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List: insight-users
Subject: Re: [Insight-users] What is the pipeline inside the itkGradientMagnitudeRecursiveGaussianImageFilter
From: "Xiaopeng Yang" <yxp233 () postech ! ac ! kr>
Date: 2012-12-17 23:05:14
Message-ID: 021001cddcaa$f92cdb70$eb869250$ () ac ! kr
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Hi,
Is my question too difficult? Please do me a favor to check my question. Any
idea would be very much appreciated. Or except ITK Software Guide, is there
any other manual which introduces the
itkGradientMagnitudeRecursiveGaussianImageFilter in very detail, including
pipeline and formulas?
Thank you so much!
Best,
Xiaopeng
From: insight-users-bounces@itk.org [mailto:insight-users-bounces@itk.org]
On Behalf Of Xiaopeng Yang
Sent: Monday, December 17, 2012 9:14 PM
To: insight-users@itk.org; 'Insight Developers'
Subject: [Insight-users] What is the pipeline inside the
itkGradientMagnitudeRecursiveGaussianImageFilter?
Dear All,
I am trying to look through the
itkGradientMagnitudeRecursiveGaussianImageFilter to figure out the pipeline
of this filter to visualize the computation process of image gradient
calculation from a CT volume dataset using this filter. However, the source
code of this filter makes me confused about the pipeline in this filter due
to my limited programming skill.
This filter consists of two major steps as far as I know: 1) image smoothing
using itkRecursiveGaussianImageFilter, and 2) image gradient calculation
using a finite difference method (Does anybody know what formula was used
for the finite difference method? I checked the source code but could not
get it).
For step 1, I wrote a code to get the smoothed image. But I am not sure
whether my code would get the same smoothed image as
itkGradientMagnitudeRecursiveGaussianImageFilter or not. Please check my
code and point out which part I missed or is not correct. Thank you very
much!
// Setup types
typedef itk::Image< float, 3 > FloatImageType;
typedef itk::Image< unsigned char, 3 > UnsignedCharImageType;
typedef itk::ImageFileReader< FloatImageType > readerType;
typedef itk::RecursiveGaussianImageFilter<
FloatImageType, FloatImageType > filterType;
// Create and setup a reader
readerType::Pointer reader = readerType::New();
reader->SetFileName( "D:/Hybrid Method/Hybrid/LEJ/Diffusion_filter/3D.dcm"
);
// Create and setup a gaussian filter
filterType::Pointer m_DerivativeFilter = filterType::New();
m_DerivativeFilter->SetInput( reader->GetOutput() );
//m_DerivativeFilter->SetDirection(1); // "x" axis
m_DerivativeFilter->SetFirstOrder();
m_DerivativeFilter->SetSigma(1.3);
m_DerivativeFilter->SetNormalizeAcrossScale(true);
m_DerivativeFilter->ReleaseDataFlagOn();
filterType::Pointer m_SmoothingFilters[2];
for( unsigned int i = 0; i< 2; i++ )
{
m_SmoothingFilters[ i ] = filterType::New();
m_SmoothingFilters[ i ]->SetZeroOrder();
m_SmoothingFilters[ i ]->SetNormalizeAcrossScale( true );
m_SmoothingFilters[ i ]->SetSigma( 1.3 );
}
m_SmoothingFilters[0]->SetInput( m_DerivativeFilter->GetOutput() );
for( unsigned int i = 1; i< 2; i++ )
{
m_SmoothingFilters[ i ]->SetInput(
m_SmoothingFilters[i-1]->GetOutput() );
}
typedef itk::CastImageFilter< FloatImageType, UnsignedCharImageType >
CastFilterType;
CastFilterType::Pointer caster1 = CastFilterType::New();
caster1->SetInput( m_SmoothingFilters[1]->GetOutput() );
typedef itk::ImageFileWriter< UnsignedCharImageType > WriterType;
WriterType::Pointer writer1 = WriterType::New();
writer1->SetFileName( "RecusiveGaussian.dcm" );
writer1->SetInput(caster1->GetOutput());
writer1->Update();
return EXIT_SUCCESS;
Best regards,
Xiaopeng
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class=WordSection1><div><p class=MsoNormal><span \
style='color:#1F497D'>Hi,<o:p></o:p></span></p><p class=MsoNormal><span \
style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span \
style='color:#1F497D'>Is my question too difficult? Please do me a favor to check my \
question. Any idea would be very much appreciated. Or except ITK Software Guide, is \
there any other manual which introduces the \
itkGradientMagnitudeRecursiveGaussianImageFilter in very detail, including pipeline \
and formulas?<o:p></o:p></span></p><p class=MsoNormal><span \
style='color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span \
style='color:#1F497D'>Thank you so much!<o:p></o:p></span></p><p \
class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><p \
class=MsoNormal><span style='color:#1F497D'>Best,<o:p></o:p></span></p><p \
class=MsoNormal><span style='color:#1F497D'>Xiaopeng</span><span \
style='font-family:"Arial","sans-serif";color:#1F497D'><o:p></o:p></span></p></div><p \
class=MsoNormal><span style='color:#1F497D'><o:p> </o:p></span></p><div><div \
style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p \
class=MsoNormal><b><span \
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span \
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> \
insight-users-bounces@itk.org [mailto:insight-users-bounces@itk.org] <b>On Behalf Of \
</b>Xiaopeng Yang<br><b>Sent:</b> Monday, December 17, 2012 9:14 PM<br><b>To:</b> \
insight-users@itk.org; 'Insight Developers'<br><b>Subject:</b> [Insight-users] What \
is the pipeline inside the \
itkGradientMagnitudeRecursiveGaussianImageFilter?<o:p></o:p></span></p></div></div><p \
class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Dear All,<o:p></o:p></p><p \
class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am trying to look through \
the itkGradientMagnitudeRecursiveGaussianImageFilter to figure out the pipeline of \
this filter to visualize the computation process of image gradient calculation from a \
CT volume dataset using this filter. However, the source code of this filter makes me \
confused about the pipeline in this filter due to my limited programming \
skill.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>This \
filter consists of two major steps as far as I know: 1) image smoothing using \
itkRecursiveGaussianImageFilter, and 2) image gradient calculation using a finite \
difference method (Does anybody know what formula was used for the finite difference \
method? I checked the source code but could not get it). <o:p></o:p></p><p \
class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>For step 1, I wrote a code to \
get the smoothed image. But I am not sure whether my code would get the same smoothed \
image as itkGradientMagnitudeRecursiveGaussianImageFilter or not. Please check my \
code and point out which part I missed or is not correct. Thank you very \
much!<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun;color:green'>// Setup \
types<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>typedef</span> itk::Image< <span \
style='color:blue'>float</span>, 3 > \
FloatImageType;<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
<span style='color:blue'>typedef</span> itk::Image< <span \
style='color:blue'>unsigned</span> <span style='color:blue'>char</span>, 3 \
> UnsignedCharImageType;<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>typedef</span> itk::ImageFileReader< FloatImageType > \
readerType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>typedef</span> \
itk::RecursiveGaussianImageFilter<<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
FloatImageType, FloatImageType > filterType;<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span style='color:green'>// \
Create and setup a reader<o:p></o:p></span></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
readerType::Pointer reader = readerType::New();<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> reader->SetFileName( <span \
style='color:#A31515'>"D:/Hybrid \
Method/Hybrid/LEJ/Diffusion_filter/3D.dcm"</span> );<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span style='color:green'>// \
Create and setup a gaussian filter<o:p></o:p></span></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
filterType::Pointer m_DerivativeFilter = filterType::New();<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> m_DerivativeFilter->SetInput( \
reader->GetOutput() );<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
<span style='color:green'>//m_DerivativeFilter->SetDirection(1); // "x" \
axis<o:p></o:p></span></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_DerivativeFilter->SetFirstOrder();<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
m_DerivativeFilter->SetSigma(1.3);<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
m_DerivativeFilter->SetNormalizeAcrossScale(<span \
style='color:blue'>true</span>);<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
m_DerivativeFilter->ReleaseDataFlagOn();<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span style='font-size:9.0pt;font-family:NSimSun'> \
<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> filterType::Pointer \
m_SmoothingFilters[2]; <o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>for</span>( <span style='color:blue'>unsigned</span> <span \
style='color:blue'>int</span> i = 0; i< 2; i++ )<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> {<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[ i ] = filterType::New();<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[ i ]->SetZeroOrder();<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[ i ]->SetNormalizeAcrossScale( <span \
style='color:blue'>true</span> ); <o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[ i ]->SetSigma( 1.3 );<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> }<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[0]->SetInput( m_DerivativeFilter->GetOutput() \
);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>for</span>( <span style='color:blue'>unsigned</span> <span \
style='color:blue'>int</span> i = 1; i< 2; i++ )<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> {<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
m_SmoothingFilters[ i ]->SetInput( m_SmoothingFilters[i-1]->GetOutput() \
);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> }<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>typedef</span> itk::CastImageFilter< FloatImageType, \
UnsignedCharImageType ><o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
&n \
bsp; &nbs \
p; \
CastFilterType;<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> CastFilterType::Pointer caster1 = \
CastFilterType::New();<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> caster1->SetInput( \
m_SmoothingFilters[1]->GetOutput() ); <span \
style='color:green'><o:p></o:p></span></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> <span \
style='color:blue'>typedef</span> itk::ImageFileWriter< \
UnsignedCharImageType > WriterType;<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> WriterType::Pointer writer1 = \
WriterType::New();<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> writer1->SetFileName( <span \
style='color:#A31515'>"RecusiveGaussian.dcm"</span> \
);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
writer1->SetInput(caster1->GetOutput());<o:p></o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'> \
writer1->Update();<o:p></o:p></span></p><p class=MsoNormal \
style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-autospace:none'><span \
style='font-size:9.0pt;font-family:NSimSun'><o:p> </o:p></span></p><p \
class=MsoNormal style='text-indent:9.0pt'><span \
style='font-size:9.0pt;font-family:NSimSun;color:blue'>return</span><span \
style='font-size:9.0pt;font-family:NSimSun'> EXIT_SUCCESS;<o:p></o:p></span></p><p \
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