I am actually new to matlab.
I am trying to run this matlab project in octave on my ubuntu machine. It has a function with name 'bm3d_thr' used in one of the files (line 342 of BM3D-Net/library/bm3d-denoising/BM3D.m file) as shown below:
y_hat = bm3d_thr(z, hadper_trans_single_den, Nstep, N1, N2, lambda_thr2D,...
lambda_thr3D, tau_match*N1*N1/(255*255), (Ns-1)/2, (sigma/255), thrToIncStep, single(Tfor), single(Tinv)', inverse_hadper_trans_single_den, single(thr_mask), Wwin2D, smallLN, stepFS );
Also I have the corresponding mex file (with name 'bm3d_thr.mexa64') in my octave path.
Issue is when i try to run the project(by saying 'demo'), it gives following error:
error: 'bm3d_thr' undefined near line 342 column 9
error: called from
BM3D at line 342 column 7
bm3d_net_res at line 5 column 7
demo at line 9 column 7
Can someone please help me to figure out what is going wrong here and make it work. I guess the problem is that mex file was not compiled on my machine but authors haven't provided the source code for this mex file.
Any help would be appreciated.
Thanks in advance.
Binary MEX files from Matlab are not compatible with Octave. You need to recompile all the MEX files in your project from source using Octave's mex or mkoctfile --mex commands.
If the authors have not provided the source for this MEX file, you are SOL. Post an Issue on their GitHub repo asking for the source code. And good luck. :)
Related
I am trying to use MATLAB in Colab. MATLAB is run in Colab through Octave. I have to use the MR8fast() filter, which in turn uses anigauss.c. I could successfully compile anigauss.c using
mkoctfile --mex -DMATLAB_MEX_FILE anigauss.c. anigauss.mex and anigauss.o files are created in the content folder in Colab. But while running the code which uses this function, its throwing an error
error: Invalid use of Script /content/anigauss.m in index expression
error: called from
MR8fast at line 20 column 13
How can I fix this error? Any help in this regard is greatly appreciated.
I have a script in matlab that calls other libraries. I use matlab version 2012a on linux . I get below error and I don't know how to fix it.
The error is :
Invalid MEX-file '/home/XXX/nearest_neighbors.mexa64':
libflann.so.1.8: cannot open shared object file: No such file or
directory
Error in flann_search (line 82)
[indices,dists] = nearest_neighbors('find_nn', data, testset, n, params);
Error in MyScript (line 73)
[nresult, ndists] = flann_search(Ntraindata', Ntraindata', resu.KNN, struct('algorithm','composite',...
That library you are referring to - https://github.com/mariusmuja/flann/ - has the nearest_neighbors function written in MEX code. MEX code is C code that is used to interface with MATLAB. People usually write heavily computationally burdening code over in MEX as it is known to handle loops and other things faster. The inputs come from MATLAB and are sent to this MEX function, and the outputs come from the MEX function and are piped back to MATLAB. It's basically a nice black box where you can use it just like any other MATLAB function. In fact, a lot of the functions that come shipped with MATLAB have MEX wrappers written to promote acceleration.
You are getting that error because you need to compile the nearest_neighbors function so that there is a MEX wrapper that can be called in MATLAB. That wrapper is missing because you haven't compiled the code.
First, you need to set up MEX. Make sure you have a compiler that is compatible with your version of MATLAB. You can do that by visiting this link:
http://www.mathworks.com/support/compilers/R20xxy/index.html
xx is the version number that belongs to your MATLAB and y is the character code that comes after it. For example, if you are using R2013a, you would visit:
http://www.mathworks.com/support/compilers/R2013a/index.html
Once you're there, go to your Operating System and ensure you have one of those supported compilers installed. Once you have that installed, go into MATLAB, and in the command prompt, type in:
mex -setup
This will allow you to set up MEX and choose the compiler you want. Given your error, you're using Linux 64-bit, so it should be very easy for you to get GCC. Just make sure that you choose a version of GCC that is compatible with your version of MATLAB. Once you choose the compiler, you can compile the code by doing this in the command prompt:
>> mex -v -O nearest_neighbors.cpp
This should generate the nearest_neighbors MEX file for you. Once that's done, you can now run the code.
For more detailed instructions, check out FLANN's user manual - http://people.cs.ubc.ca/~mariusm/uploads/FLANN/flann_manual-1.8.4.pdf - It tells you how to build and compile it for MATLAB use.
Good luck!
I've downloadad the SUN benchmark code from MIT:
version 2:
http://people.csail.mit.edu/jxiao/SUN/source_code/
Once I download the 15 image dataset and run the function:
compute_features.m
I get an Invalid MEX file error:
Invalid MEX-file
'/home/arturo/Documents/Virality/reddit_data/SUN_source_code_v2/code/OpenCVmexWrapper/cvlib_mex.mexa64':
libcv.so.1: cannot open shared object file: No such file or directory
The file /home/arturo/Documents/Virality/reddit_data/SUN_source_code_v2/code/OpenCVmexWrapper/cvlib_mex.mexa64 actually does exist, so I'm thinking the problem hast to do with libcv.so.1, or the .mexa64 file is broken (which is very unlikely)
I read something about adding a path via LD_LIBRARY_PATH when I googled the error, but I'm not sure what path I should exactly add, at least temporarily. I have opencv installed along with its library, so I'm not sure what the problem is. My current system is Ubuntu 12.04 64bit.
There's a similar question here, but the answer says that for their specific case they have the source code of the MEX files posted, which is not the same fortune I have: running old mex file on new matlab releases
Found the answer. The key is to link explicitly to the folder the file 'libcv.so.1' is in just before running matlab.
so in the matlab folder:
LD_LIBRARY_PATH=/home/arturDocuments/Virality/reddit_data/SUN_source_code_v2/code/scene_sun ./matlab
And in matlab:
matlab>> compute_feature
Compling the source code in the other folders is also necessary.(vlfeat,VOC,libsvm). As well as editing the path in the function im2superpixels # GeometricContext_dhoiem from :
segcmd = '../segment_pedro/segment 0.8 100 100';
to:
segcmd = '/YOUR_PATH/SUN_source_code_v2/code/segment_pedro/segment/ 0.8 100 100';
*(The folder is one level above.)
I'm using libvm-3.11. I downloaded it here and extracted. Then I set path in Matlab. After that whenever I run my program, it gives the same error always.
??? Invalid MEX-file 'E:\Gomu\Gomu General\final yr
Project\proj\libsvm-3.11\windows\svmtrain.mexw32': The specified module could not be found.
Error in ==> trysvm at 6
svmStruct = svmtrain(T,TrainMat,'showplot',true);
What should I do?
read the README file and compile the C files using mex. Mex files are platform/MATLAB version dependent. The binary download doesn't always work for everybody.
This is Subhash. I am having problem in linking fortran-matlab mex files.
I am running MATLAB R2010a. I am trying to mex fortran subroutines in MATLAB. I have installed MSYS, MinGW and gfortran. I have also downloaded and extracted gnumex in the c:\documents\MATLAB folder. I entered gnumex to run the installation settings.
At this point, I see a window pop-up and I entered the following:
MinGW's root directory ---> Pointed towards c:\mingw b) Cygwin's
root directory -----> left blank c)
Path to g95.exe ------> c:\mingw\bin
path to gfortran.exe ------> c:\program files\gfortran\bin e)
path to gnumex utilities ------> c:\users.....\matlab\gnumex
environment linking type ------> MinGW
generate mex dll or engine-----> mex
language for compilation -------> fortran 77
add stub ------> no
optimization level -----> -O3
path for libraries and .def files
c:\users...\Roaming\MathWorks\MATLAB\R2010a\gnumex
Mex options file to create:
c\users...\Roaming\MathWorks\MATLAB\R2010a\mexopts.bat
The above is my installation setup for mex with gnumex. When I hit make options file, an warning message pops out which says
" cannot corret mex.pl .....
"cannot open c:...\R2010a\bin\mex.pl for writing"
and when I hit ok, again it pops out saying to confirm overwrite of mexopts.bat .
I hit confirm and the opt file is created.
At this point I should have my mex setup ready. But, when I run the fortran mex examples xtimesy.f, etc.. ( I use mex filename.f at the command prompt) and I get the following error
g77: getValidInputLinkLibraries: No such file or directory
c:\prog~1\MATLAB\R2010A\BIN\MEX.PL: Error: Link of 'xtimesy.mexw32' failed.
Error using ---> mex at 222
unable to complete successfully.
I tried this uninstalling several times, but ended up with the same error.
Could anyone please let me know where am I going wrong. Is this not the correct procedure to link the g77? Please throw some light on this.
I appreciate your time..
Thanks.
I recently tried to mex some fortran routines and failed due to the poor support for fortran compilers by matlab in windows. I got around the problem by using f2c to convert the fortran to C code, then creating a gateway routine in C which calls the automatically generated C code functions and mexing the resul using the visual studio 2008 compiler which integrates nicely with matlab (the free express edition version is sufficient, you will also be able to use it for debugging).
You can get f2c from http://www.netlib.org/f2c/. You must link the produced C code to the f2c library, which you may also have to build from the sources.
I know this all sounds very complicated, but it was easiest solution I found.