//腐蚀操作
void segmentation::erosionOperation()//未用到
{
const unsigned int Dimension = 3;
typedef unsigned char InputPixelType;
typedef unsigned char OutputPixelType;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
typedef itk::BinaryThresholdImageFilter< InputImageType, InputImageType > ThresholdFilterType;
typedef itk::BinaryBallStructuringElement<
InputPixelType,
Dimension > StructuringElementType;
typedef itk::BinaryErodeImageFilter<
InputImageType,
OutputImageType,
StructuringElementType > ErodeFilterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writerErosion = WriterType::New();
ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
ErodeFilterType::Pointer binaryErode = ErodeFilterType::New();
StructuringElementType structuringElementErosion;
reader->SetFileName( initFileName );//读入二值图
reader->Update();
InputImageType::Pointer inputImage = InputImageType::New();
InputImageType::IndexType voxelIndex;
inputImage = reader->GetOutput();
InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
long vol = 0;
unsigned char temp;
float r;
for(int z = 0; z < imgSize[2]; z++)
for(int y = 0; y < imgSize[1]; y++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[1] = y;
voxelIndex[2] = z;
temp = inputImage->GetPixel(voxelIndex);
if(temp == 255)// 255 for PED
vol += 1;
}
r = pow((3 * vol) / (4 * PI), (1.0 / 3)) ;
r = r / 20;//experiment data
structuringElementErosion.SetRadius( r ); // 3x3 structuring element
structuringElementErosion.CreateStructuringElement();
binaryErode->SetKernel( structuringElementErosion );
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
string erosionFileName;
erosionFileName = filePrefix + "_erosionResult.mhd";
strcpy(outputFileName, erosionFileName.c_str());//string to char*
writerErosion->SetFileName(outputFileName);
const InputPixelType lowerThreshold = 255;
const InputPixelType upperThreshold = 255;
thresholder->SetInput( reader->GetOutput() );
InputPixelType background = 0;
InputPixelType foreground = 255;
thresholder->SetOutsideValue( background );
thresholder->SetInsideValue( foreground );
thresholder->SetLowerThreshold( lowerThreshold );
thresholder->SetUpperThreshold( upperThreshold );
binaryErode->SetInput( thresholder->GetOutput() );
binaryErode->SetErodeValue( foreground );
writerErosion->SetInput( binaryErode->GetOutput() );
writerErosion->Update();
//binaryErode->GetOutput()->GetPixel(index);//获取像素值失败
//腐蚀结果叠加到原图
typedef itk::Image< unsigned short, Dimension > OriginalImageType;
typedef itk::ImageFileReader<OriginalImageType>OriginalReaderType;
OriginalReaderType::Pointer orignalImgreader = OriginalReaderType::New();
OriginalImageType::Pointer originalImage = OriginalImageType::New();
OriginalReaderType::IndexType originalImgVoxelIndex;
reader->SetFileName(outputFileName);//读入腐蚀结果图像
reader->Update();
inputImage = reader->GetOutput();
orignalImgreader->SetFileName(inputFileName);//读入原图像
orignalImgreader->Update();
originalImage = orignalImgreader->GetOutput();
for(int z = 0; z < imgSize[2]; z++)
for(int y = 0; y < imgSize[1]; y++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[1] = y;
voxelIndex[2] = z;
originalImgVoxelIndex[0] = x;
originalImgVoxelIndex[1] = y;
originalImgVoxelIndex[2] = z;
temp = inputImage->GetPixel(voxelIndex);
if(temp == 255)
originalImage->SetPixel(originalImgVoxelIndex, 65535);
}
//输出结果
typedef itk::ImageFileWriter<OriginalImageType>NewWriterType;
NewWriterType::Pointer writer = NewWriterType::New();
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
filePrefix = filePrefix + "_refinedResult.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
writer->SetFileName(outputFileName);
writer->SetInput(originalImage);
writer->Update();
emit returnInternalFileName(initResultFileName);//更新原视图
emit returnOutputFileName(outputFileName);//显示结果图
}
void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (workingSlice.IsNull())
return; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry *sliceGeometry = workingSlice->GetGeometry();
itk::Index<3> projectedPointIn2D;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D);
if (!sliceGeometry->IsIndexInside(projectedPointIn2D))
{
MITK_ERROR << "point apparently not inside segmentation slice" << std::endl;
return; // can't use that as a seed point
}
typedef itk::Image<DefaultSegmentationDataType, 2> InputImageType;
typedef InputImageType::IndexType IndexType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// convert world coordinates to image indices
IndexType seedIndex;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex);
// perform region growing in desired segmented region
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(workingSlice, itkImage);
regionGrower->SetInput(itkImage);
regionGrower->AddSeed(seedIndex);
InputImageType::PixelType bound = itkImage->GetPixel(seedIndex);
regionGrower->SetLower(bound);
regionGrower->SetUpper(bound);
regionGrower->SetReplaceValue(1);
itk::BinaryFillholeImageFilter<InputImageType>::Pointer fillHolesFilter =
itk::BinaryFillholeImageFilter<InputImageType>::New();
fillHolesFilter->SetInput(regionGrower->GetOutput());
fillHolesFilter->SetForegroundValue(1);
// Store result and preview
mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput());
resultImage->SetGeometry(workingSlice->GetGeometry());
// Get the current working color
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New();
contourextractor->SetInput(resultImage);
contourextractor->Update();
mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput();
FeedbackContourTool::SetFeedbackContour(awesomeContour);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void segmentation::on_abnormalRegionSegButton_clicked()
{
fstream fin11, fin12;
char* s11Txt = ("../data/ped/txt/15715_11.txt");//s11.txt
char* s12Txt = ("../data/ped/txt/15715_12.txt");
int (*s11)[512] = new int[64][512];
int (*s12)[512] = new int[64][512];
int (*p)[512] = new int[64][512];
//read TXT
fin11.open(s11Txt, ios::in);
fin12.open(s12Txt, ios::in);
//get the p matrix
for(int z = 0; z < 64; z++)
{
for(int x = 0; x < 512; x++)
{
fin11>>s11[z][x];
fin12>>s12[z][x];
if(s12[z][x] - s11[z][x] > 5) //5 threshold
p[z][x] = 1;
else
p[z][x] = 0;
}
}
fin11.close();
fin12.close();
//read filtered MHD data
typedef itk::Image<unsigned short, 3>InputImageType;
typedef itk::Image<unsigned short, 3>OutputImageType;
typedef itk::Image<unsigned char, 3>InitOutputImageType;
InputImageType::Pointer inputImage = InputImageType::New();
OutputImageType::Pointer outputImage = OutputImageType::New();
InitOutputImageType::Pointer initOutputImage = InitOutputImageType::New();
typedef itk::ImageFileReader<InputImageType>ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFileName);//读入原图像
reader->Update();
inputImage = reader->GetOutput();
InputImageType::IndexType voxelIndex;
InitOutputImageType::IndexType initvoxelIndex;
OutputImageType::IndexType newvoxelIndex;
InputImageType::SizeType imgSize = inputImage->GetLargestPossibleRegion().GetSize();
OutputImageType::IndexType index;
index[0] = 0;
index[1] = 0;
index[2] = 0;
OutputImageType::SizeType size;
size[0] = imgSize[0];
size[1] = imgSize[1];
size[2] = imgSize[2];
//create a region for initial result
InitOutputImageType::RegionType initRegion;
initRegion.SetIndex(index);
initRegion.SetSize(size);
initOutputImage->SetRegions( initRegion);
initOutputImage->Allocate();
//create a region for enhance result
OutputImageType::RegionType region;
region.SetIndex(index);
region.SetSize(size);
outputImage->SetRegions(region);
outputImage->Allocate();
//Initial result for PED segmentation (a binary image)
for(int z = 0; z < imgSize[2]; z++)
for(int x = 0; x < imgSize[0]; x++)
{
initvoxelIndex[0] = x;
initvoxelIndex[2] = z;
for(int y = 0; y < imgSize[1]; y++)
{
//set all background a black region
initvoxelIndex[1] = y;
initOutputImage->SetPixel(initvoxelIndex, 0);
}
//set the same intensity for all PED region (empirical value)
if(p[z][x] == 1)
{
for(int y = s11[z][x]; y <= s12[z][x]; y++)
{
initvoxelIndex[1] = y;
initOutputImage->SetPixel(initvoxelIndex, 255);//亮区域
}
}
}
//输出中间分割结果
//文件前缀名
filePrefix = inputFileName;//char* to string
filePrefix = filePrefix.substr(0, filePrefix.length() - 4);
string strInitFileName;
strInitFileName = filePrefix + "_initBinaryImg.mhd";
strcpy(initFileName, strInitFileName.c_str());//string to char*
typedef itk::ImageFileWriter<InitOutputImageType>InitWriterType;
InitWriterType::Pointer initWriter = InitWriterType::New();
initWriter->SetFileName(initFileName);//生成二值图
initWriter->SetInput(initOutputImage);
initWriter->Update();
//Enhance PED region and overlay it on the original image
for(int z = 0; z < imgSize[2]; z++)
for(int x = 0; x < imgSize[0]; x++)
{
voxelIndex[0] = x;
voxelIndex[2] = z;
newvoxelIndex[0] = x;
newvoxelIndex[2] = z;
for(int y = 0; y < imgSize[1]; y++)
{
voxelIndex[1] = y;
newvoxelIndex[1] = y;
outputImage->SetPixel(newvoxelIndex, inputImage->GetPixel(voxelIndex));
}
//set the same intensity for all PED region (empirical value)
if(p[z][x] == 1)
{
for(int y = s11[z][x]; y <= s12[z][x]; y++)
{
newvoxelIndex[1] = y;
outputImage->SetPixel(newvoxelIndex, 65535);//亮区域
}
}
}
//释放内存不能缺省
delete[]s11;
delete[]s12;
delete[]p;
typedef itk::ImageFileWriter<OutputImageType>WriterType;
WriterType::Pointer writer = WriterType::New();
filePrefix = filePrefix + "_initResult.mhd";
strcpy(outputFileName, filePrefix.c_str());//string to char*
initResultFileName = outputFileName;//输出初始分割结果，二值图重叠在原图像上面
writer->SetFileName(outputFileName);
writer->SetInput(outputImage);
writer->Update();
emit returnOutputFileName(outputFileName);//发出信号
}