Mac OS Issue #25
Comments
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Hi, Apologies for the late response. I've tested the import on OS X 10.11.5 using python 3.5.1 (pyminc has been made Python3 compatible) using the minc-toolkit packages from here: http://bic-mni.github.io and am not seeing the same issues. The LD_LIBRARY_PATH for the above package is: /opt/minc-itk4/lib So exporting the LD_LIBRARY_PATH as follows: export LD_LIBRARY_PATH=/opt/minc-itk4/lib:$LD_LIBRARY_PATH should do the trick. Can I ask how you've installed the MINC libraries? |
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My impression was that this wouldn't work anymore on macs ... @cfhammill ? |
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I worked when I just tried it... :-) Perhaps because it's a slightly outdated version of the Mac OS? |
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Did the issue happen before you set the LD_LIBRARY_PATH Matthijs? LD_LIBRARY_PATH shouldn't |
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Before setting the LD_LIBRARY_PATH I got the error: Afterwards I had no errors at all loading pyminc.volumes.factory |
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I think I've made some progress. I can now run "from pyminc.volumes.factory import *"; however, this only works from within python. If I generate a python script, which works on linux without any issues, then run it on my local machine -- using minctools installed as described above. I've also set the LD_LIBRARY_PATH in bash. File "./create_noise.py", line 7, in I am running on 10.12, which may be the issue. |
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What did you set your LD_LIBRARY_PATH to? And what is the full name of the MINC library you have installed on the Mac? |
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echo $LD_LIBRARY_PATH returns: /opt/minc-itk4/lib:
In that directory, there are 4 libminc files:
/opt/minc-itk4/lib/libminc2.5.0.1.dylib
/opt/minc-itk4/lib/libminc_io.5.0.1.dylib
/opt/minc-itk4/lib/libminc2.dylib /opt/minc-itk4/lib/libminc_io.dylib
iPython works fine.
pyminc.__path__ returns ['/usr/local/lib/python2.7/site-packages/pyminc']
================
In Python, I get errors:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/pyminc/volumes/factory.py",
line 3, in <module>
from .volumes import mincException,mincVolume
File "/usr/local/lib/python2.7/site-packages/pyminc/volumes/volumes.py",
line 1, in <module>
from .libpyminc2 import *
File
"/usr/local/lib/python2.7/site-packages/pyminc/volumes/libpyminc2.py", line
4, in <module>
from ctypes.util import find_library
File
"/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/util.py",
line 2, in <module>
import subprocess
File
"/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 75, in <module>
import pickle
File
"/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py",
line 1272, in <module>
import binascii as _binascii
ImportError:
dlopen(/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so,
2): Library not loaded: libz.1.dylib
Referenced from:
/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/binascii.so
Reason: image not found
===================================
If I call a python script, I also get errors:
Something went wrong loading shared libraries ...Traceback (most recent
call last):
File "./stc.py", line 7, in <module>
from pyminc.volumes.factory import *
File "/usr/local/lib/python2.7/site-packages/pyminc/volumes/factory.py",
line 3, in <module>
from .volumes import mincException,mincVolume
File "/usr/local/lib/python2.7/site-packages/pyminc/volumes/volumes.py",
line 1, in <module>
from .libpyminc2 import *
File
"/usr/local/lib/python2.7/site-packages/pyminc/volumes/libpyminc2.py", line
18, in <module>
libminc = cdll.LoadLibrary("libminc2.so")
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py",
line 443, in LoadLibrary
return self._dlltype(name)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py",
line 365, in __init__
self._handle = _dlopen(self._name, mode)
OSError: dlopen(libminc2.so, 6): image not found
Best Regards,
Donald McLaren, PhD
…On Fri, Feb 10, 2017 at 3:29 PM, Matthijs van Eede ***@***.*** > wrote:
What did you set your LD_LIBRARY_PATH to? And what is the full name of the
MINC library you have installed on the Mac?
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I'm getting the same kinds of errors when I'm using python 2.7. However, using python 3.5.1 resolves them. Can you give that a try? |
Using: from pyminc.volumes.factory import *
Leads to the following issue:
/Users/mclaren/ in ()
----> 1 from pyminc.volumes.factory import *
/usr/local/lib/python2.7/site-packages/pyminc/volumes/factory.py in ()
1 """factories for creating mincVolumes"""
2
----> 3 from .volumes import mincException,mincVolume
4
5 def volumeFromFile(filename, dtype="float", readonly=True, labels=False):
/usr/local/lib/python2.7/site-packages/pyminc/volumes/volumes.py in ()
----> 1 from .libpyminc2 import *
2 from .hyperslab import HyperSlab
3 import operator
4 import os
5 import sys
/usr/local/lib/python2.7/site-packages/pyminc/volumes/libpyminc2.py in ()
107 # argument declarations - not really necessary but does make
--> 109 libminc.miopen_volume.argtypes = [c_stringy, c_int, POINTER(mihandle)]
110 libminc.miget_real_value.argtypes = [mihandle, location, c_int, POINTER(voxel)]
111 libminc.miget_volume_dimensions.argtypes = [mihandle, c_int, c_int, c_int,
/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/ctypes/init.pyc in getattr(self, name)
376 if name.startswith('') and name.endswith(''):
377 raise AttributeError(name)
--> 378 func = self.getitem(name)
379 setattr(self, name, func)
380 return func
/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/ctypes/init.pyc in getitem(self, name_or_ordinal)
381
382 def getitem(self, name_or_ordinal):
--> 383 func = self._FuncPtr((name_or_ordinal, self))
384 if not isinstance(name_or_ordinal, (int, long)):
385 func.name = name_or_ordinal
AttributeError: dlsym(0x102fdc290, miopen_volume): symbol not found
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