[vtkusers] correction of spacing

[Dominik Szczerba]

you need something like:

vtkImageData* image = reader->GetOutput();
image->SetSpacing(spacing);
// check with image->GetSpacing(spacing);

Dominik

Bartosz Wiklak wrote:
> 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?
>>>>> _______________________________________________
>>>>> This is the private VTK discussion list.
>>>>> Please keep messages on-topic. Check the FAQ at:
>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>
>>>> --
>>>> 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
>>
> 

-- 
Dominik Szczerba, PhD
Computational Physics Group
IT'IS Foundation
http://www.itis.ethz.ch