[vtkusers] (dcmtk -> vtkImageData) for Volume rendering

[Mallikarjun K]

Hello Cory,

Yes,the first image looks like a human head but it is surrounded by some
other gray/balck colored stuff.I think you are right,it is the issue with
color/opacity maps.The data is in the range of 0-65536(unsigned short).
Below are the color and opacity maps I applied.

                //setup opacity
d->m_opacityTransferFunction->AddPoint(132.108911, 0.000000);
d->m_opacityTransferFunction->AddPoint(197.063492, 0.041333);
d->m_opacityTransferFunction->AddPoint(1087.917989, 0.700000);
//setup gradient opacity
d->m_gradientTransferFunction->AddPoint(560.695000, 1.000000);

// Setup color
d->m_colorTransferFunction->AddRGBPoint(176.881890, 0.650980, 0.000000,
0.000000);
d->m_colorTransferFunction->AddRGBPoint(239.427822, 0.933333, 0.000000,
0.000000);
d->m_colorTransferFunction->AddRGBPoint(301.973753, 1.000000, 0.800000,
0.062745);
d->m_colorTransferFunction->AddRGBPoint(495.866142, 1.000000, 0.905882,
0.666667);
d->m_colorTransferFunction->AddRGBPoint(677.249344, 1.000000, 0.882353,
0.215686);
d->m_colorTransferFunction->AddRGBPoint(808.595801, 1.000000, 1.000000,
1.000000);

What should I do to eliminate gray/balck colored stuff ? please guide me.

Thank you.
Regards,
Mallikarjun



On Wed, Feb 10, 2016 at 7:18 PM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> Mallikarjun,
>
> Could you clarify for me whether the first image at all looks like a human
> head? Is the issue that the color/opacity maps do not appear to be applied
> correctly, or that the data is just completely strange when reading from
> dcmtk?
>
> If it is the latter, I have a couple guesses:
>
> - maybe your dimensions are off from what dcmtk tells you
> - maybe dcmtk's conventions for voxel order are different from VTK
>
> Cory
>
> On Wed, Feb 10, 2016 at 2:40 AM, Mallikarjun K <mallikarjun49 at gmail.com>
> wrote:
>
>> Hello Cory Quammen,
>>
>> Thanks for the response and suggestions.We are kind of established in
>> using dcmtk in our project,So couldn't use vtk-dicom for time being.
>>
>> Below is the code snippet which I used to get dcmtk data to vtk:
>>
>>
>> vtkDataArray* scalars = 0;
>>
>>
>>
>> switch (dicomDataType)
>> {
>> case TYPE_U32Data:
>> scalars = vtkUnsignedIntArray::New();
>> ((vtkUnsignedIntArray*)(scalars))->SetArray((unsigned int*)dicomData,
>> dicomDataSize, 1);//dicomData is the data from dcmtk
>> break;
>> case TYPE_U8Data:
>> scalars = vtkUnsignedCharArray::New();
>> ((vtkUnsignedCharArray*)(scalars))->SetArray((unsigned char*)dicomData,
>> dicomDataSize, 1);
>> break;
>> case TYPE_U16Data:
>> scalars = vtkUnsignedShortArray::New();
>> ((vtkUnsignedShortArray*)(scalars))->SetArray((unsigned short*)dicomData,
>> dicomDataSize, 1);
>> break;
>> case TYPE_S16Data:
>> scalars = vtkShortArray::New();
>> ((vtkShortArray*)(scalars))->SetArray((short*)dicomData, dicomDataSize,
>> 1);
>> break;
>> }
>> scalars->SetNumberOfComponents(1);
>> double range[2];
>> scalars->GetRange(range);
>> m_imageData = vtkImageData::New();
>> m_imageData->SetDimensions(dimensions);
>> m_imageData->SetSpacing(spacing);
>> m_imageData->GetPointData()->SetScalars(scalars);
>> scalars->Delete();
>> m_imageData->GetPointData()->GetScalars()->SetName("VR Cuboid");
>>
>>
>> Thanks&Regards,
>> Mallikarjun
>>
>>
>>
>> On Tue, Feb 9, 2016 at 8:47 PM, Cory Quammen <cory.quammen at kitware.com>
>> wrote:
>>
>>> How are you getting the data from dcmtk to VTK? Code would be helpful.
>>>
>>> As an aside, you may be interested in David Gobbi's excellent DICOM
>>> reader for VTK.
>>>
>>> https://github.com/dgobbi/vtk-dicom
>>>
>>> I believe you can build this within VTK by enabling the Module_vtkDICOM
>>> option.
>>>
>>> Best,
>>> Cory
>>>
>>> On Tue, Feb 9, 2016 at 8:25 AM, Mallikarjun K <mallikarjun49 at gmail.com>
>>> wrote:
>>>
>>>> Hello All,
>>>> I used dcmtk to read dicom raw data and applied Modality LUT and
>>>> created a vtkImageData. When I used this data for Volume
>>>> Rendering(vtkGPUVolumeRayCastMapper), I am getting the following output.
>>>>
>>>>
>>>> [image: Inline image 2]
>>>>
>>>>
>>>> When I used vtkDicomImageReader's output for Volume rendering ,I am
>>>> getting the following output.
>>>>
>>>> [image: Inline image 1]
>>>>
>>>> Can anyone give some pointers why this is happening?
>>>>
>>>> Thanks in advance..
>>>> --
>>>> *With Kind Regards:*
>>>> Mallikarjun
>>>>
>>>>
>>>>
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>>>>
>>>
>>>
>>> --
>>> Cory Quammen
>>> R&D Engineer
>>> Kitware, Inc.
>>>
>>
>>
>>
>> --
>> *With Kind Regards:*
>> Mallikarjuna K,
>> 07795531103/09908238861.
>>
>>
>
>
> --
> Cory Quammen
> R&D Engineer
> Kitware, Inc.
>



-- 
*With Kind Regards:*
Mallikarjuna K,
07795531103/09908238861.
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