Re: [ITK-users] [ITK] Image conversion from 3D volume to 2D slices

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Definitions of RescaleFilterType and FilterType should be like this:

typedef itk::RescaleIntensityImageFilter< InputImageType, OutputImageType >
RescaleFilterType;
typedef itk::ExtractImageFilter< OutputImageType, OutputImageType >
FilterType;

On Wed, May 8, 2019 at 1:54 PM Shrabani Ghosh <[email protected]>
wrote:

> I did it like this and I am getting images like this now.
> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>
>
>
> int main( int argc, char ** argv )
> {
>
>   //typedef signed short        InputPixelType;
>   /*typedef unsigned char       InputPixelType;
>   typedef unsigned char        OutputPixelType;*/
>   typedef signed short       InputPixelType;
>   typedef unsigned char      OutputPixelType;
>   typedef itk::Image< InputPixelType,  3 >    InputImageType;
>   typedef itk::Image< OutputPixelType, 2 >    OutputImageType;
>   typedef itk::ImageFileReader< InputImageType  >  ReaderType;
>   typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>   const char * inputFilename  = "G:/My Drive/BMES2019/New
> folder/subject1.nii";
>
>   {
>                 int i = 1;
>
>                         std::string str="input//";
>                         std::string s1="slice";
>                         std::string s2 = std::to_string(i);
>                         std::string s3=".png";
>                         std::string s4=str+s1+s2+s3;
>                         const char *mycharp = s4.c_str();
>
>   const char * outputFilename = mycharp;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>   reader->SetFileName( inputFilename  );
>   writer->SetFileName( outputFilename );
>
>    typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType
> > RescaleFilterType;
>    RescaleFilterType::Pointer rescalefilter = RescaleFilterType::New();
>    rescalefilter->SetInput( reader->GetOutput() );
>
>   typedef itk::ExtractImageFilter< InputImageType,
>                                    OutputImageType > FilterType;
>   FilterType::Pointer filter = FilterType::New();
>   filter->InPlaceOn();
>   filter->SetDirectionCollapseToSubmatrix();
>    reader->UpdateOutputInformation();
>   InputImageType::RegionType inputRegion =
>            reader->GetOutput()->GetLargestPossibleRegion();
>
>   InputImageType::SizeType size = inputRegion.GetSize();
>   size[2] = 0;
>
>   InputImageType::IndexType start = inputRegion.GetIndex();
>   const unsigned int sliceNumber = stoi(s2);//atoi(argv[3]);
>   start[2] = sliceNumber;
>
>   InputImageType::RegionType desiredRegion;
>   desiredRegion.SetSize(  size  );
>   desiredRegion.SetIndex( start );
>
>   filter->SetExtractionRegion( desiredRegion );
>
>   filter->SetInput( rescalefilter->GetOutput() );
>   writer->SetInput( filter->GetOutput() );
>    try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & err )
>     {
>     std::cerr << "ExceptionObject caught !" << std::endl;
>     std::cerr << err << std::endl;
>         getchar();
>     return EXIT_FAILURE;
>     }
>     }
>   return EXIT_SUCCESS;
> }
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
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>
> Visit other Kitware open-source projects at
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<div dir=3D"ltr"><div dir=3D"ltr"><div class=3D"gmail_default" style=3D"fon=
t-family:verdana,sans-serif;font-size:small">Definitions of=C2=A0<span styl=
e=3D"font-family:monospace,monospace">RescaleFilterType</span>=C2=A0and=C2=
=A0<span style=3D"font-family:monospace,monospace">FilterType</span>=C2=A0s=
hould be like this:</div><div class=3D"gmail_default" style=3D"font-family:=
verdana,sans-serif;font-size:small"><br></div><div class=3D"gmail_default" =
style=3D"font-size:small"><div class=3D"gmail_default" style=3D""><font fac=
e=3D"monospace, monospace">typedef itk::RescaleIntensityImageFilter&lt; Inp=
utImageType, OutputImageType &gt; RescaleFilterType;</font></div><div class=
=3D"gmail_default" style=3D""><font face=3D"monospace, monospace">typedef i=
tk::ExtractImageFilter&lt; OutputImageType, OutputImageType &gt; FilterType=
;</font></div></div></div></div><br><div class=3D"gmail_quote"><div dir=3D"=
ltr" class=3D"gmail_attr">On Wed, May 8, 2019 at 1:54 PM Shrabani Ghosh &lt=
;<a href=3D"mailto:[email protected]">[email protected]</a>&gt; w=
rote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0p=
x 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I did it l=
ike this and I am getting images like this now. <br>
&lt;<a href=3D"http://itk-insight-users.2283740.n2.nabble.com/file/t396636/=
slice1.png" rel=3D"noreferrer" target=3D"_blank">http://itk-insight-users.2=
283740.n2.nabble.com/file/t396636/slice1.png</a>&gt; <br>
<br>
<br>
<br>
int main( int argc, char ** argv )<br>
{<br>
<br>
=C2=A0 //typedef signed short=C2=A0 =C2=A0 =C2=A0 =C2=A0 InputPixelType;<br=
>
=C2=A0 /*typedef unsigned char=C2=A0 =C2=A0 =C2=A0 =C2=A0InputPixelType;<br=
>
=C2=A0 typedef unsigned char=C2=A0 =C2=A0 =C2=A0 =C2=A0 OutputPixelType;*/<=
br>
=C2=A0 typedef signed short=C2=A0 =C2=A0 =C2=A0 =C2=A0InputPixelType;<br>
=C2=A0 typedef unsigned char=C2=A0 =C2=A0 =C2=A0 OutputPixelType;<br>
=C2=A0 typedef itk::Image&lt; InputPixelType,=C2=A0 3 &gt;=C2=A0 =C2=A0 Inp=
utImageType;<br>
=C2=A0 typedef itk::Image&lt; OutputPixelType, 2 &gt;=C2=A0 =C2=A0 OutputIm=
ageType;<br>
=C2=A0 typedef itk::ImageFileReader&lt; InputImageType=C2=A0 &gt;=C2=A0 Rea=
derType;<br>
=C2=A0 typedef itk::ImageFileWriter&lt; OutputImageType &gt;=C2=A0 WriterTy=
pe;<br>
=C2=A0 const char * inputFilename=C2=A0 =3D &quot;G:/My Drive/BMES2019/New<=
br>
folder/subject1.nii&quot;;<br>
<br>
=C2=A0 {<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 int i =3D 1;<br>
<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 std::string str=3D&quot;input//&quot;;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 std::string s1=3D&quot;slice&quot;;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 std::string s2 =3D std::to_string(i);<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 std::string s3=3D&quot;.png&quot;;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 std::string s4=3Dstr+s1+s2+s3;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 const char *mycharp =3D s4.c_str();<br>
<br>
=C2=A0 const char * outputFilename =3D mycharp;<br>
<br>
=C2=A0 ReaderType::Pointer reader =3D ReaderType::New();<br>
=C2=A0 WriterType::Pointer writer =3D WriterType::New();<br>
<br>
=C2=A0 reader-&gt;SetFileName( inputFilename=C2=A0 );<br>
=C2=A0 writer-&gt;SetFileName( outputFilename );<br>
<br>
=C2=A0 =C2=A0typedef itk::RescaleIntensityImageFilter&lt; InputImageType, I=
nputImageType<br>
&gt; RescaleFilterType;<br>
=C2=A0 =C2=A0RescaleFilterType::Pointer rescalefilter =3D RescaleFilterType=
::New();<br>
=C2=A0 =C2=A0rescalefilter-&gt;SetInput( reader-&gt;GetOutput() );<br>
<br>
=C2=A0 typedef itk::ExtractImageFilter&lt; InputImageType,<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0OutputImageType &gt; Fi=
lterType;<br>
=C2=A0 FilterType::Pointer filter =3D FilterType::New();<br>
=C2=A0 filter-&gt;InPlaceOn();<br>
=C2=A0 filter-&gt;SetDirectionCollapseToSubmatrix();<br>
=C2=A0 =C2=A0reader-&gt;UpdateOutputInformation();<br>
=C2=A0 InputImageType::RegionType inputRegion =3D<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0reader-&gt;GetOutput()-&gt;GetLarg=
estPossibleRegion();<br>
<br>
=C2=A0 InputImageType::SizeType size =3D inputRegion.GetSize();<br>
=C2=A0 size[2] =3D 0;<br>
<br>
=C2=A0 InputImageType::IndexType start =3D inputRegion.GetIndex();<br>
=C2=A0 const unsigned int sliceNumber =3D stoi(s2);//atoi(argv[3]);<br>
=C2=A0 start[2] =3D sliceNumber;<br>
<br>
=C2=A0 InputImageType::RegionType desiredRegion;<br>
=C2=A0 desiredRegion.SetSize(=C2=A0 size=C2=A0 );<br>
=C2=A0 desiredRegion.SetIndex( start );<br>
<br>
=C2=A0 filter-&gt;SetExtractionRegion( desiredRegion );<br>
<br>
=C2=A0 filter-&gt;SetInput( rescalefilter-&gt;GetOutput() );<br>
=C2=A0 writer-&gt;SetInput( filter-&gt;GetOutput() );<br>
=C2=A0 =C2=A0try<br>
=C2=A0 =C2=A0 {<br>
=C2=A0 =C2=A0 writer-&gt;Update();<br>
=C2=A0 =C2=A0 }<br>
=C2=A0 catch( itk::ExceptionObject &amp; err )<br>
=C2=A0 =C2=A0 {<br>
=C2=A0 =C2=A0 std::cerr &lt;&lt; &quot;ExceptionObject caught !&quot; &lt;&=
lt; std::endl;<br>
=C2=A0 =C2=A0 std::cerr &lt;&lt; err &lt;&lt; std::endl;<br>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 getchar();<br>
=C2=A0 =C2=A0 return EXIT_FAILURE;<br>
=C2=A0 =C2=A0 }<br>
=C2=A0 =C2=A0 }<br>
=C2=A0 return EXIT_SUCCESS;<br>
}<br>
<br>
<br>
<br>
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