[Insight-users] setting the spacing when writing an image to
disk : FastMarchingImageFilter
Luis Ibanez
luis.ibanez at kitware.com
Sun, 25 Apr 2004 09:59:26 -0400
Hi Lucas,
Lydia already solved your problem 5 weeks ago:
http://www.itk.org/cgi-bin/cvsweb.cgi/Insight/Code/Algorithms/itkFastMarchingImageFilter.txx.diff?r1=1.44&r2=1.45&cvsroot=Insight
That was done in order to fix Bug #624:
http://www.itk.org/Bug/bug.php?op=show&bugid=624&pos=16
You must now call the functions
fastMarchingFilter->SetOutputSpacing( ... )
fastMarchingFilter->SetOutputOrigin( ... )
fastMarchingFilter->SetOutputRegion( ... )
from Doxygen:
http://www.itk.org/Insight/Doxygen/html/classitk_1_1FastMarchingImageFilter.html
"The output largeset possible, spacing and origin is
computed as follows. If the speed image is NULL or
if the OverrideOutputInformation is true, the output
information is set from user specified parameters.
These parameters can be specified using methods
SetOutputRegion(), SetOutputSpacing() and SetOutputOrigin().
Else if the speed image is not NULL, the output information
is copied from the input speed image."
--
Of course, you must make sure that you use a CVS checkout
posterior to March 18 2004. (When that changes were made).
Regards,
Luis
-----------------------
Lucas Lorenzo wrote:
> I think I know what's the problem ... although I don't know yet how to
> solve it.
> In this application there's no input to the FastMarchingImageFilter so
> there's no way to inherit the spacing from the original image.
> The output size is set explicitly with the SetOutputSize member function
> but there's no member function to set the spacing explicitly.
> The code is the following one:
>
>
> typedef itk::FastMarchingImageFilter<InternalImageType>
> FastMarchingFilterType;
> FastMarchingFilterType::Pointer fastMarching =
> FastMarchingFilterType::New();
>
> typedef FastMarchingFilterType::NodeContainer NodeContainer;
> typedef FastMarchingFilterType::NodeType NodeType;
>
> NodeContainer::Pointer seeds = NodeContainer::New();
>
> // Choose an initial contour that is the objet to be segmented
> // The initial contour is a circle centered at {x_ini,y_ini} with radius
> // 2.0
>
> int x_ini = std::atoi(argv[10]);
> int y_ini = std::atoi(argv[11]);
> InternalImageType::IndexType seedPosition;
> seedPosition[0] = x_ini;
> seedPosition[1] = y_ini;
>
> NodeType node;
> node.SetValue( -2.0 );
> node.SetIndex( seedPosition );
>
> seeds->Initialize();
> seeds->InsertElement( 0, node );
>
> fastMarching->SetTrialPoints( seeds );
> fastMarching->SetSpeedConstant( 1.0 );
>
> //original reader reads the input image to be segmented
> OriginalImageType::RegionType inputRegion =
> original_reader->GetOutput()->GetLargestPossibleRegion();
> OriginalImageType::SizeType imageSize = inputRegion.GetSize();
> fastMarching->SetOutputSize( imageSize );
>
> try
> {
> fastMarching->Update();
> }
> catch( itk::ExceptionObject & exp )
> {
> std::cerr << "Exception caught ! fastMarching" << std::endl;
> std::cerr << exp << std::endl;
> return -1;
> }
>
> If you have any suggestions please let me know.
> Thanks,
>
> Lucas
>
>
> On Apr 24, 2004, at 11:26 AM, Luis Ibanez wrote:
>
>
> Hi Lucas,
>
> Thanks for letting us know.
>
> The message you get about regions is normal,
> it is a remanent of a debugging effort that
> we should now remove.
>
>
> About your code: please try the following,
> just after calling Update in the FastMarching
> filter add the two lines:
>
> fastMarching->GetInput()->Print( std::cout );
> fastMarching->GetOutput()->Print( std::cout );
>
> I'm wandering if the spacing of the image is
> getting lost before it arrives to the fastMarching
> filter.
>
>
> Please let us know what you find.
>
>
> Thanks
>
>
> Luis
>
>
> ---------------------------------------------
> Lucas Lorenzo wrote:
>
> Hi Luis,
> I followed your directives and it does work fine.
> I'll go over my code again and if I find what's wrong I'll let
> you know.
> Also, if you have further suggestions please let me know.
> One last comment: the following message keeps appearing when I
> run this program with my vtk file:
> lucas:Borrar> FastMarchingImageFilter slc05fr_filt06.vtk out.vtk
> 114 115 0.75 -0.4 12 10 11
> inputRequestedRegion: ImageRegion (0xbfffed60)
> Dimension: 2
> Index: [-1, -1]
> Size: [258, 258]
> largestPossibleRegion: ImageRegion (0x11004fc)
> Dimension: 2
> Index: [0, 0]
> Size: [256, 256]
> I don't know if this is useful but the header for the vtk file
> is as follows:
> # vtk DataFile Version 3.0
> VTK File Generated by Insight Segmentation and Registration
> Toolkit (ITK)
> BINARY
> DATASET STRUCTURED_POINTS
> DIMENSIONS 256 256 1
> SPACING 1.33 1.33 1.0
> ORIGIN 0 0 0.0
> POINT_DATA 65536
> SCALARS scalars unsigned_short 1
> LOOKUP_TABLE default
> Thanks,
> Lucas
> On Apr 23, 2004, at 3:43 PM, Luis Ibanez wrote:
> Hi Lucas,
> I just tested the capability of the FastMarching filter for using
> the Image Spacing, and it is working fine with the CVS version.
> Something else should be happening in your installation.
> Please do the following test:
> 1) Compile the example:
> Insight/Examples/Segmentation/
> FastMarchingImageFitler.cxx
> 2) Provide as input the .vtk image you have with pixel spacing
> different from unit
> 3) Check if the output image carries the same spacing as the
> input one.
> This tests works for me both for .vtk and .mhd (MetaImage)
> images.
> Please let us know what you find.
> Thanks
> ----------------------
> Lucas Lorenzo wrote:
> Sorry, I kept making the same mistake once and once again. I
> guess that what I meant was obvious but let's clarify it anyway:
> when I talk about the "header files" I meant the headers for the
> image files (in vtk format).
> Cheers,
> Lucas
> On Apr 22, 2004, at 10:49 AM, Lucas Lorenzo wrote:
> Hi Luis,
> I'm attaching the file GeoACPSLS.cxx (which is a modified
> version of
> itkGeodesicActiveContourShapePriorLevelSetImageFilterTest.cxx).
> When compiling against released version 1.6 the output after
> running
> one single iteration is as follows (as you see all image files are
> in vtk format):
> lucas:GeodesicAcContPrSh> GeoACPSLS PrincipalModes_fr06 5 0.75 -0.4
> 12 0.2 2.0 0.15 0.8 1 slc5_fr_filt09.vtk 112 120
> Potential map created successfully !
> ../DATAP091703/Anatomical/SLICE_05/PrincipalModes_fr06/mean.vtk
> shape components set successfully !
> Filter parameters set successfully !
> Thresholder parameters set successfully !
> 1: [0.00025, 0, 0, 0, 0, 0, 0] 0.185567
> The input file header is:
> # vtk DataFile Version 3.0
> VTK File Generated by Insight Segmentation and Registration Toolkit
> (ITK)
> BINARY
> DATASET STRUCTURED_POINTS
> DIMENSIONS 256 256 1
> SPACING 1.33 1.33 1.0
> ORIGIN 0 0 0.0
> POINT_DATA 65536
> SCALARS scalars unsigned_short 1
> LOOKUP_TABLE default
> And the header file for the vtk image resulting from the fast
> marching algorithm is like this:
> # vtk DataFile Version 3.0
> VTK File Generated by Insight Segmentation and Registration Toolkit
> (ITK)
> BINARY
> DATASET STRUCTURED_POINTS
> DIMENSIONS 256 256 1
> SPACING 1 1 1.0
> ORIGIN 0 0 0.0
> POINT_DATA 65536
> SCALARS scalars float 1
> LOOKUP_TABLE default
> When compiling against the CVS copy I checked out about one week
> and
> a half ago the output is like this:
> lucas:GeodesicAcContPrSh> GeoACPSLS PrincipalModes_fr06 5 0.75 -0.4
> 12 0.2 2.0 0.15 0.8 1 slc5_fr_filt09.vtk 112 120
> Potential map created successfully !
> ../DATAP091703/Anatomical/SLICE_05/PrincipalModes_fr06/mean.vtk
> shape components set successfully !
> Filter parameters set successfully !
> Thresholder parameters set successfully !
> inputRequestedRegion: ImageRegion (0xbfffeb80)
> Dimension: 2
> Index: [-1, -1]
> Size: [258, 258]
> largestPossibleRegion: ImageRegion (0x1101f1c)
> Dimension: 2
> Index: [0, 0]
> Size: [256, 256]
> inputRequestedRegion: ImageRegion (0xbfffeb80)
> Dimension: 2
> Index: [-1, -1]
> Size: [258, 258]
> largestPossibleRegion: ImageRegion (0x1101f1c)
> Dimension: 2
> Index: [0, 0]
> Size: [256, 256]
> 1: [0.00025, 0, 0, 0, 0, 0, 0] 0.185567
> And the header files are still as before (that is, the spacing
> problem still exists).
> I hope that this information is clear enough. If not, please let me
> know.
> Thanks for your help,
> Lucas
> <GeoACPSLS.cxx>
> On Apr 21, 2004, at 7:51 PM, Luis Ibanez wrote:
> Hi Lucas,
> Can you please post a minimal (working) example
> of code that illustrates this behavior. We need
> some initial code for reproducing the problem
> that you report.
> Thanks
> Luis
> -----------------------
> Lucas Lorenzo wrote:
> HI Luis,
> I've checked out a CVS copy last week and I still have the
> same problem.
> Also now, when running my code the following messages appear:
> inputRequestedRegion: ImageRegion (0xbfffeb70)
> Dimension: 2
> Index: [-1, -1]
> Size: [258, 258]
> largestPossibleRegion: ImageRegion (0x1101c5c)
> Dimension: 2
> Index: [0, 0]
> Size: [256, 256]
> inputRequestedRegion: ImageRegion (0xbfffeb70)
> Dimension: 2
> Index: [-1, -1]
> Size: [258, 258]
> largestPossibleRegion: ImageRegion (0x1101c5c)
> Dimension: 2
> Index: [0, 0]
> Size: [256, 256]
> Do you have any suggestions ?
> Thanks,
> Lucas
> On Feb 19, 2004, at 12:05 AM, Luis Ibanez wrote:
> Hi Lucas,
> The changes to the FastMarchingImageFilter have
> been commited. The output image now uses the
> spacing and origin of the input image.
> Please let us know if you find any problem.
> Thanks
> Luis
> ------------------------
> Lucas Lorenzo wrote:
> Hi Luis,
> sorry for answering so late.
> I've tried what you suggested but I have a run time
> error "Abort trap" when trying to apply the
> GetOutput() method to my FastMarchingImageFilter
> object.
> Let me know if there are any other changes we could
> try.
> Thanks,
> Lucas
> On Feb 11, 2004, at 5:58 AM, Luis Ibanez wrote:
> Hi Lucas,
> Thanks for pointing this out.
> Please try the following:
> Edit the file:
> Insight/Code/Algorithms/
> itkFastMarchingImageFilter.txx
> Go to to line : 150
> and after the statement
> output->Allocate();
> add
> output->CopyInformation( this->GetInput() );
> Then, go to line : 157
> and after the statement
> m_LabelImage->Allocate();
> add
> m_LabelImage->CopyInformation( this->GetInput() );
> This should copy the origin and spacing
> of the input image into the output and
> label images.
> Then recompile your application and try
> running it to see if the correct spacing
> appears in the file.
> Please let us know what you find, so we proceed
> to do the same changes in the repository.
> Thanks
> Luis
> ----------------------
> Lucas Lorenzo wrote:
> 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
> 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
> _______________________________________________
> 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
> 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
> 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
>