【发布时间】：2015-08-16 18:47:01
【问题描述】：
我想在 MATLAB 中使用 http://www.losonczylab.org/sima/1.2/。
我可以从 python 运行它。
我可以在 MATLAB 中导入示例依赖项。
$ /opt/local/bin/python
Python 2.7.9 (default, Dec 13 2014, 15:13:49)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from sima import sequence
>>> sequence
<module 'sima.sequence' from '/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/sequence.pyc'>
>>> from sima import ImagingDataset
>>> ImagingDataset
<class 'sima.imaging.ImagingDataset'>
在 MATLAB 中：
>> pyversion /opt/local/bin/python
>> pyversion
version: '2.7'
executable: '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Cont...'
library: '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib'
home: '/opt/local/Library/Frameworks/Python.framework/Versions/2.7'
isloaded: 0
>> import py.picos.tools.available_solvers
>> available_solvers
ans =
Python list with no properties.
['cvxopt', 'mosek7']
>> import py.numpy.empty
>> empty(0)
ans =
Python ndarray with properties:
T: [1x1 py.numpy.ndarray]
base: [1x1 py.NoneType]
ctypes: [1x1 py.numpy.core._internal._ctypes]
data: [1x0 py.buffer]
dtype: [1x1 py.numpy.dtype]
flags: [1x1 py.numpy.flagsobj]
flat: [1x1 py.numpy.flatiter]
imag: [1x1 py.numpy.ndarray]
itemsize: 8
nbytes: 0
ndim: 1
real: [1x1 py.numpy.ndarray]
shape: [1x1 py.tuple]
size: 0
strides: [1x1 py.tuple]
[]
>> import py.sima.sequence
Error using import
Import argument 'py.sima.sequence' cannot be found or cannot be imported.
>> import py.sima.Sequence
Error using import
Import argument 'py.sima.Sequence' cannot be found or cannot be imported.
>> import py.sima.Sequence.create
Error using import
Import argument 'py.sima.Sequence.create' cannot be found or cannot be imported.
>> import py.sima.sequence.create
Error using import
Import argument 'py.sima.sequence.create' cannot be found or cannot be imported.
>> import py.sima.sequence
Error using import
Import argument 'py.sima.sequence' cannot be found or cannot be imported.
>> import py.sima.Sequence
Error using import
Import argument 'py.sima.Sequence' cannot be found or cannot be imported.
>> import py.sima.ImagingDataset
Error using import
Import argument 'py.sima.ImagingDataset' cannot be found or cannot be imported.
>> import py.sima.imagingdataset
Error using import
Import argument 'py.sima.imagingdataset' cannot be found or cannot be imported.
>> import py.sima
Error using import
Import argument 'py.sima' cannot be found or cannot be imported.
我怎样才能知道为什么sima无法导入？
sima 正在路上：
>> pp = py.pprint.PrettyPrinter
pp =
Python PrettyPrinter with no properties.
<pprint.PrettyPrinter instance at 0x129425bd8>
>> pp.pprint(py.sys.path)
['',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload',
'/Users/eflister/Library/Python/2.7/lib/python/site-packages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages']
我想出了以下乏味的方法来查找问题导入 - 有没有更好的方法？
- 定义一个模块，如http://www.mathworks.com/help/matlab/matlab_external/call-user-defined-custom-module.html
- 复制从 MATLAB 不会加载的库中的源文件导入
- 注释掉可疑导入，直到 MATLAB 调用模块成功
- 重命名模块并重复（成功加载后，MATLAB 必须重新启动才能看到新的更改）
我只需要这样做 29 次即可隔离 sima 中的以下有问题的导入。 :)
from PIL import Image
from skimage.measure import approximate_polygon
from skimage.measure import find_contours
from skimage.filter import threshold_otsu
from skimage import transform as tf
from sklearn.decomposition import FastICA
import scipy.io
from scipy.stats import uniform
from scipy.linalg import inv
from scipy.sparse.linalg import eigsh, eigs
from scipy.sparse.linalg import inv
from scipy import ndimage
from scipy.ndimage import measurements
import cv2
# note the following are OK:
from scipy.linalg import eig, eigh, norm
from scipy import sparse
from multiprocessing import Pool
import multiprocessing.util as util
在 python 中运行此代码显示没有导入异常：
lines = """
import h5py
from PIL import Image
from skimage.measure import approximate_polygon
from skimage.measure import find_contours
from skimage.filter import threshold_otsu
from skimage import transform as tf
from sklearn.decomposition import FastICA
import scipy.io
from scipy.stats import uniform
from scipy.linalg import inv
from scipy.sparse.linalg import eigsh, eigs
from scipy.sparse.linalg import inv
from scipy import ndimage
from scipy.ndimage import measurements
import cv2
"""
def tryImport(i):
try:
exec(i)
except ImportError as e:
print i
print e
print
map(tryImport, filter(lambda x: len(x) > 0, lines.splitlines()))
但在 MATLAB 中，它给出了输出：
import h5py
cannot import name _errors
from PIL import Image
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PIL/_imaging.so, 2): Library not loaded: /opt/local/lib/libtiff.5.dylib
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PIL/_imaging.so
Reason: Incompatible library version: _imaging.so requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0
from skimage.measure import approximate_polygon
cannot import name _ni_support
from skimage.measure import find_contours
cannot import name _ni_support
from skimage.filter import threshold_otsu
cannot import name _ni_support
from skimage import transform as tf
cannot import name hough_ellipse
from sklearn.decomposition import FastICA
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_lbfgsb.so, 2): Symbol not found: __gfortran_transfer_character_write
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_lbfgsb.so
Expected in: /Applications/MATLAB_R2015a.app/sys/os/maci64/libgfortran.3.dylib
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/optimize/_lbfgsb.so
import scipy.io
cannot import name doccer
from scipy.stats import uniform
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so, 2): Symbol not found: __gfortran_stop_numeric_f08
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so
Expected in: /Applications/MATLAB_R2015a.app/sys/os/maci64/libgfortran.3.dylib
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so
from scipy.sparse.linalg import eigsh, eigs
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so, 2): Symbol not found: __gfortran_transfer_array_write
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
Expected in: /Applications/MATLAB_R2015a.app/sys/os/maci64/libgfortran.3.dylib
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
from scipy.sparse.linalg import inv
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so, 2): Symbol not found: __gfortran_transfer_array_write
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
Expected in: /Applications/MATLAB_R2015a.app/sys/os/maci64/libgfortran.3.dylib
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
from scipy import ndimage
cannot import name _ni_support
from scipy.ndimage import measurements
cannot import name _ni_support
import cv2
dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/cv2.so, 2): Library not loaded: /opt/local/lib/libtiff.5.dylib
Referenced from: /opt/local/lib/libopencv_highgui.2.4.dylib
Reason: Incompatible library version: libopencv_highgui.2.4.dylib requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0
我发现这个方法显示了matlab的错误：
>> py.importlib.import_module('sima')
Python Error: cannot import name hough_ellipse
那么从这里开始还有希望吗？
我不太了解这些错误，据我所知，其中一些是：
matlab 的 libtiff.5.dylib 提供 6.0.0 版本，但是 PIL 和 opencv 需要 >= 8.0.0
matlab 的 libgfortran.3.dylib 不适用于 scipy 的 _lbfgsb.so、_ufuncs.so、_arpack.so
是否有某种方法可以针对 MATLAB 的库编译 scipy/PIL/opencv？
会非常痛苦吗？ :)
我找到了以下第 3 方 python-from-matlab 桥：
- http://algoholic.eu/matpy/ -- numpy.ndarray 集成
- https://github.com/kw/pymex -- numpy.ndarray 集成，近期开发较少，但看起来也不错
- https://github.com/pv/pythoncall -- 更老了，看起来不够精致
- https://code.google.com/p/python-matlab-wormholes/ -- 也是旧的，ndarray 唯一的，基于 TCP 的双向
还有其他需要考虑的吗？对于这种情况最有希望的意见/经验？我猜是matpy...
pymex 是 no good
matpy 不好：
>> py_shell
py> import sima
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/__init__.py", line 6, in <module>
from sima.imaging import ImagingDataset
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/imaging.py", line 26, in <module>
import h5py
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/h5py/__init__.py", line 23, in <module>
from . import _conv
File "h5py/h5t.pxd", line 14, in init h5py._conv (/opt/local/var/macports/build/_opt_mports_dports_python_py-h5py/py27-h5py/work/h5py-2.5.0/h5py/_conv.c:6958)
File "h5py/h5t.pyx", line 139, in init h5py.h5t (/opt/local/var/macports/build/_opt_mports_dports_python_py-h5py/py27-h5py/work/h5py-2.5.0/h5py/h5t.c:20282)
File "h5py/h5t.pyx", line 73, in h5py.h5t.lockid (/opt/local/var/macports/build/_opt_mports_dports_python_py-h5py/py27-h5py/work/h5py-2.5.0/h5py/h5t.c:2562)
File "h5py/h5t.pyx", line 42, in h5py.h5t.typewrap (/opt/local/var/macports/build/_opt_mports_dports_python_py-h5py/py27-h5py/work/h5py-2.5.0/h5py/h5t.c:2196)
RuntimeError: Interface initialization failed (Not a datatype object)
py> import sima
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/__init__.py", line 6, in <module>
from sima.imaging import ImagingDataset
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/imaging.py", line 33, in <module>
import sima.misc
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/misc/__init__.py", line 21, in <module>
from skimage import transform as tf
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skimage/transform/__init__.py", line 1, in <module>
from ._hough_transform import (hough_ellipse, hough_line,
File "skimage/transform/_hough_transform.pyx", line 13, in init skimage.transform._hough_transform (skimage/transform/_hough_transform.c:22321)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skimage/draw/__init__.py", line 2, in <module>
from .draw3d import ellipsoid, ellipsoid_stats
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skimage/draw/draw3d.py", line 3, in <module>
from scipy.special import (ellipkinc as ellip_F, ellipeinc as ellip_E)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/__init__.py", line 586, in <module>
from ._ufuncs import *
ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so, 2): Symbol not found: __gfortran_stop_numeric_f08
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so
Expected in: /Applications/MATLAB_R2015a.app/sys/os/maci64/libgfortran.3.dylib
in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/special/_ufuncs.so
py> import sima
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/__init__.py", line 6, in <module>
from sima.imaging import ImagingDataset
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/imaging.py", line 33, in <module>
import sima.misc
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/misc/__init__.py", line 21, in <module>
from skimage import transform as tf
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skimage/transform/__init__.py", line 1, in <module>
from ._hough_transform import (hough_ellipse, hough_line,
ImportError: cannot import name hough_ellipse
py> import sima
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/__init__.py", line 6, in <module>
from sima.imaging import ImagingDataset
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/imaging.py", line 33, in <module>
import sima.misc
File "/Users/eflister/Library/Python/2.7/lib/python/site-packages/sima/misc/__init__.py", line 21, in <module>
from skimage import transform as tf
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/skimage/transform/__init__.py", line 1, in <module>
from ._hough_transform import (hough_ellipse, hough_line,
ImportError: cannot import name hough_ellipse
py> import picos.tools
py> print picos.tools.available_solvers()
['cvxopt', 'mosek7']
我开始认为虫洞到一个单独的进程听起来不错...
但是如何使用LD_PRELOAD 来启动具有更新的 libgfortran 和 libtiff 的 matlab？
我想要的版本位于：
/opt/local/lib/libgcc/libgfortran.3.dylib
/opt/local/lib/libtiff.5.dylib
在新的 matlab 会话中，以下内容没有帮助。
>> setenv('DYLD_LIBRARY_PATH',['/opt/local/lib:' getenv('DYLD_LIBRARY_PATH')])
>> getenv('DYLD_LIBRARY_PATH')
ans =
/opt/local/lib:/Applications/MATLAB_R2015a.app/sys/os/maci64:/Applications/MATLAB_R2015a.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2015a.app/bin/maci64:/Applications/MATLAB_R2015a.app/extern/lib/maci64:/Applications/MATLAB_R2015a.app/runtime/maci64:/Applications/MATLAB_R2015a.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2015a.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2015a.app/sys/java/jre/maci64/jre/lib/./lib/jli
但是！！！
~$ DYLD_INSERT_LIBRARIES=/opt/local/lib/libgcc/libgfortran.3.dylib:/opt/local/lib/libtiff.5.dylib /Applications/MATLAB_R2015a.app/bin/matlab
解决所有导入问题！！！
>> import py.sima
Error using import
Import argument 'py.sima' cannot be found or cannot be imported.
>> import py.sima.Sequence % succeeds!
>> import py.sima.ImagingDataset % succeeds!
>> x = py.sima.ImagingDataset([1,2],'~')
Python Error: ImagingDataset objects must be initialized with a list of sequences.
>> x = py.numpy.random.random([2,3,4])
x =
Python ndarray with properties:
T: [1x1 py.numpy.ndarray]
base: [1x1 py.NoneType]
ctypes: [1x1 py.numpy.core._internal._ctypes]
data: [1x192 py.buffer]
dtype: [1x1 py.numpy.dtype]
flags: [1x1 py.numpy.flagsobj]
flat: [1x1 py.numpy.flatiter]
imag: [1x1 py.numpy.ndarray]
itemsize: 8
nbytes: 192
ndim: 3
real: [1x1 py.numpy.ndarray]
shape: [1x3 py.tuple]
size: 24
strides: [1x3 py.tuple]
[[[ 0.4158531 0.18912596 0.20743597 0.92631168]
[ 0.0371785 0.48093953 0.88221637 0.85687334]
[ 0.2267605 0.79464779 0.97438662 0.47791076]]
[[ 0.05602249 0.06596678 0.05691491 0.02706325]
[ 0.28477145 0.74781928 0.56700236 0.14500885]
[ 0.87999554 0.78932748 0.24473039 0.18383564]]]
>> x = py.sima.Sequence.create('ndarray',x)
The class "py.sima.Sequence" is undefined.
Perhaps Java is not running.
>> py.sima.segment.STICA()
ans =
Python STICA with no properties.
<sima.segment.stica.STICA object at 0x138e15890>
>> py.sima.segment.PlaneCA1PC()
ans =
Python PlaneCA1PC with no properties.
<sima.segment.ca1pc.PlaneCA1PC object at 0x138e158d0>
我们终于如此接近了。但是为什么我不能让sima.Sequence.create() 运行！？？！
【问题讨论】：
-
好像不是these
-
import py.scipy.io.loadmat也以同样的方式失败，但import py.scipy.constants.pi和import py.scipy.cluster.hierarchy.fcluster没问题。 -
为什么
py.pprint.PrettyPrinter.pprint(py.sys.path)会失败并出现The class py.pprint.PrettyPrinter has no property or method named 'pprint'.当这工作时：pp = py.pprint.PrettyPrinter; pp.pprint(py.sys.path)？ -
在我看来，您在一个 python 安装 (
/Users/eflister/Library/Python/2.7/lib/python/) 中安装了 sima，但 matlab 使用的是不同的 python (/opt/local/Library/Frameworks/Python.framework/Versions/2.7)。我不确定细节，但您可能需要在 matlab 正在使用的 python 中安装 sima 或切换 matlab 以使用另一个。 -
@Kyle - 这些只是
/opt/local/bin/python路径上的两个地方，我更新了 OP 以反映这一点
标签： python matlab linker shared-libraries dyld