site-packages/numpy/core/include -I/home/appl/usr/local/include/python2.7 -c pyhdf/hdfext_wrap.c -o build/temp.linux-x86_64-2.7/pyhdf/hdfext_wrap.o" failed with exit status 1

How to deal with pyhdf-0.8.3? I complete with all (ZILB, SZIP and JPEG)

Alyson Douglas · Answer 5 · Wed Jul 31 2019 02:48:59 GMT+0800 (China Standard Time)

Is there a better fix for this? Im currently getting my error too and no amount of uninstalling/reinstalling seems to be fixing it.

Fazlul Shahriar · Answer 6 · Wed Jul 31 2019 02:57:33 GMT+0800 (China Standard Time)

@AlysonR Use conda so you don't have to worry about these issues. See top of installation guide: http://fhs.github.io/pyhdf/install.html

Mohammad Ghaemi · Answer 7 · Fri Jul 02 2021 08:49:57 GMT+0800 (China Standard Time)

I installed using conda install -c conda-forge pyhdf and still got the _No module named 'hdfext' error.

rippleofheart · Answer 8 · Sun Sep 18 2022 09:43:20 GMT+0800 (China Standard Time)

Hello，Could you share the _hdftext.so to me? Or tell me how to find it, please?

812515548 · Answer 9 · Fri Nov 25 2022 20:40:50 GMT+0800 (China Standard Time)

Thanks. I copied the file to the site-packages directory manually and it works now. So it turns out that the file was not copied to the directory automatically._hdfext.so``.so

Thank you!

Hello my friend，I have the same problem, Could you please share the _hdftext.so to me? or tell me how to download it, please?

M-ych · Answer 10 · Sat Jun 03 2023 10:59:12 GMT+0800 (China Standard Time)

Thanks. I copied the file to the site-packages directory manually and it works now. So it turns out that the file was not copied to the directory automatically. _hdfext.so.so ``
Thank you!

Hello my friend，I have the same problem, Could you please share the _hdftext.so to me? or tell me how to download it, please?

Hello, friend. Have you resolved your issue? I encountered the same problem as you did.