[vtkusers] Announcement: New image rendering classes for VTK

Tue Jun 28 11:40:31 EDT 2011

Hi David,

I am interested in this too:
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

Currently I resample the image so it has identity transformation. But this
is lossy and ugly.

Does the above approach affect the polygonal actors in the scene (segmented
parts of the image)?

Regards,
Dženan

On Mon, Jun 27, 2011 at 19:29, 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
> -----------------------------------------------------------------
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.vtk.org/pipermail/vtkusers/attachments/20110628/08e084ac/attachment.htm>