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• No acceleration for OpenGL and ImportError for modules that exist

  - by Aku

  I'm writing a program using wxPython and OpenGL. The program works, but without any antialiasing, and I get these error messages: (I'm using ArchLinux) INFO:OpenGL.acceleratesupport:No OpenGL_accelerate module loaded: No module named OpenGL_accelerate INFO:OpenGL.formathandler:Unable to load registered array format handler numpy: Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/OpenGL/arrays/formathandler.py", line 44, in loadPlugin plugin_class = entrypoint.load() File "/usr/lib/python2.6/site-packages/OpenGL/plugins.py", line 14, in load return importByName( self.import_path ) File "/usr/lib/python2.6/site-packages/OpenGL/plugins.py", line 28, in importByName module = __import__( ".".join(moduleName), {}, {}, moduleName) File "/usr/lib/python2.6/site-packages/OpenGL/arrays/numpymodule.py", line 11, in <module> raise ImportError( """No numpy module present: %s"""%(err)) ImportError: No numpy module present: No module named numpy INFO:OpenGL.formathandler:Unable to load registered array format handler numeric: Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/OpenGL/arrays/formathandler.py", line 44, in loadPlugin plugin_class = entrypoint.load() File "/usr/lib/python2.6/site-packages/OpenGL/plugins.py", line 14, in load return importByName( self.import_path ) File "/usr/lib/python2.6/site-packages/OpenGL/plugins.py", line 28, in importByName module = __import__( ".".join(moduleName), {}, {}, moduleName) File "/usr/lib/python2.6/site-packages/OpenGL/arrays/numeric.py", line 15, in <module> raise ImportError( """No Numeric module present: %s"""%(err)) ImportError: No Numeric module present: No module named Numeric However, when I look into my site-packages folder, I see those modules present there. I have a wxPython demo program that uses GLCanvas, and it works fine, without any errors. My program is quite similar to the GLCanvas demo, involving just translations, rotations, drawing quads and some basic lighting. What am I doing wrong here? (The code is over 200 lines, if necessary I'll edit this and put it here.)

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• Matplotlib and WSGI/mod_python not working on Apache.

  - by Luiz C.

  Everything works as supposed to on the Django development server. In Apache, the django app also works except when matplotlib is used. Here's the error I get: No module named multiarray. Exception Type: ImportError Exception Value: No module named multiarray Exception Location: /usr/share/pyshared/numpy/core/numerictypes.py in <module>, line 81 Python Executable: /usr/bin/python Python Version: 2.6.4 From the python shell, both statements work: import numpy.core.multiarray and import multiarray. Any ideas? Thanks As I'm looking over the numpy files, I found the multiarray module, which has an extension of 'so'. My guess, is that mod_python is not reading these files.

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• How to incorporate existing open source software from a licensing perspective?

  - by Matt

  I'm working on software that uses the following libraries: Biopython SciPy NumPy All of the above have licenses similar to MIT or BSD. Three scenarios: First, if I don't redistribute those dependencies, and only my code, then all I need is my own copyright and license (planing on using the MIT License) for my code. Correct? What if I use py2exe or py2app to create a binary executable to distribute so as to make it easy for people to run the application without needing to install python and all the dependencies. Of course this also means that my binary file(s) contains python itself (along with any other packages I might have performed a pip install xyz). What if I bundle Biopython, SciPy, and NumPy binaries in my package? In the latter two cases, what do I need to do to comply with copyright laws.

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• mayavi2 installing has problem (ubuntu 12.04)

  - by user98865

  I'm using ubuntu 12.04 and python 2.7.3-0ubuntu2 is already installed. I have a problem during installing mayavi2 from ubuntu software center. Error message is : Package dependencies cannot be resolved This error could be caused by required additional software packages which are missing or not installable. Furthermore there could be a conflict between software packages which are not allowed to be installed at the same time. Details: The following packages have unmet dependencies mayavi2: Depends: python-numpy (= 1:1.6.1) but 1:1.6.1-6ubuntu1 is to be installed Depends: python-numpy-abi9 but it is a virtual package Depends: python (< 2.8) but 2.7.3-0ubuntu2 is to be installed Depends: python-vtk (= 5.4.2-5) but 5.8.0-5 is to be installed I've searched to solve this problem for a long time but I didn't solve yet. What can I do?

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• Compiling scipy on Windows 32-bit: linker error with libf77blas.a

  - by Sridhar Ratnakumar

  Has anyone tried compiling SciPy 0.7.1 on Windows using numpy-1.3.0 that was built with the pre-built ATLAS libraries (atlas3.6.0_WinNT_P4SSE2.zip) linked in the installation document. I get the following linker error, and have no ideas as to how to fix this issue. $ python setup.py config --compiler=mingw32 build --compiler=mingw32 install --root=i [...] creating build\temp.win32-2.6\Release creating build\temp.win32-2.6\Release\scipy creating build\temp.win32-2.6\Release\scipy\integrate compile options: '-DNO_ATLAS_INFO=2 -I"C:\Documents and Settings\apy\Application Data\Python\Python26\site-packages\numpy\core\inc lude" -IC:\Python26\include -IC:\Python26\PC -c' gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes -DNO_ATLAS_INFO=2 -I"C:\Documents and Settings\apy\Application Data\Python\Python26\ site-packages\numpy\core\include" -IC:\Python26\include -IC:\Python26\PC -c scipy\integrate\_odepackmo dule.c -o build\temp.win32-2.6\Release\scipy\integrate\_odepackmodule.o C:\MinGW\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\temp.win32-2.6\Release\scipy\integrate\_odepackmodule .o -LC:\atlas3.6.0_WinNT_P4SSE2 -LC:\MinGW\lib -LC:\MinGW\lib\gcc\mingw32\3.4.5 -LC:\Python26\libs -LC:\Act ivePython32Python26\PCbuild -Lbuild\temp.win32-2.6 -lodepack -llinpack_lite -lmach -latlas -lcblas -lf77blas -llapack -lpython26 - lg2c -o build\lib.win32-2.6\scipy\integrate\_odepack.pyd C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_daxpy.o):ATL_F77wrap_axpy.c:(.text+0x3c): undefined reference to `ATL _daxpy' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_dscal.o):ATL_F77wrap_scal.c:(.text+0x26): undefined reference to `ATL _dscal' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_dcopy.o):ATL_F77wrap_copy.c:(.text+0x3d): undefined reference to `ATL _dcopy' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_idamax.o):ATL_F77wrap_amax.c:(.text+0x1e): undefined reference to `AT L_idamax' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_ddot.o):ATL_F77wrap_dot.c:(.text+0x36): undefined reference to `ATL_d dot' collect2: ld returned 1 exit status error: Command "C:\MinGW\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\temp.win32-2.6\Release\scipy\integrat e\_odepackmodule.o -LC:\atlas3.6.0_WinNT_P4SSE2 -LC:\MinGW\lib -LC:\MinGW\lib\gcc\mingw32\3.4.5 -LC:\Python 26\libs -LC:\Python26\PCbuild -Lbuild\temp.win32-2.6 -lodepack -llinpack_lite -lmach -latlas -lcblas -lf77blas -llap ack -lpython26 -lg2c -o build\lib.win32-2.6\scipy\integrate\_odepack.pyd" failed with exit status 1 Does anyone know what could have gone wrong here? Looking for ATL_daxpy, for example, in libf77blas.a resulted in: $ strings libf77blas.a | grep -i daxpy _daxpy_ _atl_f77wrap_daxpy_ ATL_F77wrap_daxpy.o/ daxpy.o/ 1081731936 1003 513 100755 420 ` daxpy.f _daxpy_ _atl_f77wrap_daxpy_ _atl_f77wrap_daxpy_ _ATL_daxpy There is _ATL_daxpy, but no ATL_daxpy.

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• Multiple Unpacking Assignment in Python when you don't know the sequence length

  - by doug

  The textbook examples of multiple unpacking assignment are something like: import numpy as NP M = NP.arange(5) a, b, c, d, e = M # so of course, a = 0, b = 1, etc. M = NP.arange(20).reshape(5, 4) # numpy 5x4 array a, b, c, d, e = M # here, a = M[0,:], b = M[1,:], etc. (ie, a single row of M is assigned each to a through e) (My Q is not numpy specfic; indeed, i would prefer a pure python solution.) W/r/t the piece of code i'm looking at now, i see two complications on that straightforward scenario: i usually won't know the shape of M; and i want to unpack a certain number of items (definitely less than all items) and i want to put the remainder into a single container so back to the 5x4 array above, what i would very much like to be able to do is, for instance, assign the first three rows of M to a, b, and c respectively (exactly as above) and the rest of the rows (i have no idea how many there will be, just some positive integer) to a single container, all_the_rest = []. I'm not sure if i have explained this clearly; in any event, if i get feedback i'll promptly edit my Question.

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• Compiling scipy on Windows 32-bit

  - by Sridhar Ratnakumar

  Has anyone tried compiling SciPy on Windows using numpy-1.3.0 that was built with the pre-built ATLAS libraries (atlas3.6.0_WinNT_P4SSE2.zip) linked in the installation document. I get the following linker error, and have no ideas as to how to fix this issue. $ python setup.py config --compiler=mingw32 build --compiler=mingw32 install --root=i [...] creating build\temp.win32-2.6\Release creating build\temp.win32-2.6\Release\scipy creating build\temp.win32-2.6\Release\scipy\integrate compile options: '-DNO_ATLAS_INFO=2 -I"C:\Documents and Settings\apy\Application Data\Python\Python26\site-packages\numpy\core\inc lude" -IC:\Python26\include -IC:\Python26\PC -c' gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes -DNO_ATLAS_INFO=2 -I"C:\Documents and Settings\apy\Application Data\Python\Python26\ site-packages\numpy\core\include" -IC:\Python26\include -IC:\Python26\PC -c scipy\integrate\_odepackmo dule.c -o build\temp.win32-2.6\Release\scipy\integrate\_odepackmodule.o C:\MinGW\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\temp.win32-2.6\Release\scipy\integrate\_odepackmodule .o -LC:\atlas3.6.0_WinNT_P4SSE2 -LC:\MinGW\lib -LC:\MinGW\lib\gcc\mingw32\3.4.5 -LC:\Python26\libs -LC:\Act ivePython32Python26\PCbuild -Lbuild\temp.win32-2.6 -lodepack -llinpack_lite -lmach -latlas -lcblas -lf77blas -llapack -lpython26 - lg2c -o build\lib.win32-2.6\scipy\integrate\_odepack.pyd C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_daxpy.o):ATL_F77wrap_axpy.c:(.text+0x3c): undefined reference to `ATL _daxpy' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_dscal.o):ATL_F77wrap_scal.c:(.text+0x26): undefined reference to `ATL _dscal' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_dcopy.o):ATL_F77wrap_copy.c:(.text+0x3d): undefined reference to `ATL _dcopy' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_idamax.o):ATL_F77wrap_amax.c:(.text+0x1e): undefined reference to `AT L_idamax' C:\atlas3.6.0_WinNT_P4SSE2/libf77blas.a(ATL_F77wrap_ddot.o):ATL_F77wrap_dot.c:(.text+0x36): undefined reference to `ATL_d dot' collect2: ld returned 1 exit status error: Command "C:\MinGW\bin\g77.exe -g -Wall -mno-cygwin -g -Wall -mno-cygwin -shared build\temp.win32-2.6\Release\scipy\integrat e\_odepackmodule.o -LC:\atlas3.6.0_WinNT_P4SSE2 -LC:\MinGW\lib -LC:\MinGW\lib\gcc\mingw32\3.4.5 -LC:\Python 26\libs -LC:\Python26\PCbuild -Lbuild\temp.win32-2.6 -lodepack -llinpack_lite -lmach -latlas -lcblas -lf77blas -llap ack -lpython26 -lg2c -o build\lib.win32-2.6\scipy\integrate\_odepack.pyd" failed with exit status 1 Does anyone know what could have gone wrong here?

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• Python Speeding Up Retrieving data from extremely large string

  - by Burninghelix123

  I have a list I converted to a very very long string as I am trying to edit it, as you can gather it's called tempString. It works as of now it just takes way to long to operate, probably because it is several different regex subs. They are as follow: tempString = ','.join(str(n) for n in coords) tempString = re.sub(',{2,6}', '_', tempString) tempString = re.sub("[^0-9\-\.\_]", ",", tempString) tempString = re.sub(',+', ',', tempString) clean1 = re.findall(('[-+]?[0-9]*\.?[0-9]+,[-+]?[0-9]*\.?[0-9]+,' '[-+]?[0-9]*\.?[0-9]+'), tempString) tempString = '_'.join(str(n) for n in clean1) tempString = re.sub(',', ' ', tempString) Basically it's a long string containing commas and about 1-5 million sets of 4 floats/ints (mixture of both possible),: -5.65500020981,6.88999986649,-0.454999923706,1,,,-5.65500020981,6.95499992371,-0.454999923706,1,,, The 4th number in each set I don't need/want, i'm essentially just trying to split the string into a list with 3 floats in each separated by a space. The above code works flawlessly but as you can imagine is quite time consuming on large strings. I have done a lot of research on here for a solution but they all seem geared towards words, i.e. swapping out one word for another. EDIT: Ok so this is the solution i'm currently using: def getValues(s): output = [] while s: # get the three values you want, discard the 3 commas, and the # remainder of the string v1, v2, v3, _, _, _, s = s.split(',', 6) output.append("%s %s %s" % (v1.strip(), v2.strip(), v3.strip())) return output coords = getValues(tempString) Anyone have any advice to speed this up even farther? After running some tests It still takes much longer than i'm hoping for. I've been glancing at numPy, but I honestly have absolutely no idea how to the above with it, I understand that after the above has been done and the values are cleaned up i could use them more efficiently with numPy, but not sure how NumPy could apply to the above. The above to clean through 50k sets takes around 20 minutes, I cant imagine how long it would be on my full string of 1 million sets. I'ts just surprising that the program that originally exported the data took only around 30 secs for the 1 million sets

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• How do I tell if a Python pip install is working correctly or hanging?

  - by wobbily_col

  I am trying to install the python pandas package in a virtualenv using pip. On my development machine it installed correctly, but now I am trying on the server, it gets so far then it seems to get stuck: warnings.warn(LapackSrcNotFoundError.__doc__) /apps/PYTHON/2.7.3/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) non-existing path in 'numpy/distutils': 'site.cfg' non-existing path in 'numpy/lib': 'benchmarks' Could not locate executable gfortran Could not locate executable f95 Found executable /apps/modules/wrappers/fortran/ifort Top shows ifort running at 46% cpu. Is there any way I can tell if this is working correctly (can I check files it is updating for example), or if it is stuck in a loop? It has been running for 40 minutes so far.

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• Creating Python C module from Fortran sources on Ubuntu 10.04 LTS

  - by Botondus

  In a project I work on we use a Python C module compiled from Fortran with f2py. I've had no issues building it on Windows 7 32bit (using mingw32) and on the servers it's built on 32bit Linux. But I've recently installed Ubuntu 10.04 LTS 64bit on my laptop that I use for development, and when I build it I get a lot of warnings (even though I've apparently installed all gcc/fortran libraries/compilers), but it does finish the build. However when I try to use the built module in the application, most of it seems to run well but then it crashes with an error: * glibc detected /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000006a44760 ** Warnings on running *f2py -c -m module_name ./fortran/source.f90* customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler Could not locate executable g77 Found executable /usr/bin/f77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgf90 Could not locate executable pgf77 customize AbsoftFCompiler Could not locate executable f90 absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found customize NAGFCompiler Found executable /usr/bin/f95 customize VastFCompiler customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler Could not locate executable efort Could not locate executable efc customize IntelEM64TFCompiler customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext I have tried building a 32bit version by installing the gfortran multilib packages and running f2py with -m32 option (but with no success): f2py -c -m module_name ./fortran/source.f90 --f77flags="-m32" --f90flags="-m32" Any suggestions on what I could try to either build 32bit version or correctly build the 64bit version? Edit: It looks like it crashes right at the end of a subroutine. The 'write' executes fine... which is strange. write(6,*)'Eh=',Eh end subroutine calcolo_involucro The full backtrace is very long and I'm not sure if it's any help, but here it is: *** glibc detected *** /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000007884690 *** ======= Backtrace: ========= /lib/libc.so.6(+0x775b6)[0x7fe24f8f05b6] /lib/libc.so.6(cfree+0x73)[0x7fe24f8f6e53] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4183c)[0x7fe24a18183c] /home/botondus/Envs/gasit/bin/python[0x46a50d] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4fbd8)[0x7fe24a18fbd8] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x5aded)[0x7fe24a19aded] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x516e)[0x4a7c5e] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python[0x537620] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python[0x427dff] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python[0x477bff] /home/botondus/Envs/gasit/bin/python[0x46f47f] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python[0x537620] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x4a1b03] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x2ee94)[0x7fe24a16ee94] /home/botondus/Envs/gasit/bin/python(_PyObject_Str+0x61)[0x454a81] /home/botondus/Envs/gasit/bin/python(PyObject_Str+0xa)[0x454b3a] /home/botondus/Envs/gasit/bin/python[0x461ad3] /home/botondus/Envs/gasit/bin/python[0x46f3b3] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550] ======= Memory map: ======== 00400000-0061c000 r-xp 00000000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0081b000-0081c000 r--p 0021b000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0081c000-0087e000 rw-p 0021c000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0087e000-0088d000 rw-p 00000000 00:00 0 01877000-07a83000 rw-p 00000000 00:00 0 [heap] 7fe240000000-7fe240021000 rw-p 00000000 00:00 0 7fe240021000-7fe244000000 ---p 00000000 00:00 0 7fe247631000-7fe2476b1000 r-xp 00000000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2476b1000-7fe2478b1000 ---p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b1000-7fe2478b6000 r--p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b6000-7fe2478b7000 rw-p 00085000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b7000-7fe2478bb000 r-xp 00000000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe2478bb000-7fe247aba000 ---p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247aba000-7fe247abb000 r--p 00003000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247abb000-7fe247abc000 rw-p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247abc000-7fe247abf000 r-xp 00000000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247abf000-7fe247cbf000 ---p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cbf000-7fe247cc0000 r--p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cc0000-7fe247cc1000 rw-p 00004000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cc1000-7fe247cc5000 r-xp 00000000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247cc5000-7fe247ec4000 ---p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec4000-7fe247ec5000 r--p 00003000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec5000-7fe247ec6000 rw-p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec6000-7fe24800c000 r-xp 00000000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe24800c000-7fe24820b000 ---p 00146000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe24820b000-7fe248213000 r--p 00145000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe248213000-7fe248215000 rw-p 0014d000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe248215000-7fe248216000 rw-p 00000000 00:00 0 7fe248216000-7fe248229000 r-xp 00000000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248229000-7fe248428000 ---p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248428000-7fe248429000 r--p 00012000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248429000-7fe24842a000 rw-p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe24842a000-7fe248464000 r-xp 00000000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248464000-7fe248663000 ---p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248663000-7fe248664000 r--p 00039000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248664000-7fe248665000 rw-p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248665000-7fe24876e000 r-xp 00000000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24876e000-7fe24896d000 ---p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24896d000-7fe24896e000 r--p 00108000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24896e000-7fe248999000 rw-p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe248999000-7fe2489a7000 rw-p 00000000 00:00 0 7fe2489a7000-7fe2489bd000 r-xp 00000000 08:03 132934 /lib/libgcc_s.so.1

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• Python: x-y-plot with matplotlib

  - by kame

  I want to plot some data. The first column contains the x-data. But matplotlib doesnt plot this. Where is my mistake? #fresnel formula import numpy as np from numpy import cos from scipy import * from pylab import plot, show, ylim, yticks from matplotlib import * from pprint import pprint n1 = 1.0 n2 = 1.5 #alpha, beta, intensity data = [ [10, 22, 4.3], [20, 42, 4.2], [30, 62, 3.6], [40, 83, 1.3], [45, 102, 2.8], [50, 123, 3.0], [60, 143, 3.2], [70, 163, 3.8], ] for i in range(len(data)): rhotang1 = (n1 * cos(data[i][0]) - n2 * cos(data[i][1])) rhotang2 = (n1 * cos(data[i][0]) + n2 * cos(data[i][1])) rhotang = rhotang1 / rhotang2 data[i].append(rhotang) #append 4th value pprint(data) x = data[:][0] y1 = data[:][2] y3 = data[:][3] plot(x, y1, x, y3) show() EDIT: http://paste.pocoo.org/show/205534/ But it doesnt work.

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• Idiomatic way to do list/dict in Cython?

  - by ramanujan

  My problem: I've found that processing large data sets with raw C++ using the STL map and vector can often be considerably faster (and with lower memory footprint) than using Cython. I figure that part of this speed penalty is due to using Python lists and dicts, and that there might be some tricks to use less encumbered data structures in Cython. For example, this page (http://wiki.cython.org/tutorials/numpy) shows how to make numpy arrays very fast in Cython by predefining the size and types of the ND array. Question: Is there any way to do something similar with lists/dicts, e.g. by stating roughly how many elements or (key,value) pairs you expect to have in them? That is, is there an idiomatic way to convert lists/dicts to (fast) data structures in Cython? If not I guess I'll just have to write it in C++ and wrap in a Cython import.

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• Converting python objects for rpy2

  - by bgbg

  The following code is supposed to created a heatmap in rpy2 import numpy as np from rpy2.robjects import r data = np.random.random((10,10)) r.heatmap(data) However, it results in the following error Traceback (most recent call last): File "z.py", line 8, in <module> labRow=rowNames, labCol=colNames) File "C:\Python25\lib\site-packages\rpy2\robjects\__init__.py", line 418, in __call__ new_args = [conversion.py2ri(a) for a in args] File "C:\Python25\lib\site-packages\rpy2\robjects\__init__.py", line 93, in default_py2ri raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o)))) ValueError: Nothing can be done for the type <type 'numpy.ndarray'> at the moment. From the documentation I learn that r.heatmap expects "a numeric matrix". How do I convert np.array to the required data type?

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• Graphing a line and scatter points using Matplotlib?

  - by Patrick O'Doherty

  Hi guys I'm using matplotlib at the moment to try and visualise some data I am working on. I'm trying to plot around 6500 points and the line y = x on the same graph but am having some trouble in doing so. I can only seem to get the points to render and not the line itself. I know matplotlib doesn't plot equations as such rather just a set of points so I'm trying to use and identical set of points for x and y co-ordinates to produce the line. The following is my code from matplotlib import pyplot import numpy from pymongo import * class Store(object): """docstring for Store""" def __init__(self): super(Store, self).__init__() c = Connection() ucd = c.ucd self.tweets = ucd.tweets def fetch(self): x = [] y = [] for t in self.tweets.find(): x.append(t['positive']) y.append(t['negative']) return [x,y] if __name__ == '__main__': c = Store() array = c.fetch() t = numpy.arange(0., 0.03, 1) pyplot.plot(array[0], array[1], 'ro', t, t, 'b--') pyplot.show() Any suggestions would be appreciated, Patrick

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• Converting excel files to python to frequency

  - by Jacob

  Essentially I've got an excel files with voltage in the first column, and time in the second. I want to find the period of the voltages, as it returns a graph of voltage in y axis and time in x axis with a periodicity, looking similar to a sine function. To find the frequency I have uploaded my excel file to python as I think this will make it easier- there may be something I've missed that will simplify this. So far in python I have: import xlrd import numpy as N import numpy.fft as F import matplotlib.pyplot as P wb = xlrd.open_workbook('temp7.xls') #LOADING EXCEL FILE wb.sheet_names() sh = wb.sheet_by_index(0) first_column = sh.col_values(1) #VALUES FROM EXCEL second_column = sh.col_values(2) #VALUES FROM EXCEL Now how do I find the frequency from this? Huge thanks to anyone who can help! Jacob

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• pyplot: really slow creating heatmaps

  - by cvondrick

  I have a loop that executes the body about 200 times. In each loop iteration, it does a sophisticated calculation, and then as debugging, I wish to produce a heatmap of a NxM matrix. But, generating this heatmap is unbearably slow and significantly slow downs an already slow algorithm. My code is along the lines: import numpy import matplotlib.pyplot as plt for i in range(200): matrix = complex_calculation() plt.set_cmap("gray") plt.imshow(matrix) plt.savefig("frame{0}.png".format(i)) The matrix, from numpy, is not huge --- 300 x 600 of doubles. Even if I do not save the figure and instead update an on-screen plot, it's even slower. Surely I must be abusing pyplot. (Matlab can do this, no problem.) How do I speed this up?

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• Python Imaging: YCbCr problems

  - by daver

  Hi, I'm doing some image processing in Python using PIL, I need to extract the luminance layer from a series of images, and do some processing on that using numpy, then put the edited luminance layer back into the image and save it. The problem is, I can't seem to get any meaningful representation of my Image in a YCbCr format, or at least I don't understand what PIL is giving me in YCbCr. PIL documentation claims YCbCr format gives three channels, but when I grab the data out of the image using np.asarray, I get 4 channels. Ok, so I figure one must be alpha. Here is some code I'm using to test this process: import Image as im import numpy as np pengIm = im.open("Data\\Test\\Penguins.bmp") yIm = pengIm.convert("YCbCr") testIm = np.asarray(yIm) grey = testIm[:,:,0] grey = grey.astype('uint8') greyIm = im.fromarray(grey, "L") greyIm.save("Data\\Test\\grey.bmp") I'm expecting a greyscale version of my image, but what I get is this jumbled up mess: http://i.imgur.com/zlhIh.png Can anybody explain to me where I'm going wrong? The same code in matlab works exactly as I expect.

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• How to import a module from a directory?

  - by Roman

  On my system I have two versions of Python (to call them I type python and python2 in the command line). When I use the first version of Python, I cannot import sklearn module but I can do it in the second version of Python. I would like to use the first version of python (because other modules are available there) and, at the same time, I would like to be able to import sklearn from this version of Python. My solution was to use: import sys sys.path.append('location_of_the_sklearn_module') To find the location of the sklearn module I started a python session (using the second version of python, in which sklearn works). The I type: import sklearn sklearn.__file__ As a result I got: /home/name/my_name/numpy/local/lib/python2.7/site-packages/sklearn/__init__.pyc In the session of the first version of Python I tried: import sys sys.path.append('/home/name/my_name/numpy/local/lib/python2.7/site-packages/sklearn') import sklearn Unfortunately it did not work. As a result I got: ImportError: No module named sklearn Does anybody know what I am doing wrong and if it is possible to reach the goal in the way I try?

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• Calculating the null space of a matrix

  - by Ainsworth

  I'm attempting to solve a set of equations of the form Ax = 0. A is known 6x6 matrix and I've written the below code using SVD to get the vector x which works to a certain extent. The answer is approximately correct but not good enough to be useful to me, how can I improve the precision of the calculation? Lowering eps below 1.e-4 causes the function to fail. from numpy.linalg import * from numpy import * A = matrix([[0.624010149127497 ,0.020915658603923 ,0.838082638087629 ,62.0778180312547 ,-0.336 ,0], [0.669649399820597 ,0.344105317421833 ,0.0543868015800246 ,49.0194290212841 ,-0.267 ,0], [0.473153758252885 ,0.366893577716959 ,0.924972565581684 ,186.071352614705 ,-1 ,0], [0.0759305208803158 ,0.356365401030535 ,0.126682113674883 ,175.292109352674 ,0 ,-5.201], [0.91160934274653 ,0.32447818779582 ,0.741382053883291 ,0.11536775372698 ,0 ,-0.034], [0.480860406786873 ,0.903499596111067 ,0.542581424762866 ,32.782593418975 ,0 ,-1]]) def null(A, eps=1e-3): u,s,vh = svd(A,full_matrices=1,compute_uv=1) null_space = compress(s <= eps, vh, axis=0) return null_space.T NS = null(A) print "Null space equals ",NS,"\n" print dot(A,NS)

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• python how to put data on y-axis when plotting histogram

  - by user3041107

  I don't quite understand how to control y - axis when using plt.hist plot in python. I read my .txt data file - it contains 10 columns with various data. If I want to plot distribution of strain on x axis I take column n.5. But what kind of value appears on y axis ??? Don't understand that. here is the code: import numpy import matplotlib.pyplot as plt from pylab import * from scipy.stats import norm import sys strain = [] infile = sys.argv[1] for line in infile: ret = numpy.loadtxt(infile) strain += list(ret[:,5]) fig = plt.figure() plt.hist(strain, bins = 20) plt.show() Thanks for help!

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• Strange python error

  - by Werner

  Hi, I am trying to write a python program that calculates a histogram, given a list of numbers like: 1 3 2 3 4 5 3.2 4 2 2 so the input parameters are the filename and the number of intervals. The program code is: #!/usr/bin/env python import os, sys, re, string, array, math import numpy Lista = [] db = sys.argv[1] db_file = open(db,"r") ic=0 nintervals= int(sys.argv[2]) while 1: line = db_file.readline() if not line: break ll=string.split(line) #print ll[6] Lista.insert(ic,float(ll[0])) ic=ic+1 lmin=min(Lista) print "min= ",lmin lmax=max(Lista) print "max= ",lmax width=666.666 width=(lmax-lmin)/nintervals print "width= ",width nelements=len(Lista) print "nelements= ",nelements print " " Histogram = numpy.zeros(shape=(nintervals)) for item in Lista: #print item int_number = 1 + int((item-lmin)/width) print " " print "item,lmin= ",item,lmin print "(item-lmin)/width= ",(item-lmin)," / ",width," ====== ",(float(item)-float(lmin))/float(width) print "int((item-lmin)/width)= ",int((item-lmin)/width) print item , " belongs to interval ", int_number, " which is from ", lmin+width*(int_number-1), " to ",lmin+width*int_number Histogram[int_number] = Histogram[int_number] + 1 4 but somehow I am completely lost, I get strange errors, can anybody help¿ Thanks

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• error installing python wrapper for openkinect

  - by auraham

  I tried to install python wrappers for OpenKinect on Ubuntu 12.04, but I can't due this error: $ sudo apt-get install python2.7-dev python2.7-dev : Depends: libexpat1-dev but it is not going to be installed Depends: libssl-dev but it is not going to be installed E: Unable to correct problems, you have held broken packages. Python wrapper requires these dependencies: Cython python-dev (error above) python-numpy how can I install python-dev?

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• Opening cursor files in a graphics editor?

  - by sdaau

  I'm looking at /usr/share/icons/DMZ-White/cursors, and there is: $ tree -s /usr/share/icons/DMZ-White/ /usr/share/icons/DMZ-White/ +-- [ 4096] cursors ¦   +-- [ 14] 00008160000006810000408080010102 -> v_double_arrow ... ¦   +-- [ 5] 9d800788f1b08800ae810202380a0822 -> hand2 ¦   +-- [ 8] arrow -> left_ptr ¦   +-- [ 15776] bd_double_arrow ¦   +-- [ 15776] bottom_left_corner ¦   +-- [ 15776] bottom_right_corner ¦   +-- [ 15776] bottom_side ... ... a bunch of files without extension, that GIMP cannot open. Is there an editor where these files can be opened - or at least a converter to something like .png? I can note that ImageMagick display also failed to open these files... Found also Gursor Maker - Cursor Editor for X11/GTK+; got the CVS code from SourceForge - it still uses Numeric (the old name of numpy), so to run it, you'll have to do: #from Numeric import * from numpy import * ... in xcurio.py, curxp.py, gimp.py, colorfunc.py - and comment the #from xml.dom.ext.reader import Sax2 in lsproj.py. With that, I got it running 11.04: ... but cannot get any files to open? So I thought I should grep for paths, nothing much came up - and when I looked into cursordefs.py, I simply had to paste this: CURSOR_ICON = gtk.gdk.pixbuf_new_from_xpm_data([ "10 16 3 1", " c None", ". c #000000", "+ c #FFFFFF", ".. ", ".+. ", ".++. ", ".+++. ", ".++++. ", ".+++++. ", ".++++++. ", ".+++++++. ", ".++++++++.", ".+++++....", ".++.++. ", ".+. .++. ", ".. .++. ", " .++. ", " .++. ", " .. "]) Heh :) In any case, doesn't look like it will be much usable on newer Ubuntus, unfortunately... Just tested XMC plugin as well - on 11.04, has to be built from source (from the link in the accepted answer); the requirements on my system resolved to: sudo apt-get install libgimp2.0-dev libglib2.0-0-dbg libglib2.0-0-refdbg libglib2.0-cil-dev libgtk2.0-0-dbg libgtk2.0-cil-dev ... after that, the configure/make procedure in the INSTALL file works. Note that this plugin is a bit "sneaky": ... that is, you should use "All files" (as there are no extensions); cursor previews at first will not be rendered. Then open one cursor file; after it has been opened, then there is a preview in the File/Open dialog; but other than that, it works fine...

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• How do I put YAML code in GitHub MarkDown?

  - by rutherford

  Following YAML snippet that I'm trying to place in my markdown formatted readme: ``` libraries: - name: numpy version: "1.6.1" ``` Tried the above with both no and 2 trailing spaces at the end of each line. Both turn out on a single line. Obviously I want them on 3 separate lines in my README.md. How? edit: note tried adding 'yaml' as the optional lang parameter but no dice either.

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• apache pointing to the wrong version of python on ubuntu how do I change?

  - by one

  I am setting up a flask application on and Ubuntu 12.04.3 LTS EC2 instance and everything seemed to be working well (i.e. I could get to the webpage via the publicly available url) until I tried to import a module (e.g. numpy) and realised the apache python differs from the one I used to compile the mod_wsgi and also the one I am using I am running apache2. The apache2 logs show the warnings (specifically the last line shows the path hasnt changed): [warn] mod_wsgi: Compiled for Python/2.7.5. [warn] mod_wsgi: Runtime using Python/2.7.3. [warn] mod_wsgi: Python module path '/usr/lib/python2.7/:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib$ I have tried to set the path in my virtual host conf (my python is located in /home/ubuntu/anaconda/bin along with all of the other libraries): WSGIPythonHome /home/ubuntu/anaconda WSGIPythonPath /home/ubuntu/anaconda <VirtualHost *:80> ServerName xx-xx-xxx-xxx-xxx.compute-1.amazonaws.com ServerAdmin [email protected] WSGIScriptAlias / /var/www/microblog/microblog.wsgi <Directory /var/www/microblog/app/> Order allow,deny Allow from all </Directory> Alias /static /var/www/microblog/app/static <Directory /var/www/FlaskApp/FlaskApp/static/> Order allow,deny Allow from all </Directory> ErrorLog ${APACHE_LOG_DIR}/error.log LogLevel warn CustomLog ${APACHE_LOG_DIR}/access.log combined </VirtualHost> But I still get the warnings and the apache python path hasnt changed - where do I need to put the relevant directives to point apache at my python version and modules (e.g. scipy, numpy etc)? Separately, could I have avoided this using virtual environments? Thanks in advance.

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