[vtkusers] Volume origin,bounds, extent question
Eric E. Monson
emonson at cs.duke.edu
Tue Jan 20 22:03:42 EST 2009
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).
>>>>>>>>
>>>>>>>>
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>>>>>>
>>>>
>>>>
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>>
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