Mailman 3 March 2010 - SciPy-User

Re: [SciPy-User] helmert implementation (7 parameters - geometric transformation)
by Ewald Zietsman 02 Mar '10

02 Mar '10

Hi, I see your coordinates are very big numbers. These can lead to an ill-conditioned (AtA) matrix which can lead to a wrong inverse. Try using cholesky decomposition instead of using linalg.inv. The method is outlined here http://en.wikipedia.org/wiki/Cholesky_decomposition and numpy has routines for doing just this. The other option is to subtract the centre-of-mass from your coordinates i.e. P1 -> P1x - P1xave, P1y - P1yave etc. Do the same for P2. Calculate the transformation again. The shifts should now be zero but your rotations and scale should be statistically independent and correct. The difference between the two coordinate systems' centres of mass gives the shifts. Transformations far away from the origin rarely behaves well. Good luck. >> >>> Hi All, >>> >>> i'm tring to implement a function to perform a geometric trasformation >>> between a set of points in 2 different reference systems >>> >>> it is a 7 parameters trasformation (helmert) , based on last square method >>> it use as input 2 set of x,y,z coordinates in 2 different reference >>> systems >>> and give as output 7 parameters needed to performs transformation >>> from one reference system to the other one. >>> >>> http://en.wikipedia.org/wiki/Helmert_transformation >>> >>> this function is used in geodesy to "reproject" coordinates between 2 >>> different Datum >>> >>> i wrote it as : >>> >>> import numpy as np >>> from scipy import linalg >>> >>> def helmert(p1, p2): >>> L = np.loadtxt(p1) >>> A = np.zeros((3*L.shape[0],7),float) >>> A[ ::3, 0] = 1.0 >>> A[1::3, 1] = 1.0 >>> A[2::3, 2] = 1.0 >>> A[ ::3, 3] = L[:,0] >>> A[1::3, 3] = L[:,1] >>> A[2::3, 3] = L[:,2] >>> A[1::3, 4] = L[:,2] >>> A[2::3, 4] = -L[:,1] >>> A[ ::3, 5] = -L[:,2] >>> A[2::3, 5] = L[:,0] >>> A[ ::3, 6] = L[:,1] >>> A[1::3, 6] = -L[:,0] >>> G = np.loadtxt(p2) >>> Y = np.zeros((3*G.shape[0],1),float) >>> Y[ ::3, 0] = G[:,0] - L[:,0] >>> Y[1::3, 0] = G[:,1] - L[:,1] >>> Y[2::3, 0] = G[:,2] - L[:,2] >>> N = np.dot(A.T.conj(), A) >>> T = np.dot(A.T.conj(), Y) >>> C = np.dot(linalg.inv(N), T) >>> print C >>> >>> >>> from a pdf i find online >>> it has numerical examples >>> and i get different results :'( >>> >>> >>> p1 : >>> >>> 4402553.334 727053.937 4542823.474 >>> 4399375.347 703845.876 4549215.105 >>> 4412911.150 701094.435 4536518.139 >>> >>> >>> p2 : >>> >>> 4402553.569 727053.737 4542823.332 >>> 4399375.518 703845.639 4549214.880 >>> 4412911.336 701094.214 4536517.955 >>> >>> >>> pdf results : >>> >>> x0 -9.256 m >>> y0 -23.701 m >>> z0 16.792 m >>> Rx -0.0001990982 rad >>> Ry 0.0001778762 rad >>> Rz 0.00015 rad >>> ? 0.00000046 >>> >>> >> The angles here look like degrees, not radians. Also, the last factor is >> pretty definitely wrong. It is given directly as the square root of the >> ratio of the variance of the two sets of vectors around their means minus 1. >> For instance >> >> sqrt(pt2.var(0).sum()/pt1.var(0).sum()) - 1 >> >> >>> >>> my results : >>> >>> [[ -9.91564629e+00] >>> [ -2.36172028e+01] >>> [ 1.57283853e+01] >>> [ -2.68063331e-07] >>> [ 3.04330048e-06] >>> [ -2.76148185e-06] >>> [ -2.31598150e-06]] >>> >>> >>> >> And my result agrees with neither ;) BTW, are you going from pt2 -> pt1 or >> vice versa? >>

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Re: [SciPy-User] scikits.learn installation
by David Trethewey 02 Mar '10

02 Mar '10

Problem is sorted now, thanks for your help. David > > Message: 5 > Date: Tue, 2 Mar 2010 06:45:08 -0500 > From: josef.pktd(a)gmail.com > Subject: Re: [SciPy-User] scikits.learn installation > To: SciPy Users List <scipy-user(a)scipy.org> > Message-ID: > <1cd32cbb1003020345k7d51d85ah5fd703139a20afbc(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Tue, Mar 2, 2010 at 6:02 AM, David Trethewey <dlrt2(a)ast.cam.ac.uk> wrote: > >> I installed the python headers and libboost. It now compiles without >> error but still when I actually try to import the em module I get the >> same error message; >> >>>>>> import scipy >>>>>> import numpy >>>>>> from scikits.learn.machine import em >>>>>> >>>>>> >>> Traceback (most recent call last): >>> ?File "<stdin>", line 1, in <module> >>> ?File "scikits/learn/machine/em/__init__.py", line 8, in <module> >>> ? ?from online_em import OnGMM as _OnGMM >>> ?File "scikits/learn/machine/em/online_em.py", line 164, in <module> >>> ? ?import _rawden >>> ImportError: No module named _rawden >>> > > You could search the source and build directories for *.pyd . > It happened to me in the pre-release version that the pyd files didn't > get copied correctly to the install directories. > > Josef > > >>> David Trethewey >>> Institute of Astronomy, Cambridge, UK >>> >>> >>> >>> >> >> scipy-user-request(a)scipy.org wrote: >> >>> Send SciPy-User mailing list submissions to >>> ? ? ? scipy-user(a)scipy.org >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> ? ? ? http://mail.scipy.org/mailman/listinfo/scipy-user >>> or, via email, send a message with subject or body 'help' to >>> ? ? ? scipy-user-request(a)scipy.org >>> >>> You can reach the person managing the list at >>> ? ? ? scipy-user-owner(a)scipy.org >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of SciPy-User digest..." >>> >>> >>> Today's Topics: >>> >>> ? ?1. Re: Error on importing scikits.learn (David Trethewey) >>> ? ?2. Re: Error on importing scikits.learn (David Trethewey) >>> ? ?3. Re: Error on importing scikits.learn (Helge Reikeras) >>> ? ?4. ANN: SfePy 2010.1 (Robert Cimrman) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Mon, 01 Mar 2010 11:46:42 +0000 >>> From: David Trethewey <dlrt2(a)ast.cam.ac.uk> >>> Subject: Re: [SciPy-User] Error on importing scikits.learn >>> To: scipy-user(a)scipy.org >>> Message-ID: <4B8BA922.6010900(a)ast.cam.ac.uk> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> I get the following error message when attempting to import the >>> expectation maximisation (em) module from scikits.learn : >>> >>> >>>>>>> import scipy >>>>>>> import numpy >>>>>>> from scikits.learn.machine import em >>>>>>> >>>>>>> >>>> Traceback (most recent call last): >>>> ?File "<stdin>", line 1, in <module> >>>> ?File "scikits/learn/machine/em/__init__.py", line 8, in <module> >>>> ? ?from online_em import OnGMM as _OnGMM >>>> ?File "scikits/learn/machine/em/online_em.py", line 164, in <module> >>>> ? ?import _rawden >>>> ImportError: No module named _rawden >>>> >>>> Does anyone know what this _rawden module is and why might it not be >>>> found? >>>> >>>> David Trethewey >>>> Institute of Astronomy, Cambridge, UK >>>> >>>> >>>> >>>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Mon, 01 Mar 2010 11:51:14 +0000 >>> From: David Trethewey <dlrt2(a)ast.cam.ac.uk> >>> Subject: Re: [SciPy-User] Error on importing scikits.learn >>> To: scipy-user(a)scipy.org >>> Message-ID: <4B8BAA32.3000004(a)ast.cam.ac.uk> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> I have traced it back to an error in compiling scikits.learn itself: >>> >>> building 'scikits.learn.machine.em._rawden' extension >>> compiling C sources >>> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 >>> -Wall -Wstrict-prototypes -fPIC >>> >>> compile options: '-I/usr/lib/python2.6/dist-packages/numpy/core/include >>> -I/usr/include/python2.6 -c' >>> gcc: scikits/learn/machine/em/src/pure_den.c >>> scikits/learn/machine/em/src/pure_den.c:7:20: error: Python.h: No such >>> file or directory >>> >>> David >>> >>> David Trethewey wrote: >>> >>> >>>> I get the following error message when attempting to import the >>>> expectation maximisation (em) module from scikits.learn : >>>> >>>> >>>>>>>> import scipy >>>>>>>> import numpy >>>>>>>> from scikits.learn.machine import em >>>>>>>> >>>>>>>> >>>>> Traceback (most recent call last): >>>>> ?File "<stdin>", line 1, in <module> >>>>> ?File "scikits/learn/machine/em/__init__.py", line 8, in <module> >>>>> ? ?from online_em import OnGMM as _OnGMM >>>>> ?File "scikits/learn/machine/em/online_em.py", line 164, in <module> >>>>> ? ?import _rawden >>>>> ImportError: No module named _rawden >>>>> >>>>> Does anyone know what this _rawden module is and why might it not be >>>>> found? >>>>> >>>>> David Trethewey >>>>> Institute of Astronomy, Cambridge, UK >>>>> >>>>> >>>>> >>>>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Mon, 01 Mar 2010 13:55:01 +0200 >>> From: "Helge Reikeras" <helge.reikeras(a)gmail.com> >>> Subject: Re: [SciPy-User] Error on importing scikits.learn >>> To: "SciPy Users List" <scipy-user(a)scipy.org> >>> Message-ID: <op.u8v0pqws9y0l3i@helge-desktop> >>> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes >>> >>> On Mon, 01 Mar 2010 13:51:14 +0200, David Trethewey <dlrt2(a)ast.cam.ac.uk> >>> wrote: >>> >>> >>> >>>> compile options: '-I/usr/lib/python2.6/dist-packages/numpy/core/include >>>> -I/usr/include/python2.6 -c' >>>> gcc: scikits/learn/machine/em/src/pure_den.c >>>> scikits/learn/machine/em/src/pure_den.c:7:20: error: Python.h: No such >>>> file or directory >>>> >>>> >>> This is because you don't have the Python header files installed. You need >>> to install these somehow. E.g. if you are running Ubuntu you do "sudo >>> apt-get install python-dev". >>> >>> >>> >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User(a)scipy.org >> http://mail.scipy.org/mailman/listinfo/scipy-user >> >> > > > ------------------------------ > > _______________________________________________ > SciPy-User mailing list > SciPy-User(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user > > > End of SciPy-User Digest, Vol 79, Issue 3 > ***************************************** >

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segfaults with weave.inline
by Pitam Mitra 02 Mar '10

02 Mar '10

Hi, I am creating a new median filter for an astronomy application. Due to speed issues, I decided to code it with weave.inline. However, I have run into segfaults and I have no clue what to do next. I am sorry if this is the wrong section to post this - I searched the site, I could not find any forum. :( Any help is appreciated!! Here is the output: *** glibc detected *** python: free(): invalid next size (fast): 0x09746358 *** ======= Backtrace: ========= /lib/libc.so.6[0x428751] /usr/lib/python2.6/site-packages/numpy/core/multiarray.so(+0x3643c)[0x8db43c] /usr/lib/libpython2.6.so.1.0[0x3669924] /usr/lib/libpython2.6.so.1.0[0x3656559] /usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x5359)[0x36c8fc9] /usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x7aa)[0x36c9e4a] /usr/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x64)[0x36c9fb4] /usr/lib/libpython2.6.so.1.0[0x36e525c] /usr/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0x93)[0x36e5323] /usr/lib/libpython2.6.so.1.0(PyRun_SimpleFileExFlags+0xe1)[0x36e68c1] /usr/lib/libpython2.6.so.1.0(PyRun_AnyFileExFlags+0x82)[0x36e7162] /usr/lib/libpython2.6.so.1.0(Py_Main+0xb95)[0x36f3bd5] python(main+0x28)[0x80485c8] /lib/libc.so.6(__libc_start_main+0xe6)[0x3d0bb6] python[0x8048501] Then there is a huge memory map. The full output can be seen here:http://www.pastebay.com/88049 and the code here: http://www.pastebay.com/88050 Regards Pitam

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Re: [SciPy-User] scikits.learn installation
by David Trethewey 02 Mar '10

02 Mar '10

I installed the python headers and libboost. It now compiles without error but still when I actually try to import the em module I get the same error message; >>>> import scipy >>>> import numpy >>>> from scikits.learn.machine import em >>>> > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "scikits/learn/machine/em/__init__.py", line 8, in <module> > from online_em import OnGMM as _OnGMM > File "scikits/learn/machine/em/online_em.py", line 164, in <module> > import _rawden > ImportError: No module named _rawden > > > David Trethewey > Institute of Astronomy, Cambridge, UK > > > scipy-user-request(a)scipy.org wrote: > Send SciPy-User mailing list submissions to > scipy-user(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-user > or, via email, send a message with subject or body 'help' to > scipy-user-request(a)scipy.org > > You can reach the person managing the list at > scipy-user-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-User digest..." > > > Today's Topics: > > 1. Re: Error on importing scikits.learn (David Trethewey) > 2. Re: Error on importing scikits.learn (David Trethewey) > 3. Re: Error on importing scikits.learn (Helge Reikeras) > 4. ANN: SfePy 2010.1 (Robert Cimrman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 01 Mar 2010 11:46:42 +0000 > From: David Trethewey <dlrt2(a)ast.cam.ac.uk> > Subject: Re: [SciPy-User] Error on importing scikits.learn > To: scipy-user(a)scipy.org > Message-ID: <4B8BA922.6010900(a)ast.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I get the following error message when attempting to import the > expectation maximisation (em) module from scikits.learn : > >>>>> import scipy >>>>> import numpy >>>>> from scikits.learn.machine import em >>>>> >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "scikits/learn/machine/em/__init__.py", line 8, in <module> >> from online_em import OnGMM as _OnGMM >> File "scikits/learn/machine/em/online_em.py", line 164, in <module> >> import _rawden >> ImportError: No module named _rawden >> >> Does anyone know what this _rawden module is and why might it not be >> found? >> >> David Trethewey >> Institute of Astronomy, Cambridge, UK >> >> >> > > > > ------------------------------ > > Message: 2 > Date: Mon, 01 Mar 2010 11:51:14 +0000 > From: David Trethewey <dlrt2(a)ast.cam.ac.uk> > Subject: Re: [SciPy-User] Error on importing scikits.learn > To: scipy-user(a)scipy.org > Message-ID: <4B8BAA32.3000004(a)ast.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I have traced it back to an error in compiling scikits.learn itself: > > building 'scikits.learn.machine.em._rawden' extension > compiling C sources > C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 > -Wall -Wstrict-prototypes -fPIC > > compile options: '-I/usr/lib/python2.6/dist-packages/numpy/core/include > -I/usr/include/python2.6 -c' > gcc: scikits/learn/machine/em/src/pure_den.c > scikits/learn/machine/em/src/pure_den.c:7:20: error: Python.h: No such > file or directory > > David > > David Trethewey wrote: > >> I get the following error message when attempting to import the >> expectation maximisation (em) module from scikits.learn : >> >>>>>> import scipy >>>>>> import numpy >>>>>> from scikits.learn.machine import em >>>>>> >>> Traceback (most recent call last): >>> File "<stdin>", line 1, in <module> >>> File "scikits/learn/machine/em/__init__.py", line 8, in <module> >>> from online_em import OnGMM as _OnGMM >>> File "scikits/learn/machine/em/online_em.py", line 164, in <module> >>> import _rawden >>> ImportError: No module named _rawden >>> >>> Does anyone know what this _rawden module is and why might it not be >>> found? >>> >>> David Trethewey >>> Institute of Astronomy, Cambridge, UK >>> >>> >>> >> > > > > ------------------------------ > > Message: 3 > Date: Mon, 01 Mar 2010 13:55:01 +0200 > From: "Helge Reikeras" <helge.reikeras(a)gmail.com> > Subject: Re: [SciPy-User] Error on importing scikits.learn > To: "SciPy Users List" <scipy-user(a)scipy.org> > Message-ID: <op.u8v0pqws9y0l3i@helge-desktop> > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > On Mon, 01 Mar 2010 13:51:14 +0200, David Trethewey <dlrt2(a)ast.cam.ac.uk> > wrote: > > >> compile options: '-I/usr/lib/python2.6/dist-packages/numpy/core/include >> -I/usr/include/python2.6 -c' >> gcc: scikits/learn/machine/em/src/pure_den.c >> scikits/learn/machine/em/src/pure_den.c:7:20: error: Python.h: No such >> file or directory >> > > This is because you don't have the Python header files installed. You need > to install these somehow. E.g. if you are running Ubuntu you do "sudo > apt-get install python-dev". > >

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helmert implementation (7 parameters - geometric transformation)
by Massimo Di Stefano 01 Mar '10

01 Mar '10

Hi All, i'm tring to implement a function to perform a geometric trasformation between a set of points in 2 different reference systems it is a 7 parameters trasformation (helmert) , based on last square method it use as input 2 set of x,y,z coordinates in 2 different reference systems and give as output 7 parameters needed to performs transformation from one reference system to the other one. http://en.wikipedia.org/wiki/Helmert_transformation this function is used in geodesy to "reproject" coordinates between 2 different Datum i wrote it as : import numpy as np from scipy import linalg def helmert(p1, p2): L = np.loadtxt(p1) A = np.zeros((3*L.shape[0],7),float) A[ ::3, 0] = 1.0 A[1::3, 1] = 1.0 A[2::3, 2] = 1.0 A[ ::3, 3] = L[:,0] A[1::3, 3] = L[:,1] A[2::3, 3] = L[:,2] A[1::3, 4] = L[:,2] A[2::3, 4] = -L[:,1] A[ ::3, 5] = -L[:,2] A[2::3, 5] = L[:,0] A[ ::3, 6] = L[:,1] A[1::3, 6] = -L[:,0] G = np.loadtxt(p2) Y = np.zeros((3*G.shape[0],1),float) Y[ ::3, 0] = G[:,0] - L[:,0] Y[1::3, 0] = G[:,1] - L[:,1] Y[2::3, 0] = G[:,2] - L[:,2] N = np.dot(A.T.conj(), A) T = np.dot(A.T.conj(), Y) C = np.dot(linalg.inv(N), T) print C from a pdf i find online it has numerical examples and i get different results :'( p1 : 4402553.334 727053.937 4542823.474 4399375.347 703845.876 4549215.105 4412911.150 701094.435 4536518.139 p2 : 4402553.569 727053.737 4542823.332 4399375.518 703845.639 4549214.880 4412911.336 701094.214 4536517.955 pdf results : x0 -9.256 m y0 -23.701 m z0 16.792 m Rx -0.0001990982 rad Ry 0.0001778762 rad Rz 0.00015 rad μ 0.00000046 my results : [[ -9.91564629e+00] [ -2.36172028e+01] [ 1.57283853e+01] [ -2.68063331e-07] [ 3.04330048e-06] [ -2.76148185e-06] [ -2.31598150e-06]] anyone here can give it a try ? the results seems wrong but i haveb't yet find a solution. thanks to ALL! regards, Massimo.

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scipy.io.wavfile versus audiolab
by Nils Wagner 01 Mar '10

01 Mar '10

Hi all, what are the differences between audiolab and scipy.io.wavfile ? Nils

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ANN: SfePy 2010.1
by Robert Cimrman 01 Mar '10

01 Mar '10

I am pleased to announce release 2010.1 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method. The code is based on NumPy and SciPy packages. It is distributed under the new BSD license. Mailing lists, issue tracking, git repository: http://sfepy.org Home page: http://sfepy.kme.zcu.cz Documentation: http://docs.sfepy.org/doc Contributors to this release: Vladimír Lukeš, Logan Sorenson. Highlights of this release -------------------------- - new sphinx-based documentation - refactoring of base functions (polynomial spaces) and element geometry description - interpolation between different meshes - terms for describing perfusion and active fibres in the total Lagrangian formulation (applicable, for example, to active muscle tissue models) Major improvements ------------------ Apart from many bug-fixes, let us mention: - data probing: - automatic refinement of probe points, speed-up - postprocessing and visualization: - VTK source construction for any format supported by MeshIO classes: - this means displaying meshes in formats Mayavi knows nothing about - graphical logging: - support logging to a text file, vertical line plot, allow several Log instances - new examples: - application of the theory of homogenization to elasticity - perfusion, active fibres - new tests and many new terms For more information on this release, see http://sfepy.googlecode.com/svn/web/releases/2010.1_RELEASE_NOTES.txt (full release notes, rather long). Best regards, Robert Cimrman

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Re: [SciPy-User] Error on importing scikits.learn
by David Trethewey 01 Mar '10

01 Mar '10

I get the following error message when attempting to import the expectation maximisation (em) module from scikits.learn : > > >>> import scipy > >>> import numpy > >>> from scikits.learn.machine import em > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "scikits/learn/machine/em/__init__.py", line 8, in <module> > from online_em import OnGMM as _OnGMM > File "scikits/learn/machine/em/online_em.py", line 164, in <module> > import _rawden > ImportError: No module named _rawden > > Does anyone know what this _rawden module is and why might it not be > found? > > David Trethewey > Institute of Astronomy, Cambridge, UK > >

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