[Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to Read MAT Files

Thu Mar 26 16:52:12 CET 2015

It turns out this wasn't really a Rcpp issue, but I want to post the
solution, in case someone stumbles on this thread while trying to use the
MAT-file API with MinGW. It turns out I was just linking against the wrong
libraries. My original library directory was
C:/MATLAB2013a/extern/lib/win64/microsoft,
but the correct one is C:/MATLAB2013a/bin/win64. (Where "C:/MATLAB2013a"
should be replaced by the root of your MATLAB installation.)

- Elliot

On Wed, Mar 25, 2015 at 12:57 PM, Elliot Joel Bernstein <ejb6 at cornell.edu>
wrote:

> John -
>
> One quick follow-up about the warnings: I think they have to do with
> loading cell arrays. Basically, all the actual data ends up in the #refs#
> field, in what seems like an arbitrary order, and the field that should
> contain the data is all NAs. Do you know if there's any way to get around
> that? I think all the cell arrays being saved contain only strings, so I
> can change things in MATLAB to save them as char arrays if necessary.
>
> Thanks.
>
> - Elliot
>
> On Wed, Mar 25, 2015 at 12:26 PM, Elliot Joel Bernstein <ejb6 at cornell.edu>
> wrote:
>
>> John -
>>
>> Thanks for the suggestions. I tried taking not only Rcpp but R out of the
>> loop, and just compiling from the command line with MinGW. That crashed as
>> well, so I think there's probably a compatibility issue with MATLAB's API
>> and MinGW. I'll contact Mathworks tech support to try and get some help
>> with that.
>>
>> Regarding v7.3...my files aren't all v7.3, but I could definitely save
>> them all that way, which might be the easiest solution. I tried what you
>> suggested with some of my real data files, which contain two variables
>> each: a matrix and a struct. I get the following warnings:
>>
>> > data <- h5dump("z:/temp/test73.mat", bit64conversion='double')
>> Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
>> by NA's
>> Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
>> by NA's
>> Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced
>> by NA's
>>
>> The data look OK, as far as I can tell. (The matrix is 411x30927, so it's
>> not like I can check every element, but I don't see anything obviously
>> wrong.) In addition to the two variables I was expecting, the result has
>> two additional elements, #refs# and #subsystem. I'm not actually sure how
>> to see what they contain, since the names include the comment character.
>> Can I safely ignore those warnings?
>>
>> Thanks.
>>
>> - Elliot
>>
>>
>> On Wed, Mar 25, 2015 at 11:09 AM, John Buonagurio <
>> jbuonagurio at exponent.com> wrote:
>>
>>> Elliot,
>>>
>>> How are you building the executable? Did you make sure to include all
>>> dependencies in the search path (run depends.exe against libmat.dll and
>>> libmx.dll)? Did you make sure to set the appropriate architecture e.g. -m64
>>> in CFLAGS? I don't have access to the MAT-File libraries to test this
>>> myself.
>>>
>>> Start simple and take Rcpp out of the equation. Call matOpen from a
>>> simple C function with type void. Does it work with dyn.load() and .C()?
>>>
>>> If you are *only* working with v7.3 files which are based on HDF5, you
>>> may be able to avoid this issue and access them using rhdf5:
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("rhdf5")
>>> library(rhdf5)
>>> h5dump("file.mat", load=FALSE)
>>>
>>> John
>>>
>>> From: rcpp-devel-bounces at lists.r-forge.r-project.org [mailto:
>>> rcpp-devel-bounces at lists.r-forge.r-project.org] On Behalf Of Elliot
>>> Joel Bernstein
>>> Sent: Wednesday, March 25, 2015 9:28 AM
>>> To: Dale Smith
>>> Cc: xian at unm.edu; rcpp-devel at lists.r-forge.r-project.org
>>> Subject: Re: [Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to
>>> Read MAT Files
>>>
>>> Dale -
>>>
>>> Thank you for the suggestion. I have MATLAB and the MATLAB libraries,
>>> and I am not looking to redistribute anything. I just have a lot of data in
>>> MAT files that I would like to be able to load analyze in R. I am able to
>>> compile and link against the MATLAB libraries, but the code crashes when I
>>> run it. I looked into the Octave FAQ. It looks like they don't handle v7.3
>>> files either, and I don't think they provide an API that I could access
>>> from R/C++.
>>>
>>> - Elliot
>>>
>>> On Wed, Mar 25, 2015 at 8:36 AM, Dale Smith <DSmith at nexidia.com> wrote:
>>> mat.h is a header file which comes with MATLAB. I don't think the
>>> license allows redistribution, and you would not be able to compile without
>>> the MATLAB libraries.
>>>
>>> An alternative may be Octave since it will read .mat files. Perhaps
>>> someone can email the name of the header file used from the Octave
>>> distribution?
>>>
>>>
>>> http://stackoverflow.com/questions/9915658/how-do-you-open-mat-files-in-octave
>>>
>>> This also offers a viable way to test this type of code for those who
>>> don't have MATLAB.
>>>
>>> Dale Smith, Ph.D. | Data Scientist | nexidia | office: +1 404 495 7220
>>> ext 4008 | fax: +1 404 495 7221 | nexidia.com
>>>
>>>
>>> -----Original Message-----
>>> From: rcpp-devel-bounces at lists.r-forge.r-project.org [mailto:
>>> rcpp-devel-bounces at lists.r-forge.r-project.org] On Behalf Of Christian
>>> Gunning
>>> Sent: Wednesday, March 25, 2015 8:08 AM
>>> To: rcpp-devel at lists.r-forge.r-project.org
>>> Subject: [Rcpp-devel] R.e. Using Rcpp and MATLAB MAT-File API to Read
>>> MAT Files
>>>
>>> Can you provide a link to the mat.h file referenced in the source (which
>>> I assume is the same as the API mentioned below)?
>>>
>>> Also, see Dirk's comments about compilers here:
>>> http://stackoverflow.com/questions/10723165/using-visual-c-with-r
>>> and here:
>>> dirk.eddelbuettel.com/code/rcpp/Rcpp-FAQ.pdf
>>>
>>> Best,
>>> Christian
>>>
>>> > I'm trying to use the MATLAB Mat-File API to read data from MAT files
>>> > into R. (I've tried using the R.matlab package, but the matrices I'm
>>> > loading can be very large, and that method was too slow. In addition,
>>> > some of the files I'm loading are v7.3 MAT files, which are not
>>> > supported by the package.) I wrote the following simple function to
>>> > start testing. It works fine if I compile without the Rcpp parts in
>>> > Visual Studio (i.e. I can call matOpen and get a nonzero pointer), but
>>> > when I run in R it crashes my R session without displaying "Test".
>>> >
>>> > #include <Rcpp.h>
>>> > #include "mat.h"
>>> >
>>> > using namespace Rcpp;
>>> >
>>> > // [[Rcpp::export]]
>>> > NumericVector rcpp_mat_load() {
>>> >
>>> >     MATFile* mf = matOpen("z:/temp/test.mat", "r");
>>> >     printf("Test\n");
>>> >     double val = 10;
>>> >     NumericVector y = NumericVector::create(val);
>>> >     return y;
>>> > }
>>>
>>> --
>>> A man, a plan, a cat, a ham, a yak, a yam, a hat, a canal – Panama!
>>> _______________________________________________
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>>>
>>
>
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