[vtkusers] Volume origin,bounds, extent question
Kall, Bruce A.
kall at mayo.edu
Mon Jan 19 17:04:37 EST 2009
Eric,
Thanks. Unfortunately my rotations are quite small (in one particular
volume,
rotating about the center of the volume):
Rotate around Z by: 0.6467807 degrees
Rotate around X by: -0.18608 degrees
Rotate around Y by: -0.49602 degrees
It's enough though that if not done, coordinates of voxels on the other
side of the volume are incorrect (using an origin of lower left in vtk).
Seems
like vtk just increments each voxel by the spacing to get from
the lower left to the upper right coordinate. But even with these small
angular
rotations, over a 256x256x86 volume with a voxel size of 0.977 it puts
me off by about 3mm on the other size from what coordinates are supposed
to be.
Any other suggestions?
Bruce
Eric E. Monson wrote:
> Hey Bruce,
>
> (try to keep the discussion on-list)
>
> So what is your original align_matrix[][] -- is the issue that it's
> being changed after you assign the values to "matrix"?
>
> My suggestion was to use vtkTransform itself to calculate the
> transformation matrix. If you only do rotations in 90 degree
> increments and scalings of +/- 1, then the matrix will still be a
> permutation matrix. As I understand it, there is nothing that forces
> the transformation matrix in vtkTransform to be a permutation matrix,
> though, since it can do "a full range of linear (also known as affine)
> coordinate transformations in three dimesions". SetTransform()
> requires a permutation matrix, though, and I'm not sure how that is
> enforced.
>
> e.g. If you do:
>
> xform = vtk.vtkTransform()::New();
> xform->RotateX(90);
> xform->Scale(1, 1, -1);
>
> the matrix will be:
>
> 1 0 0 0
> 0 -1.99673e-16 1 0
> 0 1 1.99673e-16 0
> 0 0 0 1
>
> Which would hopefully still qualify for the SetTransform() input.
>
> -Eric
>
>
> On Jan 19, 2009, at 1:23 PM, Kall, Bruce A. wrote:
>
>> Eric,
>>
>> Thanks. I think this is what I tried, but what I am getting back
>> after the SetTransform is the same xform
>> which is not a permutation matrix (e.g., sum in all rows is 1.0). Is
>> there some step I am missing? I'm sending
>> in my matrix (I called it align_matrix which is double
>> align_matrix[4][4]) and then read back what my image
>> reader has:
>>
>> Here's a code snippet right after I've calculated the transform I want:
>>
>>> matrix = vtkMatrix4x4::New();
>>> matrix->Identity();
>>>
>>> fprintf(stderr,"Setting VTK Matrix to align_matrix\n");
>>> for(i = 0; i < 4; i++)
>>> {
>>> for(j = 0; j < 4; j++)
>>> {
>>> matrix->SetElement(i,j,align_matrix[i][j]);
>>> }
>>> }
>>>
>>> printf("\n\n");
>>> printf("FINAL VTK MATRIX Before Install\n");
>>> for(i = 0;i < 4;i++)
>>> {
>>> for(j = 0;j < 4;j++)
>>> {
>>> e = matrix->GetElement(i,j);
>>> fprintf(stderr,"%12.5f ",e);
>>> }
>>> printf("\n");
>>> }
>>> printf("\n\n");
>>>
>>>
>>> xform = vtkTransform::New();
>>> xform->SetMatrix(matrix);
>>> original_volume_reader->SetTransform(xform);
>>> original_volume_reader->Update();
>>>
>>> vtkTransform *read_back_xform = original_volume_reader->GetTransform();
>>> vtkMatrix4x4 *read_back_matrix = read_back_xform->GetMatrix();
>>>
>>> printf("\n\n");
>>> printf("Image Reader Transform\n");
>>> double row_sum;
>>> for(i = 0;i < 4;i++)
>>> {
>>> row_sum = 0.0;
>>> for(j = 0;j < 4;j++)
>>> {
>>> e = read_back_matrix->GetElement(i,j);
>>> row_sum = row_sum + e;
>>> fprintf(stderr,"%12.5f ",e);
>>> }
>>> printf(" row_sum[%12.5f]\n",row_sum);
>>> }
>>> printf("\n\n");
>>>
>> and this is the output I get:
>>
>> Setting VTK Matrix to align_matrix
>>
>>
>> FINAL VTK Affine MATRIX Before Install
>> 0.99990 0.01129 -0.00862 0.00000
>> -0.01126 0.99993 0.00335 0.00000 0.00866
>> -0.00325 0.99996 0.00000 -1.05445 1.22598
>> -0.63108 1.00000
>>
>>
>>
>> Image Reader Transform
>> 0.99990 0.01129 -0.00862 0.00000
>> row_sum[ 1.00257]
>> -0.01126 0.99993 0.00335 0.00000
>> row_sum[ 0.99202]
>> 0.00866 -0.00325 0.99996 0.00000
>> row_sum[ 1.00537]
>> -1.05445 1.22598 -0.63108 1.00000
>> row_sum[ 0.54045]
>>
>> My image volume is now a bunch of dots. If I send in an identity
>> matrix, it renders
>> correctly, but with the wrong coordinates.
>>
>> Am I missing a step that converts the matrix into a permutation matrix?
>>
>> Thanks in advance for any suggestions,
>> Bruce
>>
>>
>>
>> Eric E. Monson wrote:
>>> Hey Bruce,
>>>
>>> I'm not an expert in this, but it looks like you can create a
>>> vtkTransform object, set the rotation and translation on that
>>> object, and then feed this to the SetTransform method of your
>>> reader. This makes it easy to construct the required permutation
>>> matrix using a more intuitive interface (as long as what you're
>>> trying to do is really an affine transformation).
>>>
>>> Talk to you later,
>>> -Eric
>>>
>>> ------------------------------------------------------
>>> Eric E Monson
>>> Duke Visualization Technology Group
>>>
>>>
>>> On Jan 16, 2009, at 4:47 PM, Kall, Bruce A. wrote:
>>>
>>>> Anybody have any thoughts on my question from the other day?
>>>> The only thing I can find in vtkImageReader is the SetTransform
>>>> but that has to be a permutation matrix. I need to rotate/translate.
>>>> I've got the transform calculated, I just don't know where to apply
>>>> it.
>>>>
>>>> Thanks,
>>>> Bruce
>>>>
>>>>
>>>>
>>>>> I'm reading in a premade (raw) image volume. I know the voxel size
>>>>> (same for all dimensions) as
>>>>> well as the coordinates of all 8 corners of the volume. I'm using
>>>>> vtkImageReader.
>>>>>
>>>>> This only seems to allow me to set the coordinate of the lower
>>>>> left voxel and the voxel size.
>>>>>
>>>>> How do you set the coordinate for another corner (e.g., upper
>>>>> right) so the coordinates
>>>>> run in the direction I want using the fixed voxel size I have?
>>>>> Right now it seems to just
>>>>> increment in the x,y,z dimensions by the voxel size and the
>>>>> coordinate of the upper right
>>>>> is not correct (my volume is slightly oblique for lack of a better
>>>>> phrase).
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
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>>>
>
>
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