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On Tue, Nov 13, 2018 at 11:58 AM Flandin, Guillaume <[log in to unmask]> wrote:

Hi Arnold,

That's some progress... If you run the following:
dat = file_array('test.dat',[1 1],'FLOAT32-LE',352);
dat(1) = 1;
dat(1)
and the first two lines are executed without error (i.e. it created a
file test.dat of 356 bytes) then it means that you don't observe the
error you initially reported any more (that concerned mat2file).

Now the error you have when running the third line means that there is
an issue with file2mat... Could you comment lines 92,98-100 here:
https://github.com/andersonwinkler/PALM/blob/master/fileio/%40file_array/subsref.m#L92-L100
in case a more interesting error message is displayed?

Best regards,
Guillaume.

On 13/11/2018 17:14, Arnold Evia wrote:
>
> Thanks, that fixed that issue.
>
> When I type the final command "dat(1)", this error appears:
>>> dat(1)
> error: multifile2mat: =: nonconformant arguments (op1 is 1x1, op2 is 0x0)
> error: called from
>     subsref>multifile2mat at line 179 column 26
>     subsref>subfun at line 99 column 7
>     subsref at line 65 column 7
>
> Best,
> Arnold
>
>
> On Tue, Nov 13, 2018 at 4:13 AM Flandin, Guillaume <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Arnold,
>
> Thanks, this is useful. This time, I think you came across an Octave bug
> that was fixed in the latest version, 4.4.1:
>    https://savannah.gnu.org/bugs/?53856
> A workaround would be to delete mat2file.m, file2mat.m and init.m from
> @file_array/private. Could you try to do this, restart Octave and let us
> know what the error message is afterwards?
>
> Best regards,
> Guillaume.
>
>
> On 13/11/2018 08:26, Arnold Evia wrote:
> > Hello Guillaume,
> >
> > I ran the commands that you used to reinstall octave,
> liboctave-dev, and
> > PALM.
> > I also ran mkoctfile on all three .c files, and confirmed that the mex
> > files exist.
> > After that, there are some differences in our setup. In my setup, I am
> > using Octave 4.2.2 and gcc 5.5.
> >
> > I tried the commands you used, and "dat(1) = 1;" returns this:
> > error: mat2file.c not compiled - see Makefile
> > error: called from
> >     mat2file at line 16 column 1
> >     subsasgn>subfun at line 164 column 5
> >     subsasgn at line 88 column 9
> >
> > I don't know why it's a different error.
> > What do you advise for this error?
> >
> > Best,
> > Arnold
> >
> >
> > On Fri, Nov 9, 2018 at 6:46 AM Flandin, Guillaume
> <[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
> >
> > Hi Arnold,
> >
> > I don't think I can understand what is going on without
> reproducing the
> > error. You mentioned using Ubuntu 16.4 so I set up a Docker
> container
> > with stock Octave:
> >
> > ========= Dockerfile =========
> > FROM ubuntu:16.04
> >
> > RUN apt-get update && apt-get -y install \
> >   octave liboctave-dev git
> >
> > RUN git clone https://github.com/andersonwinkler/PALM.git \
> >   && cd /PALM/fileio/@file_array/private \
> >   && rm *.mex* *.o \
> >   && mkoctfile --mex file2mat.c \
> >   && mkoctfile --mex mat2file.c \
> >   && mkoctfile --mex init.c
> >
> > ENTRYPOINT ["octave"]
> > ==============================
> >
> > This contains Octave 4.0.0 and gcc 5.4.0. I run the following:
> >    docker build -t palm/oct .
> >    docker run -ti palm/oct
> > and at the Octave prompt, I type:
> >    cd /PALM/fileio;
> >    dat = file_array('test.dat',[1 1],'FLOAT32-LE',352);
> >    dat(1) = 1;
> >    dat(1)
> >
> > My understanding from the email exchange with Melanni is that
> the code
> > above triggers the error "mat2file: Can not yet write logical
> data." but
> > it works here. Is there any difference you can think of
> between this and
> > your current installation?
> >
> > Best regards,
> > Guillaume.
> >
> >
> > On 08/11/2018 20:38, Arnold Evia wrote:
> > > Hello Guillaume and Melanni,
> > >
> > > I already had liboctave-dev installed.
> > > I reinstalled it and ran the commands, and still have the
> same issue.
> > >
> > > Best,
> > > -Arnold
> > >
> > > On Tue, Nov 6, 2018 at 6:28 AM Flandin, Guillaume
> > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>> wrote:
> > >
> > > Hi Arnold and Melanni,
> > >
> > > I still cannot make sense of the errors you report. In order
> > to compile
> > > MEX files for Octave, you indeed need to install
> > liboctave-dev, which
> > > will provide the mkoctfile command.
> > >
> > > In a terminal (not within Octave), do the following:
> > > * cd PALM/fileio/@file_array/private/
> > > * rm *.mex*
> > > * mkoctfile --mex file2mat.c
> > >    mkoctfile --mex mat2file.c
> > >    mkoctfile --mex init.c
> > > This should have created three files with a .mex extension.
> > >
> > > Run Octave/PALM and let us know what happens.
> > >
> > > Best regards,
> > > Guillaume.
> > >
> > >
> > > On 01/11/2018 18:50, melanni nanni wrote:
> > > > Hi Arnold,
> > > >
> > > > I also observed that it was a mkoctfile dependent on
> the version
> > > of gcc
> > > > in my case, I installed liboctave-dev, then compile it
> from
> > terminal.
> > > >
> > > > Best,
> > > >
> > > > Melanni
> > > >
> > > >
> > >
> >
>    ------------------------------------------------------------------------
> > > > *De:* FSL - FMRIB's Software Library
> <[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>> en
> > nombre de
> > > > Arnold Evia <[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
> > > > *Enviado:* jueves, 1 de noviembre de 2018 07:19 p. m.
> > > > *Para:* [log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > > *Asunto:* Re: [FSL] Error in mat2file using Palm
> > > >
> > > > I am compiling for Octave on Ubuntu 16.04. When I
> compiled the
> > > file for
> > > > Octave in the terminal, compilation completed with no
> errors or
> > > > warnings, and I still had the problem.
> > > > I also tried compiling without the 'platform=octave'
> tag, hoping
> > > to get
> > > > some information on what could be going wrong.
> > > >
> > > > -Arnold
> > > >
> > > >
> > > > On Thu, Nov 1, 2018 at 7:28 AM Flandin, Guillaume
> > > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>> wrote:
> > > >
> > > > Hi Arnold,
> > > >
> > > > Are you compiling for MATLAB or Octave? The issue
> > observed by
> > > Melanni
> > > > was with Octave. Here you are compiling with mex
> from the
> > > terminal, so
> > > > it is aiming at compiling for MATLAB (*.mexa64).
> > > > Also, which version of Ubuntu are you using?
> > > >
> > > > Best regards,
> > > > Guillaume.
> > > >
> > > >
> > > > On 31/10/2018 19:59, Arnold Evia wrote:
> > > > > Compiling the file using terminal didn't make a
> > difference.
> > > > > Still observe the same behavior.
> > > > >
> > > > > I tried compiling without the platform tags,
> and got the
> > > > following result:
> > > > >
> > > > > rm -f file2mat.mexa64 mat2file.mexa64 init.mexa64
> > > > > mex -O -largeArrayDims file2mat.c
> > > > > Building with 'gcc'.
> > > > > Warning: You are using gcc version '5.5.0'. The
> version of
> > > gcc is not
> > > > > supported. The version currently supported with
> MEX is
> > > '6.3.x'. For a
> > > > > list of currently supported compilers see:
> > > > >
> > https://www.mathworks.com/support/compilers/current_release
> > > >
> > >
> >
>     <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > > > > MEX completed successfully.
> > > > > mex -O -largeArrayDims mat2file.c
> > > > > Building with 'gcc'.
> > > > > Warning: You are using gcc version '5.5.0'. The
> version of
> > > gcc is not
> > > > > supported. The version currently supported with
> MEX is
> > > '6.3.x'. For a
> > > > > list of currently supported compilers see:
> > > > >
> > https://www.mathworks.com/support/compilers/current_release
> > > >
> > >
> >
>     <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > > > > MEX completed successfully.
> > > > > mex -O -largeArrayDims init.c
> > > > > Building with 'gcc'.
> > > > > Warning: You are using gcc version '5.5.0'. The
> version of
> > > gcc is not
> > > > > supported. The version currently supported with
> MEX is
> > > '6.3.x'. For a
> > > > > list of currently supported compilers see:
> > > > >
> > https://www.mathworks.com/support/compilers/current_release
> > > >
> > >
> >
>     <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > > > > MEX completed successfully.
> > > > >
> > > > > Is mkoctfile dependent on the version of gcc?
> > > > > If so, then I will try again after updating gcc.
> > > > >
> > > > > Arnold M. Evia, Ph.D.
> > > > > Senior Research Associate
> > > > > Department of Biomedical Engineering
> > > > > Medical Imaging Research Center
> > > > > Illinois Institute of Technology
> > > > > http://www.iit.edu/~mri/
> > > >
> > >
> >
>     <https://nam04.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.iit.edu%2F~mri%2F&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=JhxZ6Y0BLpowwAZsauK6yOmJj%2FfMD2wWCPDUhPQYxvY%3D&reserved=0>
> > > > >
> > > > >
> > > > > On Wed, Oct 31, 2018 at 7:37 AM Flandin, Guillaume
> > > > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
> > > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>>> wrote:
> > > > >
> > > > > Hi Arnold,
> > > > >
> > > > > Thanks, we went down the same road with Melanni
> > last week,
> > > > and, while I
> > > > > am still trying to understand what the
> problem is
> > (somehow
> > > > related to
> > > > > memory alignment), the issue was disappearing if
> > the MEX
> > > file were
> > > > > compiled from a terminal:
> > > > >    mkoctfile --mex mat2file.c
> > > > > instead of invoking mex() within octave:
> > > > >    mex mat2file.c
> > > > > It shouldn't make any difference (check the
> source
> > code of
> > > > mex.m) but
> > > > > apparently it does... I would be curious if
> you can
> > > reproduce
> > > > the same
> > > > > phenomenon.
> > > > >
> > > > > Best regards,
> > > > > Guillaume.
> > > > >
> > > > >
> > > > > On 30/10/2018 21:33, Arnold Evia wrote:
> > > > > > Hello Guillaume and Melanni,
> > > > > >
> > > > > > I am also having the same issue as Melanni
> using
> > PALM
> > > in Ubuntu.
> > > > > > I tried the commands that you suggested,
> and got the
> > > same output
> > > > > as Melanni.
> > > > > >
> > > > > > After some debugging, I may have found a
> clue as
> > to what's
> > > > happening.
> > > > > > In mat2file.c, I placed a few print statements
> > for some
> > > > variables
> > > > > right before the error message (line 252):
> > > > > >
> > > > > > printf("code = %d\n",map->dtype->code);
> > > > > > printf("bits = %d\n",map->dtype->bits);
> > > > > > printf("channels =
> %d\n",map->dtype->channels);
> > > > > >
> > > > > > if (map->dtype == NULL)
> > > mexErrMsgTxt("Unrecognised
> > > > > 'dtype' value.");
> > > > > > if (map->dtype->bits % 8)
> mexErrMsgTxt("Can
> > > not yet
> > > > write
> > > > > logical data.");
> > > > > > if (map->dtype->channels != 1)
> mexErrMsgTxt("Can
> > > not yet
> > > > write
> > > > > complex data.");
> > > > > >
> > > > > > The program returned unusual numbers:
> > > > > >
> > > > > > code = 16
> > > > > > bits = 32726
> > > > > > channels = 7
> > > > > > Error using subsasgn>subfun
> > > > >
> > > >
> > >
> >
>      ([log in to unmask]:168)
> > > > > > mat2file: Can not yet write logical data.
> > > > > >
> > > > > > Running the program again with the same
> parameters,
> > > values for
> > > > > code and channels stays constant, but the value
> > for bits
> > > would
> > > > change:
> > > > > >
> > > > > > code = 16
> > > > > > bits = 32696
> > > > > > channels = 7
> > > > > > Error using subsasgn>subfun
> > > > >
> > > >
> > >
> >
>      ([log in to unmask]:168)
> > > > > > mat2file: Can not yet write complex data.
> > > > > >
> > > > > > As you can see, sometimes bits will be
> divisible
> > by 8,
> > > and the
> > > > > program returns a different error.
> > > > > > There is a table in the script that
> defines the
> > values
> > > for bits,
> > > > > and channels for a specific code.
> > > > > > In this case, bits should be 32, and channels
> > should be 1.
> > > > > > I don't know why bits and channels are
> being set to
> > > incorrect
> > > > > values, and I hope this sheds some light.
> > > > > >
> > > > > > -Arnold Evia
> > > > > >
> > > > >
> > > > > --
> > > > > Guillaume Flandin, PhD
> > > > > Wellcome Centre for Human Neuroimaging
> > > > > UCL Queen Square Institute of Neurology
> > > > > London WC1N 3BG
> > > > >
> > > >
> > > > --
> > > > Guillaume Flandin, PhD
> > > > Wellcome Centre for Human Neuroimaging
> > > > UCL Queen Square Institute of Neurology
> > > > London WC1N 3BG
> > > >
> > > >
> > > >
> > >
> >
>    ------------------------------------------------------------------------
> > > >
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> > > >
> > >
> >
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> > > >
> > > >
> > > >
> > > >
> > >
> >
>    ------------------------------------------------------------------------
> > > >
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> > > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> > > >
> > >
> > > --
> > > Guillaume Flandin, PhD
> > > Wellcome Centre for Human Neuroimaging
> > > UCL Queen Square Institute of Neurology
> > > London WC1N 3BG
> > >
> > >
> >
>    ########################################################################
> > >
> > > To unsubscribe from the FSL list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> > >
> > >
> > >
> >
>   ------------------------------------------------------------------------
> > >
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> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> > >
> >
> > --
> > Guillaume Flandin, PhD
> > Wellcome Centre for Human Neuroimaging
> > UCL Queen Square Institute of Neurology
> > London WC1N 3BG
> >
> >
>   ########################################################################
> >
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> >
> >
> >
> ------------------------------------------------------------------------
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> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG
>
> ########################################################################
>
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--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG

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