[vtkusers] Re: Re: Re: Creating a Volume from 2D BMP files.
Ashish Singh
mrasingh at gmail.com
Thu Sep 14 01:02:18 EDT 2006
Hi Yixun,
I am using the volumerendering library as you mentioned. But still I am
getting the following errors.
1)ERROR: In ..\..\IO\vtkDICOMImageReader.cxx, line 255
vtkDICOMImageReader (0033C900): Either a filename was not specified or the
specified directory does not contain any DICOM images.
2)ERROR: In ..\..\VolumeRendering\vtkVolumeRayCastMapper.cxx, line 326
vtkVolumeRayCastMapper (02953718): Cannot volume render data of type short,
only unsigned char or unsigned short.
The 2nd error keeps repeating itself again and again.
How can I rectify these errors?
My code is as follows:
-----
#include "vtkConeSource.h"
#include "vtkPolyDataMapper.h "
#include "vtkRenderWindow.h"
#include "vtkCamera.h"
#include "vtkActor.h"#include "vtkImageActor.h"
#include "vtkOutlineFilter.h"
#include " vtkProperty.h"
#include "vtkPolyDataNormals.h"
#include "vtkContourFilter.h"
#include "vtkDataSetMapper.h"
#include "vtkImageMapper.h"
#include "vtkPiecewiseFunction.h "
#include "vtkVolumeProperty.h"
#include "vtkRenderer.h"
#include "conio.h"
#include "vtkDICOMImageReader.h"
#include "vtkImageViewer2.h"
#include " vtkJPEGReader.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkVolumeMapper.h"
#include "vtkActor2D.h"
#include "vtkPolyDataMapper.h"
#include "vtkVolumeRayCastCompositeFunction.h "
#include "vtkVolumeRayCastMapper.h"
void main()
{
vtkRenderer *arenderer = vtkRenderer::New();
vtkRenderWindow *renwin = vtkRenderWindow::New();
vtkDICOMImageReader *img1=vtkDICOMImageReader::New();
img1->SetFilePrefix("D:\\testimages\\dicomset\\IM");
img1->SetFilePattern("%s%d.dcm");
img1->SetFileNameSliceOffset(1);
img1->SetFileNameSliceSpacing(1);
img1->SetDataExtent(0,511,0,511,1,10);//512x512 images and 10 slices
img1->SetDataSpacing(360.0/512,360.0/512,1.0); //my image is 36cm x 36cm
and 512x512
img1->SetDataOrigin(0.0,0.0,0.0);
img1->Update();
vtkVolume *vol=vtkVolume::New();
vtkVolumeRayCastMapper *volumemapper = vtkVolumeRayCastMapper::New();
vtkVolumeRayCastCompositeFunction
*rcf=vtkVolumeRayCastCompositeFunction::New();
volumemapper->SetVolumeRayCastFunction(rcf);
volumemapper->SetInput(img1->GetOutput());
vol->SetMapper(volumemapper);
vtkCamera *cam=vtkCamera::New();
cam->SetViewUp(0,0,-1);
cam->SetPosition(0,1,0);
cam->SetFocalPoint(0,0,0);
cam->ComputeViewPlaneNormal();
arenderer->AddActor(vol);
arenderer->SetActiveCamera(cam);
arenderer->ResetCamera();
arenderer->SetBackground(1,1,1);
renwin->AddRenderer(arenderer);
vtkRenderWindowInteractor *iren=vtkRenderWindowInteractor::New();
iren->SetRenderWindow(renwin);
renwin->Render();
iren->Initialize();
iren->Start();
img1->Delete();
iren->Delete();
}
--------
I would appreciate all help.
Thanks,
Ashish
On 9/13/06, Yixun Liu <yxliu at fudan.edu.cn> wrote:
>
> Hi,
> When you update vtk from 4.2 to 5.0 the old rendering.lib has been
> replaced with volumerendering.lib, so be sure that you use the
> volumerendering.lib instead of rendering.lib in you project configuration.
>
> Cheers,
>
> Yixun
>
> ----- Original Message -----
> *From:* Ashish Singh <mrasingh at gmail.com>
> *To:* vtkusers at vtk.org
> *Cc:* Yixun Liu <yxliu at fudan.edu.cn> ; Amy Squillacote<amy.squillacote at kitware.com>
> *Sent:* Thursday, September 14, 2006 1:23 AM
> *Subject:* Re: [vtkusers] Re: Re: Re: Creating a Volume from 2D BMP files.
>
> Hi Amy,
>
> I don't remember if VTK_USE_RENDERING variable was ON or not. Is there a
> way to confirm that? However I am able to compile and run other programs
> from the examples/tutorials directory such as cones etc. as well as read and
> display single dicom image and interact with it using
> renderwindowinteractor.
>
> Here is my cmakelists.txt file for cone example:
> ---
> PROJECT (Step1)
>
> FIND_PACKAGE(VTK REQUIRED)
> IF(NOT VTK_USE_RENDERING)
> MESSAGE(FATAL_ERROR "Example ${PROJECT_NAME} requires
> VTK_USE_RENDERING.")
> ENDIF(NOT VTK_USE_RENDERING)
> INCLUDE(${VTK_USE_FILE})
>
> ADD_EXECUTABLE(Cone Cone.cxx)
> TARGET_LINK_LIBRARIES(Cone vtkRendering)
> ----
> This works fine.
>
> The cmakelists.txt file that I use for dicom volume problem is :
> ----
> PROJECT (multiimagereader)
>
> INCLUDE (${CMAKE_ROOT}/Modules/FindVTK.cmake)
> IF (USE_VTK_FILE)
> INCLUDE(${USE_VTK_FILE})
> ENDIF (USE_VTK_FILE)
>
> ADD_EXECUTABLE(multiimagereader multiimagereader.cxx )
> TARGET_LINK_LIBRARIES(multiimagereader vtkRendering)
> ----
> Is there anything that I need to modify in this file?
>
> Thanks,
> Ashish
>
>
> On 9/13/06, Amy Squillacote <amy.squillacote at kitware.com> wrote:
> >
> > Hi Ashish,
> >
> > When you built VTK, was the VTK_USE_RENDERING CMake variable set to ON?
> > If it was, are you linking against the vtkVolumeRendering library?
> >
> > - Amy
> >
> > Ashish Singh wrote:
> >
> > Hi Yixun and Sharwari,
> >
> > I am trying to solve exactly similar problem but using DICOM images
> > rather than bmp. But I am getting errors and I can't figure out why. My code
> > is based on your previous conversation so far. The error that I get is:
> > (1)error LNK2019: unresolved external symbol "public: static class
> > vtkVolumeRayCastCompositeFunction * __cdecl
> > vtkVolumeRayCastCompositeFunction::New(void)"
> > (?New at vtkVolumeRayCastCompositeFunction@@SAPAV1 at XZ ) referenced in
> > function _main
> > (2)error LNK2019: unresolved external symbol "public: static class
> > vtkVolumeRayCastMapper * __cdecl vtkVolumeRayCastMapper::New(void)"
> > (?New at vtkVolumeRayCastMapper@@SAPAV1 at XZ) referenced in function _main
> > (3)fatal error LNK1120: 2 unresolved externals
> >
> > Can you please help me figure out what's going wrong here?
> >
> > My code is as follows:
> > -----
> > #include "vtkConeSource.h"
> > #include "vtkPolyDataMapper.h "
> > #include "vtkRenderWindow.h"
> > #include "vtkCamera.h"
> > #include "vtkActor.h"
> > #include "vtkImageActor.h"
> > #include "vtkOutlineFilter.h"
> > #include " vtkProperty.h"
> > #include "vtkPolyDataNormals.h"
> > #include "vtkContourFilter.h"
> > #include "vtkDataSetMapper.h"
> > #include "vtkImageMapper.h"
> > #include "vtkPiecewiseFunction.h "
> > #include "vtkVolumeProperty.h"
> > #include "vtkRenderer.h"
> > #include "conio.h"
> > #include "vtkDICOMImageReader.h"
> > #include "vtkImageViewer2.h"
> > #include " vtkJPEGReader.h"
> > #include "vtkRenderWindowInteractor.h"
> > #include "vtkVolumeMapper.h"
> > #include "vtkActor2D.h"
> > #include "vtkPolyDataMapper.h"
> > #include "vtkVolumeRayCastCompositeFunction.h "
> > #include "vtkVolumeRayCastMapper.h"
> >
> > void main()
> > {
> >
> > vtkRenderer *arenderer = vtkRenderer::New();
> > vtkRenderWindow *renwin = vtkRenderWindow::New();
> > vtkDICOMImageReader *img1=vtkDICOMImageReader::New();
> >
> > img1->SetFilePrefix("D:\\testimages\\dicomset\\IM");
> > img1->SetFilePattern("%s%d.dcm");
> > img1->SetFileNameSliceOffset(1);
> > img1->SetFileNameSliceSpacing(1);
> > img1->SetDataExtent(0,511,0,511,1,10);//512x512 images and 10 slices
> > img1->SetDataSpacing(360.0/512,360.0/512,1.0); //my image is 36cm x
> > 36cm and 512x512
> > img1->SetDataOrigin(0.0,0.0,0.0);
> > img1->Update();
> >
> > vtkVolume *vol=vtkVolume::New();
> > vtkVolumeRayCastMapper *volumemapper = vtkVolumeRayCastMapper::New();
> > vtkVolumeRayCastCompositeFunction
> > *rcf=vtkVolumeRayCastCompositeFunction::New();
> > volumemapper->SetVolumeRayCastFunction(rcf);
> > volumemapper->SetInput(img1->GetOutput());
> > vol->SetMapper(volumemapper);
> >
> > vtkCamera *cam=vtkCamera::New();
> > cam->SetViewUp(0,0,-1);
> > cam->SetPosition(0,1,0);
> > cam->SetFocalPoint(0,0,0);
> > cam->ComputeViewPlaneNormal();
> >
> > arenderer->AddActor(vol);
> > arenderer->SetActiveCamera(cam);
> > arenderer->ResetCamera();
> > arenderer->SetBackground(1,1,1);
> >
> > renwin->AddRenderer(arenderer);
> > vtkRenderWindowInteractor *iren=vtkRenderWindowInteractor::New();
> > iren->SetRenderWindow(renwin);
> > renwin->Render();
> > iren->Initialize();
> > iren->Start();
> >
> > img1->Delete();
> > iren->Delete();
> > }
> > --------
> > I would really appreciate if anyone can help me.
> >
> > Regards,
> > Ashish
> >
> > On 9/7/06, Sharwari Mavalankar < sharwari at gmail.com> wrote:
> > >
> > > hi Yixun,
> > > I'll try and look into why the volume appears darker.
> > >
> > > However I'll there are many lines that are appearing on the volume
> > > (they look like striations).
> > > Do you know what the reason for that could be?
> > >
> > >
> > > Also if I have to visualize color bmp slices (24 bit ) I need vtkFixedPointVolumeRayCastMapper
> > > right?
> > > Thanks
> > > Sharwari
> > >
> > >
> > > On 9/6/06, Yixun Liu <yxliu at fudan.edu.cn > wrote:
> > > >
> > > > Hi,
> > > > You are right and alwayse taking mm as the unit.
> > > > SpacingX = 5.12*10/256;
> > > > SpacingY = 5.12*10/256;
> > > >
> > > > Many reason can make the volume look darker.
> > > > You can change the opacity and color interpolation function to
> > > > adjust the appearance of the volume. If you use shade you can also change
> > > > ambient or diffusion coefficient to make the volume look more lighter.
> > > > Another method is to change the vtkLight in the renderer. vtkLightis a virtual light for 3D rendering. It provides methods to locate and point
> > > > the light, turn it on and off, and set its brightness and color.
> > > >
> > > > Cheers,
> > > >
> > > > Yixun Liu
> > > > ----- Original Message -----
> > > > *From:* Sharwari Mavalankar <sharwari at gmail.com>
> > > > *To:* Yixun Liu <yxliu at fudan.edu.cn>
> > > > *Cc:* VTK <vtkusers at vtk.org>
> > > > *Sent:* Thursday, September 07, 2006 1:43 AM
> > > > *Subject:* Re: Re: Re: Creating a Volume from 2D BMP files.
> > > >
> > > >
> > > > hi Yixun,
> > > > Thank you very much for your email.
> > > > What exactly do you mean by the physical size of the image?
> > > > Does it mean the size of the image in cm or mm?
> > > >
> > > > For example if my original images are 5.12 cm * 5.12 cm and are 256
> > > > * 256 images.
> > > > What will the data spacing be?
> > > >
> > > >
> > > > Also can you tell me the reason why the 3D volume seems darker than
> > > > the original images?
> > > > Is there any way I can scale the intensity of the images?
> > > > Thanks again,
> > > > Sharwari
> > > >
> > > >
> > > > On 9/3/06, Yixun Liu <yxliu at fudan.edu.cn > wrote:
> > > > >
> > > > > Hi,
> > > > > If you read color bmp files you should update vtk to 5.0 version
> > > > > and use vtkFixedPointVolumeRayCastMapper(see last mail). Otherwise, you
> > > > > should not call
> > > > > br->SetNumberOfScalarComponents(3);
> > > > >
> > > > > 1. You can decide the physical spacing accroding to the image
> > > > > extent(pixel unit) and its physical size(mm): spacing = size/(extent-1); If
> > > > > no physical size you have to give a estimation for the spacing.
> > > > >
> > > > > 2.The point1 and point2 will define a linear opacity function,
> > > > > which can be interpolated from the two points. For example, define two
> > > > > points (intensity1, opacity1)and (intensity2, opacity2) you can get the
> > > > > opacity3 at intensity3 by opacity3 =
> > > > > (intensity3-intensity1)/(intensity2-intensity1)*(opacity2-opacity1) +
> > > > > opacity1
> > > > >
> > > > > Hope it help.
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Yixun Liu
> > > > >
> > > > > ----- Original Message -----
> > > > > *From:* Sharwari Mavalankar <sharwari at gmail.com>
> > > > > *To:* Yixun Liu <yxliu at fudan.edu.cn>
> > > > > *Cc:* VTK <vtkusers at vtk.org>
> > > > > *Sent:* Monday, September 04, 2006 6:50 AM
> > > > > *Subject:* Re: Re: Creating a Volume from 2D BMP files.
> > > > >
> > > > >
> > > > > hi Yixun,
> > > > > I implemented the suggestions that you had made.
> > > > > Now I am getting a 3D volume but it doesnt look anything like the
> > > > > original 2D slices.
> > > > > It is much darker in appearance and it's got lines all over it (
> > > > > it looks as though it's some kind of aliasing).
> > > > >
> > > > > I have the following questions to ask you
> > > > > 1.While using the function SetDataSpacing(x,y,z) how do I decide
> > > > > the values of the parameters x,y and z.
> > > > >
> > > > > 2.While using the Addpoint() function of class
> > > > > vtkPiecewiseFunction what do the two parameters in the Addpoint function
> > > > > mean?
> > > > > How do they affect the output?
> > > > >
> > > > >
> > > > > This is code I have used. Do let me know if you can make any more
> > > > > sugestions.
> > > > >
> > > > >
> > > > >
> > > > > //This program reads a single BMP file and plots it as an image.
> > > > > //The same program will be extended to read multiple images and
> > > > > create a 3D volume out of 2D slices.
> > > > >
> > > > >
> > > > > #include "vtkRenderer.h"
> > > > > #include "vtkRenderWindow.h"
> > > > > #include "vtkRenderWindowInteractor.h"
> > > > > #include "vtkBMPReader.h"
> > > > > #include "vtkPolyDataMapper.h"
> > > > > #include "vtkActor.h"
> > > > > #include "vtkActor2D.h"
> > > > > #include "vtkImageActor.h"
> > > > > #include "vtkOutlineFilter.h"
> > > > > #include "vtkCamera.h"
> > > > > #include "vtkProperty.h"
> > > > > #include "vtkPolyDataNormals.h"
> > > > > #include "vtkContourFilter.h"
> > > > > #include "vtkDataSetMapper.h"
> > > > > #include "vtkImageMapper.h"
> > > > > #include "vtkVolumeMapper.h"
> > > > > #include " vtkVolumeRayCastMapper.h"
> > > > > #include "vtkVolumeRayCastCompositeFunction.h"
> > > > > #include "vtkPiecewiseFunction.h"
> > > > > #include "vtkVolumeProperty.h"
> > > > >
> > > > >
> > > > > void main (void)
> > > > > {
> > > > >
> > > > > vtkRenderer *aRenderer = vtkRenderer::New();
> > > > > vtkRenderWindow *renWin = vtkRenderWindow::New();
> > > > >
> > > > > renWin->AddRenderer(aRenderer);
> > > > > vtkRenderWindowInteractor *iren =
> > > > > vtkRenderWindowInteractor::New();
> > > > > iren->SetRenderWindow(renWin);
> > > > >
> > > > >
> > > > > //create an instance of the class vtkBMPReader
> > > > > vtkBMPReader *br = vtkBMPReader::New();
> > > > >
> > > > > br->SetFilePrefix("C:\\Images\\conductivities\\slice");
> > > > > br->SetFilePattern("%s%d.bmp");
> > > > > br->SetFileNameSliceOffset(1);
> > > > > br->SetFileNameSliceSpacing(1);
> > > > > br->SetNumberOfScalarComponents(3);
> > > > > br->SetDataSpacing(0.4,0.4,10);
> > > > > br->SetDataOrigin(0,0,0);
> > > > > br->SetDataExtent(0,255,0,255,0,7);
> > > > > br->Update();
> > > > >
> > > > > vtkPiecewiseFunction *opacityTransferFunction =
> > > > > vtkPiecewiseFunction::New();
> > > > > opacityTransferFunction->AddPoint(20,0.2);
> > > > > opacityTransferFunction->AddPoint(255,1.0);
> > > > >
> > > > > vtkVolumeProperty *volumeProperty = vtkVolumeProperty::New();
> > > > > volumeProperty->SetScalarOpacity(opacityTransferFunction);
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > vtkVolumeRayCastMapper *VolumeMapper =
> > > > > vtkVolumeRayCastMapper::New();
> > > > > vtkVolumeRayCastCompositeFunction *RayCastFunction =
> > > > > vtkVolumeRayCastCompositeFunction::New();
> > > > > VolumeMapper->SetVolumeRayCastFunction(RayCastFunction);
> > > > > VolumeMapper->SetInput(br->GetOutput());
> > > > >
> > > > >
> > > > > vtkVolume *volume = vtkVolume::New();
> > > > >
> > > > > VolumeMapper->SetInput(br->GetOutput());
> > > > > volume->SetMapper(VolumeMapper);
> > > > >
> > > > > vtkCamera *aCamera = vtkCamera::New();
> > > > > aCamera->SetViewUp (0, 0,-1);
> > > > > aCamera->SetPosition (0, 1, 0);
> > > > > aCamera->SetFocalPoint (0, 0, 0);
> > > > > aCamera->ComputeViewPlaneNormal();
> > > > >
> > > > >
> > > > > aRenderer->AddActor(volume);
> > > > > aRenderer->SetActiveCamera(aCamera);
> > > > > aRenderer->ResetCamera ();
> > > > > aRenderer->SetBackground(1,1,1);
> > > > > renWin->Render();
> > > > >
> > > > > iren->Initialize();
> > > > > iren->Start();
> > > > >
> > > > > }
> > > > >
> > > > > Thanks again for all your help.
> > > > > Sharwari
> > > > >
> > > > >
> > > > > On 8/31/06, Yixun Liu <yxliu at fudan.edu.cn > wrote:
> > > > > >
> > > > > > Hi,
> > > > > > Assuming image is 256x256x100. The first file name is image1 and
> > > > > > the last file name is image100. So, SetDataExtent(0, 255, 0, 255, 1, 100);
> > > > > > The access violation may be caused by wrong extent setting.
> > > > > >
> > > > > > If you use vtkVolume, use vtkVolumeRayCastMapper(vtk4.2.2)
> > > > > > or use vtkFixedPointVolumeRayCastMapper(vtk5.0). Note that if
> > > > > > you use vtkFixedPointVolumeRayCastMapper you no need to call
> > > > > > SetVolumeRayCastFunction();
> > > > > >
> > > > > > Hope it help.
> > > > > >
> > > > > > Yixun Liu
> > > > > >
> > > > > > ----- Original Message -----
> > > > > > *From:* Sharwari Mavalankar <sharwari at gmail.com>
> > > > > > *To:* Yixun Liu <yxliu at fudan.edu.cn>
> > > > > > *Cc:* VTK <vtkusers at vtk.org>
> > > > > > *Sent:* Thursday, August 31, 2006 6:37 PM
> > > > > > *Subject:* Re: Creating a Volume from 2D BMP files.
> > > > > >
> > > > > >
> > > > > > hi Yixun,
> > > > > > Thanks for your email.I had a couple of more questions though.
> > > > > > 1.I do not want to visualize colour slices.They are grey level
> > > > > > images.
> > > > > >
> > > > > > 2.Also if I put SetDataExtent() before the Update() then I am
> > > > > > getting an access violation error.What does the Update function
> > > > > > do exactly?
> > > > > > Also can you tell me what the five parameters in SetDataExtent()
> > > > > > mean?
> > > > > >
> > > > > > 3.If I use vtkVolume what mapper should I use to visualize the
> > > > > > slices?
> > > > > >
> > > > > >
> > > > > > Thanks again for all your help.
> > > > > > Sharwari
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 8/23/06, Yixun Liu <yxliu at fudan.edu.cn > wrote:
> > > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > If you want to visualize color slices, you need to
> > > > > > > 1. read these slices. You need to put the SetDataExtent(0,
> > > > > > > 111, 0, 127, 1, 300);
> > > > > > > before Update();
> > > > > > >
> > > > > > > vtkTIFFReader *v16 = vtkTIFFReader::New();
> > > > > > >
> > > > > > > v16->SetFilePrefix("D:\\MyVC\\VTKtest\\Raycasting\\Data\\BrainColor\\brain");
> > > > > > > v16->SetFilePattern("%s%d.TIF");
> > > > > > > v16->SetDataExtent(0, 111, 0, 127, 1, 300);
> > > > > > > v16->SetDataSpacing(1.2,1.2,0.5);
> > > > > > > v16->SetDataOrigin(0.0, 0.0, 0.0);
> > > > > > > v16->SetNumberOfScalarComponents(3);
> > > > > > > v16->Update();
> > > > > > >
> > > > > > > 2. Add the 4th component. The first three components are color
> > > > > > > and the 4th is used to map to opacity. I compute the luminancy according to
> > > > > > > the firft three components and take it as the 4th component.
> > > > > > >
> > > > > > > 3. Opacity map using vtkPiecewiseFunction
> > > > > > >
> > > > > > > 4. no need color map function
> > > > > > >
> > > > > > > 5. you need vtk5.0
> > > > > > >
> > > > > > > Regads,
> > > > > > >
> > > > > > > Yixun Liu
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > >
> > > _______________________________________________
> > > This is the private VTK discussion list.
> > > Please keep messages on-topic. Check the FAQ at:
> > > http://www.vtk.org/Wiki/VTK_FAQ
> > > Follow this link to subscribe/unsubscribe:
> > > http://www.vtk.org/mailman/listinfo/vtkusers
> > >
> > >
> > >
> > ------------------------------
> >
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