No subject

Fri May 8 15:29:31 EDT 2009

simpler.

-Curtis

On Wed, May 13, 2009 at 3:04 AM, Daniel James White <white at mpi-cbg.de>wrote:

> Dear Curtis,
>
>
>> BIO-FORMATS IN ITK
>>
>> On Tue, May 12, 2009 at 6:38 AM, alex gouaillard <
>> Alexandre_Gouaillard at hms.harvard.edu> wrote:
>> curtis any news on the wrapping (in C++) and using the IO mechanism in
>> ITK? More specifically, anything we could do to help you?
>>
>> Yes!
>>
>> The C++ bindings are completely functional on Windows (with Visual C++),
>> and Mac OS X and Linux (with gcc).
>>
>> The ITK plugin is functional on Mac OS X and Linux, but I hit a roadblock
>> on Windows.
>>
>
> Windows often proves to be the problematic platform.....
> What is the problem specifically?
>
>
>>
>> For the past month or so I have been swamped with other projects and have
>> not had time to investigate further. If anyone on this list wants to try the
>> C++ bindings and the ITK plugin themselves, I would be extremely
>> appreciative.
>>  * If you are a scientist who needs to access life sciences data within
>> ITK, the plugin is likely to be useful as-is.
>>  * If you are a C++ software developer, I come from a primarily Java
>> background and have no prior experience with CMake, so I would highly value
>> any improvements or "best practices" fixes to my build system.
>>
>
> I hope we can start leveraging your work into BioImageXD as soon as we can.
> We are coming up to a major release, so it might not make it into that
> (especially if its not really working on windoze)
>
> but in  the medium - long term we are very keen to use bio-Formats in
> BioImageXD
>
> cheers
>
> Dan
>
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49  (0)351 210 2627 (Work phone at MPI-CBG)
> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net       BioImageXD
> http://pacific.mpi-cbg.de Fiji  Fiji is just ImageJ - Batteries Included
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
>
>
>
>
>
>
>
>
>

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Hi Dan,<br><br><div class=3D"gmail_quote"><blockquote class=3D"gmail_quote"=
 style=3D"border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.=
8ex; padding-left: 1ex;">Windows often proves to be the problematic platfor=
m.....<br>

What is the problem specifically? 
</blockquote><div> My Jace generated proxy headers produce many errors d=
uring compilation; e.g.: Compiling... 
itkBioFormatsImageIOFactory.cxx 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/java/awt/Tr=
ansparency.h(75)
: error C2059: syntax error : &#39;constant&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/java/awt/Tr=
ansparency.h(75)
: error C2238: unexpected token(s) preceding &#39;;&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/loci/format=
s/TiffTools.h(862)
: warning C4003: not enough actual parameters for macro &#39;RGB&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/loci/format=
s/TiffTools.h(862) : error C2059: syntax error : &#39;(&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/loci/format=
s/TiffTools.h(862) : error C2059: syntax error : &#39;(&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/loci/format=
s/TiffTools.h(862) : error C2059: syntax error : &#39;)&#39; 
C:\svn\java\components\native\bf-cpp\proxies\include\jace/proxy/loci/format=
s/TiffTools.h(862)
: error C2143: syntax error : missing &#39;)&#39; before &#39;|&#39; 
... It&#39;s strange because these are the same headers used in the =
C++ bindings layer, and that code compiles without any problem. (For what i=
t&#39;s worth, I am using Visual C++ 2008 Express.) It could be a mi=
sconfiguration of my Bio-Formats ITK project, fixed with tweaks to the CMak=
e file. Or it could be a bug in Jace requiring further investigation. I hav=
en&#39;t had time to find out.

<br></div><blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid=
 rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I hope =
we can start leveraging your work into BioImageXD as soon as we can.<br>
We are coming up to a major release, so it might not make it into that (esp=
ecially if its not really working on windoze)<br>
<br>
but in =A0the medium - long term we are very keen to use bio-Formats in Bio=
ImageXD<br></blockquote></div><br>From what Pasi said, it looks like your t=
ransition to Java will make things simpler.<br><br>-Curtis<br><br><div clas=
s=3D"gmail_quote">

On Wed, May 13, 2009 at 3:04 AM, Daniel James White <span dir=3D"ltr">&lt;<=
a href=3D"mailto:white at mpi-cbg.de">white at mpi-cbg.de</a>&gt;</span> wrote:<b=
r><blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204=
, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

Dear Curtis, 
 
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
 
BIO-FORMATS IN ITK 
 
On Tue, May 12, 2009 at 6:38 AM, alex gouaillard &lt;<a href=3D"mailto:Alex=
andre_Gouaillard at hms.harvard.edu" target=3D"_blank">Alexandre_Gouaillard at hm=
s.harvard.edu</a>&gt; wrote: 
curtis any news on the wrapping (in C++) and using the IO mechanism in ITK?=
 More specifically, anything we could do to help you? 
 
Yes! 
 
The C++ bindings are completely functional on Windows (with Visual C++), an=
d Mac OS X and Linux (with gcc). 
 
The ITK plugin is functional on Mac OS X and Linux, but I hit a roadblock o=
n Windows. 
</blockquote>
 
Windows often proves to be the problematic platform..... 
What is the problem specifically? 
 
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
 
 
For the past month or so I have been swamped with other projects and have n=
ot had time to investigate further. If anyone on this list wants to try the=
 C++ bindings and the ITK plugin themselves, I would be extremely appreciat=
ive.

 =A0* If you are a scientist who needs to access life sciences data within =
ITK, the plugin is likely to be useful as-is.<br>
 =A0* If you are a C++ software developer, I come from a primarily Java bac=
kground and have no prior experience with CMake, so I would highly value an=
y improvements or &quot;best practices&quot; fixes to my build system.<br>

</blockquote>
<br>
I hope we can start leveraging your work into BioImageXD as soon as we can.=
<br>
We are coming up to a major release, so it might not make it into that (esp=
ecially if its not really working on windoze)<br>
<br>
but in =A0the medium - long term we are very keen to use bio-Formats in Bio=
ImageXD<br>
<br>
cheers<br>
<br>
Dan<br>
<br>
<br>
<br>
<br>
Dr. Daniel James White BSc. (Hons.) PhD<br>
Senior Microscopist / Image Visualisation, Processing and Analysis<br>
Light Microscopy and Image Processing Facilities<br>
Max Planck Institute of Molecular Cell Biology and Genetics<br>
Pfotenhauerstrasse 108<br>
01307 DRESDEN<br>
Germany<br>
<br>
+49 (0)15114966933 (German Mobile)<br>
+49 =A0(0)351 210 2627 (Work phone at MPI-CBG)<br>
+49 =A0(0)351 210 1078 (Fax MPI-CBG LMF)<br>
<br>
<a href=3D"http://www.bioimagexd.net" target=3D"_blank">http://www.bioimage=
xd.net</a> =A0 =A0 =A0 BioImageXD<br>
<a href=3D"http://pacific.mpi-cbg.de" target=3D"_blank">http://pacific.mpi-=
cbg.de</a> Fiji =A0Fiji is just ImageJ - Batteries Included<br>
<a href=3D"http://www.chalkie.org.uk" target=3D"_blank">http://www.chalkie.=
org.uk</a><br>
<a href=3D"mailto:dan at chalkie.org.uk" target=3D"_blank">dan at chalkie.org.uk<=
/a><br>
( <a href=3D"mailto:white at mpi-cbg.de" target=3D"_blank">white at mpi-cbg.de</a=
> )<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</blockquote></div><br>

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