[vtkusers] Problems with TIFF Writer while writing a volume

[Amy Squillacote]

Hi Enkelejda,

I'm not sure whether this is what's causing your problems, but 
FileDimensionality for the vtkTIFFReader should be set to 2 if you're 
reading a series of images. This is because each of the tiff images you 
are reading contains a 2D slice of your 3D dataset, so the 
dimensionality of the data in each file is 2D.

- Amy

Enkelejda Tafaj wrote:
> Hi,
>
> I'm using the vtkTIFFWriter to convert a 8-bit tiff image sequence into a volume. In my application I go through following steps:
>
> 1. Using the vtkTiffReader I first read a sequence of 50 8-bit tiff images. Thereby I'm setting the file dimensionality to 3.
>
> 2. In a second step I'm using a Gaussian filter to smooth the image stack. 
>
> 3. At the end i would like to write out the filter result as a volume. If i use the TIFFWriter like below, it writes out a concatenation of the image sequence along the y axis. I don't get a volume but one very long image. 
>
> What am I doing wrong? 
>
> Thanks for your help!
>
> Enkelejda
>
>
>
>   // 1. reading image sequence
>   vtkTIFFReader *imageReader = vtkTIFFReader::New();
>   imageReader->SetFilePrefix("image_");
>   imageReader->SetFilePattern("%s%.d.tif");
>   imageReader->SetFileDimensionality(3);
>   imageReader->SetDataExtent(0,299,0,299,1,50);
>   imageReader->SetDataSpacing(1,1,1);
>   imageReader->SetDataByteOrderToLittleEndian();
>   imageReader->UpdateWholeExtent();
>   
>   // 2. Some Filtering-... 
>   vtkImageMedian3D *filter = vtkImageMedian3D::New();
>   filter->SetKernelSize(3,3,3);
>   filter->SetInputConnection(imageReader->GetOutputPort());
>   filter->UpdateWholeExtent();
>
>   // 3. write out the result as a volume
>   vtkTIFFWriter *volumeWriter = vtkTIFFWriter::New();
>   volumeWriter->SetInputConnection(filter->GetOutputPort());
>   volumeWriter->SetFileDimensionality(3);
>   volumeWriter->SetFileName("test_volume.tif");
>   volumeWriter->Write();
>   
>   

-- 
Amy Squillacote
Kitware, Inc.
28 Corporate Drive
Clifton Park, NY 12065
Phone: (518) 371-3971 x106