[Insight-users] setting the spacing when writing an image to disk
Lucas Lorenzo
lucas at cvrti.utah.edu
Sat, 24 Apr 2004 14:28:51 -0600
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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
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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
<fontfamily><param>Hei</param>SetOutputSize</fontfamily> member
function but there's no member function to set the spacing explicitly.
The code is the following one:
<fontfamily><param>Hei</param> 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;
} </fontfamily>
If you have any suggestions please let me know.
Thanks,
Lucas
On Apr 24, 2004, at 11:26 AM, Luis Ibanez wrote:
<excerpt>
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:
<excerpt>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
</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
--Apple-Mail-20--695367076--