[vtkusers] Volume origin,bounds, extent question
Kall, Bruce A.
kall at mayo.edu
Mon Jan 26 15:15:20 EST 2009
Since I've not solved this issue and from what I can tell a large volume
in an unstructured grid
would be slow to volume render, am I better off rotating my volume so it
is axis-aligned? Is
there an easy way to do this in vtk?
Bruce
Eric E. Monson wrote:
> Hey Bruce,
>
> I hope that through my ignorance I haven't led you too far astray. I
> tried this tonight, too, and can't get it to work. I think I've come
> up with the reason, but someone else might want to speak up to
> confirm. After swearing for a while I remembered a recent thread on
> the VTK mailing list and found at least a possible direction.
>
> http://www.vtk.org/pipermail/vtkusers/2008-November/098299.html
>
> This says that you can't create a non-axis-aligned vtkImageData. This
> would explain why you can't apply a vtkTransformFilter to an ImageData
> set -- because most of the transformations would break the constraints
> of ImageData. Instead, "You could use a vtkStructuredGrid. You can
> place the points of the regular grid anywhere you like, so it would be
> easy to construct a rotated grid."
>
> I'm a little too tired to work this out tonight, but if you read your
> data into a vtkStructuredGrid, you could construct the correct rotated
> array right from the beginning. I think you should also be able to
> apply a vtkTransformFilter to the structured grid since vtkPolyData,
> vtkStructuredGrid and vtkUnstructuredGrid all derive from vtkPointSet,
> and vtkTransformFilter derives from vtkPointSetAlgorithm.
>
> Hope I've helped more than hurt,
> -Eric
>
>
> On Jan 20, 2009, at 4:42 PM, Kall, Bruce A. wrote:
>
>> Eric,
>>
>> Thanks. This doesn't seem to have any effect on my volume. Here's a
>> snippet:
>>
>>> xform_filter = vtkTransformFilter::New();
>>> xform_filter_xform = vtkTransform::New();
>>>
>>> xform_filter_xform->Identity();
>>> xform_filter_xform->Translate(0.0,0.0,25.0);
>>>
>>> xform_filter->SetInputConnection(original_volume_reader->GetOutputPort());
>>>
>>> xform_filter->SetTransform(xform_filter_xform);
>> If I add a xform_filter->Update(), I get the following error:
>>
>>> vtkStreamingDemandDrivenPipeline (0x1af4b540): Algorithm
>>> vtkTransformFilter(0x1af4b680) returned failure for request:
>>> vtkInformation (0x1af4c4a0)
>>> Debug: Off
>>> Modified Time: 1217
>>> Reference Count: 1
>>> Registered Events: (none)
>>> Request: REQUEST_DATA_OBJECT
>>> FORWARD_DIRECTION: 0
>>> FROM_OUTPUT_PORT: 0
>>> ALGORITHM_AFTER_FORWARD: 1
>>
>> I must be missing a step?
>>
>> Bruce
>>
>>
>> Eric E. Monson wrote:
>>> Hey Bruce,
>>>
>>> It really doesn't sound like this should be a problem if you're
>>> really talking about rotating the whole volume, even by these small
>>> amounts. Since this transformation, as you saw before, doesn't fit
>>> the definition of a permutation, I think you just need to apply a
>>> vtkTransformFilter to your data after the reader pulls it in.
>>>
>>> xform = vtkTransform()::New();
>>> xform->RotateZ(0.6467807);
>>> xform->RotateX(-0.18608);
>>> xform->RotateY(-0.49602);
>>>
>>> xformFilter = vtkTransformFilter()::New();
>>> xformFilter->SetInputConnection(original_volume_reader->GetOutputPort());
>>>
>>> xformFilter->SetTransform(xform);
>>>
>>> Talk to you later,
>>> -Eric
>>>
>>>
>>> On Jan 19, 2009, at 5:04 PM, Kall, Bruce A. wrote:
>>>
>>>> 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).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> This is the private VTK discussion list.
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>>>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>
>>>>>
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>>>
>>>
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