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<font color="#000000"><small><font face="Helvetica, Arial, sans-serif">Hi
Geatan,<br>
<br>
I am in the process of reviewing your Insight Journal article "WrapITK".<br>
<br>
While compiling and installing WrapITK I have come across a number of
issues. For your information my system details are as follows:<br>
</font></small></font>
<ul>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">Operating System=Windows XP SP2</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">CMake=CMake 2.4.2</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">Compiler=Microsoft.NET 2003
(7.1.3088)</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">ITK=InsightToolkit-2.8.1</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">CableSwig=CVS checkout on 10th
July 2006, 9:30AM (GMT+10:00)</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">WrapITK=Nightly archive from
<a class="moz-txt-link-freetext" href="http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/WrapITK.tar.gz">http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/WrapITK.tar.gz</a>
downloaded on 10th July 2006, 8:45AM (GMT+10:00)</font></small></font></li>
<li><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">Python=Python 2.4.3 (#69, Mar 29
2006, 17:35:34) [MSC v.1310 32 bit (Intel)] on win32</font></small></font></li>
</ul>
<font color="#000000"><small><font face="Helvetica, Arial, sans-serif"><br>
<b>1. Error accessing __FUNCSIG__:</b><br>
For some reason while compiling <font
face="Courier New, Courier, monospace">_IOPython</font> I received the
following error:<br>
<font face="Courier New, Courier, monospace"><font color="#666666">In
file included from
C:/Dan/Tools/ITK/src/WrapITK/Modules/IO/wrap_ITKIOBase.cxx:64:<br>
C:/Dan/Tools/ITK/src/InsightToolkit-2.8.1/Code/IO/itkGDCMSeriesFileNames.h:
In<br>
member function `void
itk::GDCMSeriesFileNames::SetInputDirectory(const <br>
char*)':<br>
C:/Dan/Tools/ITK/src/InsightToolkit-2.8.1/Code/IO/itkGDCMSeriesFileNames.h:73:
error: `<br>
__FUNCSIG__' undeclared (first use this function)<br>
C:/Dan/Tools/ITK/src/InsightToolkit-2.8.1/Code/IO/itkGDCMSeriesFileNames.h:73:
error: (Each<br>
undeclared identifier is reported only once for each function it
appears <br>
in.)<br>
Project : error PRJ0019: A tool returned an error code from "Generating
wrap_ITKIOBase.xml"</font><font face="Helvetica, Arial, sans-serif"><br>
<br>
When I comment out the offending line, the project compiles fine:<br>
<font color="#666666" face="Courier New, Courier, monospace">/** Set
the directory that contains the DICOM series. */<br>
void SetInputDirectory (const char * name)<br>
{<br>
if( !name )<br>
{<br>
itkExceptionMacro(<<"SetInputDirectory() received a NULL
string"); //<<< commenting this fixes it<br>
}<br>
std::string fname = name;<br>
this->SetInputDirectory( fname );<br>
}</font><br>
<br>
Note that <font face="Courier New, Courier, monospace">itkExceptionMacro</font>
expands based on <font face="Courier New, Courier, monospace">itkMacro.h</font>:<br>
<font color="#666666" face="Courier New, Courier, monospace">#define
itkExceptionMacro(x) \<br>
{ \<br>
::itk::OStringStream message; \<br>
message << "itk::ERROR: " << this->GetNameOfClass() \<br>
<< "(" << this << "): " x; \<br>
::itk::ExceptionObject e_(__FILE__, __LINE__,
message.str().c_str(),ITK_LOCATION); \<br>
throw e_; /* Explicit naming to work around Intel compiler bug. */ \<br>
}</font><br>
<br>
and <font face="Courier New, Courier, monospace">ITK_LOCATION</font>
is expanded based on <font face="Courier New, Courier, monospace">itkMacro.h</font>:<br>
<font color="#666666" face="Courier New, Courier, monospace">#if
defined(ITK_CPP_FUNCTION)<br>
#if defined(__BORLANDC__)<br>
#define ITK_LOCATION __FUNC__<br>
#elif defined(_WIN32) && !defined(__MINGW32__) &&
!defined(__CYGWIN__)<br>
#define ITK_LOCATION __FUNCSIG__ // <<< this line is
obviously being used by the macro<br>
#elif defined(__GNUC__)<br>
#define ITK_LOCATION __PRETTY_FUNCTION__<br>
#else<br>
#define ITK_LOCATION __FUNCTION__<br>
#endif<br>
#else<br>
#define ITK_LOCATION "unknown"<br>
#endif</font><br>
<br>
This error is quite interesting (ie. baffling) because I can compile
other ITK code containing __FUNCSIG__ just fine. I don't understand why
the __FUNCSIG__ macro is not recognised in this instance. Any
thoughts/ideas/help?? I don't envisage needing to use
itk::GDCMSeriesFileNames so it is not a major issue for me.<br>
<br>
<b>2. Object file format limit exceeded:</b><br>
During my first attempt to configure/compile WrapITK I used the default
settings, EXCEPT that I set<font face="Courier New, Courier, monospace">
WRAP_unsigned_short=ON.</font><br>
<br>
Doing this caused the follow error during compilation of <font
face="Courier New, Courier, monospace">_BasePython</font>:<br>
<font color="#666666" face="Courier New, Courier, monospace">c:\dan\tools\itk\src\insighttoolkit-2.8.1\code\common\itksmartpointer.h(55)
: fatal error C1128: object file format limit exceeded : more than
65,279 sections</font><br>
<br>
The Microsoft documentation says the following about C1128:<br>
<font color="#666666" face="Courier New, Courier, monospace">An .obj
file exceeded the number of allowable sections, a COFF object file
format limitation.<br>
Reaching this section limitation can be the result of using /Gy and a
debug build; /Gy causes functions to go into their own COMDAT sections.
In a debug build, there is a debug info section for each COMDAT
function.<br>
C1128 can also be caused when there are too many inline functions.<br>
To correct this error, divide your source file into multiple source
code files.</font><br>
<br>
I reset the project to use the default CMake settings (ie.
WRAP_unsigned_short=OFF) and this error went away. Perhaps when
wrapping with lots of types (eg. default types + 1) I am reaching the
object file limitations?? Maybe breaking _BasePython into 2 or more
projects would solve the issue (if possible)?<br>
<br>
<b>3. </b></font></font></font></small></font><b><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif">Ambiguous call to overloaded
function </font></font></font></small></font><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif">'sqrt':</font></font></font></small></font></b><br>
<font color="#000000"><small><font face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif">While compiling <font
face="Courier New, Courier, monospace">_DistanceMapPython</font> I
encountered the following error:<br>
<font color="#666666" face="Courier New, Courier, monospace">wrap_itkSignedMaurerDistanceMapImageFilterPython.cxx<br>
c:\Dan\Tools\ITK\src\InsightToolkit-2.8.1\Code\BasicFilters\itkSignedMaurerDistanceMapImageFilter.txx(241)
: error C2668: 'sqrt' : ambiguous call to overloaded function<br>
C:\Program Files\Microsoft Visual Studio .NET
2003\Vc7\include\math.h(626): could be 'long double sqrt(long double)'<br>
C:\Program Files\Microsoft Visual Studio .NET
2003\Vc7\include\math.h(578): or 'float sqrt(float)'<br>
C:\Program Files\Microsoft Visual Studio .NET
2003\Vc7\include\math.h(200): or 'double sqrt(double)'<br>
while trying to match the argument list '(unsigned short)'<br>
C:\Program Files\Microsoft Visual Studio .NET
2003\Vc7\include\xmemory(156) : while compiling class-template member
function 'void
itk::SignedMaurerDistanceMapImageFilter<TInputImage,TOutputImage>::GenerateData(void)'<br>
with<br>
[<br>
TInputImage=itk::Image<short,3>,<br>
TOutputImage=itk::Image<short,3><br>
]<br>
wrap_itkSignedMaurerDistanceMapImageFilterPython.cxx(10865) :
see reference to class template instantiation
'itk::SignedMaurerDistanceMapImageFilter<TInputImage,TOutputImage>'
being compiled<br>
with<br>
[<br>
TInputImage=itk::Image<short,3>,<br>
TOutputImage=itk::Image<short,3><br>
]</font><br>
<br>
I fixed this by editing </font></font></font></small></font><font
color="#000000"><small><font face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace">itkSignedMaurerDistanceMapImageFilter.txx</font></font></font></font></small></font><font
color="#000000"><small><font face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif"> to explicitly casting to double
before the call to sqrt.<br>
<br>
<b>4. C</b></font></font></font></small></font><b><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif">annot access protected member </font></font></font></small></font></b><font
color="#000000"><small><font face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif"><b>EnlargeOutputRequestedRegion:</b><br>
While compiling <font face="Courier New, Courier, monospace">_SegmentationAndThresholdPython</font>
I encountered the following error:<br>
</font></font></font></small></font><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">wrap_itkScalarConnectedComponentImageFilterPython.cxx(11151)
: error C2248:
'itk::ConnectedComponentImageFilter<TInputImage,TOutputImage,TMaskImage>::EnlargeOutputRequestedRegion'
: cannot access protected member declared in class
'itk::ConnectedComponentImageFilter<TInputImage,TOutputImage,TMaskImage>'<br>
with<br>
[<br>
TInputImage=itk::Image<short,2>,<br>
TOutputImage=itk::Image<short,2>,<br>
TMaskImage=itk::Image<short,2><br>
]<br>
and<br>
[<br>
TInputImage=itk::Image<short,2>,<br>
TOutputImage=itk::Image<short,2>,<br>
TMaskImage=itk::Image<short,2><br>
]<br>
c:\Dan\Tools\ITK\src\InsightToolkit-2.8.1\Code\BasicFilters\itkConnectedComponentImageFilter.h(149)
: see declaration of
'itk::ConnectedComponentImageFilter<TInputImage,TOutputImage,TMaskImage>::EnlargeOutputRequestedRegion'<br>
with<br>
[<br>
TInputImage=itk::Image<short,2>,<br>
TOutputImage=itk::Image<short,2>,<br>
TMaskImage=itk::Image<short,2><br>
]</font><br>
<br>
To temporarily fix this and continue with the compile I renamed <font
face="Courier New, Courier, monospace">wrap_itkScalarConnectedComponentImageFilter.cmake</font>
to ensure it was not included. After re-configuring with CMake this
project compiled correctly.<br>
<br>
<b>5. Python installation:</b><br>
When I install WrapITK (ie. build the INSTALL project) it copies the
created files to the <font face="Courier New, Courier, monospace">CMAKE_INSTALL_PREFIX
/ WRAP_ITK_INSTALL_PREFIX</font> folder (in my case <font
face="Courier New, Courier, monospace">C:/Program Files/WrapITK/lib/InsightToolkit/WrapITK/Python</font>).<br>
<br>
However, the Python site-packages WrapITK.pth file does not contain the
correct paths for usage. The generated WrapITK.pth file is:<br>
<font color="#666666" face="Courier New, Courier, monospace"><font
color="#009900"># Python pth file to add WrapITK's path to sys.path.</font><br>
C:/Program Files/WrapITK//lib/InsightToolkit/WrapITK/Python</font><br>
which does not allow Python access to all the files. I manually changed
WrapITK.pth to:<br>
</font></font></font></small></font><font color="#666666"
face="Courier New, Courier, monospace"><small><font color="#009900">#
Python pth file to add WrapITK's path to sys.path.</font><br>
C:/Program Files/WrapITK/lib/InsightToolkit/WrapITK/Python</small><br>
</font><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif"><font
face="Courier New, Courier, monospace"><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">C:/Program
Files/WrapITK/lib/InsightToolkit/WrapITK/lib</font><br>
to make it work correctly.<br>
<br>
Also, the <font face="Courier New, Courier, monospace">SwigRuntimePython.dll</font>
file is copied to the <font face="Courier New, Courier, monospace">C:/Program
Files/WrapITK/bin</font> folder and is not accessible to Python. I had
to manually copy this file to </font></font></font></small></font><font
color="#000000" face="Courier New, Courier, monospace"><small>C:/Program
Files/WrapITK/lib/InsightToolkit/WrapITK/Python<font
face="Helvetica, Arial, sans-serif"> to ensure Python finds it.<br>
<br>
Finally, some required Python files (<font
face="Courier New, Courier, monospace">itk.py</font>, <font
face="Courier New, Courier, monospace">itkBase.py</font>, <font
face="Courier New, Courier, monospace">itkTemplate.py</font>, <font
face="Courier New, Courier, monospace">itktesting.py</font>, and <font
face="Courier New, Courier, monospace">itkTypes.py</font>) were not
copied to the installation folder. I manually copied these in order for
Python to automatically detect WrapITK.<br>
<br>
<b>6. String formatting:</b><br>
It seems the formatting for the itkExtras function <font
face="Courier New, Courier, monospace">auto_progress(bool)</font> is
not correct. I'm not a Python guru, so perhaps it's something at my
end? The follow results don't look very nice to me:<br>
</font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">>>> imagetype =
itk.Image[itk.UC, 2]<br>
>>> reader =
itk.ImageFileReader[imagetype].New(FileName="c:/temp/input.png")<br>
</font></font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">>>>
itk.auto_progress(True)</font></font></small></font><br>
<font color="#000000" face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">>>> filter =
itk.GradientMagnitudeImageFilter[imagetype,
imagetype].New(Input=reader.GetOutput())<br>
>>> filter.Update()</font><font color="#666666"
face="Courier New, Courier, monospace"><br>
</font><font color="#666666" face="Courier New, Courier, monospace"> ←[2000D←[KitkGradientMagnitudeImageFilterIUC2IUC2:
0.000000 ←[2000D←[KitkGradie<br>
ntMagnitudeImageFilterIUC2IUC2: 0.009979
←[2000D←[KitkGradientMagnitudeImageFilt<br>
erIUC2IUC2: 0.019958 ←[2000D←[KitkGradientMagnitudeImageFilterIUC2IUC2:
0.029938<br>
←[2000D←[KitkGradientMagnitudeImageFilterIUC2IUC2: 0.039917
←[2000D←[KitkGradie<br>
ntMagnitudeImageFilterIUC2IUC2: 0.049896
←[2000D←[KitkGradientMagnitudeImageFilt<br>
erIUC2IUC2: 0.059875 ←[2000D←[KitkGradientMagnitudeImageFilterIUC2IUC2:
0.069855<br>
←[2000D←[KitkGradientMagnitudeImageFilterIUC2IUC2: 0.079834
←[2000D←[KitkGradie<br>
...</font><br>
<br>
Also, the output of the below example is not correct:<br>
<font color="#666666" face="Courier New, Courier, monospace">>>>
print itk.size(reader)<br>
ÓýB♠e [256, 256]></font><br>
<br>
</font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif">The above example should be:<br>
</font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><font color="#666666"
face="Courier New, Courier, monospace">>>> print
itk.size(reader)<br>
<Size [256, 256]><br>
<br>
</font></font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif">Perhaps I have the wrong string
encoding specified? Or perhaps <font color="#000000"
face="Courier New, Courier, monospace">print </font>does not work on
Python win32? Any thoughts/help?<br>
</font></small></font><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><br>
<br>
</font></small></font><font color="#000000"><small><font
face="Helvetica, Arial, sans-serif">Geatan, </font></small></font><font
color="#000000" face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif">please feel free to contact me if
you require any further clarification on the issues described above. <br>
<br>
Besides these minor issues, WrapITK is fantastic - thanks for the nice
addition to ITK! I'll be posting my review to the article soon.<br>
<br>
Cheers<br>
<br>
Dan Mueller<br>
PhD Student<br>
Queensland University of Technology (QUT)<br>
Brisbane, Australia<br>
</font></small></font><small><font face="Helvetica, Arial, sans-serif">CRICOS
No: 00213J
</font></small><font color="#000000"
face="Courier New, Courier, monospace"><small><font
face="Helvetica, Arial, sans-serif"><br>
</font></small></font>
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