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

[rama]

Hi,

I tried the SetCenter(...) method that you suggestd, but I am still not 
getting rotations about that point.

So, I have a cube of 160 X 144 X 208 pixels and I want to rotate it by 
the point (80, 72, 104) around X-Axis.

Here is the code that I wrote for setting the CenterPoint,

TransformType::InputPointType centerPoint;
centerPoint[0] = (xNumPixels/2) * PixelXWidth;
centerPoint[1] = - (yNumPixels/2) * PixelYWidth;
centerPoint[2] = (zNumPixels/2) * PixelZWidth;
transform->SetCenter(centerPoint);

I did this before I set the rotation values. Also, here I don't have two 
images, like one fixed and other moving. I only have one single cube and 
just I want to rotate it.

But with the addition of above lines of code before setting the rotation 
values (transform->SetRotation3D(rotation, angle, false)) doesn't make 
any difference. Still the image is rotating about one of the corners of 
the image. Not about its center point.

Please see the images before and after rotations. 
http://www.funnotes.net/img-before-rot.JPG    
http://www.funnotes.net/img-after-rot.JPG  . This image is a Left side 
view of the 3D cube (middle slice).

You can see that image rotation is done about the Top-Left corner of the 
image and not about the center point of the image (the center point of 
cross).

Can you please suggest what to do here.

thank you,
Rama.

Marius Staring wrote:

> No I mean
>
>    affinetransform->SetCenter( 
> fixedImage->TransformIndexToPhysicalPoint( centerInIndices ) );
>
> See also
>
>    
> http://www.itk.org/Doxygen/html/classitk_1_1MatrixOffsetTransformBase.html#z1307_0 
>
>
> for what the SetCenter() does
>
> Regards,
>
> Marius
>
> rama wrote:
>
>> 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.
>>>>
>>>> _______________________________________________
>>>> Insight-users mailing list
>>>> Insight-users at itk.org
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>>
>>
>>
>