[Insight-users] Insight-users Digest, Vol 62, Issue 111

[Darren Weber]

On Tue, Jun 30, 2009 at 1:20 AM, Daniel James White <white at mpi-cbg.de>wrote:

> Hi Darren and All,
>
>>
>>  Hi Darren,
>>>
>>> I'm a little puzzled by the farsight build wiki.  It appears to be
>>> nothing
>>>
>>>> more than an ITK build, so what's special about "farsight" that it
>>>> should be
>>>> identified as something more than Insight (ITK)?
>>>>
>>>>
>>> FARSIGHT is an effort to provide an image analysis toolkit for
>>> microscopy,
>>> based on ITK. There is an (incomplete) list of modules included in
>>> FARSIGHT
>>> listed at:
>>>
>>>  http://www.farsight-toolkit.org/wiki/Table_of_Contents
>>>
>>> It is still very early days for FARSIGHT, with the SVN repository just
>>> opening up in recent weeks, so everything is still pretty rough around
>>> the
>>> edges.
>>>
>>> Badri Roysam, the head of the project, can comment further on goals and
>>> directions if you are interested.
>>>
>>>
>>
>> I am working with microscopy data also, so I will keep an eye on this
>> while
>> I'm working with this data.
>>
>> Have you looked at the BioImageXD development?  I wonder if your work will
>> benefit from more collaboration on that front.  Although I read in another
>> thread that they want to move to java, instead of a python platform.  BTW,
>> the MacPort for InsightToolkit wraps in java, but I've not tested any of
>> that wrapping to see if it works.
>>
>> I take it that most of the FARSIGHT work will be in python, and the
>> MacPort
>> for InsightToolkit does use WrapITK with python25 (it should be fairly
>> easy
>> to provide python26 or python3x wrapping whenever they are reliable or
>> preferred platforms).
>>
>>
> Its true that the medium long term plan is to move / rebuild from scratch
> BioImageXD using java
> wrapping.
>
> That said the current python version is under very active development right
> now,
> with a release for windows 32 bit comming pretty soon as we fgix the las
> bugs.
>
> The OSX version is proving more problematic as we are struggling to get
> py2app to build a working 32bit OSX .app bundle.
> We have a developer on that task, but nay tips would be welcome!
>

I don't know for sure.  Maybe you can check some of the MacPort software to
find a similar package and see how it works.  Maybe wxMaxima or something
that is using wxPython.



>
>>  As for OSX, there are no build instructions (most of the linux
>>> instructions
>>>
>>>> might apply, but actually it's a lot more complicated because OSX can an
>>>> rpath nightmare when it comes to shared libs).  I think the entire
>>>> farsight
>>>> build wiki could be replaced, for OSX, with a one line MacPorts command:
>>>>
>>>> sudo port install InsightToolkit
>>>>
>>>> This will probably do everything at all stages identified on this wiki
>>>> thread:
>>>>
>>>>
>>> As far as compililng ITK, yes, if the MacPorts version of ITK includes
>>> the
>>> CableSWIG stuff with WrapITK. (My understanding is that FARSIGHT needs
>>> that
>>> for its Python interface.)
>>>
>>> There are still more instructions to be written on compiling FARSIGHT
>>> itself, once all the dependencies are set up.
>>>
>>>
>>
> in BioImageXD we have ben using custom VTK and ITK builds (using Wrap ITK)
> and we have custom kits for VTK and ITK that link to those.
>
> We would like to be able to use a mac ports build of VTK and ITK
> as it would make life simpler, but i dint know if that will work for us or
> not,
> i never tried.
>


Please give it a try, if you can.  It would make porting BXD a lot easier.
Using custom VTK and ITK builds will make a port for BXD a huge, very time
consuming build on MacPorts.  It would have to replicate all the work of the
VTK and ITK ports and then some.  I guess you arrived at this point for a
windows development environment where your goal is to build once on your
local dev system and then distribute binary builds (maybe static builds).
The shared lib approach is more efficient in an open-source distribution
(MacPorts, Debian, etc.), but it's a bit more difficult to manage
development dependencies.



>> Ah, ha.  I look forward to learning more about this.  Wherever possible,
>> I'll try to provide support for release versions in MacPorts.  I will need
>> to know more about your development process and dependencies.  If you
>> develop with any release version of ITK as a dependency, that will be easy
>> to define as a dependency for a FARSIGHT port in MacPorts and it will then
>> inherit all the dependencies of ITK (the InsightToolkit port).  For
>> example:
>>
>> $ port deps InsightToolkit
>> InsightToolkit has build dependencies on:
>>   cmake
>>   gmake
>>   gawk
>>   bison
>> InsightToolkit has library dependencies on:
>>   xorg-libs
>>   ossp-uuid
>>   guile
>>   tcl
>>   python25
>>
>> If you have a separate svn and development modules from the ITK cvs, I
>> would
>> assume a new port for FARSIGHT will be required in MacPorts.  I should
>> suggest that for any porting system (MacPorts, FreeBSD, Debian, etc.), it
>> would be optimal to have a FARSIGHT dependency on a release version of
>> ITK,
>> rather than an entire, customized ITK development tree that needs to be
>> built especially for FARSIGHT.  (FYI, for example, wxPython packages the
>> entire wxWidgets in its distribution, rather than just a dependency on the
>> wxWidgets library, and that's a pain for porting systems.)  In other
>> words,
>> if you need to make changes to ITK, it would be preferable to make them in
>> the ITK cvs for their next release (ie, make the change upstream).  If you
>> have custom code based on ITK, it's preferable to link against the release
>> version and subclass or something within your own library path, until you
>> can commit upstream to ITK (I guess BioImageXD may do something like this;
>> someday I should put together a MacPort for that project).
>>
>
> for a mac ports of BioImageXD you might want to wait until we have big
> tested and fixed the upcoming version.
> Not sure how long that will take, but for now, the OSX version  still a bit
> too alpha, and not really even beta.
>
> We are aiming for a production quality release this time.
>
> The tricky but will be the custom ITK and VTK C++ kits we have in the svn.
>
> I would be very happy to see a mac ports version of BXD in the future.
> It hasnt been tested for a X11 build for a very long time.. no idea of it
> works.
> We use Carbon  - wxPython for the GUI.
>


At the moment, VTK and ITK are built with cocoa, by default, but there are
options for x11 or carbon.  I've not tested those options in the vtk 5.4 and
itk 3.12 or 3.14 ports.

At the moment, wxpython is in the port named py-wxpython at version 2.8.9.2
in python25 and 2.8.9.1 in python26 (wxWidgets is at 2.8.9).  There are some
ports for py2app too.

If you develop against MacPorts libs, you might get the benefit of binary
packages too, see
http://guide.macports.org/#using.binaries.binary-packages

Best,
Darren
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