[Insight-users] Re: Writing 3D image from text file?

[Luis Ibanez]

Hi Ekta,

What is the message that the exception give you ?


You are probably having trouble because you are using a
PNG fileformat in order to save a 3D image.


          PNG only supports 2D images.


You may want to use a different file format, such as
VTK, MetaImage or Analyze, for saving your image.

You will find a list of the file format supported
in the ITK Software Guide:


    http://www.itk.org/ItkSoftwareGuide.pdf

in the Chapter "Reading and Writing Images"



    Regards,



       Luis



------------------
ekta amar wrote:
> Dear Luis,
> 
> The answers to all of your questions is Yes..I want to see points (text 
> file) which are in space as pixels in 3D image.
> 
> As per told by you I tried to write an image (/just one single point for 
> try/) but unable to write it...
> I used the command *writer -> SetInput(image)* where /*image*/ is 
> variable where my pixel index and pixel value is stored.
> 
> I'm not able to write the image. Everytime I'm getting error Exception 
> object caught.
> 
> Following is my code I used to write.
> 
> Please go through it and let me know where I'm doing wrong.
> 
> In case I've to read points from file then I've to modify the 
> pixelIndex? Is it right?  
> 
> 
> #include "itkImage.h"
> 
> #include "itkPoint.h"
> 
> #include " itkImageFileWriter.h"
> 
>  int main()
> 
> {
> 
> typedef itk::Image< unsigned short, 3 > ImageType;
> 
> ImageType::Pointer image = ImageType::New();
> 
> ImageType::IndexType start;
> 
> ImageType::SizeType size;
> 
> size[0] = 200; // size along X
> 
> size[1] = 200; // size along Y
> 
> size[2] = 200; // 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 );
> 
> 
> 
> image->SetRegions( region );
> 
> image->Allocate();
> 
> image->FillBuffer( 0 );
> 
> 
> 
> ImageType::SpacingType spacing;
> 
> spacing[0]= 0.33;
> 
> spacing[1]= 0.33;
> 
> spacing[2]= 1.20;
> 
> image ->SetSpacing( spacing );
> 
> ImageType::PointType origin;
> 
> origin[0] = 0;
> 
> origin[1] = 0;
> 
> origin[2] = 0;
> 
> image -> SetOrigin (origin);
> 
> typedef itk::Point< float, ImageType::ImageDimension > PointType;
> 
> PointType point;
> 
> point[0] = 1.45;
> 
> point[1] = 7.21;
> 
> point[2] = 9.28;
> 
> ImageType::IndexType pixelIndex;
> 
> bool isInside = image -> TransformPhysicalPointToIndex ( point, 
> pixelIndex );
> 
> if (isInside)
> 
> {
> 
> ImageType::PixelType pixelValue = image ->GetPixel(pixelIndex);
> 
> pixelValue += 5;
> 
> image -> SetPixel( pixelIndex, pixelValue );
> 
> }
> 
> typedef itk::ImageFileWriter< ImageType > WriterType;
> 
> WriterType::Pointer writer = WriterType::New();
> 
> char pic[200] = " try12.png";
> 
> const char * outputFilename = pic;
> 
> writer->SetFileName( outputFilename );
> 
> *writer ->SetInput(image ); //Not able to write image..
> *
> try
> 
> {
> 
> writer->Update();
> 
> std::cerr << "Success" << std::endl;
> 
> }
> 
> catch( itk::ExceptionObject & err )
> 
> {
> 
> std::cerr << "ExceptionObject caught !" << std::endl;
> 
> std::cerr << err << std::endl;
> 
> return EXIT_FAILURE;
> 
> }
> 
> 
> 
> return 0;
> 
> }
>  
> Please tell how can I modify this writer command to write the image 
> properly.
>  
> Thanks,
> Ekta
>  
> ----- Original Message -----
> From: "Luis Ibanez" <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>>
> To: "Ekta Amar" <amar.3 at osu.edu <mailto:amar.3 at osu.edu>>
> Cc: "ITK" <Insight-users at itk.org <mailto:Insight-users at itk.org>>
> Sent: Friday, December 29, 2006 11:14 AM
> Subject: Re: Writing 3D image from text file?
> 
>  
>  >
>  > Hi Ekta,
>  >
>  > What are the x,y,z coordinates representing ?
>  >
>  > Points in space ?
>  >
>  > Would you like to see them as pixels turned on in a 3D image ?
>  >
>  > You could do
>  >
>  > 1) Create an image whose physical extent covers all the points.
>  > 2) Initialize the image pixels to zero
>  > 3) Do a for loop over all the points and invoke the image method
>  >    PhysicalPointToIndex(), then take that index and invoke the
>  >    image method SetPixe(index,value) in order to set the pixel to
>  >    a high value.
>  > 4) Write the image to a file using the ImageFileWriter
>  >
>  >
>  >
>  > Regards,
>  >
>  >
>  >    Luis
>  >
>  >
>  >
>  > ---------------
>  > Ekta Amar wrote:
>  >> Hello Luis,
>  >> 
>  >> Is there any way I can read a text file having x, y, and z co-ordinates
>  >> and write it as a 3D image?
>  >> 
>  >> I'm able to read a text file but I'm not getting how can I 
> make/write  a
>  >> 3D image from that text file.
>  >> 
>  >> I tried using Image2.cxx example which explains reading from a file but
>  >> when I'm using .txt file to read it is giving me error, which I can
>  >> understand is not correct format.
>  >> 
>  >> Is there a way I can read text file and create a 3D image from that.
>  >> 
>  >> Please help me,
>  >> 
>  >> Thanks,
>  >> Ekta
>  >>
>