Re: how to make mexbiosig work on mxe-octave

[Alois Schlögl]

On 5/10/19 1:51 PM, JohnD wrote:
>
>> -----Original Message-----
>> From: Alois Schloegl [mailto:address@hidden
>> Sent: Friday, May 10, 2019 5:15 AM
>> To: JohnD; address@hidden
>> Subject: Re: how to make mexbiosig work on mxe-octave
>>
>> On 09.05.19 19:45, JohnD wrote:
>>>
>>>> -----Original Message-----
>>>> From: Alois Schlögl [mailto:address@hidden
>>>> Sent: Sunday, May 05, 2019 5:36 PM
>>>> To: JohnD; address@hidden
>>>> Subject: Re: how to make mexbiosig work on mxe-octave
>>>>
>>>> On 5/3/19 5:48 PM, JohnD wrote:
>>>>>> -----Original Message-----
>>>>>> From: Alois Schlögl [mailto:address@hidden
>>>>>> Sent: Friday, May 03, 2019 11:22 AM
>>>>>> To: JohnD; address@hidden
>>>>>> Subject: Re: how to make mexbiosig work on mxe-octave
>>>>>>
>>>>>> On 01.05.19 22:12, JohnD wrote:
>>>>>>>> ------------------------------
>>>>>>>>
>>>>>>>> Message: 2
>>>>>>>> Date: Wed, 1 May 2019 01:20:49 +0200
>>>>>>>> From: Alois Schl?gl <address@hidden>
>>>>>>>> To: <address@hidden>
>>>>>>>> Subject: how to make mexbiosig work on mxe-octave
>>>>>>>> Message-ID: <3780f755-22ea-4001-b7c8-
>>>>>> address@hidden>
>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>
>>>>>>>>
>>>>>>>> Dear maintainers of MXE-OCTAVE,
>>>>>>>>
>>>>>>>>
>>>>>>>> mexbiosig [1] is a mex-file for loading about 50 different Biosig
>>>>>>>> data formats [2] into octave. mexbiosig can than be installed in
>>>>>>>> octave with
>>>>>> ?
>>>>>>>>     pkg install mexbiosig-X.Y.Z.src.tar.gz
>>>>>>>>
>>>>>>>> but requires that? libbiosig [1] is available on the host platform.
>>>>>>>> libbiosig for windows can be compiled with mxe [3,4,5]. I tried to
>>>>>>>> compile libbiosig within mxe-octave. However, this was not
>>>>>>>> successful (I just copied src/libbiosig.mk from [5] into a recent
>>>>>>>> mxe-octave directory and tried to run "make libbiosig" in the same
>>>>>>>> way as I used to this
>>>>>> mxe.
>>>>>>>> It fails with the message "make: *** No rule to make target
>>>>>>>> 'libbiosig'.? Stop."
>>>>>>>>
>>>>>>>> Therefore, I'm asking:
>>>>>>>>
>>>>>>>> 1) how to compile libbiosig within mxe-octave ? What do I miss here ?
>>>>>>>>
>>>>>>>> 2) would you consider including libbiosig into the official
>>>>>>>> mxe-octave repository ? What is needed to include this in Octave
>>>>>>>> for
>>>>>> windows ?
>>>>>>>> The procedure to install mexbiosig in Octave is working fine on?
>>>>>>>> Linux and macOS through homebrew. It would be great if mexbiosig
>>>>>>>> could be also provided to Octave users on Windows. Could you help
>>>>>>>> me with
>>>>>> that ?
>>>>>>>> Best regards,
>>>>>>>>
>>>>>>>> ? Alois
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [1] http://biosig.sourceforge.net/download.html
>>>>>>>>
>>>>>>>> [2] http://pub.ist.ac.at/~schloegl/biosig/TESTED
>>>>>>>>
>>>>>>>> [3] https://mxe.cc/
>>>>>>>>
>>>>>>>> [4] https://github.com/schloegl/mxe
>>>>>>>>
>>>>>>>> [5] https://github.com/schloegl/mxe/blob/master/src/libbiosig.mk
>>>>>>>>
>>>>>>>>
>>>>>>>> -------------- next part -------------- An HTML attachment was
>>>>>>>> scrubbed...
>>>>>>> Looks like from biosig4c++, you should be running make -f
>>>>>>> Makefile.win32 It currently fails in the build though with error:
>>>>>>> conflicting types for 'sopen'
>>>>>>>
>>>>>> Dear John,
>>>>>>
>>>>>>
>>>>>> Yes, it's possible to cross-compile libbiosig on linux for windows.
>>>>>> Usually, I do this with mxe.
>>>>>>    git clone https://github.com/schloegl/mxe.git
>>>>>>    cd mxe
>>>>>>    make libbiosig
>>>>>>
>>>>>> The approach if "make -f Makefile.win32" is not supported anymore,
>>>>>> but should be replaced with something like
>>>>>>     TARGET=$(TARGET) CROSS=$(TARGET) make libbiosig
>>>>>>
>>>>>> Currently, I'm trying with the attached makefile which I put into
>>>>>>     mxe-octave/src/libbiosig.mk
>>>>>> and apply to attached patch
>>>>>>
>>>>>> When trying to run
>>>>>>     mxe-octave$ make libbiosig
>>>>>> it does not do much. Any idea what else is needed ?
>>>>>>
>>>>>>
>>>>>> Best, Alois
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> Im assuming you ran configure in the mxe-octave directory and its not
>> issues
>>>> with that.
>>>>
>>>> I was not aware about the need to run configure (thanks for the hint).
>>>>
>>>> And yes is does not show any issues.
>>>>
>>>>
>>>>> Mxe-octave was based on an older version of mxe, where I believe there
>> was
>>>> only a PKG_BUILD target being called, so you need to create a section for:
>>>>> define $(PKG)_BUILD
>>>>> endef
>>>>>
>>>>> and in it call the correct target build
>>>>>
>>>>>
>>>>> Some of the dependencies you have haven't been built in a long time, so
>> may
>>>> be rather out of date, or no longer compile in mxe-octave, but I guess you
>> will
>>>> find that out soon enough if that’s the case.
>>>>
>>>>
>>>> The attached patches and make file compiles libbiosig v1.9.4 . I had to
>> disable
>>>> dicom waveform support, but libbiosig will still be quite useful.
>>>>
>>>> Could you include these in mxe-octave ?
>>>>
>>>>
>>>> Cheers,
>>>>
>>>>    Alois
>>>>
>>>
>>>
>>> That’s still  didn’t work for me in mxe-octave, however I managed to get
>> something working for em and pushed:
>>> https://hg.octave.org/mxe-octave/rev/01ced4433575
>>>
>>>
>>
>> Dear John D.,
>>
>>
>> looks good to me. For testing this, the following commands should run
>> without error:
>>
>> %%% installing mexbiosig %%%
>> pkg install
>> https://pub.ist.ac.at/~schloegl/biosig/prereleases/mexbiosig-1.9.4.src.tar.gz
>>
>> %%% load mexbiosig %%%
>> pkg load mexbiosig
>>
>> %%% check mexSLOAD - it shows how to use mexSLOAD %%%
>> mexSLOAD
>>
>> %%% load data [1] using mexSLOAD %%%
>> [s,HDR]=mexSLOAD('SC4002E0-PSG.edf');
>>
>> % this fails for me when I build mxe-octave and run it on Windows
>> plot(s(1:1e5,1))
>>
>>
>>
>>
>> Best,
>>    Alois
>>
>>
>>
>> [1]
>> https://alpha.physionet.org/static/published-projects/sleep-edfx/1.0.0/sleep-
>> cassette/SC4002E0-PSG.edf
>>
>>
>>
> I had verified pkg install worked butb was nt sure on the functions, but this 
> works for me in dev octave 5.1.1:
>
>>> [s,HDR]=mexSLOAD('SC4002E0-PSG.edf');
> ERROR 3: Error SOPEN(READ); Cannot open file.
>
>>> urlwrite 
>>> ('https://physionet.org/pn6/sleep-edfx/sleep-cassette/SC4002E0-PSG.edf', 
>>> 'SC4002E0-PSG.edf')
>>> [s,HDR]=mexSLOAD('SC4002E0-PSG.edf');
> Warning mexSLOAD: Overflowdetection not supported in file SC4002E0-PSG.edf


That is ok. The warning is expected for this type of file. The warning
can be disabled with

[s,HDR]=mexSLOAD('SC4002E0-PSG.edf',0,'OVERFLOWDETECTION:OFF');



Attached is a version for building libbiosig.dll. I guess, this might be useful 
in mxe-octave. 




Cheers,
   Alois

libbiosig.mk
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