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  • Integrating GSL onto iPhone Xcode

    - by zeroinverse
    I have been trying to integrate GSL (Gnu Scientific Library) into an iPhone project using Xcode. The challenge is GSL has all the modules in different folders, yet when their header files are reference, they often reference instead of or . At least with I could use Xcode's recursive header file search to find it. But with , basically file not found. Does anyone have an easy way to address the hierarchical GSL structure to compile into Xcode? I can do it the tedious way of fixing all the #INCLUDE lines but hoping there is a better alternative. This way, I can more easily update GSL when changes are made by the community. NOTE: I found Xcode needs to find the right header file locations (make sure to adjust your TARGET Build settings, not just your Project Build settings).

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  • GSL interpolation error, values must be x values must be monotonically increasing

    - by pyCthon
    Hi my problem is that my data set is monotonically increasing but towards the end the of the data it looks like it does below ,where some of the x[i-1] = x[i] as shown below. This causes an error to be raised in GSL because it thinks that the values are not monotonically increasing. Is there a solution, fix or work around for this problem? the values are already double precision ,this particular data set starts at 9.86553e-06 and ends at .999999 would the only solution be to offset every value in a for loop? 0.999981 0.999981 0.999981 0.999982 0.999982 0.999983 0.999983 0.999983 0.999984 0.999984 0.999985 0.999985 0.999985

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  • GSL Uniform Random Number Generator

    - by Jamaia
    I want to use GSL's uniform random number generator. On their website, they include this sample code: #include <stdio.h> #include <gsl/gsl_rng.h> int main (void) { const gsl_rng_type * T; gsl_rng * r; int i, n = 10; gsl_rng_env_setup(); T = gsl_rng_default; r = gsl_rng_alloc (T); for (i = 0; i < n; i++) { double u = gsl_rng_uniform (r); printf ("%.5f\n", u); } gsl_rng_free (r); return 0; } However, this does not rely on any seed and so, the same random numbers will be produced each time. They also specify the following: The generator itself can be changed using the environment variable GSL_RNG_TYPE. Here is the output of the program using a seed value of 123 and the multiple-recursive generator mrg, $ GSL_RNG_SEED=123 GSL_RNG_TYPE=mrg ./a.out But I don't understand how to implement this. Any ideas as to what modifications I can make to the above code to incorporate the seed?

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  • How to configure path or set environment variables for installation?

    - by Orr22
    I'm aiming to install APE in Ubuntu 14.04 LTS, a simple code for pseudopotential generation. I'm having this error message while running ./configure: checking for gsl-config... no checking for GSL - version >= 1.0... no *** The gsl-config script installed by GSL could not be found *** If GSL was installed in PREFIX, make sure PREFIX/bin is in *** your path, or set the GSL_CONFIG environment variable to the *** full path to gsl-config. configure: error: could not find required gsl library I checked and I have the GSL already installed: :~/Programas/ape-2.2.0$ dpkg -l | grep gsl ii libgsl0ldbl 1.16+dfsg-1ubuntu1 i386 GNU Scientific Library (GSL) -- library package So I have the library but the program installation isn't finding it. Any help? Thanks in advance

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  • GSL-GNU in Visual studio

    - by Arman
    I have visual studio 2008, I want to integrate GSL library in my project, kindly give me some guidelines so that I can make it possible. I have added the GSL library but the following error come. Error 1 error LNK2028: unresolved token (0A000010) "extern "C" void __cdecl gsl_matrix_set(struct gsl_matrix *,unsigned int,unsigned int,double)" (?gsl_matrix_set@@$$J0YAXPAUgsl_matrix@@IIN@Z) referenced in function "int __cdecl main(void)" (?main@@$$HYAHXZ) Error 2 error LNK2028: unresolved token (0A000011) "extern "C" struct gsl_matrix * __cdecl gsl_matrix_alloc(unsigned int,unsigned int)" (?gsl_matrix_alloc@@$$J0YAPAUgsl_matrix@@II@Z) referenced in function "int __cdecl main(void)" (?main@@$$HYAHXZ) Error 3 error LNK2028: unresolved token (0A000014) "extern "C" double __cdecl gsl_matrix_get(struct gsl_matrix const *,unsigned int,unsigned int)" (?gsl_matrix_get@@$$J0YANPBUgsl_matrix@@II@Z) referenced in function "int __cdecl main(void)" (?main@@$$HYAHXZ) Error 4 error LNK2019: unresolved external symbol "extern "C" double __cdecl gsl_matrix_get(struct gsl_matrix const *,unsigned int,unsigned int)" (?gsl_matrix_get@@$$J0YANPBUgsl_matrix@@II@Z) referenced in function "int __cdecl main(void)" (?main@@$$HYAHXZ) Error 5 error LNK2019: unresolved external symbol "extern "C" void __cdecl gsl_matrix_set(struct gsl_matrix *,unsigned int,unsigned int,double)" (?gsl_matrix_set@@$$J0YAXPAUgsl_matrix@@IIN@Z) referenced in function "int __cdecl main(void)" (?main@@$$HYAHXZ)

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  • Implementation of GNU Scientific Library?

    - by anon
    Does anyone know a collection of articles or books that describes the implementation of the GNU Scientific Library? This question is not about using the GSL; it's about how the GSL is implemented, their design decisions / tradeoffs. Thanks!

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  • Most efficient way to solve system of equations involving the digamma function?

    - by Neil G
    What is the most efficient way to solve system of equations involving the digamma function? I have a vector v and I want to solve for a vector w such that for all i: digamma(sum(w)) - digamma(w_i) = v_i and w_i 0 I found the gsl function gsl_sf_psi, which is the digamma function. Is there an identity I can use to reduce the equations? Is my best bet to use a solver? I am using C++0x; which solver is easiest to use and fast?

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  • What is the most efficient way to solve system of equations containing the digamma function?

    - by Neil G
    What is the most efficient way to solve system of equations involving the digamma function? I have a vector v and I want to solve for a vector w such that for all i: digamma(sum(w)) - digamma(w_i) = v_i and w_i 0 I found the gsl function gsl_sf_psi, which is the digamma function (calculated using some kind of series.) Is there an identity I can use to reduce the equations? Is my best bet to use a solver? I am using C++0x; which solver is easiest to use and fast?

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  • Generating a random displacement on the unit sphere

    - by becko
    Given a unit vector n, I need to generate, as fast as possible, another random unit vector m. The deviation of m from n should be on the order of a positive parameter sigma, and the distribution of m on the unit sphere should be symmetrical around n. I have no specific requirements on the representation of unit vectors, so you can use spherical angles, Cartesian coordinates, or whatever turns out to be convenient. Also, there are no precise requirements on the probability distributions used, as long as it decays when m deviates more than sigma from n. I am working with gsl and C. I have come up with a somewhat convoluted method using Cartesian coordinates. I will post it later if it is useful, but I would like to see people's ideas.

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  • Random numbers from binomial distribution

    - by Sarah
    I need to generate quickly lots of random numbers from binomial distributions for dramatically different trial sizes (most, however, will be small). I was hoping not to have to code an algorithm by hand (see, e.g., this related discussion from November), because I'm a novice programmer and don't like reinventing wheels. It appears Boost does not supply a generator for binomially distributed variates, but TR1 and GSL do. Is there a good reason to choose one over the other, or is it better that I write something customized to my situation? I don't know if this makes sense, but I'll alternate between generating numbers from uniform distributions and binomial distributions throughout the program, and I'd like for them to share the same seed and to minimize overhead. I'd love some advice or examples for what I should be considering.

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  • How can I apply a PSSM efficiently?

    - by flies
    I am fitting for position specific scoring matrices (PSSM aka Position Specific Weight Matrices). The fit I'm using is like simulated annealing, where I the perturb the PSSM, compare the prediction to experiment and accept the change if it improves agreement. This means I apply the PSSM millions of times per fit; performance is critical. In my particular problem, I'm applying a PSSM for an object of length L (~8 bp) at every position of a DNA sequence of length M (~30 bp) (so there are M-L+1 valid positions). I need an efficient algorithm to apply a PSSM. Can anyone help improve performance? My best idea is to convert the DNA into some kind of a matrix so that applying the PSSM is matrix multiplication. There are efficient linear algebra libraries out there (e.g. BLAS), but I'm not sure how best to turn an M-length DNA sequence into a matrix M x 4 matrix and then apply the PSSM at each position. The solution needs to work for higher order/dinucleotide terms in the PSSM - presumably this means representing the sequence-matrix for mono-nucleotides and separately for dinucleotides. My current solution iterates over each position m, then over each letter in word from m to m+L-1, adding the corresponding term in the matrix. I'm storing the matrix as a multi-dimensional STL vector, and profiling has revealed that a lot of the computation time is just accessing the elements of the PSSM (with similar performance bottlenecks accessing the DNA sequence). If someone has an idea besides matrix multiplication, I'm all ears.

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  • Problem in Building mplsh-run in lshkit

    - by Yijinsei
    Hi guy, been trying out this for quite some time but I'm still unable to built mplsh-run from lshkit Not sure if this would help to explain my situation during the building process /tmp/cc17kth4.o: In function `lshkit::MultiProbeLshRecallTable::reset(lshkit::MultiProbeLshModel, unsigned int, double, double)': mplsh-run.cpp:(.text._ZN6lshkit24MultiProbeLshRecallTable5resetENS_18MultiProbeLshModelEjdd[lshkit::MultiProbeLshRecallTable::reset(lshkit::MultiProbeLshModel, unsigned int, double, double)]+0x230): undefined reference to `lshkit::MultiProbeLshModel::recall(double) const' /tmp/cc17kth4.o: In function `void lshkit::MultiProbeLshIndex<unsigned int>::query_recall<lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> > >(float const*, float, lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> >&) const': mplsh-run.cpp:(.text._ZNK6lshkit18MultiProbeLshIndexIjE12query_recallINS_11TopkScannerINS_6MatrixIfE8AccessorENS_6metric5l2sqrIfEEEEEEvPKffRT_[void lshkit::MultiProbeLshIndex<unsigned int>::query_recall<lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> > >(float const*, float, lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> >&) const]+0x2c4): undefined reference to `lshkit::MultiProbeLsh::genProbeSequence(float const*, std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int) const' /tmp/cc17kth4.o: In function `void lshkit::MultiProbeLshIndex<unsigned int>::query<lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> > >(float const*, unsigned int, lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> >&)': mplsh-run.cpp:(.text._ZN6lshkit18MultiProbeLshIndexIjE5queryINS_11TopkScannerINS_6MatrixIfE8AccessorENS_6metric5l2sqrIfEEEEEEvPKfjRT_[void lshkit::MultiProbeLshIndex<unsigned int>::query<lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> > >(float const*, unsigned int, lshkit::TopkScanner<lshkit::Matrix<float>::Accessor, lshkit::metric::l2sqr<float> >&)]+0x4a): undefined reference to `lshkit::MultiProbeLsh::genProbeSequence(float const*, std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int) const' collect2: ld returned 1 exit status the command that i used to built mplsh-run is g++ -I./lshkit/include -L/usr/lib -lm -lgsl -lgslcblas -lboost_program_options-mt mplsh-run.cpp Do you guys have any clue on how I could solve this?

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  • Installing GNU scientific library and linking to programme

    - by jack
    I am trying to install a statistical program which requires GNU Scientific Library (GSL). I have successfully installed GSL through the yum command, but my statistical program gives an error when I try to run make install. I think there is a linking problem. How can I solve it? $ sudo yum install gsl.x86_64 Installed: gsl.x86_64 0:1.15-3.fc16 Dependency Installed: atlas.x86_64 0:3.8.4-1.fc16 $ tar -xvzf prog.tgz $ cd prog $ make $ gcc -O3 -Wall -Wshadow -pedantic -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DVER32 -I/opt/local/include/ -L/opt/local/lib/ -c -o prog.o prog.c In file included from prog.c:16:0: prog.h:7:30: fatal error: gsl/gsl_sf_gamma.h: No such file or directory compilation terminated. make: *** [prog.o] Error 1

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  • NetUserGetLocalGroups - how to call it?

    - by SteveL
    Hi, I am using Delphi 2010, latest version (from repository) of JEDI WinAPI and Windows Security Code Library (WSCL). I don't know how to call the NetUserSetGroups function. The way I am doing it, it is throwing an exception: Access violation at address 5B8760BE in module 'netapi32.dll'. Write of address 00000000. Following is my code: unit uFunc; interface uses Windows, SysUtils, JwaWindows, JwsclSid, Classes; function UserExists(const username: PChar): boolean; stdcall; function AddUser(const username, password: PChar; resetpassword: boolean): boolean; stdcall; //function AddLogonAsAService(ID: pchar): boolean; implementation uses Dialogs; // Returns true if the username exists on the local computer function UserExists(const username: PChar): boolean; stdcall; var NetApiStatus: NET_API_STATUS; ui: PUSER_INFO_0; begin NetApiStatus := NetUserGetInfo(nil, PWideChar(username), 0, PByte(ui)); if Assigned(ui) then NetApiBufferFree(ui); if (NetApiStatus <> NERR_Success) and (NetApiStatus <> NERR_UserNotFound) then RaiseLastOSError(NetApiStatus); Result := (NetApiStatus = NERR_Success); end; function AddPrivilegeToAccount(AAccountName, APrivilege: String): DWORD; var lStatus: TNTStatus; lObjectAttributes: TLsaObjectAttributes; lPolicyHandle: TLsaHandle; lPrivilege: TLsaUnicodeString; lSid: PSID; lSidLen: DWORD; lTmpDomain: String; lTmpDomainLen: DWORD; lTmpSidNameUse: TSidNameUse; lPrivilegeWStr: String; begin ZeroMemory(@lObjectAttributes, SizeOf(lObjectAttributes)); lStatus := LsaOpenPolicy(nil, lObjectAttributes, POLICY_LOOKUP_NAMES, lPolicyHandle); if lStatus <> STATUS_SUCCESS then begin Result := LsaNtStatusToWinError(lStatus); Exit; end; try lTmpDomainLen := DNLEN; // In 'clear code' this should be get by LookupAccountName SetLength(lTmpDomain, lTmpDomainLen); lSidLen := SECURITY_MAX_SID_SIZE; GetMem(lSid, lSidLen); try if LookupAccountName(nil, PChar(AAccountName), lSid, lSidLen, PChar(lTmpDomain), lTmpDomainLen, lTmpSidNameUse) then begin lPrivilegeWStr := APrivilege; lPrivilege.Buffer := PWideChar(lPrivilegeWStr); lPrivilege.Length := Length(lPrivilegeWStr) * SizeOf(Char); lPrivilege.MaximumLength := lPrivilege.Length; lStatus := LsaAddAccountRights(lPolicyHandle, lSid, @lPrivilege, 1); Result := LsaNtStatusToWinError(lStatus); end else Result := GetLastError; finally FreeMem(lSid); end; finally LsaClose(lPolicyHandle); end; end; //if user does not exists, create a local username with the supplied password //if resetpassword, then reset password to the supplied parameter //add the user to the local administrators group (note that this must work //on all languages, use the SID of the group) //give the user the "run as a service" privilege. //enable the user if it is disabled. function AddUser(const username, password: PChar; resetpassword: boolean): boolean; stdcall; var NetApiStatus: NET_API_STATUS; UserInfo1003: USER_INFO_1003; // UserInfo1005: USER_INFO_1005; ui: USER_INFO_1; grp: String; sidstring: String; lgmi3: LOCALGROUP_MEMBERS_INFO_3; jwSid: TJwSecurityID; dwEntriesRead, dwEntriesTotal: PDWORD; lgi01: LOCALGROUP_USERS_INFO_0; plgi01 : PLOCALGROUP_USERS_INFO_0; i: Integer; gsl: TStringList; begin if UserExists(username) then begin if resetpassword then begin NetApiStatus := NetUserChangePassword(nil, PChar(username), PChar(''), PChar(password)); // If old password is incorrect then force password change if (NetApiStatus = ERROR_INVALID_PASSWORD) then begin UserInfo1003.usri1003_password := PChar(password); NetApiStatus := NetUserSetInfo(nil, PChar(username), 1003, @UserInfo1003, nil); end; if (NetApiStatus <> NERR_Success) and (NetApiStatus <> NERR_UserNotFound) then RaiseLastOSError(NetApiStatus); // UserInfo1005.usri1005_priv := USER_PRIV_ADMIN; // NetApiStatus := NetApiStatus and NetUserSetInfo(nil, PChar(username), 1005, @UserInfo1005, nil); end; end else begin ui.usri1_name := PChar(username); ui.usri1_password := PChar(Password); ui.usri1_password_age := 0; // ignored in this call ui.usri1_priv := USER_PRIV_USER; // ui.usri1_home_dir := nil; ui.usri1_comment := PChar(''); ui.usri1_flags := UF_SCRIPT or UF_DONT_EXPIRE_PASSWD; ui.usri1_script_path := nil; NetApiStatus := NetUserAdd(nil, 1, @ui, nil); if NetApiStatus <> NERR_Success then RaiseLastOSError(NetApiStatus); end; Result := (NetApiStatus = NERR_Success); //check if user already belongs to Administrators group if Result then begin sidstring := 'S-1-5-32-544'; //Local Administrators group jwSid := TJwSecurityID.Create(sidstring); try grp := jwSid.GetAccountName(''); finally jwSid.Free; end; gsl := TStringList.Create; try // New(plgi01); NetApiStatus := NetUserGetLocalGroups(nil, PChar(username), 0, LG_INCLUDE_INDIRECT, PByte(plgi01), MAX_PREFERRED_LENGTH, dwEntriesRead, dwEntriesTotal); if NetApiStatus = NERR_SUCCESS then showmessage('messg ' + IntTostr(dwEntriesRead^)); for i := 0 to dwEntriesRead^ - 1 do begin gsl.Add(PLOCALGROUP_USERS_INFO_0(plgi01)^.lgrui0_name); Inc(Integer(plgi01), SizeOf(Pointer)); end; Result := (NetApiStatus = NERR_Success); NetAPIBufferFree(plgi01); if Result then Result := gsl.Find(grp, i); finally gsl.Free; end; end; //Add user to administrators group if Result then begin lgmi3.lgrmi3_domainandname := PChar(UserName); NetApiStatus := NetLocalGroupAddMembers(nil, PChar(grp), 3, @lgmi3, 1); if NetApiStatus <> NERR_Success then RaiseLastOSError(NetApiStatus); end; Result := (NetApiStatus = NERR_Success); try AddPrivilegeToAccount(UserName, 'SeServiceLogonRight'); except // showmessage('messg in an Excecpt'); end; end; end. Would appreciate if someone could kindly show me how I can call this function? Thanks in advance.

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  • Where can I find simple beta cdf implementation.

    - by Gacek
    I need to use beta distribution and inverse beta distribution in my project. There is quite good but complicated implementation in GSL, but I don't want to use such a big library only to get one function. I would like to either, implement it on my own or link some simple library. Do you know any sources that could help me? I'm looking for any books/articles about numerical approximation of beta PDF, libraries where it could be implemented. Any other suggestions would be also appreciated. Any programming language, but C++/C# preffered.

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  • Should I bundle C libraries with my Python application?

    - by oceanhug
    If I have a Python package that depends on some C libraries (like say the Gnu Scientific Library (GSL) for numerical computations), is it a good idea to bundle the library with my code? I'd like to make my package as easy to install as possible for users and I don't want them to have to download C libraries by hand and supply include-paths. Also I could always ensure that the version of the library that I ship is compatible with my code. However, is it possible that there are clashes if the user has the library installed already, or ar there any other reasons why I shouldn't do this? I know that I can make it easier for users by just providing a binary distribution, but I'd like to avoid having to maintain binary distributions for all possible OSs. So, I'd like to stick to a source distribution, but for the user (who proudly owns a C compiler) installation should be as easy as python setup.py install.

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  • C++ vs Matlab vs Python as a main language for Computer Vision Postgraduate

    - by Hough
    Hi all, Firstly, sorry for a somewhat long question but I think that many people are in the same situation as me and hopefully they can also gain some benefit from this. I'll be starting my PhD very soon which involve the fields of computer vision, pattern recognition and machine learning. Currently, I'm using opencv (2.1) C++ interface and I especially like its powerful Mat class and the overloaded operations available for matrix and image seamless operations and transformations. I've also tried (and implemented many small vision projects) using opencv python interface (new bindings; opencv 2.1) and I really enjoy python's ability to integrate opencv, numpy, scipy and matplotlib. But recently, I went back to opencv C++ interface because I felt that the official python new bindings were not stable enough and no overloaded operations are available for matrices and images, not to mention the lack of machine learning modules and slow speeds in certain operations. I've also used Matlab extensively in the past and although I've used mex files and other means to speed up the program, I just felt that Matlab's performance was inadequate for real-time vision tasks, be it for fast prototyping or not. When the project becomes larger and larger, many tasks have to be re-written in C and compiled into Mex files increasingly and Matlab becomes nothing more than a glue language. Here comes the sub-questions: For postgrad studies in these fields (machine learning, vision, pattern recognition), what is your main or ideal programming language for rapid prototyping of ideas and testing algorithms contained in papers? For postgrad studies, can you list down the pros and cons of using the following languages? C++ (with opencv + gsl + svmlib + other libraries) vs Matlab (with all its toolboxes) vs python (with the imcomplete opencv bindings + numpy + scipy + matplotlib). Are there computer vision PhD/postgrad students here who are using only C++ (with all its availabe libraries including opencv) without even needing to resort to Matlab or python? In other words, given the current existing computer vision or machine learning libraries, is C++ alone sufficient for fast prototyping of ideas? If you're currently using Java or C# for your postgrad work, can you list down the reasons why they should be used and how they compare to other languages in terms of available libraries? What is the de facto vision/machine learning programming language and its associated libraries used in your university research group? Thanks in advance.

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  • C++ vs Matlab vs Python as a main language for Computer Vision Research

    - by Hough
    Hi all, Firstly, sorry for a somewhat long question but I think that many people are in the same situation as me and hopefully they can also gain some benefit from this. I'll be starting my PhD very soon which involves the fields of computer vision, pattern recognition and machine learning. Currently, I'm using opencv (2.1) C++ interface and I especially like its powerful Mat class and the overloaded operations available for matrix and image operations and seamless transformations. I've also tried (and implemented many small vision projects) using opencv python interface (new bindings; opencv 2.1) and I really enjoy python's ability to integrate opencv, numpy, scipy and matplotlib. But recently, I went back to opencv C++ interface because I felt that the official python new bindings were not stable enough and no overloaded operations are available for matrices and images, not to mention the lack of machine learning modules and slow speeds in certain operations. I've also used Matlab extensively in the past and although I've used mex files and other means to speed up the program, I just felt that Matlab's performance was inadequate for real-time vision tasks, be it for fast prototyping or not. When the project becomes larger and larger, many tasks have to be re-written in C and compiled into Mex files increasingly and Matlab becomes nothing more than a glue language. Here comes the sub-questions: For carrying out research in these fields (machine learning, vision, pattern recognition), what is your main or ideal programming language for rapid prototyping of ideas and testing algorithms contained in papers? For computer vision research work, can you list down the pros and cons of using the following languages? C++ (with opencv + gsl + svmlib + other libraries) vs Matlab (with all its toolboxes) vs python (with the imcomplete opencv bindings + numpy + scipy + matplotlib). Are there computer vision PhD/postgrad students here who are using only C++ (with all its availabe libraries including opencv) without even needing to resort to Matlab or python? In other words, given the current existing computer vision or machine learning libraries, is C++ alone sufficient for fast prototyping of ideas? If you're currently using Java or C# for your research, can you list down the reasons why they should be used and how they compare to other languages in terms of available libraries? What is the de facto vision/machine learning programming language and its associated libraries used in your research group? Thanks in advance. Edit: As suggested, I've opened the question to both academic and non-academic computer vision/machine learning/pattern recognition researchers and groups.

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