[Insight-users] setting the spacing when writing an image to disk

[Lucas Lorenzo]

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Hi Luis,

sorry for having such a mess in my code.
I'm using an application based on  
ITK/Testing/Code/Algorithms/ 
itkGeodesicActiveContourShapePriorLevelSetImageFilterTest_2.cxx
The spacing is being carried through the pipeline with no problem,  
except when arriving to the point when I have to generate my initial  
contour (signed distance map) from a seed point using  
FastMarchingImageFilter. It is the output from this filter the one that  
has the "default" spacing (and I think that this new spacing is carried  
to the end to the output image) and I can't find any method to set the  
correct spacing.
Thanks,

Lucas


On Tuesday, February 10, 2004, at 08:38 PM, Luis Ibanez wrote:

>
> Hi Lucas,
>
> Why are you setting the spacing on the ImageIO
> object instead of the image itself ?
>
> You should just carry the spacing through the
> pipeline. Does your input image has an invalid
> spacing ?
>
> An option in that case is to use the
> ChangeInformationImageFilter
> http://www.itk.org/Insight/Doxygen/html/ 
> classitk_1_1ChangeInformationImageFilter.html
>
> This filter carries the data buffer of the
> input image to the output image, and allows
> you to alter the meta-data such as image
> origin and spacing.
>
> Please don't use this filter for processing
> images of human beings or any other living
> organisms, since chances are that you will
> make somebody operate in a liver instead of
> a lung.
>
>
> In the long term the right thing to do is
> to fix the source of your images which is
> where the real spacing information should
> be comming from.
>
>
> Regards,
>
>
>   Luis
>
>
>
> ======================================
> -------------------
> Lucas Lorenzo wrote:
>
>> Hi all,
>> I'm trying to write an image to disk in vtk format.
>> By default the spacing is set to 1 1 1. I'd like to change it so I'm  
>> doing the following:
>> /#include "itkVTKImageIO.h"
>> int main( int argc, char * argv[] )
>> {
>> /* /* Typedefs of components. */*/
>> const unsigned int ImageDimension = 2;
>> typedef unsigned char BinaryPixelType;
>> typedef itk::Image<BinaryPixelType,ImageDimension> BinaryImageType;
>> /*// read the input image and get the spacing from it:*/
>> typedef itk::VTKImageIO ImageIOType;
>> ImageIOType::Pointer IO1 = ImageIOType::New();
>> original_reader->SetImageIO(IO1);
>> double dx,dy,dz;
>> original_reader->Update();
>> dx = IO1->GetSpacing(0);
>> dy = IO1->GetSpacing(1);
>> dz = IO1->GetSpacing(2);
>> /*// here I'm omitting when I process the input image
>> // write the image to a file but perviously set the spacing
>> */
>> binary_writer->SetFileName("out.vtk");
>> binary_writer->SetInput(thresholder->GetOutput());
>> ImageIOType::Pointer IO2 = ImageIOType::New();
>> IO2->SetSpacing(0,dx);
>> IO2->SetSpacing(1,dy);
>> IO2->SetSpacing(2,dz);
>> binary_writer->SetImageIO(IO2);
>> try
>> {
>> binary_writer->Update();
>> }
>> catch( itk::ExceptionObject & exp )
>> {
>> std::cerr << "Exception caught ! binary image writer" << std::endl;
>> std::cerr << exp << std::endl;
>> return -1;
>> }
>> return 0;
>> }
>> /
>> When I execute this program I have a "segmentation fault" run time  
>> error.
>> If I ommit the line setting the spacing in the z axis ("/  
>> IO2->SetSpacing(2,dz); /") the programs executes without crashing but  
>> the spacing is not really set, that is, in the header of the output  
>> vtk file (out.vtk) you can still see "SPACING 1 1 1.0" instead of  
>> "SPACING dx dy 1.0".
>> Any clue of what am I doing wrong ?
>> Thanks,
>> Lucas Lorenzo
>> University of Utah
>> Nora Eccles Harrison CardioVascular Research and Training Institute
>> Fellows Room
>> 95 South 2000 East
>> Salt Lake City, UT 84112-5000
>> e-mail: lucas at cvrti.utah.edu
>> telephone: 801-587-9536
>
>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
Lucas Lorenzo

University of Utah
Nora Eccles Harrison CardioVascular Research and Training Institute
Fellows Room
95 South 2000 East
Salt Lake City, UT 84112-5000

e-mail:  lucas at cvrti.utah.edu
telephone: 801-587-9536

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Hi Luis,


sorry for having such a mess in my code.

I'm using an application based on
<fontfamily><param>Times New Roman</param>ITK/Testing/Code/Algorithms/itkGeodesicActiveContourShapePriorLevelSetImageFilterTest_2.cxx</fontfamily>

The spacing is being carried through the pipeline with no problem,
except when arriving to the point when I have to generate my initial
contour (signed distance map) from a seed point using
FastMarchingImageFilter. It is the output from this filter the one
that has the "default" spacing (and I think that this new spacing is
carried to the end to the output image) and I can't find any method to
set the correct spacing.

Thanks,


Lucas



On Tuesday, February 10, 2004, at 08:38 PM, Luis Ibanez wrote:


<excerpt>

Hi Lucas,


Why are you setting the spacing on the ImageIO

object instead of the image itself ?


You should just carry the spacing through the

pipeline. Does your input image has an invalid

spacing ?


An option in that case is to use the

ChangeInformationImageFilter

http://www.itk.org/Insight/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html


This filter carries the data buffer of the

input image to the output image, and allows

you to alter the meta-data such as image

origin and spacing.


Please don't use this filter for processing

images of human beings or any other living

organisms, since chances are that you will

make somebody operate in a liver instead of

a lung.



In the long term the right thing to do is

to fix the source of your images which is

where the real spacing information should

be comming from.



Regards,



  Luis




======================================

-------------------

Lucas Lorenzo wrote:


<excerpt>Hi all,

I'm trying to write an image to disk in vtk format.

By default the spacing is set to 1 1 1. I'd like to change it so I'm
doing the following:

/#include "itkVTKImageIO.h"

int main( int argc, char * argv[] )

{

/* /* Typedefs of components. */*/

const unsigned int ImageDimension = 2;

typedef unsigned char BinaryPixelType;

typedef itk::Image<<BinaryPixelType,ImageDimension> BinaryImageType;

/*// read the input image and get the spacing from it:*/

typedef itk::VTKImageIO ImageIOType;

ImageIOType::Pointer IO1 = ImageIOType::New();

original_reader->SetImageIO(IO1);

double dx,dy,dz;

original_reader->Update();

dx = IO1->GetSpacing(0);

dy = IO1->GetSpacing(1);

dz = IO1->GetSpacing(2);

/*// here I'm omitting when I process the input image

// write the image to a file but perviously set the spacing

*/

binary_writer->SetFileName("out.vtk");

binary_writer->SetInput(thresholder->GetOutput());

ImageIOType::Pointer IO2 = ImageIOType::New();

IO2->SetSpacing(0,dx);

IO2->SetSpacing(1,dy);

IO2->SetSpacing(2,dz);

binary_writer->SetImageIO(IO2);

try

{

binary_writer->Update();

}

catch( itk::ExceptionObject & exp )

{

std::cerr <<<< "Exception caught ! binary image writer" <<<< std::endl;

std::cerr <<<< exp <<<< std::endl;

return -1;

}

return 0;

}

/

When I execute this program I have a "segmentation fault" run time
error.

If I ommit the line setting the spacing in the z axis ("/
IO2->SetSpacing(2,dz); /") the programs executes without crashing but
the spacing is not really set, that is, in the header of the output
vtk file (out.vtk) you can still see "SPACING 1 1 1.0" instead of
"SPACING dx dy 1.0".

Any clue of what am I doing wrong ?

Thanks,

Lucas Lorenzo

University of Utah

Nora Eccles Harrison CardioVascular Research and Training Institute

Fellows Room

95 South 2000 East

Salt Lake City, UT 84112-5000

e-mail: lucas at cvrti.utah.edu

telephone: 801-587-9536

</excerpt>



_______________________________________________

Insight-users mailing list

Insight-users at itk.org

http://www.itk.org/mailman/listinfo/insight-users


</excerpt>Lucas Lorenzo


University of Utah

Nora Eccles Harrison CardioVascular Research and Training Institute

Fellows Room

95 South 2000 East

Salt Lake City, UT 84112-5000


e-mail:  lucas at cvrti.utah.edu

telephone: 801-587-9536


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