[vtkusers] Re: Re: Re: Creating a Volume from 2D BMP files.
Yixun Liu
yxliu at fudan.edu.cn
Thu Sep 14 01:09:39 EDT 2006
Hi,
vtkVolumeRayCastMapper does not support short type, so rescale it to unsigned short using vtkImageShiftScale or use vtkFixedPointVolumeRayCastMapper instead of vtkVolumeRayCastMapper.
Hope it help.
Yixun
----- Original Message -----
From: Ashish Singh
To: Yixun Liu ; vtkusers at vtk.org
Sent: Thursday, September 14, 2006 1:02 PM
Subject: Re: [vtkusers] Re: Re: Re: Creating a Volume from 2D BMP files.
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 "vtkVolumeRayCastCompositeFuncti
on.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
To: vtkusers at vtk.org
Cc: Yixun Liu ; Amy Squillacote
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. vtkLight is 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
To: Yixun Liu
Cc: VTK
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
To: Yixun Liu
Cc: VTK
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
To: Yixun Liu
Cc: VTK
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
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