[vtkusers] vtkImageData Beginner Question

Sat Jul 4 08:19:04 EDT 2009

Michael,

There is a confusion between physical extent (bounds) and the extent
of the indices of the image. An image's extent is the number of pixels
in each dimension regardless of the "size" if each pixel. If you have
an image that is 100 x 100 x 100 pixels and a spacing of 1 unit, that
image will have a physical size of 100 x 100 x 100 units. If the
spacing is 2 units, the size will be 200 x 200 x 200 units. The origin
locates the image in physical space. For example, the 100 x 100 x 100,
spacing 1, origin 50.5,50.5,50.5 will locate the first pixel of the
image at physical location 50.5,50.5,50.5. The physical extent of the
image is:
50.5, 50.5 + 1.0 * (100 - 1), ... but the extent of the indices is
0,99,0,99,0,99

It seems that you ask the user to input the bounds (physical extent).
To convert from bounds to indices:

index = bounds/spacing - origin

Also, look at the code in vtkImageData::AllocateScalars.

Bill

On Fri, Jul 3, 2009 at 7:01 PM, Michael
Jackson<mike.jackson at bluequartz.net> wrote:
> Ok, here is the problem, if I set my extents to 46979 48525 48443 49981 0 0
>  then the size of the image is only 1547 x 1539 pixels. It should be 7433 x
> 7394 pixels. The 1547 x 1539 is the correct _micron_ length of each side but
> this NOT the correct pixel size.
>
>  So I need to create a vtkImage object with a true pixel size of 7433 x 7394
> x 1 that represents a volume in physical space with an origin at 46979,
> 48443, 0 and a maximum at 48525, 49981, 1.
>
> I can not seem to "get there from here"..
>
> ---
> Mike Jackson                 www.bluequartz.net
>
>
>
> On Jul 3, 2009, at 6:13 PM, Francois Bertel wrote:
>
>> Hello,
>>
>> I think you should use SetExtent(), not SetDimensions().
>>
>> because the code of vtkImageData::SetDimensions() is actually:
>>
>>  SetExtent(0, dim[0]-1, 0, dim[1]-1, 0, dim[2]-1);
>>
>> Also Origin is the position in world coordinate of the point of
>> extent(0,0,0): the origin does not have to be part of the dataset, in
>> other words, the dataset extent does not have to start at (0,0,0) and
>> the origin can be outside of the dataset bounding box.
>>
>>
>> On Fri, Jul 3, 2009 at 5:50 PM, Michael
>> Jackson<mike.jackson at bluequartz.net> wrote:
>>>
>>> I have consulted all the vtk and paraview books but I am just coming up
>>> empty on this.
>>>
>>> Here is what I have: A volume of Grayscale pixels being read from a file.
>>> The data represents a volume starting at 46979 Microns in x and 48443
>>> Microns in Y. Each Slice in the z direction represents 1.2 microns. The
>>> "scaling" is 0.207987 Microns/Pixel. The volume is roughly 821 slices by
>>> about 1500 Microns in X and about 1500 Microns in Y.
>>>
>>>  Here is what I would like: This to show in a window (ParaView) so that
>>> when
>>> I set the "Show Axis" all the values are "correct", ie, the values should
>>> start at about 46979,48443,0 and go to their maximum values. Currently I
>>> have the user fill in some text fields that represent the VOI that the
>>> user
>>> would like to render. When the code hits what I have written I either get
>>> a
>>> crash or errors of the type:
>>>
>>> ERROR: In
>>> /Users/Shared/Kitware-CVS/ParaView3/VTK/Filtering/vtkImageData.cxx, line
>>> 2101
>>> vtkImageData (0x122a31b70): GetPointer: Pixel (46979, 48443, 0) not in
>>> current extent: (0, 7432, 0, 7393, 0, 1)
>>>
>>> or
>>>
>>> Warning: In
>>> /Users/Shared/Kitware-CVS/ParaView3/VTK/Filtering/vtkDataSet.cxx, line
>>> 414
>>> vtkImageData (0x12a0e5ee0): Point array RoboMet Voxels with 1 components,
>>> has 0 tuples but there are only -1048158596 points
>>>
>>>
>>> Here is the code that I am using to init the vtkImageData object during
>>> the
>>> pipeline excution:
>>>
>>> int dims[3];
>>> dims[0] = (requestedExtent[1] -
>>> requestedExtent[0])/this->CurrentScalingFactor;
>>> dims[1] = (requestedExtent[3] -
>>> requestedExtent[2])/this->CurrentScalingFactor;
>>> dims[2] =  requestedExtent[5] - requestedExtent[4] + 1;
>>> if (dims[2] == 0)
>>> {
>>> dims[2] = 1;
>>> }
>>> output->SetDimensions(dims[0], dims[1], dims[2]);
>>> output->SetSpacing(this->DataSpacing);
>>> output->SetOrigin(this->DataOrigin);
>>> output->SetScalarType(VTK_TYPE_UINT8);
>>>
>>> //output->SetExtent(requestedExtent);
>>> output->SetNumberOfScalarComponents( 1 );
>>> output->AllocateScalars();
>>> output->GetPointData()->GetScalars()->SetName("RoboMet Voxels");
>>> output->GetPointData()->SetActiveScalars("RoboMet Voxels");
>>>
>>> Here is the values of the requestedExtent when the method gets called:
>>>
>>> 46979 48525 48443 49981 0 0
>>>
>>> Any help is appreciated..
>>> _________________________________________________________
>>> Mike Jackson                  mike.jackson at bluequartz.net
>>> BlueQuartz Software                    www.bluequartz.net
>>> Principal Software Engineer                  Dayton, Ohio
>>>
>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the VTK FAQ at:
>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>
>>
>>
>>
>> --
>> François Bertel, PhD  | Kitware Inc. Suite 204
>> 1 (518) 371 3971 x113 | 28 Corporate Drive
>>                     | Clifton Park NY 12065, USA
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.vtk.org/mailman/listinfo/vtkusers
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.vtk.org/mailman/listinfo/vtkusers
>