[Insight-users] Is it silly to attempt this ?

[Emma Ryan]

Hello Luis,

  Thank you for your reply. My image is 256 x 256 x 32. I have 512Mb ram. No computer does not seem to swapping memory.
I used .mha file instead of .vtk for the deformation field and it was quick and correct.

So, does the warper not accept .vtk files ?  I tried to debug the code to see where the program  takes forever and it seemed to be in the ImageFilereader (deformation field type)

The imageReader should expect a certain byte size and I am sure there are that  many bytes in the file, so I'm not sure what the problem is.

Emma


----- Original Message ----
From: Luis Ibanez <luis.ibanez at kitware.com>
To: Emma Ryan <eryanvtk at yahoo.com>
Cc: insight-users at itk.org
Sent: Saturday, February 23, 2008 8:00:34 PM
Subject: Re: [Insight-users] Is it silly to attempt this ?




Hi 
Emma,

The 
source 
code 
that 
you 
posted 
seems 
to 
be 
reasonable.


However, 
a 
duration 
of 
2 
hours 
for 
warping 
an 
image
sounds 
like 
an 
excesive 
time.


1) 
How 
big 
is 
your 
image 
?
  
  
  
pixels 
along 
X
  
  
  
pixels 
along 
Y
  
  
  
pixels 
along 
Z


2) 
How 
much 
RAM 
do 
you 
have 
?


3) 
Have 
you 
checked 
if 
your 
computer
  
  
is 
not 
swapping 
memory 
?

  
  
(you 
can 
check 
this 
on 
Windows 
by 
looking
  
  
 
at 
the 
Task 
Manager, 
or 
in 
Linux 
by 
using
  
  
 
the 
top 
tool, 
or 
the 
system 
information 
tool.)


Please 
let 
us 
know,


  
 
Thanks


  
  
Luis


----------------
Emma 
Ryan 
wrote:
> 
Hi,
>  
>  
 
I 
am 
trying 
to 
read 
in 
a 
3D 
deformationField.vtk 
file 
and 
apply 
it 
to 
> 
a 
3D 
image. 
To 
read 
the 
deformation 
field, 
I 
use 
ImageFileReader 
> 
<deformafieldType>  
and 
then 
connect 
the 
output 
of 
this 
to 
the 
warper.
> 
> 
The 
code 
for 
this 
is 
available 
below.  
It 
seems 
to 
take 
forever 
to 
read 
> 
the 
deformation 
field 
file.  
Even 
after 
2 
hours, 
the 
reading 
is 
not 
> 
complete. 
What 
is 
going 
on 
?  
Any 
clues 
?
> 
> 
Thanks,
> 
Emma
> 
> 
> 
#if 
defined(_MSC_VER)
> 
#pragma 
warning 
( 
disable 
: 
4786 
)
> 
#endif
> 
> 
#include 
"itkImageFileReader.h"
> 
#include 
"itkImageFileWriter.h"
> 
> 
#include 
"itkImageRegionIterator.h"
> 
> 
> 
#include 
"itkCastImageFilter.h"
> 
#include 
"itkWarpImageFilter.h"
> 
#include 
"itkLinearInterpolateImageFunction.h"
> 
> 
#include 
"itkSquaredDifferenceImageFilter.h"
> 
#include 
"itkCheckerBoardImageFilter.h"
> 
#include 
"itkTimeProbe.h"  
  
  
> 
> 
#include 
"itkImageRegionIteratorWithIndex.h"
> 
#include 
"itkPointSet.h"
> 
#include 
<fstream>
> 
> 
> 
> 
int 
main( 
int 
argc, 
char 
*argv[] 
)
> 
{
>  
  
 
if( 
argc 
< 
4 
)
>  
  
 
{
>  
  
  
  
 
std::cerr 
<< 
"Missing 
Parameters 
" 
<< 
std::endl;
>  
  
  
  
 
std::cerr 
<< 
"Usage: 
" 
<< 
argv[0];
>  
  
  
  
 
std::cerr 
<< 
" 
fixedImagefile 
movingImageFile 
deformField.vtk 
";
>  
  
  
  
 
std::cerr 
<< 
" 
outputImageFile 
" 
<< 
std::endl;
>  
  
  
  
 
return 
1;
>  
  
 
}
> 
>  
  
>  
  
 
const 
unsigned 
int 
Dimension 
= 
3;
>  
  
 
typedef 
unsigned 
char 
PixelType;
> 
> 
>  
  
 
typedef 
itk::Image< 
PixelType, 
Dimension 
>  
FixedImageType;
>  
  
 
typedef 
itk::ImageFileReader< 
FixedImageType 
> 
FixedImageReaderType;
>  
  
 
FixedImageReaderType::Pointer 
fixedImageReader 
= 
> 
FixedImageReaderType::New();
>  
  
 
fixedImageReader->SetFileName( 
argv[1] 
);
> 
>  
  
>  
  
 
typedef 
itk::Image< 
PixelType, 
Dimension 
>  
MovingImageType;
>  
  
 
typedef 
itk::ImageFileReader< 
MovingImageType 
> 
MovingImageReaderType;
>  
  
 
MovingImageReaderType::Pointer 
movingImageReader 
= 
> 
MovingImageReaderType::New();
>  
  
 
movingImageReader->SetFileName( 
argv[2] 
);
> 
>  
  
  
  
 
typedef 
itk::Vector< 
float, 
Dimension 
>  
  
VectorPixelType;
>  
  
 
typedef 
itk::Image<  
VectorPixelType, 
Dimension 
> 
DeformationFieldType;
> 
>  
  
 
typedef 
itk::ImageFileReader< 
DeformationFieldType 
>  
FieldReaderType;
>  
  
 
FieldReaderType::Pointer 
fieldReader 
= 
FieldReaderType::New();
> 
>  
  
 
fieldReader->SetFileName( 
argv[3] 
);
> 
>  
 
>  
  
try 
{
> 
>  
  
 
fieldReader->Update();
>  
  
}
> 
>  
  
catch 
( 
itk::ExceptionObject 
& 
err 
)
>  
  
{
>  
  
 
std::cerr 
<< 
"ExceptionObject 
caught 
!" 
<< 
std::endl;
>  
  
 
std::cerr 
<< 
err 
<< 
std::endl;
>  
  
 
return 
-1;
>  
  
 
}
> 
> 
>  
  
>  
  
 
typedef 
itk::WarpImageFilter<MovingImageType, 
> 
MovingImageType,DeformationFieldType  
>  
  
 
WarperType;
>  
  
 
typedef 
itk::LinearInterpolateImageFunction<MovingImageType, 
double  
>  
>  
InterpolatorType;
>  
  
 
WarperType::Pointer 
warper 
= 
WarperType::New();
>  
  
 
InterpolatorType::Pointer 
interpolator 
= 
InterpolatorType::New();
>  
  
 
FixedImageType::Pointer 
fixedImage 
= 
fixedImageReader->GetOutput();
> 
>  
 
>  
  
 
warper->SetInput( 
movingImageReader->GetOutput() 
);
>  
  
 
warper->SetInterpolator( 
interpolator 
);
>  
  
 
warper->SetOutputSpacing( 
fixedImage->GetSpacing() 
);
>  
  
 
warper->SetOutputOrigin( 
fixedImage->GetOrigin() 
);
> 
>  
  
 
warper->SetDeformationField( 
fieldReader->GetOutput() 
);
> 
>  
>  
  
 
typedef  
unsigned 
char  
OutputPixelType;
>  
  
 
typedef 
itk::Image< 
OutputPixelType, 
Dimension 
> 
OutputImageType;
>  
  
 
typedef 
itk::CastImageFilter<
>  
  
  
  
 
MovingImageType,
>  
  
  
  
 
OutputImageType 
> 
CastFilterType;
>  
  
 
typedef 
itk::ImageFileWriter< 
OutputImageType 
>  
WriterType;
> 
>  
>  
  
 
WriterType::Pointer  
  
  
writer 
=  
WriterType::New();
>  
  
 
CastFilterType::Pointer  
caster 
=  
CastFilterType::New();
> 
>  
  
 
writer->SetFileName( 
argv[4] 
);
> 
>  
  
>  
  
 
caster->SetInput( 
warper->GetOutput() 
);
>  
  
 
writer->SetInput( 
caster->GetOutput()  
 
);
>  
  
 
writer->Update();
> 
>  
 
>  
  
 
return 
0;
> 
}
> 
> 
> 
> 
------------------------------------------------------------------------
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> 
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> 
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> 
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