[vtkusers] Building a volume out of DICOM images

[David Gobbi]

Someone should write a vtkAbstractImageReader, so that
the readers are no longer derived from a concrete base class.  Any
takers?

   David


On Wed, Jul 14, 2010 at 3:13 PM, Steven Chall <stevec at renci.org> wrote:
> That makes sense.  Thanks again.
>
> -----Original Message-----
> From: David Gobbi [mailto:david.gobbi at gmail.com]
> Sent: Wednesday, July 14, 2010 5:11 PM
> To: Steven Chall
> Cc: vtkusers at vtk.org
> Subject: Re: [vtkusers] Building a volume out of DICOM images
>
> 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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>>
>>
>>
>