从 .dcm 文件生成和读取 .vtk 文件,以及修改模型
Generating and reading .vtk files from .dcm files, and modifying model
想对dicom体积渲染有更深入的了解
我有一组 dicom 图像,我已经能够从中提取轴向、冠状和矢状切面,如下所示:
我一开始想从头开始生成一个 3D 模型,但似乎太难了。
所以我听说了 VTK/ITK,我一直在使用这段代码从我的图像集中生成一个 .vtk 文件:
http://www.itk.org/Doxygen46/html/IO_2DicomSeriesReadImageWrite2_8cxx-example.html
有效,但我需要一些解释:
当我用 ParaView 打开这个文件时,我得到以下结果:
首先,这可能是一个愚蠢的问题,但为什么它是蓝色的?
有没有办法切开并看到模型的内部?
我的目标是不使用 ParaView,我想制作自己的 .vtk reader,我发现这段代码我不记得在哪里,我认为它应该可以工作,但是我得到的只是绿色背景,仅此而已:
#include <vtkPolyDataReader.h>
#include <vtkSmartPointer.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkRenderWindowInteractor.h>
int main ( int argc, char *argv[] ) {
// Parse command line arguments
if (argc != 2) {
std::cerr << "Usage: " << argv[0] << " Filename(.vtk)" << std::endl;
return EXIT_FAILURE;
}
std::string filename = argv[1];
// Read all the data from the file
vtkSmartPointer<vtkPolyDataReader> reader = vtkSmartPointer<vtkPolyDataReader>::New();
reader->SetFileName(filename.c_str());
reader->Update();
// Visualize
vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
mapper->SetInputConnection(reader->GetOutputPort());
vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
actor->SetMapper(mapper);
vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
renderWindow->AddRenderer(renderer);
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
vtkSmartPointer<vtkRenderWindowInteractor>::New();
renderWindowInteractor->SetRenderWindow(renderWindow);
renderer->AddActor(actor);
renderer->SetBackground(.3, .6, .3); // Background color green
renderWindow->Render();
renderWindowInteractor->Start();
return EXIT_SUCCESS;
}
知道为什么吗?我在 ParaView 中看到我必须激活 "Volume" 模式才能看到我的模型,这里有类似的处理吗?
最后一件非常重要的事情:是否可以修改 .vtk 文件中的 3D 体积?例如,如果我想更改模型特定部分的颜色,VTK 是否提供允许这样做的工具?
这里有很多问题!
这里有一些答案。
- 渲染是蓝色的,因为查找table是paraview中的默认(从蓝色到红色)。您可以使用 color map editor
编辑它
- "cut"里面的数据确实有一些方法,请看后面贴的例子。
- 该示例不起作用,因为您正在尝试使用多数据(网格)加载 vtkImageData reader
- 这正是您必须在 Paraview 中 select "Volume" 的原因,因为您的数据是一个体积(体素的 3D 阵列)。您可以使用 VTK 中可用的任何体积映射器来执行相同的操作。
- 是的,您可以编辑音量的值,但目前这会让我们走得有点远,如果需要,我们稍后会谈到;)
这是一个完整的示例,它读取一个目录下的所有 DICOM 文件,构建一个体积,使用体积渲染器渲染它,并启用一个盒子小部件以交互方式剪辑体积。
#include "vtkBoxRepresentation.h"
#include "vtkBoxWidget2.h"
#include "vtkCamera.h"
#include "vtkColorTransferFunction.h"
#include "vtkCommand.h"
#include "vtkDICOMImageReader.h"
#include "vtkGPUVolumeRaycastMapper.h"
#include "vtkImageData.h"
#include "vtkInteractorStyle.h"
#include "vtkInteractorStyleTrackballCamera.h"
#include "vtkMath.h"
#include "vtkPiecewiseFunction.h"
#include "vtkPlanes.h"
#include "vtkRenderWindow.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkRenderer.h"
#include "vtkVolume.h"
#include "vtkVolumeProperty.h"
// Box interaction callback
class vtkBoxCallback : public vtkCommand
{
public:
static vtkBoxCallback *New(){ return new vtkBoxCallback; }
vtkGPUVolumeRayCastMapper* m_mapper;
vtkPlanes* m_planes;
virtual void Execute( vtkObject* a_caller, unsigned long, void* ){
vtkBoxWidget2* l_box_wdget = vtkBoxWidget2::SafeDownCast( a_caller );
( (vtkBoxRepresentation*)l_box_wdget->GetRepresentation() )->GetPlanes( m_planes );
this->m_mapper->SetClippingPlanes( m_planes );
}
vtkBoxCallback(){}
};
int main( int argc, char *argv[] ){
// Read volume
vtkDICOMImageReader* l_reader = vtkDICOMImageReader::New();
l_reader->SetDirectoryName( "C:/PathToDicomFiles/" );
l_reader->Update();
// Setup rendering stuff
vtkRenderer* l_renderer = vtkRenderer::New();
l_renderer->SetBackground( 0.3, 0.3, 0.3 );
vtkRenderWindow* l_render_windows = vtkRenderWindow::New();
l_render_windows->AddRenderer( l_renderer );
l_render_windows->SetSize( 900, 900 );
vtkInteractorStyleTrackballCamera* l_trackball = vtkInteractorStyleTrackballCamera::New();
vtkRenderWindowInteractor* l_iren = vtkRenderWindowInteractor::New();
l_iren->SetInteractorStyle( l_trackball );
l_iren->SetRenderWindow( l_render_windows );
l_iren->GetInteractorStyle()->SetDefaultRenderer( l_renderer );
l_iren->SetDesiredUpdateRate( 15 );
// Make sure we have an opengl context
l_render_windows->Render();
// Setup GPU volume raycast mapper
vtkGPUVolumeRayCastMapper* l_gpu_mapper = vtkGPUVolumeRayCastMapper::New();
l_gpu_mapper->SetInputConnection( l_reader->GetOutputPort() );
// Setup Volume property
// Window/Level
double wl = 260;
double ww = 270;
// Color function
vtkColorTransferFunction* l_color = vtkColorTransferFunction::New();
l_color->SetColorSpaceToRGB();
l_color->AddRGBPoint( wl - ww / 2, 0, 0, 0 );
l_color->AddRGBPoint( wl - ww / 2 + 94 * ( ww / 255.0 ), 1., 21. / 255.0, 27. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 147 * ( ww / 255.0 ), 1., 176. / 255.0, 9. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 201 * ( ww / 255.0 ), 1., 241. / 255.0, 39. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 255 * ( ww / 255.0 ), 1, 1, 1. );
l_color->Build();
// Opacity function
vtkPiecewiseFunction* l_opacity = vtkPiecewiseFunction::New();
l_opacity->AddPoint( wl - ww / 2, 0 );
l_opacity->AddPoint( wl + ww / 2, 1 );
// Volume property, light, shading
vtkVolumeProperty* l_volume_property = vtkVolumeProperty::New();
l_volume_property->SetColor( l_color );
l_volume_property->SetScalarOpacity( l_opacity );
l_volume_property->SetInterpolationTypeToLinear();
l_volume_property->ShadeOn();
l_volume_property->SetAmbient( 0.15 );
l_volume_property->SetDiffuse( 0.8 );
l_volume_property->SetSpecular( 0.25 );
l_volume_property->SetSpecularPower( 40 );
// Put everything together
vtkVolume* l_volume = vtkVolume::New();
l_volume->SetProperty( l_volume_property );
l_volume->SetMapper( l_gpu_mapper );
l_renderer->AddVolume( l_volume );
l_renderer->ResetCamera();
// setup Box interactive widget
vtkBoxRepresentation* l_box_rep = vtkBoxRepresentation::New();
l_box_rep->SetInsideOut( true );
vtkBoxWidget2* l_voi_widget = vtkBoxWidget2::New();
l_voi_widget->SetRepresentation( l_box_rep );
l_voi_widget->SetInteractor( l_iren );
l_voi_widget->GetRepresentation()->SetPlaceFactor( 1. );
l_voi_widget->GetRepresentation()->PlaceWidget( l_reader->GetOutput()->GetBounds() );
l_voi_widget->SetEnabled( true );
vtkPlanes* l_planes = vtkPlanes::New();
vtkBoxCallback* l_callback = vtkBoxCallback::New();
l_callback->m_mapper = l_gpu_mapper;
l_callback->m_planes = l_planes;
l_voi_widget->AddObserver( vtkCommand::InteractionEvent, l_callback );
// Go rendering !
l_iren->Start();
// Memory cleanup
l_reader->Delete();
l_renderer->Delete();
l_render_windows->Delete();
l_trackball->Delete();
l_iren->Delete();
l_gpu_mapper->Delete();
l_color->Delete();
l_opacity->Delete();
l_volume_property->Delete();
l_volume->Delete();
l_voi_widget->Delete();
l_planes->Delete();
l_callback->Delete();
}
作为一般性建议,我建议您阅读 VTK examples,这应该可以帮助您了解所有 VTK 功能。
希望对您有所帮助:)
想对dicom体积渲染有更深入的了解
我有一组 dicom 图像,我已经能够从中提取轴向、冠状和矢状切面,如下所示:
我一开始想从头开始生成一个 3D 模型,但似乎太难了。
所以我听说了 VTK/ITK,我一直在使用这段代码从我的图像集中生成一个 .vtk 文件:
http://www.itk.org/Doxygen46/html/IO_2DicomSeriesReadImageWrite2_8cxx-example.html
有效,但我需要一些解释:
当我用 ParaView 打开这个文件时,我得到以下结果:
首先,这可能是一个愚蠢的问题,但为什么它是蓝色的?
有没有办法切开并看到模型的内部?
我的目标是不使用 ParaView,我想制作自己的 .vtk reader,我发现这段代码我不记得在哪里,我认为它应该可以工作,但是我得到的只是绿色背景,仅此而已:
#include <vtkPolyDataReader.h>
#include <vtkSmartPointer.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkRenderWindow.h>
#include <vtkRenderer.h>
#include <vtkRenderWindowInteractor.h>
int main ( int argc, char *argv[] ) {
// Parse command line arguments
if (argc != 2) {
std::cerr << "Usage: " << argv[0] << " Filename(.vtk)" << std::endl;
return EXIT_FAILURE;
}
std::string filename = argv[1];
// Read all the data from the file
vtkSmartPointer<vtkPolyDataReader> reader = vtkSmartPointer<vtkPolyDataReader>::New();
reader->SetFileName(filename.c_str());
reader->Update();
// Visualize
vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
mapper->SetInputConnection(reader->GetOutputPort());
vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
actor->SetMapper(mapper);
vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<vtkRenderWindow>::New();
renderWindow->AddRenderer(renderer);
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
vtkSmartPointer<vtkRenderWindowInteractor>::New();
renderWindowInteractor->SetRenderWindow(renderWindow);
renderer->AddActor(actor);
renderer->SetBackground(.3, .6, .3); // Background color green
renderWindow->Render();
renderWindowInteractor->Start();
return EXIT_SUCCESS;
}
知道为什么吗?我在 ParaView 中看到我必须激活 "Volume" 模式才能看到我的模型,这里有类似的处理吗?
最后一件非常重要的事情:是否可以修改 .vtk 文件中的 3D 体积?例如,如果我想更改模型特定部分的颜色,VTK 是否提供允许这样做的工具?
这里有很多问题! 这里有一些答案。
- 渲染是蓝色的,因为查找table是paraview中的默认(从蓝色到红色)。您可以使用 color map editor 编辑它
- "cut"里面的数据确实有一些方法,请看后面贴的例子。
- 该示例不起作用,因为您正在尝试使用多数据(网格)加载 vtkImageData reader
- 这正是您必须在 Paraview 中 select "Volume" 的原因,因为您的数据是一个体积(体素的 3D 阵列)。您可以使用 VTK 中可用的任何体积映射器来执行相同的操作。
- 是的,您可以编辑音量的值,但目前这会让我们走得有点远,如果需要,我们稍后会谈到;)
这是一个完整的示例,它读取一个目录下的所有 DICOM 文件,构建一个体积,使用体积渲染器渲染它,并启用一个盒子小部件以交互方式剪辑体积。
#include "vtkBoxRepresentation.h"
#include "vtkBoxWidget2.h"
#include "vtkCamera.h"
#include "vtkColorTransferFunction.h"
#include "vtkCommand.h"
#include "vtkDICOMImageReader.h"
#include "vtkGPUVolumeRaycastMapper.h"
#include "vtkImageData.h"
#include "vtkInteractorStyle.h"
#include "vtkInteractorStyleTrackballCamera.h"
#include "vtkMath.h"
#include "vtkPiecewiseFunction.h"
#include "vtkPlanes.h"
#include "vtkRenderWindow.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkRenderer.h"
#include "vtkVolume.h"
#include "vtkVolumeProperty.h"
// Box interaction callback
class vtkBoxCallback : public vtkCommand
{
public:
static vtkBoxCallback *New(){ return new vtkBoxCallback; }
vtkGPUVolumeRayCastMapper* m_mapper;
vtkPlanes* m_planes;
virtual void Execute( vtkObject* a_caller, unsigned long, void* ){
vtkBoxWidget2* l_box_wdget = vtkBoxWidget2::SafeDownCast( a_caller );
( (vtkBoxRepresentation*)l_box_wdget->GetRepresentation() )->GetPlanes( m_planes );
this->m_mapper->SetClippingPlanes( m_planes );
}
vtkBoxCallback(){}
};
int main( int argc, char *argv[] ){
// Read volume
vtkDICOMImageReader* l_reader = vtkDICOMImageReader::New();
l_reader->SetDirectoryName( "C:/PathToDicomFiles/" );
l_reader->Update();
// Setup rendering stuff
vtkRenderer* l_renderer = vtkRenderer::New();
l_renderer->SetBackground( 0.3, 0.3, 0.3 );
vtkRenderWindow* l_render_windows = vtkRenderWindow::New();
l_render_windows->AddRenderer( l_renderer );
l_render_windows->SetSize( 900, 900 );
vtkInteractorStyleTrackballCamera* l_trackball = vtkInteractorStyleTrackballCamera::New();
vtkRenderWindowInteractor* l_iren = vtkRenderWindowInteractor::New();
l_iren->SetInteractorStyle( l_trackball );
l_iren->SetRenderWindow( l_render_windows );
l_iren->GetInteractorStyle()->SetDefaultRenderer( l_renderer );
l_iren->SetDesiredUpdateRate( 15 );
// Make sure we have an opengl context
l_render_windows->Render();
// Setup GPU volume raycast mapper
vtkGPUVolumeRayCastMapper* l_gpu_mapper = vtkGPUVolumeRayCastMapper::New();
l_gpu_mapper->SetInputConnection( l_reader->GetOutputPort() );
// Setup Volume property
// Window/Level
double wl = 260;
double ww = 270;
// Color function
vtkColorTransferFunction* l_color = vtkColorTransferFunction::New();
l_color->SetColorSpaceToRGB();
l_color->AddRGBPoint( wl - ww / 2, 0, 0, 0 );
l_color->AddRGBPoint( wl - ww / 2 + 94 * ( ww / 255.0 ), 1., 21. / 255.0, 27. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 147 * ( ww / 255.0 ), 1., 176. / 255.0, 9. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 201 * ( ww / 255.0 ), 1., 241. / 255.0, 39. / 255.0 );
l_color->AddRGBPoint( wl - ww / 2 + 255 * ( ww / 255.0 ), 1, 1, 1. );
l_color->Build();
// Opacity function
vtkPiecewiseFunction* l_opacity = vtkPiecewiseFunction::New();
l_opacity->AddPoint( wl - ww / 2, 0 );
l_opacity->AddPoint( wl + ww / 2, 1 );
// Volume property, light, shading
vtkVolumeProperty* l_volume_property = vtkVolumeProperty::New();
l_volume_property->SetColor( l_color );
l_volume_property->SetScalarOpacity( l_opacity );
l_volume_property->SetInterpolationTypeToLinear();
l_volume_property->ShadeOn();
l_volume_property->SetAmbient( 0.15 );
l_volume_property->SetDiffuse( 0.8 );
l_volume_property->SetSpecular( 0.25 );
l_volume_property->SetSpecularPower( 40 );
// Put everything together
vtkVolume* l_volume = vtkVolume::New();
l_volume->SetProperty( l_volume_property );
l_volume->SetMapper( l_gpu_mapper );
l_renderer->AddVolume( l_volume );
l_renderer->ResetCamera();
// setup Box interactive widget
vtkBoxRepresentation* l_box_rep = vtkBoxRepresentation::New();
l_box_rep->SetInsideOut( true );
vtkBoxWidget2* l_voi_widget = vtkBoxWidget2::New();
l_voi_widget->SetRepresentation( l_box_rep );
l_voi_widget->SetInteractor( l_iren );
l_voi_widget->GetRepresentation()->SetPlaceFactor( 1. );
l_voi_widget->GetRepresentation()->PlaceWidget( l_reader->GetOutput()->GetBounds() );
l_voi_widget->SetEnabled( true );
vtkPlanes* l_planes = vtkPlanes::New();
vtkBoxCallback* l_callback = vtkBoxCallback::New();
l_callback->m_mapper = l_gpu_mapper;
l_callback->m_planes = l_planes;
l_voi_widget->AddObserver( vtkCommand::InteractionEvent, l_callback );
// Go rendering !
l_iren->Start();
// Memory cleanup
l_reader->Delete();
l_renderer->Delete();
l_render_windows->Delete();
l_trackball->Delete();
l_iren->Delete();
l_gpu_mapper->Delete();
l_color->Delete();
l_opacity->Delete();
l_volume_property->Delete();
l_volume->Delete();
l_voi_widget->Delete();
l_planes->Delete();
l_callback->Delete();
}
作为一般性建议,我建议您阅读 VTK examples,这应该可以帮助您了解所有 VTK 功能。
希望对您有所帮助:)