[vtkusers] Building a volume out of DICOM images

[David Gobbi]

The Set method does set the value, but it is only used for raw data.
For any data files that have a header, the reader automatically calls
SetDataType() itself based on the information in the file header, and
ignores any value set by the user.

So it is still a set method like any other set method... it is just
that vtkDICOMReader ignores the value that you set, and sets its own
value (the correct value) instead.

   David



On Wed, Jul 14, 2010 at 3:07 PM, Steve Chall <stevec at renci.org> wrote:
> Thanks, David.  That does explain why a Set...() method may not set the
> value as I expected.  But it does conflict with my expectation that a
> Set...() method would set a value rather than simply telling me what it is.
> I guess I misunderstand the rationale behind how the method is named.  At
> any rate, you've been very helpful.  Thanks again.
>
> -Steve
>
> -----Original Message-----
> From: David Gobbi [mailto:david.gobbi at gmail.com]
> Sent: Wednesday, July 14, 2010 4:37 PM
> To: Steven Chall
> Cc: vtkusers at vtk.org
> Subject: Re: [vtkusers] Building a volume out of DICOM images
>
> Hi Steve,
>
> The reader's SetDataScalarTypeTo...() methods are used to tell the
> reader what the data type _is_, it can't change the data from one type
> to another.  These methods are meant to be used when the reader has to
> deal with raw data (specifically, when the superclass vtkImageReader
> has to deal with raw data, the vtkDICOMImageReader gets the data type
> information from the DICOM header).
>
> You need to use vtkImageShiftScale to convert the "signed short" data
> into "unsigned short".  The lowest value in a "signed short" CT file
> is usually around -1000, so a Shift of 1000 is usually needed when
> converting to unsigned, but you will need to check the actual range of
> data values stored in the file to be sure.
>
>  David
>
>
> On Wed, Jul 14, 2010 at 2:13 PM, Steven Chall <stevec at renci.org> wrote:
>> Based on
>>
> http://public.kitware.com/cgi-bin/viewcvs.cgi/*checkout*/Examples/VolumeRend
> ering/Cxx/GPURenderDemo.cxx?root=VTK&content-type=text/plain,
>> I’ve written a little app to display a volume constructed from a directory
>> of DICOM files of CT data.  I’m having no problem displaying individual
>> image files, but when I try to see the volume, it’s a different story.
> Here
>> are what I believe are the germane C++ code fragments:
>>
>>
>>
>> …
>>
>>   vtkDICOMImageReader *reader = vtkDICOMImageReader::New();
>>
>>   reader->SetDirectoryName("C:\\Documents and Settings\\Steve Chall\\My
>> Documents\\IMRT\\CT");
>>
>>   reader->Update();
>>
>>   int dataScalarType = reader->GetDataScalarType();
>>
>>   reader->SetDataScalarTypeToUnsignedShort();
>>
>>   reader->GetOutput()->SetScalarTypeToUnsignedInt();
>>
>> …
>>
>>   vtkVolume *volume = vtkVolume::New();
>>
>>   vtkVolumeRayCastMapper *mapper = vtkVolumeRayCastMapper::New();
>>
>> …
>>
>>   renderer->AddVolume( volume );
>>
>>   renderer->ResetCamera();
>>
>> …
>>
>>
>>
>> It builds and runs, but instead of displaying the volume I get the
> following
>> message:
>>
>>
>>
>> ERROR: In ..\..\VTK\VolumeRendering\vtkVolumeRayCastMapper.cxx, line 327
>>
>> vtkVolumeRayCastMapper (01F111C8): Cannot volume render data of type
> short,
>> only unsigned char or unsigned short.
>>
>>
>>
>> I’d expect the call to
>>
>> reader->SetDataScalarTypeToUnsignedShort();
>>
>> to do just that, and when I step through it in the debugger it does indeed
>> get called and does everything I’d expect except the reader’s
> DataScalarType
>> value never changes (down where the assignment should occur, in
>> vtkImageReader2::SetDataScalarType(int type)) from 4 (VTK_SHORT) to 5
>> (VTK_UNSIGNED_SHORT).
>>
>>
>>
>> Finally, here’s the method comment for void
>> vtkImageReader2::SetDataScalarType(int type):
>>
>>
>>
>> // Set the data type of pixels in the file.
>>
>> // If you want the output scalar type to have a different value, set it
>>
>> // after this method is called.
>>
>>
>>
>> And that’s what I thought
>>
>> reader->GetOutput()->SetScalarTypeToUnsignedInt();
>>
>> would do.  But no, it’s still VTK_SHORT.
>>
>>
>>
>> I’d appreciate any suggestions y’all might have.  I’m running VTK 5.4.2
> with
>> Visual C++ 2008 in WinXP SP3.  Thanks.
>>
>>
>>
>> -Steve Chall
>>
>>  Senior Research Software Developer
>>
>>  Renaissance Computing Institute (RENCI)
>>
>>  Phone: 919-681-9639
>>
>>  Email: stevec at renci.org
>>
>>
>>
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