[vtkusers] Volume origin,bounds, extent question
Eric E. Monson
emonson at cs.duke.edu
Mon Jan 19 14:37:23 EST 2009
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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