[vtkusers] correction of spacing

[Bartosz Wiklak]

Oh, I'm really NEW to VTK (2 weeks of heavy learning and some attempts
before), so please be more specific.
Why should I get mesh out, ist't it the same?:

reader->GetOutput()->SetSpacing(...)

> mesh = reader->GetOutput();
> mesh->SetSpacing(...)

?

What I should do further?

Really thanks for kind help.

On Mon, Nov 24, 2008 at 11:37 PM, Dominik Szczerba <dominik at itis.ethz.ch> wrote:
> Fist of all get the mesh out of the reader:
>
> mesh = reader->GetOutput();
> mesh->SetSpacing(...)
>
> Dominik
>
> Bartosz Wiklak wrote:
>>
>> Hi, thanks for answear
>>
>> If I understand, you suggested to use reader->Update() or
>> reader->GetOutput()->Update().
>> It doesn't work for me, I still can see that spacing is wrong.
>>
>> I'm not sure, but after some actions UpdateInformation is called
>> automatically.
>> Sample code:
>>
>>  spacing[2] = 1.5;
>>
>>  reader->GetOutput()->SetSpacing(spacing);
>>
>>  reader->Update();
>>
>>  reader->GetOutput()->UpdateInformation();
>>
>>  reader->GetOutput()->GetSpacing(spacing);
>>
>>
>> or
>>
>>  spacing[2] = 1.5;
>>
>>  reader->GetOutput()->SetSpacing(spacing);
>>
>>  reader->GetOutput()->Update();
>>
>>  reader->GetOutput()->UpdateInformation();
>>
>>  reader->GetOutput()->GetSpacing(spacing);
>>
>> Gives me spacing[2]==1.0
>>
>>
>> What can I do?
>>
>> Bartek
>>
>>
>> On Mon, Nov 24, 2008 at 7:58 PM, Dominik Szczerba <dominik at itis.ethz.ch>
>> wrote:
>>>
>>> Haha! - see my recent posts.
>>> Try updating the pipeline with the correct spacing.
>>>
>>> Dominik
>>>
>>> Bartosz Wiklak wrote:
>>>>
>>>> Hello,
>>>>
>>>> I'm using GDCM  ( vtkGDCMImageReader ) to read some MR data.
>>>> I switched  SetComputeZSpacing on, set SetZSpacingTolerance to 1e-2
>>>> and used IPPSorter.
>>>> This is my code:
>>>>
>>>>  vtkGDCMImageReader *reader = vtkGDCMImageReader::New();
>>>>
>>>>
>>>>
>>>>       std::vector<std::string> filenames;
>>>>
>>>>
>>>>
>>>>       gdcm::Directory d;
>>>>
>>>>
>>>>
>>>>       d.Load( "/home/basiek/Dokumenty/dcms/testGLOWA/1", false );
>>>>
>>>>
>>>>
>>>>       filenames = d.GetFilenames();
>>>>
>>>>       gdcm::IPPSorter s;
>>>>
>>>>       s.SetComputeZSpacing( true );
>>>>
>>>>       s.SetZSpacingTolerance( 1e-2 );
>>>>
>>>>       bool b = s.Sort( filenames );
>>>>
>>>>       if( !b )
>>>>
>>>>               {
>>>>
>>>>               std::cerr << "Failed to sort:" << "s" << std::endl;
>>>>
>>>>               return 1;
>>>>
>>>>               }
>>>>
>>>>
>>>>
>>>>       std::cout << "Sorting succeeded:" << s.GetZSpacing() << std::endl;
>>>>
>>>>       //s.Print( std::cout );
>>>>
>>>>
>>>>
>>>>       const std::vector<std::string> & sorted = s.GetFilenames();
>>>>
>>>>
>>>>
>>>>       vtkStringArray *files = vtkStringArray::New();
>>>>
>>>>       std::vector< std::string >::const_iterator it = sorted.begin();
>>>>
>>>>       for( ; it != sorted.end(); ++it)
>>>>
>>>>       {
>>>>
>>>>       const std::string &f = *it;
>>>>
>>>>       files->InsertNextValue( f.c_str() );
>>>>
>>>>       }
>>>>
>>>>       reader->SetFileNames( files );
>>>>
>>>>       reader->Update();
>>>>
>>>> I'm getting zspacing 1.5 whitch is ok, but in the
>>>> reader->GetOutput()->GetSpacing(spacing) I'm getiing spacing[2]==1.0 !
>>>>
>>>> What am I doing wrong?
>>>> I tried to set pixelspacing manually but after
>>>> reader->GetOutput()->UpdateInformation() I'm with old, wrong value
>>>> again.
>>>>
>>>> When I make reslice in coronal I have eyes shaped like ellipses. I
>>>> tired to set pixelspacing for vtkImageReslice:
>>>> reslice->SetOutputSpacing( spacing[0], spacing[1], 1.5 );
>>>>
>>>> but this also makes no difference regardless
>>>> reslice->GetOutput()->UpdateInformation().
>>>>
>>>> Can someone point me in the right direction?
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>>>>
>>> --
>>> Dominik Szczerba, PhD
>>> Computational Physics Group
>>> IT'IS Foundation
>>> http://www.itis.ethz.ch
>>>
>>
>
> --
> Dominik Szczerba, PhD
> Computational Physics Group
> IT'IS Foundation
> http://www.itis.ethz.ch
>