[vtkusers] Announcement: New image rendering classes for VTK

Mon Jun 27 14:56:39 EDT 2011

?

On 6/27/11, Lic. José M. Rodriguez Bacallao <jmrbcu at gmail.com> wrote:
> could U post a sample code of this procedure:
>
> 1) I equate the VTK world coordinate system with the DICOM patient
> coordinate system
> 2) I set the data-to-world transform from the information in the DICOM
> header
> 3) I set up the camera in my viewer to display the image in the
> desired orientation
>
> what about
> 1) The VTK image readers and importers don't deal with DICOM image
> orientation correctly
> when I read dicom series I use: vtkGDCMImageReader from gdcm project.
> Do you know if this reader handle dicom orientation?
>
> 3) For each image, you must keep a 4x4 matrix describing the DICOM
> orientation
> this need to be done for every image in a serie?
>
>
>
> On 6/27/11, David Gobbi <david.gobbi at gmail.com> wrote:
>> These are not viewer classes, they are just rendering classes and are
>> therefore completely agnostic with regards to DICOM.
>>
>> But for the record, I do not understand all the difficulty people have
>> with
>> this issue.  When I view DICOM images, I just do the following:
>> 1) I equate the VTK world coordinate system with the DICOM patient
>> coordinate system
>> 2) I set the data-to-world transform from the information in the DICOM
>> header
>> 3) I set up the camera in my viewer to display the image in the desired
>> orientation
>>
>> So please let me go on the record as saying that there is no "difference
>> between VTK coords and DICOM coords".  That is a vicious rumour that
>> people
>> spread for reasons that are beyond me.  You can define the VTK world
>> coordinate system to be whatever you want.
>>
>> The problems that people have are due to the following:
>> 1) The VTK image readers and importers don't deal with DICOM image
>> orientation correctly
>> 2) The vtkImageViewer does not deal with DICOM image orientation
>> correctly
>> 3) For each image, you must keep a 4x4 matrix describing the DICOM
>> orientation
>>
>> If someone were to fix the readers and the viewer, this DICOM vs. VTK
>> issue
>> would mostly disappear.
>>
>> Regarding the second question, it's not up to me when these go into a
>> stable
>> release, Kitware controls the release schedule ;)
>>
>>  - David
>>
>>
>>
>> On Mon, Jun 27, 2011 at 8:34 AM, Jothy <jothybasu at gmail.com> wrote:
>>
>>> I wonder whether these classes has any fix for the different coordinates
>>> used by DICOm and vtk?
>>>
>>> Thank you
>>>
>>> Jothy
>>>
>>>
>>> On Mon, Jun 27, 2011 at 3:31 PM, Lic. José M. Rodriguez Bacallao <
>>> jmrbcu at gmail.com> wrote:
>>>
>>>> so, when this classes will be available in stable vtk?
>>>>
>>>> right now I am working with an snapshot from vtk git.
>>>>
>>>> On 6/27/11, Aashish Chaudhary <aashish.chaudhary at kitware.com> wrote:
>>>> > Hi David,
>>>> >
>>>> > What Aaron said  +  Awesome!! (one more time)
>>>> >
>>>> > Looking at the features list, I think our project will be greatly
>>>> > benefited by your work. Thanks for sharing your work.
>>>> >
>>>> > Regards,
>>>> > Aashish
>>>> >
>>>> >
>>>> > On Mon, Jun 27, 2011 at 8:47 AM, Aaron Boxer <boxerab at gmail.com>
>>>> > wrote:
>>>> >> Awesome!!! Nice work; can't wait to use these classes.
>>>> >>
>>>> >> Aaron
>>>> >>
>>>> >> On Sun, Jun 26, 2011 at 6:15 PM, David Gobbi <david.gobbi at gmail.com>
>>>> >> wrote:
>>>> >>> I'm pleased to announce that I have finally completed my work on
>>>> several
>>>> >>> new
>>>> >>> image rendering classes for VTK.  They are in the VTK git
>>>> >>> development
>>>> >>> tree,
>>>> >>> and a few of you have already tried them out (if you are one of
>>>> >>> those
>>>> >>> people, note that several feature and performance enhancements were
>>>> added
>>>> >>> last week).  More info can be found at the following wiki page:
>>>> >>>
>>>> >>> http://www.vtk.org/Wiki/VTK/Image_Rendering_Classes
>>>> >>>
>>>> >>> In brief, these classes replace vtkImageActor and provide a much
>>>> higher
>>>> >>> level of functionality.  They are new VTK actor and mapper classes
>>>> >>> specifically meant for image viewing.  What they are not: they are
>>>> >>> not
>>>> >>> widgets or viewers, although they provide machinery that can be
>>>> >>> used
>>>> to
>>>> >>> write widget and viewer classes.  In other words, they are meant
>>>> >>> for
>>>> >>> people
>>>> >>> who like to roll their own image viewers.
>>>> >>>
>>>> >>> The three new classes that I recommend for people to use are the
>>>> >>> following:
>>>> >>> vtkImageSlice - the new actor class for images
>>>> >>> vtkImageResliceMapper - mapper for drawing images for MPR viewers
>>>> >>> vtkImageProperty - for controlling lookup tables, window/level,
>>>> opacity,
>>>> >>> etc
>>>> >>>
>>>> >>> Typical use cases:
>>>> >>>
>>>> >>> 1) For an MPR viewer, use vtkInteractorStyleImage and set it to
>>>> >>> your
>>>> >>> desired
>>>> >>> view orientation. Then set the following properties in
>>>> >>> vtkImageResliceMapper:
>>>> >>> mapper->SliceFacesCameraOn()
>>>> >>> mapper->SliceAtFocalPointOn()
>>>> >>> The interactor will then allow you to pan, zoom, window/level, and
>>>> >>> (in
>>>> 3D
>>>> >>> mode) rotate and slice.  See
>>>> >>> VTK/Examples/ImageProcessing/ImageInteractorReslice.py for an
>>>> >>> example.
>>>> >>>
>>>> >>> 2) For a 3D ortho object, use multiple vtkImageResliceMapper
>>>> >>> objects,
>>>> and
>>>> >>> for each one make a vtkPlane that describes the normal and position
>>>> >>> of
>>>> >>> the
>>>> >>> slice to extract. Then call these methods:
>>>> >>> mapper->SetSlicePlane(plane)
>>>> >>> mapper->ResampleToScreenPixelsOff()
>>>> >>> Turning the "ResampleToScreenPixels" option Off makes rotation
>>>> >>> faster,
>>>> so
>>>> >>> it
>>>> >>> is recommended when rotations are going to be common operations.
>>>> >>>  Example:
>>>> >>> VTK/Rendering/Testing/Cxx/TestImageResliceMapperOffAxis.cxx
>>>> >>>
>>>> >>> Features:
>>>> >>> 1) oblique views (obviously!)
>>>> >>> 2) nearest-neighbor, linear, and cubic interpolation
>>>> >>> 3) modify image orientation with respect to world coords by setting
>>>> >>> vtkImageSlice's UserMatrix
>>>> >>> 4) fully multi-threaded reslicing and color mapping operations
>>>> >>> 5) streaming, i.e. only pulls the data needed for rendering
>>>> >>> 6) works well with very large images (as long as they fit in
>>>> >>> memory)
>>>> >>> 7) LOD-style interaction (switches to faster rendering for
>>>> interaction)
>>>> >>> 8) blend images by adding multiple vtkImageSlice objects to a
>>>> >>> vtkImageStack
>>>> >>> 9) checkerboard images by setting "CheckerboardOn" in the
>>>> >>> vtkImageProperty
>>>> >>> 10) thick-slab views (see vtkImageResliceMapper for details)
>>>> >>> 11) works with vtkCellPicker for picking image voxels as points or
>>>> cells
>>>> >>>
>>>> >>> For large image viewing, on a 4GB computer (64-bit OS X) I've
>>>> displayed
>>>> >>> images up to 3GB in size with full interactivity, but YMMV.  As
>>>> >>> long
>>>> as
>>>> >>> the
>>>> >>> mapper's ResampleToScreenPixels option is On, the mapper will never
>>>> try
>>>> >>> to
>>>> >>> load the full image onto the GPU (which is what causes the
>>>> vtkImageActor
>>>> >>> to
>>>> >>> be slow for large images).  The size of the images that you can
>>>> display
>>>> >>> is
>>>> >>> limited only by main memory, I have displayed stacks of RGB images
>>>> that
>>>> >>> are
>>>> >>> 10000x10000 pixels in size.
>>>> >>>
>>>> >>> I do not plan to push these into the VTK 5.8 release (even if
>>>> >>> Kitware
>>>> >>> were
>>>> >>> to give me the go-ahead), because the VTK development tree has
>>>> diverged
>>>> >>> too
>>>> >>> far from the VTK 5.8 release tree.  These new image classes are
>>>> >>> only
>>>> >>> possible due to recent improvements that I've made to the picker,
>>>> lookup
>>>> >>> table, and image reslice classes and they probably depend on a
>>>> >>> handful
>>>> of
>>>> >>> recent changes made by other people, as well.
>>>> >>>
>>>> >>>  - David
>>>> >>> _______________________________________________
>>>> >>> 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
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > | Aashish Chaudhary
>>>> > | R&D Engineer
>>>> > | Kitware Inc.
>>>> > | www.kitware.com
>>>> > _______________________________________________
>>>> > 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
>>>> >
>>>>
>>>>
>>>> --
>>>> Lic. José M. Rodriguez Bacallao
>>>> Centro de Biofisica Medica
>>>> -----------------------------------------------------------------
>>>> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo
>>>> mismo.
>>>>
>>>> Recuerda: El arca de Noe fue construida por aficionados, el titanic
>>>> por profesionales
>>>> -----------------------------------------------------------------
>>>> _______________________________________________
>>>> 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
>>>>
>>>
>>>
>>
>
>
> --
> Lic. José M. Rodriguez Bacallao
> Centro de Biofisica Medica
> -----------------------------------------------------------------
> Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo
> mismo.
>
> Recuerda: El arca de Noe fue construida por aficionados, el titanic
> por profesionales
> -----------------------------------------------------------------
>


-- 
Lic. José M. Rodriguez Bacallao
Centro de Biofisica Medica
-----------------------------------------------------------------
Todos somos muy ignorantes, lo que ocurre es que no todos ignoramos lo mismo.

Recuerda: El arca de Noe fue construida por aficionados, el titanic
por profesionales
-----------------------------------------------------------------