[Insight-users] Image index limits
Robert.Atwood at diamond.ac.uk
Robert.Atwood at diamond.ac.uk
Tue Jan 12 07:02:25 EST 2010
Hi,
I have tried Oleksandr's program on our system ( RedHat 5.3, 32 Gb
memory, Lustre file system ) and I can report that I have observed the
problem when using .hdr format output but not with .mhd format output.
Using the .hdr format I observe exactly the same critical boundary ,
slice 104.
My ITK was built Nov 4, 2009 from cvs on that date.
Test 1: .mhd
1. Run ImageFill_Cube test.mhd
2. Use another utility to examine x-z slice y=700 -- looks correct
3. run JustReadWrite test.mhd after.mhd
4. Use another utility to examine x-z slice y=700 of after.raw -- looks
correct (see th_090_vsl_700_after.raw.jpg)
Test 2. .hdr
1. Run ImageFill_Cube test.hdr
2. Use another utility to examine x-z slice y=700 -- looks correct
3. Run JustReadWrite test.hdr after.hdr
4. Use another utility to examine x-z slice y=700 of after.img -- looks
INCORRECT ( see th_090_vsl_700_after.img.jpg)
The only difference in these tests was to use .hdr as the file format
extension rather than .mhd
I hope this helps pinpoint the problems.
Robert
-----Original Message-----
From: insight-users-bounces at itk.org
[mailto:insight-users-bounces at itk.org] On Behalf Of
Robert.Atwood at diamond.ac.uk
Sent: 11 January 2010 10:05
To: insight-users at itk.org
Subject: Re: [Insight-users] Image index limits
Hi,
I had a similar problem .. Only I attributed it to a different source
and thus did not mention it here.
If I had large multi-slice TIFF files, some later slices became entirely
zero. However if I stored the data in .raw/.mhd or in multiple
single-slice TIFF, then I had no problem.
In this case the slices were 6000x4000 and all slices after slice 10
were coming up zero.
I simply assumed that multi-slice TIFF was not suitable for this case
and didn't use this format. If in fact there's a problem in the itk
code, rather than TIFF limitations, I am happy to investigate this a
little further. I hadn't tried any other formats.
The code I was using simply reads the image then writes it , but with
axes permuted (changes a projection series into a sinogram series)
Robert
-----Original Message-----
From: insight-users-bounces at itk.org
[mailto:insight-users-bounces at itk.org] On Behalf Of Oleksandr Dzyubak
Sent: 07 January 2010 22:29
To: Bill Lorensen
Cc: insight-users at itk.org; Luis Ibanez
Subject: Re: [Insight-users] Image index limits
Hi Bill,
I am still working on a large image limitation problem.
This time let me get rid of all nuances
that keep drawing us away from the point.
First, dear ITK users, I am very sorry but to still stay on this forum
list, I have to cut attached answers. Otherwise the nabble system will
bounce me off.
Now let the party begin.
1) At this point I only use "itkImage.h" and "itkImageFileWriter.h".
I wrote a code (attached below) which allocates a 1340x1300x720 buffer
to hold a "float" pixel type, fill in some voxel values, and write the
final result down.
a) This code does not use any external image files.
b) This code first fills up the entire volume with Intensity I=100;
c) Since I already know that the "problematic boundary" is
slice# 104, I create two 100x100x100 cubes with Intensity=1000:
first cube is before the critical boundary and the second one is
after.
d) Write the result down using the "itkImageFileWriter.h"
What is the result?
Both cubes are where they supposed to be with correct intensities.
So no more discussions about Debian Linux, gcc 4.3.2 limitations,
C++ container and memory limits.
All the above supports the volumes I need and the ITK library can
perfectly handle this.
Now lets try to find out where the real problem resides.
2) At this point I am going to use "itkImage.h", "itkImageFileWriter.h".
and "itkImageFileReader.h".
I wrote a code (attached below) to make plain reading the image from a
file and writing it down to another file. Nothing fancy.
A test image is the image produced by the program above:
two cubes at the beginning and the end of the image.
What is the result?
Surprise! Second cube disappeared and all slices after the critical
boundary are empty.
Thus I conclude that these are not Gaussians and Gaussian derivatives
which generate a problem.
There is something wrong with the "itkImageFileReader.h" class.
Well, it is getting warmer.
I would predict that we can solve the problem very soon.
Bill, what would you say?
Regards,
Alex
****** Begin ImageFill_cube.cxx ***
#include "itkImage.h"
#include "itkImageFileWriter.h"
int main(int argc, char * argv[])
{
if( argc < 2 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " outputImageFile" << std::endl;
return 1;
}
const unsigned int Dimension = 3;
// typedef unsigned char PixelType;
// typedef unsigned int PixelType;
// typedef short PixelType;
typedef float PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::Pointer image = ImageType::New();
// The image region should be initialized
ImageType::IndexType start;
ImageType::SizeType size;
size[0] = 1340; // size along X
size[1] = 1300; // size along Y
size[2] = 720; // size along Z
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
ImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
// Pixel data is allocated
image->SetRegions( region );
image->Allocate();
// The image buffer is initialized to a particular value
ImageType::PixelType initialValue = 100;
image->FillBuffer( initialValue );
ImageType::IndexType pixelIndex;
ImageType::IndexType initialPixelIndex;
ImageType::PixelType pixelValue = 1000;
initialPixelIndex[0] = 670; // x position
initialPixelIndex[1] = 650; // y position
initialPixelIndex[2] = 0; // z position
std::cout << std::endl;
std::cout << "pixelIndex = " << pixelIndex << std::endl;
std::cout << std::endl;
// Lets draw two cubes 100x100x100 with intensity I=1000; // Before the
critical boundary pixelIndex[2]=104 and after.
for (int i=0; i<100; i++)
{
pixelIndex[0] = initialPixelIndex[0] + i;
for(int j=0; j<100; j++)
{
pixelIndex[1] = initialPixelIndex[1] + j;
for(int k=0; k<100; k++)
{
pixelIndex[2] = initialPixelIndex[2] + k;
image->SetPixel( pixelIndex, pixelValue );
// std::cout << "pixelIndex = " << pixelIndex << std::endl;
// std::cout << "pixelValue = " << image->GetPixel(
pixelIndex ) << std::endl;
}
}
}
initialPixelIndex[0] = 670; // x position
initialPixelIndex[1] = 650; // y position
initialPixelIndex[2] = 360; // z position
for (int i=0; i<100; i++)
{
pixelIndex[0] = initialPixelIndex[0] + i;
for(int j=0; j<100; j++)
{
pixelIndex[1] = initialPixelIndex[1] + j;
for(int k=0; k<100; k++)
{
pixelIndex[2] = initialPixelIndex[2] + k;
image->SetPixel( pixelIndex, pixelValue );
// std::cout << "pixelIndex = " << pixelIndex << std::endl;
// std::cout << "pixelValue = " << image->GetPixel(
pixelIndex ) << std::endl;
}
}
}
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[1] );
writer->SetInput( image );
try
{
writer->Update();
}
catch( itk::ExceptionObject & exp )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << exp << std::endl;
}
return EXIT_SUCCESS;
}
****** End ImageFill_cube.cxx *****
****** Begin JustReadWrite.cxx ***
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
int main( int argc, char * argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0] << std::endl;
std::cerr << " inputImageFile outputImageFile " << std::endl;
return EXIT_FAILURE;
}
const unsigned int Dimension = 3;
// typedef unsigned char PixelType;
// typedef unsigned int PixelType;
// typedef short PixelType;
typedef float PixelType;
typedef itk::Image< PixelType, Dimension > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( argv[1] );
writer->SetFileName( argv[2] );
writer->SetInput( reader->GetOutput() );
writer->Update();
try
{
writer->Update();
}
catch( itk::ExceptionObject & exp )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << exp << std::endl;
}
return EXIT_SUCCESS;
}
****** End JustReadWrite.cxx ***
Bill Lorensen wrote:
> This code is incorrect:
> for (int i=0; i<10; i++)
> {
> pixelIndex[0] += pixelIndex[0];
> ImageType::PixelType pixelValue = image->GetPixel( pixelIndex );
> std::cout << "pixelValue = " << pixelValue << std::endl;
> }
>
> pixelIndex[0] rapidly gets out of range.
>
>
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.html
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users
--
This e-mail and any attachments may contain confidential, copyright and
or privileged material, and are for the use of the intended addressee
only. If you are not the intended addressee or an authorised recipient
of the addressee please notify us of receipt by returning the e-mail and
do not use, copy, retain, distribute or disclose the information in or
attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual
and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any
attachments are free from viruses and we cannot accept liability for any
damage which you may sustain as a result of software viruses which may
be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in
England and Wales with its registered office at Diamond House, Harwell
Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
Kingdom
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.html
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
http://www.itk.org/mailman/listinfo/insight-users
--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
-------------- next part --------------
A non-text attachment was scrubbed...
Name: th_090_vsl_700_after.img.jpg
Type: image/jpeg
Size: 16726 bytes
Desc: th_090_vsl_700_after.img.jpg
URL: <http://www.itk.org/pipermail/insight-users/attachments/20100112/67487aa2/attachment-0002.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: th_090_vsl_700_after.raw.jpg
Type: image/jpeg
Size: 17348 bytes
Desc: th_090_vsl_700_after.raw.jpg
URL: <http://www.itk.org/pipermail/insight-users/attachments/20100112/67487aa2/attachment-0003.jpg>
More information about the Insight-users
mailing list