[Insight-users] Convert Zeiss .zvi files

[Darren Weber]

On Mon, Jun 29, 2009 at 12:15 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> 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).




> 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.
>


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).




>
>
> http://farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software
>>
>> The MacPorts system will take care of all the dependencies (cmake, python,
>> cableswig).  Please see this ITK wiki page for more details:
>> http://www.vtk.org/Wiki/ITK_MacPorts_Package_Maintainers
>>
>> Moreover, _please_ link to that page from the farsight tutorial on the
>> build process, it might save everyone a lot of time and headaches (because I
>> know just how painful it was to put it all together in MacPorts).
>>
>
> Noted on the Building_Software page.
>


Cool.



> If you need to develop ITK using macports, that might be done too, but it
>> requires a little bit of tweaking on the macports installation process.  The
>> macports installation uses several phases and a developer could stop after
>> the build phase.  At that point, you have a complete source tree and a
>> separate build tree.  So you could try this:
>>
>> sudo port build InsightToolkit
>>
>> Then go look in the build tree, under /opt/local/var/macports/build/
>>
>
> Cool; I saw this note on the ITK_MacPorts_Package_Maintainers page too, so
> hopefully people who care will notice that.
>

I have designed the build process in MacPorts so that it does build in a
separate path to the src path.  I put those notes together quickly, after
some reflection on my prior email about FARSIGHT, but I've never tested it,
as I'm not directly developing ITK, but rather using the library
installation.  One problem with moving the build tree somewhere else is that
the OSX convention seems to be using rpath during linking, so the build tree
has a lot of specific links within the build tree that are reset during the
"installation" (or destroot) phase and there are a ton of hacks to get the
rpath right after the destroot phase (especially for the wrapping libs).
That's the OSX nightmare that I discovered and wrangled with for a long time
before finally giving in, learning and coding it up in a MacPort.

Best, Darren
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