[vtkusers] Volume origin,bounds, extent question
Kall, Bruce A.
kall at mayo.edu
Tue Jan 20 16:42:37 EST 2009
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.
>>>>>>> Please keep messages on-topic. Check the FAQ at:
>>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>>>
>>>>>> _______________________________________________
>>>>>> This is the private VTK discussion list.
>>>>>> Please keep messages on-topic. Check the FAQ at:
>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>
>>>>>
>>>
>>>
>> _______________________________________________
>> This is the private VTK discussion list.
>> Please keep messages on-topic. Check the FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>> Follow this link to subscribe/unsubscribe:
>> http://www.vtk.org/mailman/listinfo/vtkusers
>
>
More information about the vtkusers
mailing list