Mailman 3 April 2012 - SciPy-User

linalg.eigh hangs only after importing sparse module
by Nicolas Pinto June 25, 2012

June 25, 2012

Hello, The following simple code hangs only when sparse has been imported: ``` from scipy import sparse # <<<<<<< BUG import numpy as np from scipy import linalg N = 1000 np.random.seed(42) X = np.random.random((N, N)) print X.mean() v, Q = linalg.eigh(X) print v.mean() ``` Do you think this may be related to other arpack/umfpack/etc. known failures ? Please let us know how can we help fix this issue. Thanks for your help. Regards, -- Nicolas Pinto http://web.mit.edu/pinto

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Re: [SciPy-User] sinc interpolation
by Travis Oliphant June 7, 2012

June 7, 2012

On Nov 20, 2009, at 2:26 PM, David Trem wrote: > Hello, > > Is sinc interpolation available in Scipy ? Yes, use scipy.signal.resample which uses a Fourier method to downsample or upsample a signal: from scipy.signal import resample from numpy import r_, sin from pylab import plot x = r_[0:10] y = sin(x) yy = resample(x, 100) # This is a bit tricky to get the x-samples right xx = r_[0:10:101j][:-1] plot(x,y,'ro', xx, yy) -Travis

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Python 2.7 / 64-bit
by Chris Weisiger May 6, 2012

May 6, 2012

I'm in the unfortunate situation of needing to make a OSX 64-bit version of a program that uses both Scipy/Numpy and wxWidgets. The former only has unofficial 64-bit builds and only for Python 2.6; the latter only has 64-bit builds for 2.7 -- before that, they were using Carbon for UI calls, which is 32-bit only. So there's a problem there. Hand-building my own version of either seems to be a pretty gnarly problem that I'd rather avoid if possible. Any ideas how far we are from having a 64-bit, Python2.7 build of scipy and numpy for OSX? All else being equal, I'd rather be on 2.7 than 2.6. Thanks. -Chris

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ndimage/morphology - binary dilation and erosion?
by klo uo May 6, 2012

May 6, 2012

While preparing some images for OCR, I usually discard those with low DPI, but as this happens often I thought to try some image processing and on suggestion (morphological operations) I tried ndimage.morph with idea to play around binary_dilation Images were G4 TIFFs which PIL/MPL can't decode, so I convert to 1bit PNG which I normalized after to 0 and 1. On sample img I applied: ndi.morphology.binary_dilation(img).astype(img.dtype) and ndi.morphology.binary_erosion(img).astype(img.dtype) I attached result images, and wanted to ask two question: 1. Is this result correct? From what I read today seems like what dilation does is erosion and vice versa, but I probably overlooked something 2. Does someone maybe know of better approach for enhancing original sample for OCR (except thresholding, for which I'm aware)? TIA [image: Inline image 1]

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building on Ubuntu Linux from github source : BLAS and LAPACK not getting picked up from environment variable
by hari jayaram May 1, 2012

May 1, 2012

Hi I am on 64 bit Ubuntu , python 2.6.5 , GCC 4.4.3. I want to compile my own scipy since the ubuntu package on lucid installs a scipy which does not have the scipy.optimize.curve_fit I followed the build instructions at the url below to install from the git source . http://www.scipy.org/Installing_SciPy/BuildingGeneral I could install numpy from the git source . Then I installed lapack and blas libraries in my home directory following the instructions at BuildingGeneral. I set the environment variables BLAS and LAPACK in my ~/.bashrc and sourced them and then tried the setup.py for scipy sudo python setup.py install I get the following errors implying that BLAS was not getting picked up. I even copied the libblas.a and liblapack.a files to /usr/lib, linked it to liblapack.so ...but none of these helped find lapack or blas "numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable." I am wondering if the build instructions are different for the github tree. The detailed error is given below. Thanks for your help Hari hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 208, in <module> setup_package() File "setup.py", line 199, in setup_package configuration=configuration ) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 136, in configuration config.add_subpackage('scipy') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 8, in configuration config.add_subpackage('integrate') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 325, in get_info return cl().get_info(notfound_action) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 484, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. hari@hari:~/scipy$ export BLAS=/home/hari/blas/BLAS/libblas.a hari@hari:~/scipy$ export LAPACK=/home/hari/LAPACK/lapack-3.4.0/liblapack.a hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 208, in <module> setup_package() File "setup.py", line 199, in setup_package configuration=configuration ) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 136, in configuration config.add_subpackage('scipy') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 8, in configuration config.add_subpackage('integrate') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 325, in get_info return cl().get_info(notfound_action) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 484, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable.

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setting submatrix of sparse matrix
by Duilio Tadeu April 30, 2012

April 30, 2012

Hi, I am developing a simple Finite Elements code and there a part of the code where I need to set some elements of the sparse matrix (actually a submatrix), But I could not make it work. I have tried many ways. I describe the better way I could try. The array index idx is 1x3, so idx1 and idx2 is 3x3. The (small) matrix M is 3x3. The matrix A is a sparse matrix, lil_matrix sparse matrix of scipy.sparse ###### partial code ################## M = local_matrix(x,y) M=M.ravel() idx1,idx2 = numpy.meshgrid(idx,idx) idx1=idx1.ravel() idx2=idx2.ravel() A[idx1,idx2] = A[idx1,idx2] + M ################################### In fact, I am trying to migrate from MATLAB to Scipy/Numpy, but this part is taking some time and is becoming frustrating, since I could not find any kind of way to perform this task. In MATLAB, the code would be just: M = local_matrix(x,y) A[idx,idx] = A[idx,idx] + M Which is shorter and easy. I send next the error message. Any help is welcome. Thanks, Duilio 131 idx2=idx2.ravel() 132 --> 133 A[idx1,idx2] = A[idx1,idx2] + M /usr/lib/python2.6/dist-packages/scipy/sparse/lil.pyc in __setitem__(self, index, x) 318 else: 319 for ii, jj, xx in zip(i, j, x): --> 320 self._insertat(ii, jj, xx) 321 elif isinstance(i, slice) or issequence(i): 322 rows = self.rows[i] /usr/lib/python2.6/dist-packages/scipy/sparse/lil.pyc in _insertat(self, i, j, x) 230 row = self.rows[i] 231 data = self.data[i] --> 232 self._insertat2(row, data, j, x) 233 234 def _insertat2(self, row, data, j, x): /usr/lib/python2.6/dist-packages/scipy/sparse/lil.pyc in _insertat2(self, row, data, j, x) 244 245 if not np.isscalar(x): --> 246 raise ValueError('setting an array element with a sequence') 247 248 try: ValueError: setting an array element with a sequence

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Euroscipy 2012 deadline extension: May 7th
by Emmanuelle Gouillart April 30, 2012

April 30, 2012

The committee of the Euroscipy 2012 conference has extended the deadline for abstract submission to **Monday May 7th, midnight** (Brussels time). Up to then, new abstracts may be submitted on http://www.euroscipy.org/conference/euroscipy2012, and already-submitted abstracts can be modified. We are very much looking forward to your submissions to the conference. Euroscipy 2012 is the annual European conference for scientists using Python. It will be held August 23-27 2012 in Brussels, Belgium. It is also still possible to propose sprints that will take place after the conference, please write to Berkin Malkoc (malkocb(a)itu.edu.tr) for practical organization (rooms, ...). Any other questions should be addressed exclusively to org-team(a)lists.euroscipy.org -- Emmanuelle

1 0

problem with the fmin function
by servant mathieu April 30, 2012

April 30, 2012

Dear scipy users, I'm trying to minimize a chi-square value by a simplex routine. My code contains two functions: the first one, called spotdiffusion(a, ter , v , sda , rd) generates some simulated data for a given set of parameter values. The second function, called chis ( a, ter , v , sda , rd), computes a chi-square value from the comparison of observed and simulated data, for a given set of parameter values. To do so, the chis function calls the spotdiffusion one. Here is a simplified structure of my code: def spotdiffusion (a, ter , v , sda , rd): do simulation computations returns an array of simulated data def chis (a, ter , v , sda , rd): observed data simulated_data = spotdiffusion ( a, ter , v , sda , rd) do chi-square computations returns the chi-square value (float) Now I want now to find a, ter, v, sda and rda values which minimize the chi-square. Here is my attempt: x0 = np.array ([0.11,0.25,0.35, 1.7, 0.017]) ####initial guess xopt = fmin (chis, x0, maxiter=300) However, python returns an error: Traceback (most recent call last): File "<ipython console>", line 1, in <module> File "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\startup.py", line 128, in runfile execfile(filename, glbs) File "C:\Users\mathieu\Desktop\modeling\spotlight diffusion model\fitting_spotlight.py", line 246, in <module> xopt = fmin (chis, x0, maxiter=300) File "C:\Python27\lib\site-packages\scipy\optimize\optimize.py", line 257, in fmin fsim[0] = func(x0) File "C:\Python27\lib\site-packages\scipy\optimize\optimize.py", line 176, in function_wrapper return function(x, *args) TypeError: chis() takes exactly 5 arguments (1 given) I don't understand where is my mistake. Any help would be appreciated! Cheers, Mathieu

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Alternative to R phyper
by Bruno Santos April 30, 2012

April 30, 2012

Hello everyone, I have a bit of code where I am using rpy2 to import R phyper so I can perform an hypergeometric test. Unfortunately our cluster does not have a functional installation of rpy2 working. So I am wondering if I could translate to scipy which would make the code completly independent of R. The python code I have is as following: def lphyper(self,q,m,n,k): """ self.phyper(self,q,m,n,k) Calculate p-value using R function phyper from rpy2 low-level interface. "R Documentation phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) q: vector of quantiles representing the number of white balls drawn without replacement from an urn which contains both black and white balls. m: the number of white balls in the urn. n: the number of black balls in the urn. k: the number of balls drawn from the urn. log.p: logical; if TRUE, probabilities p are given as log(p). lower.tail: logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x]. """ phyper_q = SexpVector([q,], rinterface.INTSXP) phyper_m = SexpVector([m,], rinterface.INTSXP) phyper_n = SexpVector([n,], rinterface.INTSXP) phyper_k = SexpVector([k,], rinterface.INTSXP) return phyper(phyper_q,phyper_m,phyper_n,phyper_k,**myparams)[0] I have looked to scipy.stats.hypergeom but it is giving me a different result which is also negative. > 1-phyper(45, 92, 7518, 1329) [1] 6.92113e-13 In [24]: stats.hypergeom.sf(45,(92+7518),92,1329) Out[24]: -8.4343643180773142e-12 This was supposed to be an error with an older version of scipy but I am using more recent versions of it which should not contain the error anymore: In [26]: numpy.__version__ Out[26]: '1.5.1' In [27]: scipy.__version__ Out[27]: '0.9.0' thank you very much in advance for any help. Best, Bruno

1 0

(no subject)
by Martin van Leeuwen April 28, 2012

April 28, 2012

Hi, I was trying to work with the mlab.pipeline.triangle_filter in mayavi but couldn't figure out how the method works or how to work with the returned data structure. I assume it is similar to working with the edges in the Delaunay Graph Example: http://github.enthought.com/mayavi/mayavi/auto/example_delaunay_graph.html#… , but I would need a bit more information particular to this triangle filter. The final data structure I would like to get it the triangles in is OBJ format (triangle indices into vectors array). Thanks for any help. Martin

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