[Insight-users] Compilation error with inPlace filters
Radhika Sivaramakrishna
radhika.sivaramakrishna at synarc.com
Mon, 9 Feb 2004 10:39:06 -0800
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Hi Luis,
I actually did the checkout this morning and I did see the Dashboard was
pretty green. I don't know if I am making a silly mistake or a more serious
error.
I have copied my code here which doesn't compile and gives the error
indicated below. I think the problem has something to do with the
IntImageType I put in for dealing with the Relabel.. filter.
Sorry about not putting the correct subject. Will try to make sure to do it
from now on.
Radhika
-----Original Message-----
From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
Sent: Monday, February 09, 2004 10:34 AM
To: Radhika Sivaramakrishna
Cc: ITK
Subject: Re: [Insight-users] Compilation error with inPlace filters
Hi Radhika,
A number of changes were made last week for extending
the functionality of "InPlace" filters.
You probably updated your checkout in the middle of
one of such modifications. Please trying cvs updating
to this morning (since the nightly Dashboard was quite
green today).
Regards,
Luis,
PS. Please don't reuse email threads with other subjects when
you post questions about new topics/problems. This is
confusing for anybody trying to follow a thread.
---------------------------------------
Radhika Sivaramakrishna wrote:
> Hi Luis,
> I am getting this very strange error message while compiling. Can you
> explain what this could be?
>
> /home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx: In member
> function `void itk::InPlaceImageFilter<TInputImage,
> TOutputImage>::AllocateOutputs() [with TInputImage = main(int,
> char**)::IntImageType, TOutputImage = main(int, char**)::ImageType]':
> /home/rsivaram/Insight/Code/Common/itkImageRegion.h:173:
> instantiated from here
> /home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx:76: no
> matching
> function for call to `itk::InPlaceImageFilter<main(int,
> char**)::IntImageType, main(int,
> char**)::ImageType>::GraftOutput(main(int,
> char**)::IntImageType*)'
> /home/rsivaram/Insight/Code/Common/itkImageSource.txx:95: candidates
> are: void
> itk::ImageSource<TOutputImage>::GraftOutput(TOutputImage*) [with
> TOutputImage = main(int, char**)::ImageType]
>
>
> Thanks
> Radhika
>
>
>
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charset=3Dus-ascii">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2656.87">
<TITLE>RE: [Insight-users] Compilation error with inPlace =
filters</TITLE>
</HEAD>
<BODY>
<P><FONT SIZE=3D2>Hi Luis,</FONT>
<BR><FONT SIZE=3D2>I actually did the checkout this morning and I did =
see the Dashboard was pretty green. I don't know if I am making a silly =
mistake or a more serious error.</FONT></P>
<P><FONT SIZE=3D2>I have copied my code here which doesn't compile and =
gives the error indicated below. I think the problem has something to =
do with the IntImageType I put in for dealing with the Relabel.. =
filter. </FONT></P>
<P><FONT SIZE=3D2>Sorry about not putting the correct subject. Will try =
to make sure to do it from now on.</FONT>
</P>
<P><FONT SIZE=3D2>Radhika</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Luis Ibanez [<A =
HREF=3D"mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</=
A>] </FONT>
<BR><FONT SIZE=3D2>Sent: Monday, February 09, 2004 10:34 AM</FONT>
<BR><FONT SIZE=3D2>To: Radhika Sivaramakrishna</FONT>
<BR><FONT SIZE=3D2>Cc: ITK</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [Insight-users] Compilation error with =
inPlace filters</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Hi Radhika,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>A number of changes were made last week for =
extending</FONT>
<BR><FONT SIZE=3D2>the functionality of "InPlace" =
filters.</FONT>
</P>
<P><FONT SIZE=3D2>You probably updated your checkout in the middle =
of</FONT>
<BR><FONT SIZE=3D2>one of such modifications. Please trying cvs =
updating</FONT>
<BR><FONT SIZE=3D2>to this morning (since the nightly Dashboard was =
quite</FONT>
<BR><FONT SIZE=3D2>green today).</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Regards,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Luis,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>PS. Please don't reuse email threads with other =
subjects when</FONT>
<BR><FONT SIZE=3D2> you post questions =
about new topics/problems. This is</FONT>
<BR><FONT SIZE=3D2> confusing for anybody =
trying to follow a thread.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>---------------------------------------</FONT>
<BR><FONT SIZE=3D2>Radhika Sivaramakrishna wrote:</FONT>
</P>
<P><FONT SIZE=3D2>> Hi Luis,</FONT>
<BR><FONT SIZE=3D2>> I am getting this very strange error message =
while compiling. Can you </FONT>
<BR><FONT SIZE=3D2>> explain what this could be?</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> =
/home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx: In =
member</FONT>
<BR><FONT SIZE=3D2>> function `void =
itk::InPlaceImageFilter<TInputImage,</FONT>
<BR><FONT SIZE=3D2>> =
TOutputImage>::AllocateOutputs() [with TInputImage =3D =
main(int,</FONT>
<BR><FONT SIZE=3D2>> char**)::IntImageType, =
TOutputImage =3D main(int, char**)::ImageType]':</FONT>
<BR><FONT SIZE=3D2>> =
/home/rsivaram/Insight/Code/Common/itkImageRegion.h:173: =
</FONT>
<BR><FONT SIZE=3D2>> instantiated from here</FONT>
<BR><FONT SIZE=3D2>> =
/home/rsivaram/Insight/Code/Common/itkInPlaceImageFilter.txx:76: no =
</FONT>
<BR><FONT SIZE=3D2>> matching</FONT>
<BR><FONT SIZE=3D2>> function for call to =
`itk::InPlaceImageFilter<main(int,</FONT>
<BR><FONT SIZE=3D2>> char**)::IntImageType, =
main(int, </FONT>
<BR><FONT SIZE=3D2>> =
char**)::ImageType>::GraftOutput(main(int,</FONT>
<BR><FONT SIZE=3D2>> =
char**)::IntImageType*)'</FONT>
<BR><FONT SIZE=3D2>> =
/home/rsivaram/Insight/Code/Common/itkImageSource.txx:95: candidates =
</FONT>
<BR><FONT SIZE=3D2>> are: void</FONT>
<BR><FONT SIZE=3D2>> =
itk::ImageSource<TOutputImage>::GraftOutput(TOutputImage*) =
[with</FONT>
<BR><FONT SIZE=3D2>> TOutputImage =3D main(int, =
char**)::ImageType]</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Thanks</FONT>
<BR><FONT SIZE=3D2>> Radhika</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>></FONT>
</P>
<BR>
<P><FONT =
SIZE=3D2> &nb=
sp; &nb=
sp; &nb=
sp; &nb=
sp; </FONT>
<BR><FONT =
SIZE=3D2>----------------------------------------------------- =
</FONT>
<BR><FONT SIZE=3D2>Confidentiality Notice. </FONT>
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name="HistogramThreshold.cxx"
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filename="HistogramThreshold.cxx"
#include "itkScalarImageToHistogramGenerator.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkMaskImageFilter.h"
#include "itkImageFileWriter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkHistogram.h"
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkBinaryErodeImageFilter.h"
#include "itkBinaryDilateImageFilter.h"
#include "itkBinaryBallStructuringElement.h"
int main( int argc, char * argv [] )
{
if( argc < 2 )
{
std::cerr << "Missing command line arguments" << std::endl;
std::cerr << "Usage : ImageHistogram1 inputImageFileName =
inputMaskFileName " << std::endl;
return -1;
}
typedef unsigned char PixelType;
typedef int IntType;
const unsigned int Dimension =3D 3;
typedef itk::Image<PixelType, Dimension > ImageType;
typedef itk::Image<IntType, Dimension > IntImageType;
typedef itk::Image<PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< CharImageType > WriterType;
typedef itk::MaskImageFilter<ImageType,ImageType,ImageType> =
MaskFilterType;
typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> =
BinaryThresholdFilterType;
typedef itk::ImageRegionConstIteratorWithIndex< ImageType > =
ConstIteratorType;
typedef itk::ImageRegionIteratorWithIndex< ImageType > IteratorType;
=0A=
=0A=
typedef itk::BinaryBallStructuringElement<
PixelType,
Dimension > =
StructuringElementType;
typedef itk::BinaryErodeImageFilter<
ImageType,
ImageType,
StructuringElementType> ErodeFilterType;
typedef itk::BinaryDilateImageFilter<
ImageType,
ImageType,
StructuringElementType > DilateFilterType;
typedef itk::ConnectedComponentImageFilter<ImageType,IntImageType > =
CCFilterType;
typedef itk::RelabelComponentImageFilter<IntImageType,ImageType > =
RCFilterType;
MaskFilterType::Pointer masker =3D MaskFilterType::New();
BinaryThresholdFilterType::Pointer thresholdermask =3D =
BinaryThresholdFilterType::New();
ReaderType::Pointer readerimage =3D ReaderType::New();
ReaderType::Pointer readermask =3D ReaderType::New();
WriterType::Pointer writer =3D WriterType::New();
CCFilterType::Pointer ccfilter =3D CCFilterType::New();
RCFilterType::Pointer rcfilter =3D RCFilterType::New();
ErodeFilterType::Pointer binaryErode =3D ErodeFilterType::New();
DilateFilterType::Pointer binaryDilate =3D DilateFilterType::New();
PixelType background =3D 0;
PixelType foreground =3D 255;
StructuringElementType structuringElement;
structuringElement.SetRadius( 1 ); // 3x3 structuring element
structuringElement.CreateStructuringElement();
binaryErode->SetKernel( structuringElement );
binaryDilate->SetKernel( structuringElement );
binaryErode->SetErodeValue(foreground);
binaryDilate->SetDilateValue(foreground);
thresholdermask->SetOutsideValue( background );
thresholdermask->SetInsideValue( foreground );
readerimage->SetFileName( argv[1] );
try
{
readerimage->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Problem encoutered while reading image file : " << =
argv[1] << std::endl;
std::cerr << excp << std::endl;
return -1;
}
readermask->SetFileName( argv[2] );
try
{
readermask->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Problem encoutered while reading image file : " << =
argv[1] << std::endl;
std::cerr << excp << std::endl;
return -1;
}
std::cout << " Completed reading input images " << std::endl;
readerimage->Update();
readermask->Update();
ImageType::Pointer image =3D readerimage->GetOutput();
ImageType::Pointer mask =3D readermask->GetOutput();
typedef itk::Statistics::ScalarImageToHistogramGenerator<
ImageType
> =
HistogramGeneratorType;
HistogramGeneratorType::Pointer histogramGenerator =3D =
HistogramGeneratorType::New();
masker->SetInput1(readerimage->GetOutput());
masker->SetInput2(readermask->GetOutput());
masker->Update();
histogramGenerator->SetInput( masker->GetOutput() );
histogramGenerator->SetNumberOfBins( 128 );
histogramGenerator->SetMarginalScale( 10.0 );
histogramGenerator->Compute();
typedef HistogramGeneratorType::HistogramType HistogramType;
const HistogramType * histogram =3D histogramGenerator->GetOutput();
const unsigned int histogramSize =3D histogram->Size();
std::cout << "Histogram size " << histogramSize << std::endl;
/* for( unsigned int bin=3D0; bin < histogramSize; bin++ )
{
std::cout << "bin =3D " << bin << " frequency =3D ";
std::cout << histogram->GetFrequency( bin, 0 ) << std::endl;
} */
HistogramType::ConstIterator itr =3D histogram->Begin();
HistogramType::ConstIterator end =3D histogram->End();
unsigned int bin =3D 1;
unsigned long totalhist =3D 0;
++itr; // To skip the zero count
while( itr !=3D end )
{
// std::cout << "bin =3D " << bin << " frequency =3D ";
// std::cout << itr.GetFrequency() << std::endl;
totalhist +=3D itr.GetFrequency();
++itr;
++bin;
}
std::cout << " Total " << totalhist << std::endl;
// std::cout << " Total frequency " << histogram->GetTotalFrequency() =
<< std::endl;
// std::cout << " Quantile at 90th percentile " << =
histogram->Quantile(0,0.90) << std::endl;
unsigned long probability =3D 0;
unsigned int threshold;
bin=3D1;
itr =3D histogram->Begin();
++itr; // To skip the zero count
while( (itr !=3D end) && (probability <=3D 0.90*totalhist ))
{
std::cout << "bin =3D " << bin << " frequency =3D ";
probability +=3D itr.GetFrequency();
std::cout << probability << std::endl;
threshold =3D bin*2;
++itr;
++bin;
}
std::cout << " Threshold value " << threshold << std::endl;
std::cout << " Probability value " << probability << std::endl;
ImageType::RegionType region =3D image->GetBufferedRegion();
IteratorType maskit(mask,region);
ConstIteratorType gsit(image,region);
gsit.GoToBegin();
maskit.GoToBegin();
while( ! gsit.IsAtEnd() && ! maskit.IsAtEnd())
{
if (gsit.Get() > threshold)
{
maskit.Set(0);
}
++maskit;
++gsit;
}
binaryErode->SetInput(mask);
ccfilter->SetInput(binaryErode->GetOutput());
rcfilter->SetInput(ccfilter->GetOutput());
rcfilter->Update();
thresholdermask->SetInput( rcfilter->GetOutput() );
thresholdermask->SetLowerThreshold( 1 );
thresholdermask->SetUpperThreshold( 1 );
binaryDilate->SetInput(thresholdermask->GetOutput());
writer->SetFileName("finalmask.img");
writer->SetInput(binaryDilate->GetOutput());
writer->Update();
return 0;
}
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