<DIV>Hi Luis,</DIV> <DIV> </DIV> <DIV>I'm not sure if this can help other users and can be applied in other scenarios.</DIV> <DIV>I think if I explain it first will save us from the hustle and bustle.</DIV> <DIV>1)I started by reading two DICOM CT <SPAN id=lw_1180218715_0><FONT color=#003399>datasets.To</FONT></SPAN> display simultaneously two 2D slices at the same position basically I duplicate all the CT handling code.I have m_ImageReader1+m_ImageReader2;m_ImageSpatialObject1+m_ImageSpatialObject2;</DIV> <DIV>m_ImageRepresentationAxial1+m_ImageRepresentationAxial2 and so on.The only difference is that I set </DIV> <DIV> </DIV> <DIV>m_ImageRepresentationAxial1->SetOpacity( 0.5 );</DIV> <DIV>m_ImageRepresentationAxial2->SetOpacity( 0.5 );</DIV> <DIV> </DIV> <DIV>This way I blend the two slices to get the appearance of one slice.</DIV> <DIV> </DIV> <DIV>2)In order to display a segmentation data in color I
needed to modify the igstkImageSpatialObject but adding two methods:</DIV> <DIV>void SetPseudoColorGray(){<BR> m_LUT->SetTableRange ( (m_Level - m_Window/2.0), (m_Level + m_Window/2.0) );<BR> m_LUT->SetSaturationRange (0.0, 0.0);<BR> m_LUT->SetHueRange (0.0, 0.0);<BR> m_LUT->SetValueRange (0.0, 1.0);<BR> m_LUT->SetRampToLinear();<BR>}</DIV> <DIV>void saSetPseudoColorRedBlue(){<BR> m_LUT->SetValueRange (1, 1);<BR> m_LUT->SetSaturationRange (1, 1);<BR> m_LUT->SetHueRange (0.677, 1.0);<BR> m_LUT->SetNumberOfColors(256);<BR> m_LUT->SetTableRange (0.0,255.0 );<BR> m_LUT->Build(); <BR> m_LUT->SetTableValue(0, 0.0, 0.0, 0.0, 0.1);<BR> m_LUT->SetTableValue(1, 0.3, 1.0, 0.0, 0.5);<BR> m_LUT->SetTableValue(2, 1.0, 7.0, 0.5, 0.7);<BR> m_LUT->SetTableValue(3, 0.6, 0.3, 1.0, 0.7);<BR> m_LUT->SetTableValue(4, 0.5, 1.0, 0.5,
0.2);<BR>}<BR></DIV> <DIV>I call the first one after I create m_ImageRepresentationAxial1 for CT data and second one to color my tumor data in red(actualy my second data contains 1 for tumor,2 for entrypoint area,3 for safety margin around tumor,4 for no touch zone )<BR>You presume by default that ImageSpatialobject should pseudocolor the data in gray scale.I think only CTImageSpatialobject should do that.</DIV> <DIV> </DIV> <DIV>3)If I want to display the tumor contour basically I preprocess the segmentation data with a surface extraction algorithm that does the following:for each voxel that has the value 1 for tumor check his neighbours if they are background then I keep that voxel otherwise I discard it.</DIV> <DIV> </DIV> <DIV>4)I read all my segmentation data from an "planning file" that has the next format:</DIV> <DIV>#Number of entry points<BR>1<BR>#entry points<BR>114.674 64.9553 44.9074 <BR>#ablation radius in
mm<BR>40 <BR>#Number of ablations<BR>5 <BR># x y z<BR>128.452 87.4343 35.4807<BR>135.341 98.6738 30.7674<BR>....</DIV> <DIV>and also I read separately segmentation file which is a binary file that has 0 for background,1 for tumor,2 for entry point.</DIV> <DIV> </DIV> <DIV>Inside the code I rasterize the spheres and combine the information with the segmentation file.</DIV> <DIV>I think probably an XML file that contains all this planning data with a special igstk reader that parses all this information will be more appropriate.</DIV> <DIV> </DIV> <DIV>In order to add these planning components to IGSK sandbox I have to write a basic XML Planning reader and an PlanningSpatialObject and PlanningSpatialObjectRepresentationAxial,PlanningSpatialObjectRepresentationSaggital,PlanningSpatialObjectRepresentation3D(this should display surfaces with transparency or by using raycasting).This PlanningSpatialObject should contain
an 3D image that has different values for different components.</DIV> <DIV>I'm not sure how this can help and if it fits Igstk paradigm.</DIV> <DIV> </DIV> <DIV>For my application I found that Igstk provides only a simple surgical planning(entry point and target point).</DIV> <DIV> </DIV> <DIV>Teo</DIV><BR><BR><B><I>Luis Ibanez <luis.ibanez@kitware.com></I></B> wrote: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR>Hi Ionut,<BR><BR><BR>Thanks for letting us know of your results.<BR>They look great.<BR><BR><BR>1) You could have indeed used the vtkCut filter<BR>and then follow it with the vtkDelaunay2D filter,<BR>in order to generate a triangulation of the contour.<BR>This will work fine as long as the contour is convex.<BR><BR><BR>2) I would encourage you to share this class with the<BR>community. We could rename it and put it in the<BR>IGSTK Sandbox. If you found this class useful, it
is<BR>very likely that others will do so too. By sharing the<BR>code, you will also benefit from improvements that other<BR>may make to the class.<BR><BR><BR>3) RequestSetImage() in the ImageSpatialObject is declared<BR>private for safety reasons. The purpose is to ensure that<BR>*only* image readers can put an image in an ImageSpatialObject.<BR>That is, ImageReaders are the *only trusted* source of images.<BR><BR>Remember that the purpose of IGSTK is to provide image<BR>guidance during a surgery. We don't expect that you are<BR>going to do Image Segmentation in the middle of a surgery.<BR><BR>That will be overly optimistic, and border in irresponsible.<BR><BR>We anticipate that you will perform segmentation as part<BR>of *planning* the surgery. (e.g. days or at least hours,<BR>before the actual surgical intervention). You wil save<BR>those segmentations as images or as meshes, and at the<BR>time of the surgery you will only *read* those segmentation<BR>into the
scene.<BR><BR><BR>Why is that your image is not being provided by a Reader ?<BR><BR><BR><BR>Please let us know,<BR><BR><BR>Thanks<BR><BR><BR>Luis<BR><BR><BR><BR>------------------------<BR>ionut iorgovan wrote:<BR>> Hi Luis,<BR>> <BR>> I implemented this using my idea.The reason I didn't use vtkCut is I <BR>> dont think I can use vtkCut to display tumors except as contours not as <BR>> filled polygon.(Can I do that with vtkCut?)<BR>> <BR>> _http://isiswiki.georgetown.edu/teo/rfacolor.jpg_<BR>> __ <BR>> But I didn't implemented it as a separated <BR>> igstkImageContourSpatialObjectRepresentation as you suggested , I just <BR>> modified the igstkImageSpatialObjectRepresentation :(.(because only is <BR>> for my own usage)<BR>> <BR>> My only concern is the RequestSetImage() method from <BR>> igstkImageSpatialObject require that my application is a friend of that <BR>> class.I dont understand why this method cannot be accessed
directly ?<BR>> <BR>> Teo<BR>> <BR>> */Luis Ibanez <LUIS.IBANEZ@KITWARE.COM>/* wrote:<BR>> <BR>> <BR>> Hi Teo,<BR>> <BR>> Implementing this functionality by redrawing an image<BR>> is a bit of an overkill. You can do it in a simpler<BR>> way by using creating a new image representation class<BR>> and using a vtkContour + a vtkCut filter inside.<BR>> <BR>> <BR>> 1) You can implement this functionality as a new type<BR>> of ImageRepresentation class.<BR>> <BR>> 2) If you start from the current class:<BR>> <BR>> igstkImageSpatialObjectRepresentation.<BR>> <BR>> and create a new class, with (for example) name<BR>> <BR>> igstkImageContourSpatialObjectRepresentation.<BR>> <BR>> 3) Inside that new class you remove the<BR>> <BR>> vtkImageActor<BR>> vtkLookupTable<BR>> vtkImageMapToColors<BR>> <BR>> and replace them with a vtkContour filter and<BR>> a normal vtkActor.<BR>> <BR>>
<BR>> 4) Then setup a similar pipeline to the one illustrated<BR>> in the ITK example:<BR>> <BR>> InsightApplications/Auxiliary/vtk<BR>> itkReadITKImage3DSegmentShowVTK.cxx<BR>> <BR>> 5) The image that you need to pass to the vtkContour filter<BR>> is the vtkImageData that you get from the VTKImageObserver.<BR>> <BR>> <BR>> <BR>> The reason behind the apparently complicated way of passing<BR>> images is that IGSTK does not expose ITK or VTK classes in<BR>> order to increase the safety of the software applications.<BR>> <BR>> <BR>> The igstkImage class contains internally an ITK image, and<BR>> using an ITK export + VTK import filter, it reuses the pixel<BR>> data in order to create a vtkImageData object that you can<BR>> pass to a VTK pipeline.<BR>> <BR>> <BR>> <BR>> Please let us know if you find any difficulties implementing<BR>> the igstkImageContourSpatialObjectRepresentation class.<BR>>
<BR>> <BR>> <BR>> Thanks<BR>> <BR>> <BR>> <BR>> Luis<BR>> <BR>> <BR>> <BR>> <BR>> ------------------------<BR>> ionut iorgovan wrote:<BR>> > Hi,<BR>> ><BR>> > I want to display the contour of a segmented object in<BR>> Axial,Sagittal<BR>> > and Coronal Views using igstk.<BR>> > I saw there are implemented in IGSTK sandbox some classes that start<BR>> > with Contour but they suport only mesh representation and also<BR>> there is<BR>> > no documentation how to use them, and what goes were.<BR>> ><BR>> > Therefore I tried to implement my own classes.<BR>> > I wanted to display a second transparent slice(above the CT data)<BR>> that<BR>> > shows a rasterized contour rather than a 3d object.<BR>> ><BR>> > So I wrote my own SpatialObject and SpatialObjectRepresentation.<BR>> > My workflow goes like this:<BR>> > 1.Create an empty 3D image(vtk
or itk) that has the same<BR>> dimension like<BR>> > CTSpatialObject internal image data.<BR>> > 2.Draw my countours inside this image<BR>> > 3.Pass the image to my SpatialObject in a similar fashion with<BR>> > CTImageSpatialObject.<BR>> ><BR>> > My problem is the RequestGetITKImage() with afferent event<BR>> > ITKImageModifiedEvent is not fully implemented so I<BR>> > used RequestGetVTKImage() instead and then get the<BR>> dimensions,spacing<BR>> > from the vtk image and create a new itk image.<BR>> ><BR>> > My questions are<BR>> > 1.How can I display contours in igstk(the book offers no clue on<BR>> how I<BR>> > can do this)?<BR>> > 2.Why the class has a RequestGetITKImage() and no event<BR>> > ITKImageModifiedEvent?<BR>> > 3.What is the reason behind this very complicated way of passing<BR>> image<BR>> > data between classes?<BR>> > 4.Is isgtk keeping
an internal copy of the 3d data in each class?<BR>> > 5.How a user is supposed to use correctly an Igstk<BR>> > component(methods,event,states-look in constructor for allowed<BR>> requests,<BR>> > look for allowed events)?<BR>> ><BR>> > Teo<BR>> ><BR>> ><BR>> ------------------------------------------------------------------------<BR>> > Luggage? GPS? Comic books?<BR>> > Check out fitting gifts for grads<BR>> ><BR>> > at Yahoo! Search.<BR>> ><BR>> ><BR>> ><BR>> ------------------------------------------------------------------------<BR>> ><BR>> > _______________________________________________<BR>> > IGSTK-Users mailing list<BR>> > IGSTK-Users@public.kitware.com<BR>> > http://public.kitware.com/cgi-bin/mailman/listinfo/igstk-users<BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> Get your own web
address. <BR>> <HTTP: evt="49678/*http://smallbusiness.yahoo.com/domains/?p=BESTDEAL" us.rd.yahoo.com><BR>> Have a HUGE year through Yahoo! Small Business. < <BR>> http://us.rd.yahoo.com/evt=49678/*http://smallbusiness.yahoo.com/domains/?p=BESTDEAL> <BR>> <BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> <BR>> _______________________________________________<BR>> IGSTK-Users mailing list<BR>> IGSTK-Users@public.kitware.com<BR>> http://public.kitware.com/cgi-bin/mailman/listinfo/igstk-users<BR></BLOCKQUOTE><BR><p> 
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