[Insight-users] confusion with specifying origin for 3D affine transformations - itkAffineTransform

[rama]

Hi Marius,

you mean resampler->SetCenter(...) instead of resampler->SetOrigin(...)? 
Then what about SetOrigin(...) in itk::ImportImageFilter class. What 
does it do? Is it not necessary.

Also by world coordinates, you mean the same values that I used for 
SetOrigin(...) before.
So, if I say resampler->SetOrigin((xNumPixels/2) * PixelXWidth, 
(yNumPixels/2) * PixelYWidth, (zNumPixels/2) * PixelZWidth) will it work.

Still the doubt that I have is, which point to consider as the origin 
while specifying the center point in world coordinates. If the center 
point of image in world coordinates is (0,0,0) then what is the extra 
need to specify a center point. This is bit confusing. Can you elucidate 
it please?

So, in world coordinates what will the center point of the 3D cube 
considered as by the AffineTransform class. With respect to which point 
should I specify the world coordinates of the center point.

Can you please explain it a bit more.

thank you,
Rama Aravind.

Marius Staring wrote:

> Hi Rama,
>
> you have to use SetCenter(centerpoint) and not SetOrigin(). Make sure 
> to give centerpoint in world coordinates.
>
> Regards,
>
> Marius Staring
>
> rama wrote:
>
>> Hi,
>>
>> I have a problem rotating a 3D image about ITS OWN center point 
>> around X axis (take that Z axis is pointing into the screen).
>>
>> I have a 3D image with dimensions as 160 X 144 X 208 pixels in X, Z 
>> and Y axis respectively.
>>
>> I want to rotate this image around X axis about its own center point, 
>> that is, around the middle point of the image - (80, 72, 104).  That 
>> is, the image should rotate around itself about X-Axis.
>> But I am not getting that effect. The image is always rotating around 
>> the point (0, 0, 0) of the array index.
>>
>> Here are the details.
>>
>> I am importing data from a C++ array like this using 
>> itk::ImportImageFilter class.
>>
>> typedef itk::ImportImageFilter<InputPixelType, Dimension> 
>> ImportImgFromArray;
>> ImportImgFromArray::Pointer importFilter = ImportImgFromArray::New();
>> ImportImgFromArray::SizeType size;
>> size[0]=xNumPixels;          //160
>> size[1]=yNumPixels;          //208
>> size[2]=zNumPixels;          //144
>> ImportImgFromArray::IndexType start;
>> start.Fill(0);
>> ImportImgFromArray::RegionType region;
>> region.SetIndex(start);
>> region.SetSize(size);
>> importFilter->SetRegion(region);
>> double origin[Dimension];
>> origin[0]=(xNumPixels/2) * PixelXWidth;
>> origin[1]=(yNumPixels/2) * PixelYWidth;
>> origin[2]=(zNumPixels/2) * PixelZWidth;
>> importFilter->SetOrigin(origin);
>> double spacing[Dimension];
>> spacing[0]=PixelXWidth;
>> spacing[1]=PixelYWidth;
>> spacing[2]=PixelZWidth;
>> importFilter->SetSpacing(spacing);
>> importFilter->SetImportPointer(tempBuffer, size[0]*size[1]*size[2], 
>> false);      //get data from a tempBuffer - a C++ array - there is no 
>> error here
>>
>> I am setting the transformation like this,
>>
>> typedef itk::AffineTransform<double, Dimension> TransformType;
>> TransformType::Pointer transform=TransformType::New();
>>
>> resampler->SetDefaultPixelValue(0);      //resampler is a 
>> itk::ResampleImageFilter class
>> resampler->SetSize(size);
>> origin[0]=(xNumPixels/2) * PixelXWidth;
>> origin[1]=(yNumPixels/2) * PixelYWidth;
>> origin[2]=(zNumPixels/2) * PixelZWidth;
>> resampler->SetOutputOrigin(origin);
>> resampler->SetOutputSpacing(spacing);
>>
>> TransformType::OutputVectorType translation1;
>> translation1[0]=-origin[0];
>> translation1[1]=-origin[1];
>> translation1[2]=-origin[2];
>> transform->Translate(translation1);
>>
>> TransformType::OutputVectorType rotation;
>> rotation[0]=1;   //rotate around X-Axis
>> rotation[1]=0;
>> rotation[2]=0;
>> transform->Rotate3D(rotation, 
>> m_cmnData->SagittalRotateZ(m_curDataSetListSel)*DegToRad, false);
>>
>> TransformType::OutputVectorType translation2;
>> translation2[0]=origin[0];
>> translation2[1]=origin[1];
>> translation2[2]=origin[2];
>> transform->Translate(translation2);
>> resampler->SetTransform(transform);
>>
>> resampler->SetInput(importFilter->GetOutput());
>> resampler->Update();
>>
>> These are my transformation settings. But when I try to rotate it 
>> 10degrees either CW or CCW, I am getting the rotations around the 
>> array index (0,0,0) not through the point that I specified in the image.
>>
>> I was skeptical about the before and after translations of the 
>> rotation. So, when I disabled those two translations before and after 
>> it, the image just went out of bounds and I get only a blank 3D cube.
>> When I made the origin point to (0.0, 0.0, 0.0) even then the image 
>> is just rotating around the array index (0,0,0).
>>
>> Can you please suggest me how can I get rotations for the 3D cube 
>> around its center point (that is, the center point of the cube). I 
>> want the whole cube rotate around itself about X-Axis. Can you please 
>> suggest me what to do for that.
>>
>> thank you,
>> Rama Aravind.
>>
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>