Hello everyone! If you ever wanted to call Python from MATLAB, here goes something for you. Today I’d like to present matpy – a MATLAB extension for accessing Python.
It is more or less an equivalent to pymat but the other way around. At the moment it’s for sure more low-level than an equivalent to mlabwrap would be but it could be used as a foundation for such equivalent (as pymat was used as foundation for mlabwrap).
Its core functionality is enclosed in three calls: py(‘eval’, stmt), py(‘set’, var_name, var) and var=py(‘get’, var_name). As you have probably guessed the first one evaluates whatever Python statement you throw at it. The second one sets a variable in Python environment to value taken from MATLAB (var_name specifies name of the variable and var – the value). And finally – the third one gets a variable from Python enviroment and returns its value converted to MATLAB type (again, var_name specifies name of the variable, var is the resulting MATLAB value).
matpy supports conversions of cell, numeric, logical and character MATLAB arrays. This leaves out only functions, structures and classes/objects – these cannot be transferred between Python and MATLAB environments. matpy converts arrays to numpy.ndarray with exception of character arrays – these are converted to Python strings. All numeric types are supported and the most suitable numpy.dtype is used instead of treating everything as double as is the case in many other MATLAB<->Python bridges. Also, unlike in some other interfaces – all dimensionalities are supported (2-D, 3-D, 4-D, … N-D). It maps 1:1 with numpy.ndarray functionality so it was no big deal.
Along with main MEX module there are three higher level helper functions provided – py_export(var1, …varN), py_import(var1, …varN) and py_shell(). The first two are used for mass-exporting/importing variables by name from/to MATLAB workspace. The last one starts a simple interactive Python shell (multi-line statements not supported, type ‘exit’ to go back to MATLAB).
Their usage is illustrated in this simple example using matplotlib:
>> [X,Y]=meshgrid(-10:0.1:10,-10:0.1:10);
>> Z=sin(X)+cos(Y);
>> py_export('X','Y','Z')
>> py_shell
py> import matplotlib
py> matplotlib.use('Qt4Agg')
py> import matplotlib.pyplot as plt
py> from mpl_toolkits.mplot3d import axes3d
py> f=plt.figure()
py> ax=f.gca(projection='3d')
py> cset=ax.plot_surface(X,Y,Z)
py> ax.clabel(cset,fontsize=9,inline=1)
py> plt.show()
py> exit
>>
The same code executed in non-interactive manner would have to look like this:
[X,Y]=meshgrid(-10:0.1:10,-10:0.1:10);
Z=sin(X)+cos(Y);
py_export('X','Y','Z')
stmt = sprintf(['import matplotlibn' ...
'matplotlib.use(''Qt4Agg'')n' ...
'import matplotlib.pyplot as pltn' ...
'from mpl_toolkits.mplot3d import axes3dn' ...
'f=plt.figure()n' ...
'ax=f.gca(projection=''3d'')n' ...
'cset=ax.plot_surface(X,Y,Z)n' ...
'ax.clabel(cset,fontsize=9,inline=1)n' ...
'plt.show()']);
py('eval', stmt);
So… basically that’s it. In order to run matpy you have to compile the provided py.cpp file using MEX and link against Python library. On Linux the following was sufficient:
mex py.cpp -lpython2.6
However there were some issues with dynamically loaded extensions. For this reason I had to add dlopen(‘libpython2.6.so’, RTLD_GLOBAL|RTLD_LAZY) before Py_Initialize() and exported LD_PRELOAD=”libstdc++.6.so” before running MATLAB. From what I’ve heard (will check myself tomorrow) this shouldn’t be a problem on Windows. MSVC compiler version might be though. Optimally MSVC version used to compile Python+extensions should be the same one used by your version of MATLAB to build MEX files but I’m not sure if this is really necessary.
Anyway 😉 … here goes the BSD-licensed source code:
DOWNLOAD: matpy.zip
Enjoy and let me know if you find it useful! 🙂
UPDATE 2012/05/29: I gave it a try on Windows and as expected there was no issues. Just type:
mex py.cpp -IC:/Python27/include C:/Python27/libs/python27.lib
and you are ready to go. I tested it with pythonxy distribution containing ETS (Enthought Tool Suite) with its highly renowned mayavi VTK-based 3D visualization library. It works great as can be seen in the screenshot below.
No matter what I do, I get: ImportError: /usr/lib/pymodules/python2.7/numpy/core/multiarray.so: undefined symbol: PyExc_SystemError
What am I doing wrong? I’ve compiled against Python 2.7 using the command mex py.cpp -lpython2.7 -ldl
Ahh, in this case probably this other thing I’ve changed in MEX setup was also important, sorry for not mentioning that. Under Linux I’ve appended the following line to mexopts.sh:
LDFLAGS=”$LDFLAGS -Xlinker -export-dynamic”
More about this stuff: http://stackoverflow.com/questions/4767057/embedding-python-in-c-undefined-symbol-pyexc-importerror
you might wanna wrap Linux-specific code inside a macro. Two lines would be affected: including “dlfcn.h” header, and the dlopen() call.
A bit similar: https://github.com/pv/pythoncall
a bit bloated.
I compile with: mex py.cpp -lpython2.7 -ldl
When I run:
a=1; py_export(‘a’)
I get:
Traceback (most recent call last):
File “/usr/lib/python2.7/dist-packages/numpy/__init__.py”, line 137, in
import add_newdocs
File “/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py”, line 9, in
from numpy.lib import add_newdoc
File “/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py”, line 13, in
from polynomial import *
File “/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py”, line 11, in
import numpy.core.numeric as NX
AttributeError: ‘module’ object has no attribute ‘core’
Error using py
numpy not accessible
I have already done the following:
1) Changed reference in py.cpp from libpython2.6.so to libpython2.7.so
2) Added an environment variable in the terminal with export LD_PRELOAD=”libstdc++.6.so” (& then started MATLAB)
3) Add the LDFLAGS=”$LDFLAGS -Xlinker -export-dynamic” after the other LDFLAGS in the archetecture section of my mexopts.sh
If I try to compile with just “mex py.cpp -lpython2.7”, I get a dlopen failure:
py.cpp:(.text+0x1d18): undefined reference to `dlopen’
collect2: ld returned 1 exit status
Does numpy work for you in interactive Python console?
Yes, I can succesfully do an “import numpy” in the python console. Should I have a path on the LD_PRELOAD? Also if I just run “py” from the MATLAN console, I get the “numpy not accessible”. Any troubleshooting tips/helps are much appreciated…. I would love for this to work. Thanks.
Did you also change the
#include <python2.6/Python.h>
line to:
#include <python2.7/Python.h>
?
Yes, I changed the include also. I tried it on a second machine. My process:
1) g++ is installed: whereis g++ (in terminal)
2) Verified python development environment is installed
3) In MATLAB: mex -setup and set compiler. This should create mexopts.sh in local user folder.
4) Verify arch by looking in /usr/local/MATLAB/R2011b/sys/os
5) Edit he mexopts.sh
It should be located in: ~/.matlab/R2011b/mexopts.sh (sudo gedit)
Scroll down to the case statement for the architecture
Add as a new line after the LDFLAGS=”-pthread -shared -….. line: LDFLAGS=”$LDFLAGS -Xlinker -export-dynamic”
6) Copy matpy zip and extract it into a new folder in ~/Documents/MATLAB/matpy. Add this folder to the path in MATLAB.
7) open py.cpp. Change python2.6 references to python2.7. There are 2 of these, an include python.h and the dlopen open statement.
8) Close MATLAB. In a terminal: LD_PRELOAD=”libstdc++.so.6″ /usr/local/MATLAB/R2011b//bin/matlab -desktop
9) Change MATLAB’s working directory ~/Documents/MATLAB/matpy
10) Run in MATLAB: mex py.cpp -lpython2.7 -ldl
11) Run in MATLAB: py
and I get:
Error using py
numpy not accessible
At step 10 get a couple of warnings but it seems to compile:
py.cpp: In function ‘mxArray* py2mat(PyObject*)’:
py.cpp:229:64: warning: deprecated conversion from string constant to ‘char*’
There is a typo btw in your LD_PRELOAD=”libstdc++.6.so above. I think it should be LD_PRELOAD=”libstdc++.so.6
Yes, of course it’s a typo. But otherwise your step-by-step description seems fine to me. At this point I think I would run MATLAB with strace to determine exactly what files are being loaded by the embedded Python interpreter and more precisely to get an idea of what numpy is trying to load and why it fails. I suspect it’s again some dynamic linking problem and numpy cannot load one of its modules from a shared library. I haven’t experienced it myself on any of the computers I’ve tested matpy on.
It seems something related to libgfortran
refer to http://stackoverflow.com/questions/9628273/libgfortran-version-gfortran-1-4-not-found
I did two things to make things right:
1. Solve the Mex warning due to gcc version, problem remains after this;
2. Solve the libgfortran thing according to: http://stackoverflow.com/questions/9628273/libgfortran-version-gfortran-1-4-not-found, things work out
I’m not sure only step2 is OK for this problem. If you tried out, let me know.
The previous reply only solves the problem of numpy caused by libgfortran, there is another source: libstdc, which will cause problem of qt backend.
Please refer to http://judsonsnotes.com/notes/index.php?option=com_content&view=article&id=659%3ainstalling-matlab-in-ubuntu-1110&catid=37%3atech-notes&Itemid=59 to see how to configure MATLAB to enable running external programs.
I had a similar problem that I fought with for awhile then I remembered that I had commented out one particular line that appears to have been the problem (because it is now working):
dlopen(“libpython2.7.so”, RTLD_LAZY |RTLD_GLOBAL);
I think I commented it out initially because I ran into problems with the call to dlopen.
If this doesn’t work for you I’d suggest trying to
import numpy in a simple cpp file. Something like:
// =======================================
#include
#include
using namespace std;
int main(int argc, char *argv[])
{
// Initialize the Python Interpreter
Py_Initialize();
// import numpy // Initialize the Python Interpreter
PyObject *numpy = PyImport_ImportModule(“numpy”);
if(numpy == NULL){
cout << "Import Errorn";
}else{
cout << "Numpy importedn";
}
// Finish the Python Interpreter
Py_Finalize();
return 0;
}
// =======================================
Then if you can get that to work you could wrap similar code in a mex function and see if you can get that to compile in matlab. BTW, I think the gcc call for the above call is something like:
g++ numpy_import_test.cpp -lpython2.7 -o numpy_import_test
Given that you can get it to compile, see if you can actually run it or if you get a similar error. If not then there is some goofiness in the MATLAB call to g++.
I want to also say thank you to the admin on this one. This is a great implementation, a nicer version than pymex, quicker than a jython call. I'd urge you to put it on the file exchange, it's somewhat difficult to find.
sorry the include statements were interpreted as html code, you should include
python2.7/Python.h
and
iostream
Hey, I’ve had esentially the same problems here on Ubuntu 12.10.
I cannot get this to work. But it works on Mac OSX Mountain Lion.
I tried running Matlab with strace, but this option is only available for simulink modules.
Admin: how do you run this with strace? sorry for the beginner question.
What versions and distros do you run this on? and what versions of Matlab?
Thanks
Sorry I think this is more Python embedding related problem than matpy-related problem. The best place to seek advice would be a Python forum 🙁
Hi, why not host your code in something like github, sourceforge, etc..
So that your code can make bigger difference and as a base to move forward to features like mlabwrap.
I can’t see how it fails to make a difference here 😉 It’s BSD-licensed. You’re welcome to setup a github repository yourself 🙂
Hi,
Firstly I would like to thank you for your work.
I ran into some errors compiling the mex function in Windows 64, on both 32 bit and 64 bit versions of matlab 2012b with the Visual C++ 2010 compiler and the -largeArrayDims option.
py.cpp
py.cpp(65) : error C2440: ‘initializing’ : cannot convert from ‘const mwSize *’ to ‘const int *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(129) : warning C4244: ‘argument’ : conversion from ‘__int64’ to ‘double’, possible loss of data
py.cpp(129) : warning C4244: ‘argument’ : conversion from ‘__int64’ to ‘double’, possible loss of data
py.cpp(130) : warning C4244: ‘argument’ : conversion from ‘unsigned __int64’ to ‘double’, possible loss of data
py.cpp(130) : warning C4244: ‘argument’ : conversion from ‘unsigned __int64’ to ‘double’, possible loss of data
py.cpp(182) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(183) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(183) : warning C4800: ‘long’ : forcing value to bool ‘true’ or ‘false’ (performance warning)
py.cpp(184) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(185) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(188) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(245) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(245) : warning C4800: ‘long’ : forcing value to bool ‘true’ or ‘false’ (performance warning)
py.cpp(246) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(247) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(248) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(249) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(250) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(251) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(252) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(253) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(254) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(255) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(270) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(271) : error C2664: ‘mxCreateNumericArray_730’ : cannot convert parameter 2 from ‘int *’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
py.cpp(284) : error C2664: ‘mxCreateCellArray_730’ : cannot convert parameter 2 from ‘int [2]’ to ‘const mwSize *’
Types pointed to are unrelated; conversion requires reinterpret_cast, C-style cast or function-style cast
E:MATLAB~2BINMEX.PL: Error: Compile of ‘py.cpp’ failed.
It seems like the code is trying to change “pointer to a constant integer” to simply a “pointer to integer”. It might be compiler specific to allow such a conversion (without an explicit cast)?
So which version of windows, matlab and compiler did you test it on?
Thanks,
Cres
Exactly the one you use, just without -largeArrayDims. Probably mwSize_t is defined as __int64 when using -largeArrayDims and it conflicts with lines like this:
const int *dims = mxGetDimensions(a);
You should change it to:
const mwSize_t *dims = mxGetDimensions(a);
Now it works. Thanks
Maybe an updated version to support both 32 and 64 bit would be wonderful 🙂
I’ve updated it.
Just a quick feedback, we’re using matpy to load the elefant machine learning package in python
http://elefant.developer.nicta.com.au/index.html
After working out all the setting-ups, now it works like a charm! Thanks for the great work 🙂
It’s great to hear that : )
Hi, where do you put the latest file after updating?
There’s only one matpy-related file on this blog and it’s in this post.
Yes, but the file link http://algoholic.eu/wp-content/uploads/2012/05/matpy1.zip and below update message are confusing. It seems the last update is in 2012-05.
Agreed. It _seems_ ; ) Seriously, I’m considering something like InDeferro for serving all my projects in the future. Give me some time.
I have different .cpp code, which i am trying to compile with 64-bit compiler. I am getting same type of errors. So my questions is we just need to change it with in .cpp or some other files too???
Hi,
Pardon the novice question, but I’m having trouble getting this installed. I’m running MATLAB R2011a on Mac OS X 10.8.
I type
>> mex py.cpp -I/Library/Python/2.7/
and it returns the following error message:
/Applications/MATLAB_R2011a.app/bin/mex: line 305: gcc-4.2: command not found
mex: py.cpp not a normal file or does not exist.
??? Error using ==> mex at 208
Unable to complete successfully.
It looks to me like you’re missing the XCode software package. You need it to be able to compile MEX files for MATLAB under Mac OS X.
http://www.mathworks.ch/support/compilers/R2012a/maci64.html
Turns out this error was due to a problem with the way MATLAB talks to Mac OS. I fixed it by installing the MATLAB compiler patch for OS X, here: http://www.mathworks.com/support/solutions/en/data/1-FR6LXJ/
I also needed to add the LDFLAGS=”$LDFLAGS -Xlinker -export-dynamic” line to mexopts.sh, as noted above. With that it seems to work well! Thanks for a very useful tool.
OK, I’ve encountered another problem on Mac OS X. As you probably know, OS X ships with a built-in version of Python, but the community consensus seems to be that one should not use this version but should instead get Python from python.org. OK, so I have been using the official python.org distribution for everything, and all of my modules are installed there.
When I compile with
mex py.cpp -lpython2.7 -ldl
the compiler runs, but it uses the system version of python, not the python.org version. As a result, all of the modules I care about are missing. So, somehow I need to force matpy to compile with the correct version of Python.
I tried
mex py.cpp -l/Library/Frameworks/Python.framework/Versions/2.7/bin/python
but it returns the error
ld: library not found for -l/Library/Frameworks/Python.framework/Versions/2.7/bin
I also tried
mex py.cpp -L/Library/Frameworks/Python.framework/Versions/2.7/
which returns the following long error:
Undefined symbols for architecture x86_64:
“_PyArg_ParseTuple”, referenced from:
aview_write(_object*, _object*)in py.o
“_PyBool_FromLong”, referenced from:
mat2py(mxArray_tag const*) in py.o
“_PyBool_Type”, referenced from:
py2mat(_object*) in py.o
“_PyComplex_FromDoubles”, referenced from:
mat2py(mxArray_tag const*) in py.o
“_PyComplex_ImagAsDouble”, referenced from:
py2mat(_object*) in py.o
“_PyComplex_RealAsDouble”, referenced from:
py2mat(_object*) in py.o
“_PyComplex_Type”, referenced from:
py2mat(_object*) in py.o
“_PyDict_GetItemString”, referenced from:
_mexFunction in py.o
“_PyDict_New”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyDict_SetItemString”, referenced from:
_mexFunction in py.o
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyErr_Print”, referenced from:
_mexFunction in py.o
mat2py(mxArray_tag const*) in py.o
“_PyEval_EvalCode”, referenced from:
_mexFunction in py.o
“_PyFloat_AsDouble”, referenced from:
py2mat(_object*) in py.o
“_PyFloat_FromDouble”, referenced from:
mat2py(mxArray_tag const*) in py.o
“_PyFloat_Type”, referenced from:
py2mat(_object*) in py.o
“_PyImport_AddModule”, referenced from:
_mexFunction in py.o
“_PyImport_ImportModule”, referenced from:
_mexFunction in py.o
“_PyInt_AsLong”, referenced from:
py2mat(_object*) in py.o
“_PyInt_AsUnsignedLongMask”, referenced from:
py2mat(_object*) in py.o
“_PyInt_FromLong”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyList_GetItem”, referenced from:
py2mat(_object*) in py.o
“_PyList_New”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyList_SetItem”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyLong_AsLongLong”, referenced from:
py2mat(_object*) in py.o
“_PyLong_AsUnsignedLongLong”, referenced from:
py2mat(_object*) in py.o
“_PyLong_FromLongLong”, referenced from:
mat2py(mxArray_tag const*) in py.o
“_PyLong_FromUnsignedLongLong”, referenced from:
mat2py(mxArray_tag const*) in py.o
“_PyModule_GetDict”, referenced from:
_mexFunction in py.o
“_PyObject_Call”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyObject_CallMethod”, referenced from:
py2mat(_object*) in py.o
“_PyObject_GetAttrString”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyObject_IsInstance”, referenced from:
py2mat(_object*) in py.o
“_PyObject_Str”, referenced from:
py2mat(_object*) in py.o
“_PyRun_StringFlags”, referenced from:
_mexFunction in py.o
“_PySequence_Check”, referenced from:
py2mat(_object*) in py.o
“_PySequence_GetItem”, referenced from:
py2mat(_object*) in py.o
“_PySequence_Size”, referenced from:
py2mat(_object*) in py.o
“_PyString_AsString”, referenced from:
py2mat(_object*) in py.o
“_PyString_FromString”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PySys_SetObject”, referenced from:
_mexFunction in py.o
“_PyTuple_New”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyTuple_SetItem”, referenced from:
py2mat(_object*) in py.o
mat2py(mxArray_tag const*) in py.o
“_PyType_IsSubtype”, referenced from:
py2mat(_object*) in py.o
“_Py_BuildValue”, referenced from:
aview_write(_object*, _object*)in py.o
“_Py_CompileStringFlags”, referenced from:
_mexFunction in py.o
“_Py_InitModule4_64”, referenced from:
_mexFunction in py.o
“_Py_Initialize”, referenced from:
_mexFunction in py.o
ld: symbol(s) not found for architecture x86_64
Any help would be much appreciated!
Thanks,
Dan
You should read what -L and -l mex options do first.
The first one specifies path to the directory with libraries, the second one actually links against a library so you should do mex [….] -L/path/to/dir/containing/libpython_so -lpython2.7
Also, you might want to point to the directory with correct headers for your custom python version using -I/path/to/dir/containing/Python_h
Thanks – I did read the Matlab documentation about -L and -l, but I found it rather opaque. Your explanation is clearer. It compiled successfully (and used the correct version of python) when I called
mex py.cpp -L/Library/Frameworks/Python.framework/Versions/2.7/lib -lpython2.7
Cool. I’m glad it worked in the end.
My apologies for the repeated posts… However, I think I may have found a bug. I have the numpy array x which was generated by a python module that I ran. py(‘eval’,’print(x)’) returns the following:
[ 6 6 4 5 4 4 4 3 2 1 2 3 8 3 10 6 9 9 7 8 6 5 8 7 12
6 6 4 5 4 4 4 3 2 1 2 3 8 3 10 6 6 4 5 4 4 4 3 2 1
2 3 8 3 10 6 9 9 7 8 6 5 8 7 12]
Now, I get these data into MATLAB with x = py(‘get’,’x’);
So far so good. But then I pass the data back to Python with py(‘set’,’x2′,x);
And py(‘eval’,’print(x2)’) returns this:
[[ 6]
[ 6]
[ 4]
[ 5]
[ 4]
[ 4]
[ 4]
[ 3]
[ 2]
[ 1]
[ 2]
[ 3]
[ 8]
[ 3]
[10]
[ 6]
[ 9]
[ 9]
[ 7]
[ 8]
[ 6]
[ 5]
[ 8]
[ 7]
[12]
[ 6]
[ 6]
[ 4]
[ 5]
[ 4]
[ 4]
[ 4]
[ 3]
[ 2]
[ 1]
[ 2]
[ 3]
[ 8]
[ 3]
[10]
[ 6]
[ 6]
[ 4]
[ 5]
[ 4]
[ 4]
[ 4]
[ 3]
[ 2]
[ 1]
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[ 3]
[10]
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[ 9]
[ 7]
[ 8]
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[12]]
I can easily convert these data back to their original appearance using x2 = numpy.concatenate(x2), so this is not a fatal flaw. However, I’m a little curious why it’s happening and whether it could be avoided by changing my syntax.
Thanks,
Dan
It transposes the vector. It is related to the fact that MATLAB stores matrices in column-major order. Therefore it is better to store vectors in vertical format also in Python (numpy). Then no conversion will occur.
More precisely – the first dimension in MATLAB is vertical. Therefore when you take a one-dimensional vector from Python it is vertical in MATLAB and since MATLAB doesn’t have one-dimensional matrices, just 2D with singleton dimension, it gets re-exported as vertical N rows 1 column np.array.
OK, what you said makes sense. But it seems to me that this behavior reveals a design flaw in matpy. Suppose I generate a 1-d array (i.e. a vector) of data from some process in MATLAB, and now I want to pass it to python and do something with it. Shouldn’t py(‘set’) give a python object that behaves as close as possible to the original variable in MATLAB? That would be a python list or 1-d np.array.
Or to put it a different way, if conversion of variables is “1:1” (as you claim above), then shouldn’t I be able to use data in python in exactly the format in which it is imported, rather than having to first convert it (using something like concatenate)?
I don’t mean to be overly critical, as I think you’ve made a great tool – just making a small suggestion for improvement (or at least, a suggestion for better documentation of how py(‘set’) behaves!).
I will repeat – there are no 1-d objects in MATLAB, the smallest dimensionality is 2-d which can have a singleton dimension. They’re converted 1:1 if you start from MATLAB. I have no way of determining whether I should convert 1-d object from Python to 1xN or Nx1 vector in MATLAB. This is an arbitrary decision. I chose to convert it to Nx1 vector, you can modify the code to convert it to 1xN vector if you prefer that. Alternatively when you pass it back to Python you can simply do py(‘set’, ‘x2′, x’)
Hi there,
First, thanks for providing the code and taking the time to develop it. I’m having a novice problem (novice to both mex and Python, I’m afraid, though not to MATLAB). When I run the following code to compile the function I get a string of errors. Any ideas/suggestions to get me on track? The version of Python I’m using shipped with ArcGIS. Hence the odd installation directory. But it works fine in the command prompt and through Spyder. Running windows7 x64 and 64 bit Matlab 2010b.
Many thanks again.
>> mex py.cpp -IC:/Python27/ArcGIS10.1/include C:/Python27/ArcGIS10.1/libs/python27.lib
Creating library C:UsersJeffreyAppDataLocalTempmex_spMVQ4templib.x and object C:UsersJeffreyAppDataLocalTempmex_spMVQ4templib.exp
py.obj : error LNK2019: unresolved external symbol __imp_Py_BuildValue referenced in function “struct _object * __cdecl aview_write(struct _object *,struct _object *)” (?aview_write@@YAPEAU_object@@PEAU1@0@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyArg_ParseTuple referenced in function “struct _object * __cdecl aview_write(struct _object *,struct _object *)” (?aview_write@@YAPEAU_object@@PEAU1@0@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySys_SetObject referenced in function “void __cdecl initaview(void)” (?initaview@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_Py_InitModule4_64 referenced in function “void __cdecl initaview(void)” (?initaview@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_GetAttrString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_Call referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_SetItemString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyTuple_SetItem referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyTuple_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_FromDoubles referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_FromUnsignedLongLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_FromLongLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_FromLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_FromDouble referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyErr_Print referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyBool_FromLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_SetItem referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyString_FromString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_Check referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_ImagAsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_RealAsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_AsUnsignedLongLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_AsUnsignedLongMask referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_AsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_GetItem referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_CallMethod referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_GetItem referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_Size referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_Str referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_IsInstance referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyString_AsString referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyType_IsSubtype referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_AsLongLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyBool_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_AsLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyEval_EvalCode referenced in function “void __cdecl do_get(void)” (?do_get@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_Py_CompileStringFlags referenced in function “void __cdecl do_get(void)” (?do_get@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyRun_StringFlags referenced in function “void __cdecl do_eval(void)” (?do_eval@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_GetItemString referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyImport_ImportModule referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyModule_GetDict referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyImport_AddModule referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_Py_Initialize referenced in function mexFunction
py.mexw64 : fatal error LNK1120: 47 unresolved externals
C:PROGRA~1MATLABR2010BBINMEX.PL: Error: Link of ‘py.mexw64’ failed.
??? Error using ==> mex at 208
Unable to complete successfully.
Actually this is quite bizarre. It means that all those symbols were not found in the given Python library. Just guessing – maybe ArcGIS is using 32-bit version of Python? Or Python compiled using something else than Microsoft Visual Studio? Are you using Visual Studio to compile mex files?
Thanks for getting back to me. Yes, I believe that it’s 32 bit Python:
Python 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)] on win32
Type “help”, “copyright”, “credits” or “license” for more information.
It seems that desktop ArcGIS requires 32 bit python. Since I initially started learning/using Python a month ago to access ArcGIS scripting, I need to make sure that I leave that functionality intact.
Do you think there’s a way to get your matpy function to compile correctly given this limitation? What about a separate install of 64 bit Python in a different directory? Or would that break other things in my system (e.g. Spyder, or maybe ArcGIS – I realize these questions might be off topic).
Thanks again.
64-bit MEX files cannot be linked with 32-bit libraries. Yes, separate installation of 64-bit Python should help, however, ArcGIS won’t be accessible through matpy linked against such 64-bit Python installation. It shouldn’t break anything else though.
Hi
I had need for a lower level approach to interface MATLAB to some numerical code, and I’ve bootstrapped the mexFunction and all in Cython, and some of the details you provided here were essential, e.g. the call to dlopen(). Thanks!
Now that it is working, I have noticed that calling linalg routines ends up calling into MATLAB’s MKL libraries, resulting in errors. In my main mexFunction, I’ve got a switch like
if arg1 == 'np1':
import numpy
print numpy.random.randn(3)
elif arg1 == 'np2':
from numpy import linalg, r_
A = r_[:20].reshape((4, 5))
print linalg.svd(A)[1]
and in a MATLAB session, I see
>> cymex np1
[-02.392350, 2.323590235, -02350.035]
>> cymex np2
MKL ERROR: Parameter 5 was incorrect on entry to DGESDD
[0. 0. 0. 0.]
Have you any idea how to manage the linking of the different libraries? Is it necessary to use a NumPy that has been compiled against MKL?
Thanks again for the nice work!
Sorry for the formatting; those HTML tags don’t seem to work. Please take a look at the linked gist for the actual code.
Just FYI: calling the linear algebra routines in Python embedded in Octave doesn’t seem to pose a problem.
I suspect a shared library conflict between numpy and MATLAB that doesn’t necessarily have to originate from MKL library itself, maybe from one of the common dependencies of MKL and alternative linear algebra implementation used by numpy. I think you could use step by step debugging in numpy (compiled with debugging symbols) to nail it down. Octave probably doesn’t use MKL, hence – no problems.
Hey guys,
Running Ubuntu 13.10, 64-bit, MATLAB R2013b
I contacted Tech Support at MATLAB and here is how they helped me solve the MKL issue.
Compile py.cpp making sure the code execudes the dlopen command for libpython
mex py.cpp -g -v -I/usr/include/python2.7/ -L/usr/lib -DLIBPYTHON=/usr/lib/x86_64-linux-gnu/libpython2.7.so -lpython2.7 -ldl LDFLAGS=’$LDFLAGS -Xlinker -export-dynamic’ -compatibleArrayDims
export environment variables
export LAPACK_VERBOSITY=1
export LAPACK_VERSION=/usr/lib/lapack/liblapack.so.3
export FFTW_VERSION=/usr/lib/x86_64-linux-gnu/libfftw3.so.3 #libfftw3i.so,libfftw3f.so
export BLAS_VERSION=/usr/lib/libblas.so.3
run matlab
LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/lib/x86_64-linux-gnu/libgcc_s.so.1:/usr/lib/x86_64-linux-gnu/libgfortran.so.3:/usr/lib/libblas.so.3:/usr/lib/lapack/liblapack.so.3 matlab &
The MKL error is because MATLAB uses the Intel version of LAPACK and python uses the system-wide version which is different.
You can verify that you fixed things by executing in matlab:
version -lapack
version -blas
It should say MKL before setting the env variables, and something else after. For me, the BLAS version is not recognized after the procedure, but everything seems to be working fine.
Here’s to hoping that generating python plots from matlab was totally worth the 8 hours I just spent on this!
Best,
Carlos
Many thanks, Carlos. A very useful lesson from the never-ending encyclopedia of DLL hell. Also cool that MATLAB guys treated it seriously. All the best!
I saw pymex referred to above but I think there is more than one. If people are not aware of it I think this is excellent:
https://github.com/kw/pymex
It works well (there is a fork which builds on windows) and is a bit more sophisticated – it takes care of boxing objects so you can basically use Matlab as a python environment (all your python stuff is proxied as Matlab objects and can be manipulated naturally within Matlab).
Lol. Where was it when I was looking for it? 😉 When matpy becomes insufficient for my needs, I think I will give it a try. Thanks. Boxing however is really not a priority, I think it only harms performance. It’s better to exchange variables and do your thing in big chunks of code. The functionality of copying current workspace to Python, then calling Python and copying back the results (I think I’ve spotted this in pymex) is useful – I was thinking about it myself, but didn’t have time to implement it.
Do you have any thoughts on getting interactive mode to work with matplotlib? Currently I got it working in R2011a on Linux much like your example, but the window buttons don’t function if I have run ‘ion()’. It’s still pretty functional because issuing a ‘draw()’ command still updates the figure, but people might want to zoom and/or use the save button from the figure window.
I suppose this will require threading but don’t really know how to do it.
Hmm… but does ion() work for you in Python? My impression is that people keep complaining about it even when running native Python interpreter.
Yes, ion() works as expected for me in both a normal Python shell and IPython. Also, it mostly works in matpy here. If I do something like the following …
>> X = linspace(0, 2*pi, 101);
>> Y = sin(X);
>> py_export(‘X’, ‘Y’)
>> py_shell
py> from pylab import *
py> ion()
py> h = plot(X[0], Y[0])
py> draw()
py> setp(h[0], ‘c’, ‘r’, ‘lw’, 2)
py> draw()
It draws the figure as expected on both draw() commands (first as a blue curve and then red and thicker). It’s just that the resulting window seems to have no way to obtain input from the mouse.
I can confirm that on my recent installation the drawn figure responds to the mouse, even for 3D graphics. Everything just works. Saving works, zooming works…
Does this work with Python 3?
If the Python C API hasn’t changed then I don’t see any reason why it shouldn’t.
It’s not working because the python C-Api has changed. I’ll try to make it work in python 3.4
казино рулетка игры бесплатно еще онлайн казино с выводом денег.
Thanks for the nice package. I find it useful.
I would like to be able to add debugging in my python code using pdb.set_trace(). This uses raw_input, which does not seem compatible with matpy. Have you thought about how hard it might be to allow raw_input commands to work with matpy?
I am using your package above. I modified a .py file but when I call it from Matlab it seems to call the old version instead. I import the module and reload it in Matlab but to no avail.
never mind thanks!
Hi,
I’m trying to instal MatPy on my windows 7 machine, running Matlab 2013 64 bit.
When I try the command :
mex py.cpp -IC:/Python27/include C:/Python27/libs/python27.lib
I get :
———————————————————-
Creating library C:UsersfqlAppDataLocalTemp1mex_seAMAFtemplib.x and object C:UsersfqlAppDataLocalTemp1mex_seAMAFtemplib.exp
py.obj : error LNK2019: unresolved external symbol __imp_Py_BuildValue referenced in function “struct _object * __cdecl aview_write(struct _object *,struct _object *)” (?aview_write@@YAPEAU_object@@PEAU1@0@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyArg_ParseTuple referenced in function “struct _object * __cdecl aview_write(struct _object *,struct _object *)” (?aview_write@@YAPEAU_object@@PEAU1@0@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySys_SetObject referenced in function “void __cdecl initaview(void)” (?initaview@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_Py_InitModule4_64 referenced in function “void __cdecl initaview(void)” (?initaview@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_GetAttrString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_Call referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_SetItemString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyTuple_SetItem referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyTuple_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_FromDoubles referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_FromUnsignedLongLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_FromLongLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_FromLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_FromDouble referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyErr_Print referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyBool_FromLong referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_SetItem referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_New referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyString_FromString referenced in function “struct _object * __cdecl mat2py(struct mxArray_tag const *)” (?mat2py@@YAPEAU_object@@PEBUmxArray_tag@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_Check referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_ImagAsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_RealAsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_AsUnsignedLongLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_AsUnsignedLongMask referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_AsDouble referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyList_GetItem referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_CallMethod referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_GetItem referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PySequence_Size referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_Str referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyObject_IsInstance referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyString_AsString referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyComplex_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyType_IsSubtype referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyFloat_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyLong_AsLongLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyBool_Type referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyInt_AsLong referenced in function “struct mxArray_tag * __cdecl py2mat(struct _object *)” (?py2mat@@YAPEAUmxArray_tag@@PEAU_object@@@Z)
py.obj : error LNK2019: unresolved external symbol __imp_PyEval_EvalCode referenced in function “void __cdecl do_get(void)” (?do_get@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_Py_CompileStringFlags referenced in function “void __cdecl do_get(void)” (?do_get@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyRun_StringFlags referenced in function “void __cdecl do_eval(void)” (?do_eval@@YAXXZ)
py.obj : error LNK2019: unresolved external symbol __imp_PyDict_GetItemString referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyImport_ImportModule referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyModule_GetDict referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_PyImport_AddModule referenced in function mexFunction
py.obj : error LNK2019: unresolved external symbol __imp_Py_Initialize referenced in function mexFunction
py.mexw64 : fatal error LNK1120: 47 unresolved externals
————————————————-
any idea hoe to solve “error LNK2019”
Thanks a lot !
Hello,
First of all many thanks for all your hard work on creating this, and maintaining it answering questions.
I have the same problem as reported by Flo (30 June 2013) and Jeff (2 January 2013), i.e.
LINK : warning LNK4044: unrecognized option ‘/lkernel32’; ignored
Creating library C:UsersTHANAS~1AppDataLocalTempmex_IxYcXmtemplib.x and object C:UsersTHANAS~1AppDataLocalTempmex_IxYcXmtemplib.exp
py.obj : error LNK2019: unresolved external symbol __imp_Py_BuildValue referenced in function “struct _object * __cdecl aview_write(struct _object *,struct _object *)” (?aview_write@@YAPEAU_object@@PEAU1@0@Z)
and so on for 46 more cases where the LNK2019 error appears.
I am using windows7 x64 and 64 bit Matlab 2010b.
Has anyone else had this – Jeff in particular if you read this, did you manage to solve the problem?
Many thanks
Hi,
Is there a nice way to reset the python interpreter without restarting matlab? I tried modifying your code to add a new “reset” command, which called “Py_Finalize” before setting thing up again with your call to “Py_Initialize”, but only got segmentation faults.
Thanks,
D.
Why do you need to do that? Py_Finalize() has some bugs, maybe that’s the reason. Maybe you can provide a stack trace as well, this would help to determine the cause.
Here’s the trace:
————————————————————————
Segmentation violation detected at Fri Sep 20 20:16:33 2013
————————————————————————
Configuration:
MATLAB Version: 7.11.0.584 (R2010b)
MATLAB License: 161051
Operating System: Darwin 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64
Window System: No active display
Current Visual: None
Processor ID: x86 Family 6 Model 10 Stepping 9, GenuineIntel
Virtual Machine: Java 1.6.0_51-b11-457-11M4509 with Apple Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
Default Encoding: ISO-8859-1
Fault Count: 1
Abnormal termination:
Register State (from fault):
RAX = 000000011315dde0 RBX = 000000012be13af1
RCX = 000000011315de10 RDX = 000000012be8d560
RSP = 000000012be9ccc0 RBP = 00000001245073f0
RSI = 000000012be13c95 RDI = 000000011315de00
R8 = 000000011315de30 R9 = 000000012bd6197d
R10 = 000000011315df10 R11 = 000000012be9ccc0
R12 = 000000011315df10 R13 = 000000012be9bf60
R14 = 000000011315de70 R15 = 000000012be1799e
RIP = 000000011315de70 RFL = 000000012be9ccc0
CS = 000000011315df10 FS = 000000012be9bf60 GS = 000000011315e3e0
Stack Trace (from fault):
[ 0] 0x0000000100154109 /Applications/MATLAB_R2010b.app/bin/maci64/libmwfl.dylib+00409865 fl::sysdep::osx::unwind_stack(void const**, unsigned long, unsigned long, fl::diag::thread_context const&)+000009
[ 1] 0x00000001000f803f /Applications/MATLAB_R2010b.app/bin/maci64/libmwfl.dylib+00032831 fl::diag::stacktrace_base::capture(fl::diag::thread_context const&, unsigned long)+000063
[ 2] 0x00000001001053e4 /Applications/MATLAB_R2010b.app/bin/maci64/libmwfl.dylib+00087012 fl::util::atomic_singleton<(anonymous namespace)::terminate_impl, fl::util::default_ctor_placement >::create()+003156
[ 3] 0x0000000100103e17 /Applications/MATLAB_R2010b.app/bin/maci64/libmwfl.dylib+00081431 fl::diag::terminate_log(char const*, fl::diag::thread_context const&, bool)+000199
[ 4] 0x00000001005213d2 /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00267218 mnSetCmdLineArg+000834
[ 5] 0x00007fff8ee3194a /usr/lib/system/libsystem_c.dylib+00010570 _sigtramp+000026
[ 6] 0x000000012c064310 /usr/lib/system/libsystem_c.dylib+18446603343152501520
[ 7] 0x000000012be1799e /Library/Frameworks/Python.framework/Versions/2.7/Python+01075614 initposix+000174
[ 8] 0x000000012bdebb3f /Library/Frameworks/Python.framework/Versions/2.7/Python+00895807 init_builtin+000111
[ 9] 0x000000012bdecf66 /Library/Frameworks/Python.framework/Versions/2.7/Python+00900966 load_module+000470
[ 10] 0x000000012bded32f /Library/Frameworks/Python.framework/Versions/2.7/Python+00901935 import_submodule+000383
[ 11] 0x000000012bded84a /Library/Frameworks/Python.framework/Versions/2.7/Python+00903242 load_next+000234
[ 12] 0x000000012bdee2ab /Library/Frameworks/Python.framework/Versions/2.7/Python+00905899 PyImport_ImportModuleLevel+000363
[ 13] 0x000000012bdcbfa3 /Library/Frameworks/Python.framework/Versions/2.7/Python+00765859 builtin___import__+000131
[ 14] 0x000000012bd19e12 /Library/Frameworks/Python.framework/Versions/2.7/Python+00036370 PyObject_Call+000098
[ 15] 0x000000012bdcc4e7 /Library/Frameworks/Python.framework/Versions/2.7/Python+00767207 PyEval_CallObjectWithKeywords+000087
[ 16] 0x000000012bdd12c6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00787142 PyEval_EvalFrameEx+015142
[ 17] 0x000000012bdd5ad6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00805590 PyEval_EvalCodeEx+002118
[ 18] 0x000000012bdd5bf6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00805878 PyEval_EvalCode+000054
[ 19] 0x000000012bdebcf0 /Library/Frameworks/Python.framework/Versions/2.7/Python+00896240 PyImport_ExecCodeModuleEx+000208
[ 20] 0x000000012bdeca12 /Library/Frameworks/Python.framework/Versions/2.7/Python+00899602 load_source_module+000722
[ 21] 0x000000012bded32f /Library/Frameworks/Python.framework/Versions/2.7/Python+00901935 import_submodule+000383
[ 22] 0x000000012bded84a /Library/Frameworks/Python.framework/Versions/2.7/Python+00903242 load_next+000234
[ 23] 0x000000012bdee2ab /Library/Frameworks/Python.framework/Versions/2.7/Python+00905899 PyImport_ImportModuleLevel+000363
[ 24] 0x000000012bdcbfa3 /Library/Frameworks/Python.framework/Versions/2.7/Python+00765859 builtin___import__+000131
[ 25] 0x000000012bd19e12 /Library/Frameworks/Python.framework/Versions/2.7/Python+00036370 PyObject_Call+000098
[ 26] 0x000000012bdcc4e7 /Library/Frameworks/Python.framework/Versions/2.7/Python+00767207 PyEval_CallObjectWithKeywords+000087
[ 27] 0x000000012bdd12c6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00787142 PyEval_EvalFrameEx+015142
[ 28] 0x000000012bdd5ad6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00805590 PyEval_EvalCodeEx+002118
[ 29] 0x000000012bdd5bf6 /Library/Frameworks/Python.framework/Versions/2.7/Python+00805878 PyEval_EvalCode+000054
[ 30] 0x000000012bdebcf0 /Library/Frameworks/Python.framework/Versions/2.7/Python+00896240 PyImport_ExecCodeModuleEx+000208
[ 31] 0x000000012bdeca12 /Library/Frameworks/Python.framework/Versions/2.7/Python+00899602 load_source_module+000722
[ 32] 0x000000012bded32f /Library/Frameworks/Python.framework/Versions/2.7/Python+00901935 import_submodule+000383
[ 33] 0x000000012bded84a /Library/Frameworks/Python.framework/Versions/2.7/Python+00903242 load_next+000234
[ 34] 0x000000012bdee2ab /Library/Frameworks/Python.framework/Versions/2.7/Python+00905899 PyImport_ImportModuleLevel+000363
[ 35] 0x000000012bdcbfa3 /Library/Frameworks/Python.framework/Versions/2.7/Python+00765859 builtin___import__+000131
[ 36] 0x000000012bd19e12 /Library/Frameworks/Python.framework/Versions/2.7/Python+00036370 PyObject_Call+000098
[ 37] 0x000000012bd1f1e5 /Library/Frameworks/Python.framework/Versions/2.7/Python+00057829 PyObject_CallFunction+000197
[ 38] 0x000000012bdeea4b /Library/Frameworks/Python.framework/Versions/2.7/Python+00907851 PyImport_Import+000187
[ 39] 0x000000012bdeebf8 /Library/Frameworks/Python.framework/Versions/2.7/Python+00908280 PyImport_ImportModule+000040
[ 40] 0x000000012bdfc6cc /Library/Frameworks/Python.framework/Versions/2.7/Python+00964300 Py_InitializeEx+001324
[ 41] 0x0000000104fb26ef /Users/dylan/Documents/Personal Documents/Research/Mrsic-Flogel group/Projects/RF similarity and connectivity/GIT_LSCSM/Python/matpy/py.mexmaci64+00005871 mexFunction+000143
[ 42] 0x0000000102a634da /Applications/MATLAB_R2010b.app/bin/maci64/libmex.dylib+00021722 mexRunMexFile+000090
[ 43] 0x0000000102a60ef9 /Applications/MATLAB_R2010b.app/bin/maci64/libmex.dylib+00012025 __constructor_lm_mexmaci64+000553
[ 44] 0x0000000102a61094 /Applications/MATLAB_R2010b.app/bin/maci64/libmex.dylib+00012436 __constructor_lm_mexmaci64+000964
[ 45] 0x00000001005ab881 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_dispatcher.dylib+00260225 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000321
[ 46] 0x0000000100712643 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+01144387 inValidateLoadedObject(mxArray_tag*)+001779
[ 47] 0x00000001006af7b0 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00739248 QueryMLFcnTable_m_interpreter+012000
[ 48] 0x00000001006c6340 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00832320 MathWorks::System::FatalException::~FatalException()+024080
[ 49] 0x00000001006cb2dc /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00852700 MathWorks::System::FatalException::~FatalException()+044460
[ 50] 0x00000001006c9059 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00843865 MathWorks::System::FatalException::~FatalException()+035625
[ 51] 0x00000001006c9a44 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00846404 MathWorks::System::FatalException::~FatalException()+038164
[ 52] 0x0000000100729a0a /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+01239562 inRunLoadObjFunction(mxArray_tag*)+093098
[ 53] 0x00000001005ab881 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_dispatcher.dylib+00260225 Mfh_file::dispatch_fh(int, mxArray_tag**, int, mxArray_tag**)+000321
[ 54] 0x00000001007070f3 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+01097971 inPathNotification::~inPathNotification()+033395
[ 55] 0x00000001006bf4fe /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00804094 unsigned long mdApplyToFunctions(md_match_plmmf, bool (*)(Mfh_MATLAB_fn const*), md_apply_push_pfhmf)+025614
[ 56] 0x00000001006bff91 /Applications/MATLAB_R2010b.app/bin/maci64/libmwm_interpreter.dylib+00806801 unsigned long mdApplyToFunctions(md_match_plmmf, bool (*)(Mfh_MATLAB_fn const*), md_apply_push_pfhmf)+028321
[ 57] 0x00000001004bafae /Applications/MATLAB_R2010b.app/bin/maci64/libmwbridge.dylib+00044974 mnInitializeParser(char const*, char const**)+000238
[ 58] 0x00000001004bbaa4 /Applications/MATLAB_R2010b.app/bin/maci64/libmwbridge.dylib+00047780 mnParser+000724
[ 59] 0x000000010050b329 /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00176937 mcrInstance::mnParser_on_interpreter_thread()+000041
[ 60] 0x00000001004f29ef /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00076271 MathWorks::System::SimpleException::~SimpleException()+001535
[ 61] 0x00000001004eda79 /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00055929 mvm::detail::RecursiveScopedMcrLock::~RecursiveScopedMcrLock()+002281
[ 62] 0x0000000100288a15 /Applications/MATLAB_R2010b.app/bin/maci64/libmwservices.dylib+00109077 eventqueue::UserEventQueue::pop()+000069
[ 63] 0x0000000100288461 /Applications/MATLAB_R2010b.app/bin/maci64/libmwservices.dylib+00107617 eventqueue::UserEventQueue::removeInput(int)+000337
[ 64] 0x000000010451e73c /Applications/MATLAB_R2010b.app/bin/maci64/libmwuix.dylib+00292668 sysq::ws_ppeHook::pollingPostFcn(int)+000700
[ 65] 0x00000001043f0d1a /Applications/MATLAB_R2010b.app/bin/maci64/libuij.dylib+00146714 sysq::ws_ppeHook::pollingPostFcn(int)+004330
[ 66] 0x00000001043f171c /Applications/MATLAB_R2010b.app/bin/maci64/libuij.dylib+00149276 sysq::ws_ppeHook::pollingPostFcn(int)+006892
[ 67] 0x00000001043eed67 /Applications/MATLAB_R2010b.app/bin/maci64/libuij.dylib+00138599 svWS_ProcessPendingEvents(int, int, bool)+000455
[ 68] 0x00000001004ef1f5 /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00061941 mvm::detail::RecursiveScopedMcrLock::~RecursiveScopedMcrLock()+008293
[ 69] 0x00000001004ef902 /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00063746 mvm::detail::RecursiveScopedMcrLock::~RecursiveScopedMcrLock()+010098
[ 70] 0x00000001004efc3c /Applications/MATLAB_R2010b.app/bin/maci64/libmwmcr.dylib+00064572 mvm::detail::RecursiveScopedMcrLock::~RecursiveScopedMcrLock()+010924
[ 71] 0x00007fff8ee437a2 /usr/lib/system/libsystem_c.dylib+00083874 _pthread_start+000327
[ 72] 0x00007fff8ee301e1 /usr/lib/system/libsystem_c.dylib+00004577 thread_start+000013
Hi,
I have a question about how to control which version of numpy is used by matpy. I think I have only numpy version 1.7.1, but from within the python shell accessed from py_shell, numpy.__version__ is always 1.6.1. I can’t see if or how any version of numpy is specified during compilation or on execution. Am I missing something?
D.
Hi,
I’m quite new to python. I used only Matlab before but now it is interesting for me to use SciKit from Matlab. If I use the script directly in python it works quite fine but if I try to use it with MatPy, I get the following error:
Traceback (most recent call last):
File “”, line 1, in
File “/usr/local/lib/python2.7/dist-packages/sklearn/ensemble/forest.py”, line 292, in fit
for i in xrange(n_jobs))
File “/usr/local/lib/python2.7/dist-packages/sklearn/externals/joblib/parallel.py”, line 451, in __call__
self._pool = multiprocessing.Pool(n_jobs)
File “/usr/lib/python2.7/multiprocessing/__init__.py”, line 232, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild)
File “/usr/lib/python2.7/multiprocessing/pool.py”, line 136, in __init__
self._repopulate_pool()
File “/usr/lib/python2.7/multiprocessing/pool.py”, line 199, in _repopulate_pool
w.start()
File “/usr/lib/python2.7/multiprocessing/process.py”, line 130, in start
self._popen = Popen(self)
File “/usr/lib/python2.7/multiprocessing/forking.py”, line 116, in __init__
sys.stdout.flush()
AttributeError: ‘module’ object has no attribute ‘flush’
I tried to import stdout but it doesn’t fit the problem. Any suggestions?
Regards,
Fred
What’s on that line in the script? It seems that whatever your object is, Python sees it as a module. I don’t know any module containing flush function.
I’ll check it but if I run the script without multithreading it works fine. I think it is an issue if you try to use multithreading in python from matlab.
Could be. In general, the most frequent problem I’ve observed with Python in MATLAB is that there are some conflicting DLLs in its memory space which prevent certain Python modules from loading.
Dude!, incredibly useful, and even more useful the troubleshooting of the comments, thanks!
We are running multifunction python code, something like an hour per run, from light matlab system calls. The python code creates results which have been saved in a file. Now we need to start reading the python result back to matlab while the matlab is running because because we start fitting parameters in the matlab, and then run the next set of python calls. Do you recommend matpy for such work where matlab has to wait long times for the result, or would it be simpler to just read a folder from matlab from time to time. What do you suggest?
I am very new to working with python, and know nothing about C language. I was able to successfully compile the mex file, but when I try to call the mex functions, it gives me the following error:
Invalid MEX-file
‘/home/dcui/pkg64/matlabpackages/matpy/py.mexa64’:
libpython2.7.so.1.0: cannot open
shared object file: No such file or
directory
I have tried to copy the mentioned libraries to the same folder as the compiled mex. I have also did the LD_PRELOAD, uncommenting the dlfunc and dlopen lines when compiling. My Python is 2.7, and my MATLAB is 2012b. My OS is Ubuntu 12.04 LTS.
Thanks in advance.
How about LD_LIBRARY_PATH=/wherever/your/libpython2.7.so.1.0/resides ?
Although adding LD_LIBRARY_PATH (with also PYTHONHOME) allows me to start MATLAB and compile the mex, but when I run the py_shell, MATLAB crashes, with the following error in the terminal:
ImportError: No module named site
Let me explain my situation a little bit better. I am compiling using the Anaconda python distribution, and my compile command in MATLAB is the following:
mex py.cpp -lpython2.7 -L/hsgs/projects/jhyoon1/pkg64/pythonpackages/anaconda/lib/ -I/hsgs/projects/jhyoon1/pkg64/pythonpackages/anaconda/include/python2.7/ -ldl
I know this might be due to my lack of understanding of python and computers in general, but could you help me troubleshoot this?
Thanks.
There’s not much mystery behind this. The native binary parts have to see one another (thanks to tricks with LD_PRELOAD and LD_LIBRARY_PATH) and then you have also to point the binaries to the Pythonic part of things (modules) which on my PC (Ubuntu) reside in /usr/lib/python2.7. Just look for site.py. Normally you can use the PYTHONPATH variable for pointing to that path. On the other hand when using regular Python (not Anaconda) and pythonxy it seemed to know automatically where to look for modules but this could’ve been for multiple reasons (e.g. hardcoded paths, looking in the directories where binaries were, etc.). I haven’t tested with Anaconda.
For sure your current situation is better because the mex already creates Python environment. The import error comes from Python now.
Hi — any update on the question? Would appreciate any help
Now py_import works with cell2mat (List of python vs Cell of Matlab).
My code:
function py_import(varargin)
for i=1:numel(varargin)
tmp = py(‘get’, varargin{i});
% List of list (python)
if iscell(tmp)
if iscell(tmp{1})
if iscell(tmp{1}{1}) % List of list of list
disp(‘cell of cell of cell not implemented’)
elseif size(tmp{1}(:),1)<=2 % 2 columns only
disp('cell of cell, two columns')
tmp = cell2mat(horzcat(tmp{:})')+1;
else
disp('cell of cell, sparse matrix') % Adjacency
N = numel(tmp);
A = zeros(N);
for j=1:N
s = numel(tmp{j});
for k=1:s
t = tmp{j}{k}+1;
A(j,t) = 1;
A(t,j) = 1;
end
end
tmp = A; % Matrix
end
else
disp('cell, vector')
tmp = cell2mat(tmp);
end
else
disp('scalar') % Scalar
end
assignin('base', varargin{i}, tmp);
end
end
Thanks. Worked for me on 64bit linux and matlab79 and python2.7.3.
I had to:
1) #include dlfcn.h
2) call dlopen(“libpython2.7.so” …)
3) link with -ldl
# Makefile
INCS = -I/usr/local/x64/python/2.7.3/include/python2.7/
LIBS = -L/usr/local/x64/python/2.7.3/lib/ -lpython2.7 -ldl
MEX = /usr/local/matlab.7.9/bin/mex
all:
$(MEX) py.cpp $(INCS) $(LIBS)
I am trying it on windows 7 with matlab 8.3. I compiled and started a shell sucessfully. However, when I try to py_export I get an access violation and matlab crashes.
Any help?
-Jameson
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Somewhat new to using mex in general. I get this error upon entering mex py.cpp
>> mex py.cpp
Building with ‘Xcode Clang++’.
Error using mex
/Users/samuel—-/Downloads/matpy1/py.cpp:27:10: fatal error: ‘Python.h’
file not found
#include
^
1 error generated.
Running python 3.4. changing to #include didn’t do anything. Any thoughts on what to do?
Hi,
I have been trying to get this working with R2013b and python 2.7 on ubuntu 14.04. I can compile it using
mex py.cpp -g -v -I/usr/include/python2.7 -L/usr/lib/python2.7/config-x86_64-linux-gnu/ -lpython2.7 -ldl
But when I run py_shell in matlab, I get the below…
>> py_shell
py> 5+5
Traceback (most recent call last):
File “/usr/lib/python2.7/dist-packages/numpy/__init__.py”, line 153, in
from . import add_newdocs
File “/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py”, line 13, in
from numpy.lib import add_newdoc
File “/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py”, line 8, in
from .type_check import *
File “/usr/lib/python2.7/dist-packages/numpy/lib/type_check.py”, line 11, in
import numpy.core.numeric as _nx
File “/usr/lib/python2.7/dist-packages/numpy/core/__init__.py”, line 6, in
from . import multiarray
ImportError: /usr/lib/python2.7/dist-packages/numpy/core/multiarray.so: undefined symbol: PyExc_SystemError
Error in sys.excepthook:
Traceback (most recent call last):
File “/usr/lib/python2.7/dist-packages/apport_python_hook.py”, line 63, in apport_excepthook
from apport.fileutils import likely_packaged, get_recent_crashes
File “/usr/lib/python2.7/dist-packages/apport/__init__.py”, line 5, in
from apport.report import Report
File “/usr/lib/python2.7/dist-packages/apport/report.py”, line 16, in
from xml.parsers.expat import ExpatError
File “/usr/lib/python2.7/xml/parsers/expat.py”, line 4, in
from pyexpat import *
ImportError: /usr/lib/python2.7/lib-dynload/pyexpat.x86_64-linux-gnu.so: undefined symbol: _Py_ZeroStruct
Original exception was:
Traceback (most recent call last):
File “/usr/lib/python2.7/dist-packages/numpy/__init__.py”, line 153, in
from . import add_newdocs
File “/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py”, line 13, in
from numpy.lib import add_newdoc
File “/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py”, line 8, in
from .type_check import *
File “/usr/lib/python2.7/dist-packages/numpy/lib/type_check.py”, line 11, in
import numpy.core.numeric as _nx
File “/usr/lib/python2.7/dist-packages/numpy/core/__init__.py”, line 6, in
from . import multiarray
ImportError: /usr/lib/python2.7/dist-packages/numpy/core/multiarray.so: undefined symbol: PyExc_SystemError
=============================
The entire compilation log
=============================
mex py.cpp -g -v -I/usr/include/python2.7 -L/usr/lib/python2.7/config-x86_64-linux-gnu/ -lpython2.7 -ldl
**************************************************************************
Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require
the use of -largeArrayDims and remove the -compatibleArrayDims
option. For more information, see:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html
**************************************************************************
-> mexopts.sh sourced from directory (DIR = $PREF_DIR)
FILE = /home/userName/.matlab/R2013b/mexopts.sh
—————————————————————-
-> MATLAB = /home/userName/MATLAB
-> CC = gcc
-> CC flags:
CFLAGS = -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread
CDEBUGFLAGS = -g
COPTIMFLAGS = -O -DNDEBUG
CLIBS = -Wl,-rpath-link,/home/userName/MATLAB/bin/glnxa64 -L/home/userName/MATLAB/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
arguments = -DMX_COMPAT_32
-> CXX = g++
-> CXX flags:
CXXFLAGS = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O -DNDEBUG
CXXLIBS = -Wl,-rpath-link,/home/userName/MATLAB/bin/glnxa64 -L/home/userName/MATLAB/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -Wl,-rpath-link,/home/userName/MATLAB/bin/glnxa64 -L/home/userName/MATLAB/bin/glnxa64 -lmx -lmex -lmat -lm
arguments = -DMX_COMPAT_32
-> LD = g++
-> Link flags:
LDFLAGS = -pthread -shared -Wl,–version-script,/home/userName/MATLAB/extern/lib/glnxa64/mexFunction.map -Wl,–no-undefined -Xlinker -export-dynamic
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexa64
arguments = -L/usr/lib/python2.7/config-x86_64-linux-gnu/ -lpython2.7 -ldl
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments = -L/usr/lib/python2.7/config-x86_64-linux-gnu/ -lpython2.7 -ldl
—————————————————————-
Warning: You are using gcc version “4.8.2”. The version
currently supported with MEX is “4.7.x”.
For a list of currently supported compilers see:
http://www.mathworks.com/support/compilers/current_release/
-> g++ -c -I/usr/include/python2.7 -I/home/userName/MATLAB/extern/include -I/home/userName/MATLAB/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread -DMX_COMPAT_32 -g “py.cpp”
In file included from /usr/include/python2.7/Python.h:58:0,
from py.cpp:27:
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/stringobject.h:65:5: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 1, 0)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/stringobject.h:67:5: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 1, 2)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/pyerrors.h:196:25: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 2, 3)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/pyerrors.h:321:25: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 3, 4)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/pyerrors.h:323:25: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 3, 0)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/sysmodule.h:18:4: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 1, 2)));
^
/usr/include/python2.7/pyport.h:901:44: warning: ‘mexPrintf’ is an unrecognized format function type [-Wformat=]
#define Py_GCC_ATTRIBUTE(x) __attribute__(x)
^
/usr/include/python2.7/sysmodule.h:20:4: note: in expansion of macro ‘Py_GCC_ATTRIBUTE’
Py_GCC_ATTRIBUTE((format(printf, 1, 2)));
^
py.cpp: In function ‘void initaview()’:
py.cpp:58:32: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
PySys_SetObject(“stdout”, m);
^
py.cpp:59:32: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
PySys_SetObject(“stderr”, m);
^
py.cpp: In function ‘mxArray* py2mat(PyObject*)’:
py.cpp:229:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
PyObject *list = PyObject_CallMethod(reshaped, “tolist”, NULL);
^
-> g++ -g -pthread -shared -Wl,–version-script,/home/userName/MATLAB/extern/lib/glnxa64/mexFunction.map -Wl,–no-undefined -Xlinker -export-dynamic -o “py.mexa64” py.o -L/usr/lib/python2.7/config-x86_64-linux-gnu/ -lpython2.7 -ldl -Wl,-rpath-link,/home/userName/MATLAB/bin/glnxa64 -L/home/userName/MATLAB/bin/glnxa64 -lmx -lmex -lmat -lm
I have also the same Problem. Only Ubuntu 13.10 and matlab2011 differs.
Got it working. Below are the steps I followed…
Please remember to modify the paths as required!!
1) Uncomment line 371
dlopen(“libpython2.7.so”, RTLD_LAZY |RTLD_GLOBAL);
I also modified the python lib version
2) Compile (mex) in unix shell using the below
/mex -g -v py.cpp -I/usr/include/python2.7 -L/usr/lib -DLIBPYTHON=/usr/lib/python2.7/config/libpython2.7.so ‘-lpython2.7 -ldl -Xlinker -export-dynamic’ -compatibleArrayDims
Of course you can do the same in Matlab command window
3) Export a few path variables and then run Matlab using the LD_PRELOAD trick as mentioned in the above comments
############# EXPORT #################################
export FFTW_VERSION=/usr/lib/libfftw3.so.3
export BLAS_VERSION=/usr/lib/libblas.so.3gf
export LAPACK_VERSION=/usr/lib/lapack/liblapack.so.3gf
export LAPACK_VERBOSITY=1
######################################################
# Run Matlab
LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6:/lib/x86_64-linux-gnu/libgcc_s.so.1:/usr/lib/x86_64-linux-gnu/libgfortran.so.3:/usr/lib/libblas/libblas.so.3gf:/usr/lib/liblapack.so.3gf matlab
I have just set up my system for matpy, but it still does not seem to work…
Setup:
– Windows 7 64bit
– MATLAB R2014a 64bit
– WinPython 2.7.9.2 64bit
in MATLAB:
mex py.cpp ‘-IC:Program FilesWinPython-64bit-2.7.9.2python-2.7.9.amd64include’ ‘-LC:Program FilesWinPython-64bit-2.7.9.2python-2.7.9.amd64libs’
Building with ‘Microsoft Visual C++ 2013 Professional’.
MEX completed successfully.
Now, if I type
>> py_shell
py> print “Hello, World!”
py>
nothing happens. How can I check whether my system is operational?
Hi, thank you for your awesome work! I wonder if I can run the test.py file in matlab directly?
Excuse me ,I want to know that if matpy can use scikit-learn lib just as Python as well ? Thanks~
Does this package works for python3? I’ve tried to compile using
mex py.cpp -IC:\Users\python3\include -lpython3.lib
It keeps showing that a few functions aren’t declared in this scope. For example, Py_InitModule, PyString_FromString, etc. Does it has something to with the dynamic loaded extension?
Thanks,
Abe
Great software, thank you very much! It works brilliantly and allows smooth and fast integration of python 2 code into my MATLAB routines. Have you considered building a version for python 3.6? I know the python-c interface is different there. Hope you keep up the great work!
I get the following error when running on Windows 10 64-bit. In the Matlab terminal using hte MinGW compiler add-on for MATLAB.
I put in the following:
mex py.cpp -IC:/Python27/include C:/Python27/libs/python27.lib
and got the following output:
Error using mex
In file included from
C:/ProgramData/MATLAB/SupportPackages/R2018b/3P.instrset/mingw_w64.instrset/lib/gcc/x86_64-w64-mingw32/6.3.0/include/c++/math.h:36:0,
from C:\Python27\include/pyport.h:325,
from C:\Python27\include/Python.h:58,
from
C:\Users\ychandramouli\Documents\Matlab\py.cpp:27:
C:/ProgramData/MATLAB/SupportPackages/R2018b/3P.instrset/mingw_w64.instrset/lib/gcc/x86_64-w64-mingw32/6.3.0/include/c++/cmath:1157:11:
error: ‘::hypot’ has not been declared
using ::hypot;
^~~~~
C:\Users\ychandramouli\Documents\Matlab\py.cpp: In function
‘void initaview()’:
C:\Users\ychandramouli\Documents\Matlab\py.cpp:58:32:
warning: ISO C++ forbids converting a string constant to
‘char*’ [-Wwrite-strings]
PySys_SetObject(“stdout”, m);
^
C:\Users\ychandramouli\Documents\Matlab\py.cpp:59:32:
warning: ISO C++ forbids converting a string constant to
‘char*’ [-Wwrite-strings]
PySys_SetObject(“stderr”, m);
^
C:\Users\ychandramouli\Documents\Matlab\py.cpp: In function
‘mxArray* py2mat(PyObject*)’:
C:\Users\ychandramouli\Documents\Matlab\py.cpp:229:64:
warning: ISO C++ forbids converting a string constant to
‘char*’ [-Wwrite-strings]
PyObject *list = PyObject_CallMethod(reshaped, “tolist”,
NULL);
Any idea what to change?
Спасибо!!!
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