uint ImageInstance::getPixelValue(long x, long y, EP_Representation &r) const
{
DicomImage *image;
if (rawType) image = rawImage;
else image = dcmImage;
if (image) {
const DiPixel* pixel = image->getInterData();
if (pixel && (x < (long)image->getWidth()) && (x >= 0)
&& (y < (long)image->getHeight()) && (y >= 0)) {
r = pixel->getRepresentation();
switch (r) {
case EPR_Sint8:
case EPR_Uint8:
return *((char*)(pixel->getData()) + (y * image->getWidth() + x));
case EPR_Sint16:
case EPR_Uint16:
return *((short*)(pixel->getData()) + (y * image->getWidth() + x));
case EPR_Sint32:
case EPR_Uint32:
return *((int*)(pixel->getData()) + (y * image->getWidth() + x));
}
}
}
r = (EP_Representation)-1;
return 0;
}
Dose::Dose( RTDcmtkDicomInterface* rtDoseDicom, Plan* rtPlan)
{
d = new DoseData();
d->m_dcmGeometry = vtkSmartPointer<DCMGeometry>::New();
d->m_resampledDoseCuboid = NULL;
d->m_resampled_dcm_geometry = NULL;
DcmItem *ditem = NULL;
const char * refPlanUID = NULL;
this->frameRefUID = string(rtDoseDicom->Get_FRAME_OF_REFER_UID());
this->sopUID = string(rtDoseDicom->Get_SOP_INSTANCE_UID());
this->studyUID = string(rtDoseDicom->Get_STUDY_INSTANCE_UID());
this->seriesUID = string(rtDoseDicom->Get_SERIES_INSTANCE_UID());
this->height = rtDoseDicom->Get_ROW();
this->width = rtDoseDicom->Get_COLOUMN();
double image_orientation[6] = { 0, 0, 0, 0, 0, 0 };
string imageOrientation = string(rtDoseDicom->Get_IMAGE_ORIENTATION());
vector<string> _imageOrientation;
tokenize(imageOrientation, _imageOrientation, "\\", true);
for (int i = 0; i<_imageOrientation.size(); i++)
{
image_orientation[i] = convert_to_double(_imageOrientation.at(i).c_str());
}
double xorient[3] = { image_orientation[0], image_orientation[1], image_orientation [2]};
double yorient[3] = { image_orientation[3], image_orientation[4], image_orientation [5]};
double firstImagePosition[3] = { 0, 0, 0};
double lastImagePosition[3] = { 0, 0, 0};
string imagePosition = string(rtDoseDicom->Get_IMAGE_POSITION());
vector<string> _imagePosition;
tokenize(imagePosition, _imagePosition, "\\", true);
for (int i = 0; i<_imagePosition.size(); i++)
{
firstImagePosition[i] = convert_to_double(_imagePosition.at(i).c_str());
lastImagePosition[i] = convert_to_double(_imagePosition.at(i).c_str());
}
rtDoseDicom->getMinMaxPixelValue(this->minDosePixelValue, this->maxDosePixelValue);// MinMax pixel value
this->doseGridScaling = convert_to_double(rtDoseDicom->Get_DOSEGRID_SCALING());
OFString _gridFrameOffsetVector;
vector<string> temp;
if (rtDoseDicom->dataset->findAndGetOFStringArray(DCM_GridFrameOffsetVector, _gridFrameOffsetVector).bad())
{
isMultiframe = false;
// return;
}
else
{
isMultiframe = true;
tokenize(_gridFrameOffsetVector.c_str(), temp, "\\", true);
// Convert offset vector points from string to float and store permanently.
for (int i = 0; i<temp.size(); i++)
{
this->doseGridOffsetVector.push_back(atof(temp.at(i).c_str()));
}
}
if (isMultiframe)
lastImagePosition[2] += doseGridOffsetVector.at(doseGridOffsetVector.size() - 1);
else
lastImagePosition[2] += 0;
double spacing[3] = { 0, 0, 0 };
const char* _pixelSpacing = rtDoseDicom->Get_PIXEL_SPACING();
vector<string> temp1;
tokenize(_pixelSpacing, temp1, "\\", true);
spacing[0] = convert_to_double(temp1.at(0).c_str());
spacing[1] = convert_to_double(temp1.at(1).c_str());
if (isMultiframe)
{
spacing[2] = this->doseGridOffsetVector.at(1) - this->doseGridOffsetVector.at(0);// hardcoded.
}
else
{
//this->pixelSpacing[0] = 0;
//this->pixelSpacing[1] = 0;
spacing[2] = 0;
}
int numberOfFrames = convert_to_int(rtDoseDicom->Get_NO_OF_FRAMES());
int dim[3] = { this->width, this->height, numberOfFrames };
d->m_dcmGeometry->SetImageGeometry(firstImagePosition, spacing, dim, xorient, yorient);
//Populate frame wise pixel data in map<int,void*> framePixelData;
int noOfBytes = rtDoseDicom->Get_BITS_ALLOCATED() / 8;
DJDecoderRegistration::registerCodecs();
DcmRLEDecoderRegistration::registerCodecs();
DicomImage * dicomImage = new DicomImage(&rtDoseDicom->file_format, rtDoseDicom->file_format.getDataset()->getOriginalXfer(),
CIF_UsePartialAccessToPixelData, 0, 1 /* fcount */);
DJDecoderRegistration::cleanup();
DcmRLEDecoderRegistration::cleanup();
do{
const DiPixel* diPixel = dicomImage->getInterData();
doseFrameData* dfData = new doseFrameData();
dfData->frameNumber = dicomImage->getFirstFrame();
dfData->cols = rtDoseDicom->Get_COLOUMN();
dfData->rows = rtDoseDicom->Get_ROW();
// create a vtkImage
vtkImageData* image = vtkImageData::New();
image->SetDimensions(dfData->cols, dfData->rows, 1);
image->SetSpacing(spacing[0], spacing[1], 1);
image->Initialize();
vtkDataArray* scalars = 0;
switch (diPixel->getRepresentation())
{
case EPR_Uint8:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(U8DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(U8DataType));
dfData->ORG_DicomDataType = TYPE_U8Data;*/
scalars = vtkUnsignedCharArray::New();
((vtkUnsignedCharArray*)(scalars))->SetArray((unsigned char*)diPixel->getData(), diPixel->getCount(), 1);
break;
case EPR_Sint8:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(S8DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(S8DataType));
dfData->ORG_DicomDataType = TYPE_S8Data;*/
scalars = vtkSignedCharArray::New();
((vtkSignedCharArray*)(scalars))->SetArray((signed char*)diPixel->getData(), diPixel->getCount(), 1);
break;
case EPR_Uint16:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(U16DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(U16DataType));
dfData->ORG_DicomDataType = TYPE_U16Data;*/
scalars = vtkUnsignedShortArray::New();
((vtkUnsignedShortArray*)(scalars))->SetArray((unsigned short*)diPixel->getData(), diPixel->getCount(), 1);
break;
case EPR_Sint16:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(S16DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(S16DataType));
dfData->ORG_DicomDataType = TYPE_S16Data;*/
scalars = vtkShortArray::New();
((vtkShortArray*)(scalars))->SetArray((short*)diPixel->getData(), diPixel->getCount(), 1);
break;
case EPR_Uint32:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(U32DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(U32DataType));
dfData->ORG_DicomDataType = TYPE_U32Data;*/
scalars = vtkUnsignedIntArray::New();
((vtkUnsignedIntArray*)(scalars))->SetArray((unsigned int*)diPixel->getData(), diPixel->getCount(), 1);
break;
case EPR_Sint32:
/*dfData->ORG_pixelData = calloc(diPixel->getCount(),sizeof(S32DataType));
memcpy(dfData->ORG_pixelData,diPixel->getData(),diPixel->getCount()*sizeof(S32DataType));
dfData->ORG_DicomDataType = TYPE_S32Data;*/
scalars = vtkIntArray::New();
((vtkIntArray*)(scalars))->SetArray((int*)diPixel->getData(), diPixel->getCount(), 1);
break;
default:
RAD_LOG_CRITICAL("DCMTK EP_Representation type:" << diPixel->getRepresentation() << " not supported");
}
scalars->SetNumberOfComponents(1);
image->SetDimensions(dfData->cols, dfData->rows, 1);
image->SetSpacing(spacing[0], spacing[1], 1.0);
image->GetPointData()->SetScalars(scalars);
image->GetPointData()->GetScalars()->SetName("DICOMImage");
//image->Update();
double bounds[6];
image->GetBounds(bounds);
// type cast all images to unsigned int32
vtkImageCast* imageCast = vtkImageCast::New();
imageCast->SetInputData(image);
imageCast->SetOutputScalarTypeToFloat();
imageCast->Update();
dfData->pixelData = calloc(diPixel->getCount(), sizeof(U32DataType));
dfData->dicomDataType = TYPE_U32Data;
RAD_LOG_INFO("MEMCPY pixel data for frame:" << dicomImage->getFirstFrame())
memcpy(dfData->pixelData, imageCast->GetOutput()->GetPointData()->GetScalars()->GetVoidPointer(0),
imageCast->GetOutput()->GetPointData()->GetScalars()->GetSize()*sizeof(float));
imageCast->Delete();
scalars->Delete();
image->Delete();
this->allFrameDoseData.push_back(dfData);
} while (dicomImage->processNextFrames());
/// compute cuboid
// get first dose frame data
doseFrameData* dfData = allFrameDoseData.at(0);
// create VTK Cuboid
int dimension[3] = { dfData->cols, dfData->rows, allFrameDoseData.size() };
long dicomSliceSize = dimension[0] * dimension[1];
long dicomDataSize = dimension[0] * dimension[1] * dimension[2];
long dicomDataIdx = dicomSliceSize;
void* dicomData = rad_get_memory(dicomDataSize * sizeof(float));
#ifdef ULTA
for (int i = allFrameDoseData.size() - 1; i >= 0; i--)
#else
for (int i = 0;i< allFrameDoseData.size();i++)
#endif
{
float* dicomData2 = static_cast<float*>(dicomData);
dicomData2 += dicomDataSize;
memcpy(dicomData2 - dicomDataIdx, allFrameDoseData.at(i)->pixelData, dicomSliceSize*sizeof(float));
dicomDataIdx += dicomSliceSize;
}
vtkDataArray* scalars = 0;
scalars = vtkFloatArray::New();
((vtkFloatArray*)(scalars))->SetArray((float*)dicomData, dicomDataSize, 1);
scalars->SetNumberOfComponents(1);
d->m_doseCuboid = vtkImageData::New();
d->m_doseCuboid->SetDimensions(dimension);
d->m_doseCuboid->SetSpacing(spacing);
//double lip[3] = { 0, 0, 0 };
//d->m_dcmGeometry->GetLastImagePosition(lip);
//d->m_doseCuboid->SetOrigin(firstImagePosition);
d->m_doseCuboid->GetPointData()->SetScalars(scalars);
d->m_doseCuboid->GetPointData()->GetScalars()->SetName("Dose Cuboid");
d->m_doseCuboid->Modified();
rxDose = rtPlan->getTargetPrescribedDose();
int dosemax = int(this->maxDosePixelValue * this->doseGridScaling * 10000 / rxDose);
// ISODOSE LEVEL(s) READY
this->isodoses.push_back(new isodose(dosemax, 120, 0, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(102, 170, 0, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(100, 238, 69, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(98, 255, 65, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(95, 255, 255, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(90, 0, 255, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(80, 0, 139, 0, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(70, 0, 255, 255, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(50, 0, 0, 255, "", false, 0, 0, "Built-In"));
this->isodoses.push_back(new isodose(30, 0, 0, 128, "", false, 0, 0, "Built-In"));
// Calculate cGy Value and append to names.
for (int i = 0; i<this->isodoses.size(); i++)
{
isodose* iso = this->isodoses.at(i);
iso->cGyValue = (int)(iso->level * rxDose / 100);
iso->name.append(convert_to_string(iso->level));
iso->name.append("% - ");
iso->name.append(convert_to_string(iso->cGyValue));
iso->name.append(" cGy");
iso->pixelIntensity = iso->level * rxDose / (this->doseGridScaling * 10000);
}
// load DV data
DcmItem *dvhItem = NULL;
signed long dvhCount = 0;
while (rtDoseDicom->dataset->findAndGetSequenceItem(DCM_DVHSequence, dvhItem, dvhCount++).good())
{
DVH* dh = new DVH();
DcmItem *dvhRefROISequenceItem = NULL;
// ROI Number
const char * RoiNumber = NULL;
if (dvhItem->findAndGetSequenceItem(DCM_DVHReferencedROISequence, dvhRefROISequenceItem, 0).good())
{
OFCondition status = dvhItem->findAndGetString(DCM_ReferencedROINumber, RoiNumber, true);
dh->setROINumber(convert_to_uint(RoiNumber));
}
// DVH Data
string fNm = "D:\\DVH_DICOM_";
fNm.append(convert_to_string(dvhCount));
fNm.append(".csv");
//ofstream Morison_File(fNm.c_str());
const char * dvhdata = NULL;
dvhItem->findAndGetString(DCM_DVHData, dvhdata);
vector<string> dvhdataListTemp;
tokenize(dvhdata, dvhdataListTemp, "\\");
for (int i = 0; i < dvhdataListTemp.size(); i++)
{
i++;
string volume = dvhdataListTemp.at(i);
if (0 > int(atof(volume.c_str())))
volume = "0";
dh->dvhDataList.push_back(convert_to_double(volume.c_str()));
// Morison_File << volume.c_str() << endl;
}
//Morison_File.close();
//convert volume information in dvhDataList from abosulte to percentage.
dh->setMaxDVHValue(*std::max_element(dh->dvhDataList.begin(), dh->dvhDataList.end()));
/*std::transform(dh->dvhDataList.begin(), dh->dvhDataList.end(),
dh->dvhDataList.begin(), std::bind2nd(std::divides<double>(), dh->getMaxDVHValue()));
std::transform(dh->dvhDataList.begin(), dh->dvhDataList.end(),
dh->dvhDataList.begin(), std::bind2nd(std::multiplies<double>(), 100));*/
// DVH Mini Dose
const char * dvhMinDose = NULL;
if (dvhItem->findAndGetString(DCM_DVHMinimumDose, dvhMinDose).good())
dh->setDVHMiniDose(convert_to_double(dvhMinDose));
//DVH Max Dose
const char * dvhMaxDose = NULL;
if (dvhItem->findAndGetString(DCM_DVHMaximumDose, dvhMaxDose).good())
dh->setDVHMaxDose(convert_to_double(dvhMaxDose));
//DVH Mean Dose
const char * dvhMeanDose = NULL;
if (dvhItem->findAndGetString(DCM_DVHMeanDose, dvhMeanDose).good())
dh->setDVHMeanDose(convert_to_double(dvhMeanDose));
// Structureset ref SOPUID
DcmItem *dvhRefStructureSet = NULL;
const char * structSetRefSOPUID = NULL;
if (rtDoseDicom->dataset->findAndGetSequenceItem(DCM_ReferencedStructureSetSequence, dvhRefStructureSet).good())
{
if (dvhRefStructureSet->findAndGetString(DCM_ReferencedSOPInstanceUID, structSetRefSOPUID, true).good())
dh->setStrucSetRefSopUID(string(structSetRefSOPUID));
}
this->dh.push_back(dh);
}
}