[vtkusers] Problems with TIFF Writer while writing a volume

[Cory Quammen]

It's unclear what you mean by "write out the filter result as a
volume". If you mean write it out as a sequence of 50 8-bit tiff
images, then you need to use:

volumeWriter->SetFilePrefix("test_volume");
volumeWriter->SetFilePattern("%s%d.tif");
volumeWriter->SetFileDimensionality(2);
volumeWriter->Write();

Unfortunately, this is broken last I checked, and you're program will
likely crash. However, I submitted a bug with a fix back in October
2006 (http://www.vtk.org/Bug/bug.php?op=show&bugid=3917&pos=1) which
contains a working version of vtkTIFFWriter.cxx that makes the above
code work. You could grab that if you'd like and recompile. My fix
merely duplicates what vtkPNGWriter and vtkJPGWriter do when saving a
volume as a sequence of images.

If, on the other hand, you mean that you want a single file containing
all of the images, then it seems to me that vtkTIFFWriter is doing the
correct thing by concatenating the images in the y-direction. It is
just writing pixels from each image into the file row-by-row: when it
finishes the first image, it starts back at row 0 in the second image
and continues writing, thus the concatenation along the y-axis.
Perhaps it's that your TIFF viewing program doesn't understand TIFF
volumes?

One other note: aren't the zimn and zmax arguments to
vtkTIFFReader::SetDataExtent() zero-based? That is, shouldn't your
code be

imageReader->SetDataExtent(0,299,0,299,0,49)

I wouldn't be surprised if setting the last to arguments to 1 and 50,
as you have in your example, causes problems.

-Cory

-- 
Cory Quammen
Department of Computer Science
University of North Carolina at Chapel Hill
http://www.cs.unc.edu/~cquammen

> Message: 10
> Date: Tue, 31 Jul 2007 14:22:01 +0200
> From: "Enkelejda Tafaj" <lejda at gmx.de>
> Subject: [vtkusers] Problems with TIFF  Writer while writing a volume
> To: vtkusers at vtk.org
> Message-ID: <20070731122201.118240 at gmx.net>
> Content-Type: text/plain; charset="us-ascii"
>
> 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();
>
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