/* Set a Dcm_meta struct to default values. Generates new UIDs. */
static void default_Dcm_meta(Dcm_meta *const meta) {
meta->patient_name = default_patient_name;
meta->patient_id = default_patient_id;
meta->series_descrip = default_series_descrip;
dcmGenerateUniqueIdentifier(meta->study_uid, SITE_STUDY_UID_ROOT);
dcmGenerateUniqueIdentifier(meta->series_uid, SITE_SERIES_UID_ROOT);
dcmGenerateUniqueIdentifier(meta->instance_uid, SITE_INSTANCE_UID_ROOT);
meta->instance_num = default_instance_num;
}
void DicomUtils::AddDicomElements(DcmDataset*& dataset)
{
//构建测试数据
/* 添加患者信息 */
dataset->putAndInsertUint16(DCM_AccessionNumber,0);
dataset->putAndInsertString(DCM_PatientName,"zssure",true);
dataset->putAndInsertString(DCM_PatientID,"2234");
dataset->putAndInsertString(DCM_PatientBirthDate,"20141221");
dataset->putAndInsertString(DCM_PatientSex,"M");
/* 添加Study信息 */
dataset->putAndInsertString(DCM_StudyDate,"20141221");
dataset->putAndInsertString(DCM_StudyTime,"195411");
char uid[100];
dcmGenerateUniqueIdentifier(uid,SITE_STUDY_UID_ROOT);
dataset->putAndInsertString(DCM_StudyInstanceUID,uid);
dataset->putAndInsertString(DCM_StudyID,"1111");
/* 添加Series信息 */
dataset->putAndInsertString(DCM_SeriesDate,"20141221");
dataset->putAndInsertString(DCM_SeriesTime,"195411");
memset(uid,0,sizeof(char)*100);
dcmGenerateUniqueIdentifier(uid,SITE_SERIES_UID_ROOT);
dataset->putAndInsertString(DCM_SeriesInstanceUID,uid);
/* 添加Image信息 */
dataset->putAndInsertString(DCM_ImageType,"ORIGINAL\\PRIMARY\\AXIAL");
dataset->putAndInsertString(DCM_ContentDate,"20141221");
dataset->putAndInsertString(DCM_ContentTime,"200700");
dataset->putAndInsertString(DCM_InstanceNumber,"1");
dataset->putAndInsertString(DCM_SamplesPerPixel,"1");
dataset->putAndInsertString(DCM_PhotometricInterpretation,"MONOCHROME2");
dataset->putAndInsertString(DCM_PixelSpacing,"0.3\\0.3");
dataset->putAndInsertString(DCM_BitsAllocated,"16");
dataset->putAndInsertString(DCM_BitsStored,"16");
dataset->putAndInsertString(DCM_HighBit,"15");
dataset->putAndInsertString(DCM_WindowCenter,"600");
dataset->putAndInsertString(DCM_WindowWidth,"800");
dataset->putAndInsertString(DCM_RescaleIntercept,"0");
dataset->putAndInsertString(DCM_RescaleSlope,"1");
}
Volume* VolumeBuilderFromCaptures::build()
{
Q_ASSERT(m_parentStudy);
Q_ASSERT(m_vtkImageAppend->GetNumberOfInputs());
// Creem la nova sèrie
Series *newSeries = new Series();
// Omplim la informació de la sèrie a partir de la sèrie de referència
// Assignem la modalitat segons el valor introduit. El valor per defecte és 'OT' (Other).
newSeries->setModality(m_modality);
newSeries->setSOPClassUID(QString(UID_SecondaryCaptureImageStorage));
// Generem el SeriesInstanceUID a partir del generador de DCMTK. \TODO Utilitzar el nostre UID_ROOT?
char seriesUid[100];
dcmGenerateUniqueIdentifier(seriesUid, SITE_SERIES_UID_ROOT);
newSeries->setInstanceUID(QString(seriesUid));
// \TODO Quin criteri volem seguir per donar nous noms?
newSeries->setSeriesNumber(QString("0000") + QString::number(m_parentStudy->getSeries().count()));
newSeries->setDescription(this->getSeriesDescription());
// Assignem la sèrie a l'estudi al qual partenyia l'inputVolume.
newSeries->setParentStudy(m_parentStudy);
m_parentStudy->addSeries(newSeries);
// Obtenim el nou vtkImageData a partir de la sortida del vtkImageAppend.
// Fem un flip horitzontal per tal utilitzar el mateix sistema de coordenades que DICOM.
m_vtkImageAppend->Update();
vtkSmartPointer<vtkImageData> newVtkData = vtkSmartPointer<vtkImageData>::New();
newVtkData->ShallowCopy(m_vtkImageAppend->GetOutput());
// Creem el nou volume
Volume *newVolume = new Volume();
newSeries->addVolume(newVolume);
// Generem les noves imatges a partir del vtkData generat per vtkImageAppend
int samplesPerPixel = newVtkData->GetNumberOfScalarComponents();
int bitsAllocated;
int bitsStored;
int highBit;
int pixelRepresentation;
int rows;
int columns;
// \TODO Potser podriem ser mes precisos
QString photometricInterpretation;
if (samplesPerPixel == 1)
{
photometricInterpretation = QString("MONOCHROME2");
}
else if (samplesPerPixel == 3)
{
photometricInterpretation = QString("RGB");
}
int scalarType = newVtkData->GetScalarType();
switch (scalarType)
{
//case VTK_CHAR:
//break;
case VTK_SIGNED_CHAR:
bitsAllocated = 8;
pixelRepresentation = 1;
break;
case VTK_UNSIGNED_CHAR:
bitsAllocated = 8;
pixelRepresentation = 0;
break;
case VTK_SHORT:
bitsAllocated = 16;
pixelRepresentation = 1;
break;
case VTK_UNSIGNED_SHORT:
bitsAllocated = 16;
pixelRepresentation = 0;
break;
case VTK_INT:
bitsAllocated = 32;
pixelRepresentation = 1;
break;
case VTK_UNSIGNED_INT:
bitsAllocated = 32;
pixelRepresentation = 0;
break;
// case VTK_FLOAT:
// bitsAllocated = 32;
// pixelRepresentation = 1; ?
// break;
// case VTK_DOUBLE:
// bitsAllocated = 64;
// pixelRepresentation = 1; ?
// break;
default:
DEBUG_LOG(QString("Pixel Type no suportat: ") + newVtkData->GetScalarTypeAsString());
}
bitsStored = bitsAllocated;
highBit = bitsStored - 1;
int *dimensions = newVtkData->GetDimensions();
double *spacing = newVtkData->GetSpacing();
rows = dimensions[1];
columns = dimensions[0];
Image *currentImage;
for (int i = 0; i < dimensions[2]; i++)
{
currentImage = new Image();
// Generem el SOPInstanceUID a partir del generador de DCMTK. \TODO Utilitzar el nostre UID_ROOT?
char instanceUid[100];
dcmGenerateUniqueIdentifier(instanceUid, SITE_INSTANCE_UID_ROOT);
currentImage->setSOPInstanceUID(QString(instanceUid));
newSeries->addImage(currentImage);
newVolume->addImage(currentImage);
currentImage->setParentSeries(newSeries);
currentImage->setOrderNumberInVolume(i);
currentImage->setVolumeNumberInSeries(0);
currentImage->setBitsAllocated(bitsAllocated);
currentImage->setBitsStored(bitsStored);
currentImage->setHighBit(highBit);
currentImage->setColumns(columns);
currentImage->setInstanceNumber(QString::number(i + 1));
currentImage->setPhotometricInterpretation(photometricInterpretation);
currentImage->setPixelRepresentation(pixelRepresentation);
currentImage->setPixelSpacing(spacing[0], spacing[1]);
currentImage->setRows(rows);
currentImage->setSamplesPerPixel(samplesPerPixel);
}
// Es fa després d'haver inserit les imatges perquè el nou Volume activi el flag de dades carregades.
newVolume->setData(newVtkData);
newVolume->setNumberOfPhases(1);
newVolume->setNumberOfSlicesPerPhase(newSeries->getImages().count());
// Informació de DEBUG
DEBUG_LOG(QString("\nNova sèrie generada:") +
QString("\n SeriesInstanceUID: ") + newSeries->getInstanceUID() +
QString("\n SeriesNumber: ") + newSeries->getSeriesNumber() +
QString("\n SeriesDescription: ") + newSeries->getDescription() +
QString("\n SOPClassUID: ") + newSeries->getSOPClassUID() +
QString("\n Modality: ") + newSeries->getModality() +
QString("\n SamplesPerPixel: ") + QString::number(samplesPerPixel) +
QString("\n PhotometricInterpretation: ") + photometricInterpretation +
QString("\n BitsAllocated: ") + QString::number(bitsAllocated) +
QString("\n BitsStored: ") + QString::number(bitsStored) +
QString("\n HighBit: ") + QString::number(highBit) +
QString("\n PixelRepresentation: ") + QString::number(pixelRepresentation) +
QString("\n PixelSpacing: ") + QString::number(spacing[0]) + QString(",") + QString::number(spacing[1]) +
QString("\n Num.Imatges: ") + QString::number(newSeries->getImages().count()));
return newVolume;
}
/* Helper function to write an image to a directory of DICOM files using C++ */
static int write_dcm_dir_cpp(const char *path, const Image *const im,
const Dcm_meta *const meta) {
Image slice;
// Initialize C intermediates
init_im(&slice);
// Initialize the metadata to defaults, if it is null
Dcm_meta meta_new;
set_meta_defaults(meta, &meta_new);
// Get the number of leading zeros for the file names
const int num_slices = im->nz;
const int num_zeros = static_cast<int>(ceil(log10(
static_cast<double>(num_slices))));
// Form the printf format string for file names
#define BUF_LEN 16
char format[BUF_LEN];
snprintf(format, BUF_LEN, "%%0%dd.%s", num_zeros, ext_dcm);
#undef BUF_LEN
// Resize the slice buffer
slice.nx = im->nx;
slice.ny = im->ny;
slice.nz = 1;
slice.nc = im->nc;
im_default_stride(&slice);
if (im_resize(&slice)) {
im_free(&slice);
return SIFT3D_FAILURE;
}
// Copy the units to the slice
memcpy(SIFT3D_IM_GET_UNITS(&slice), SIFT3D_IM_GET_UNITS(im),
IM_NDIMS * sizeof(double));
// Get the maximum absolute value of the whole image volume
const float max_val = im_max_abs(im);
// Write each slice
for (int i = 0; i < num_slices; i++) {
// Form the slice file name
#define BUF_LEN 1024
char buf[BUF_LEN];
snprintf(buf, BUF_LEN, format, i);
// Form the full file path
std::string fullfile(path + sepStr + buf);
// Copy the data to the slice
int x, y, z, c;
SIFT3D_IM_LOOP_START_C(&slice, x, y, z, c)
SIFT3D_IM_GET_VOX(&slice, x, y, z, c) =
SIFT3D_IM_GET_VOX(im, x, y, i, c);
SIFT3D_IM_LOOP_END_C
// Generate a new SOPInstanceUID
dcmGenerateUniqueIdentifier(meta_new.instance_uid,
SITE_INSTANCE_UID_ROOT);
// Set the instance number
const unsigned int instance = static_cast<unsigned int>(i + 1);
meta_new.instance_num = instance;
// Write the slice to a file
if (write_dcm(fullfile.c_str(), &slice, &meta_new, max_val)) {
im_free(&slice);
return SIFT3D_FAILURE;
}
}
// Clean up
im_free (&slice);
return SIFT3D_SUCCESS;
}
int gendicom(const char* file_name, const std::vector<float> &data,
unsigned int rows, unsigned int cols)
{
char uid[100];
DcmFileFormat fileformat;
DcmDataset *dataset = fileformat.getDataset();
OFCondition result = EC_Normal;
if (result.good()) result = dataset->putAndInsertString(DCM_SOPClassUID, UID_SecondaryCaptureImageStorage);
//if (result.good()) result = dataset->putAndInsertString(DCM_MediaStorageSOPClassUID, UID_SecondaryCaptureImageStorage); //same as SOP
if (result.good()) result = dataset->putAndInsertString(DCM_SOPInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
//if (result.good()) result = dataset->putAndInsertString(DCM_MediaStorageSOPInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
if (result.good()) result = dataset->putAndInsertString(DCM_SeriesInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
if (result.good()) result = dataset->putAndInsertString(DCM_StudyInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
//if (result.good()) result = dataset->putAndInsertString(DCM_TransferSyntaxUID, UID_LittleEndianExplicitTransferSyntax);
//if (result.good()) result = dataset->putAndInsertUint16(DCM_FileMetaInformationVersion, 1);
if (result.good()) result = dataset->putAndInsertString(DCM_ImageType, "DERIVED");
if (result.good()) result = dataset->putAndInsertString(DCM_Modality, "MR");
if (result.good()) result = dataset->putAndInsertString(DCM_ConversionType, "WSD");
if (result.good()) result = dataset->putAndInsertString(DCM_DerivationDescription, "IRGN Processed MR Reconstruction");
if (result.good()) result = dataset->putAndInsertString(DCM_SecondaryCaptureDeviceManufacturer, "IMT TUGRAZ");
if (result.good()) result = dataset->putAndInsertString(DCM_SecondaryCaptureDeviceManufacturerModelName, "IMT Cuda Workstation");
if (result.good()) result = dataset->putAndInsertString(DCM_PatientName, "Doe^John");
// set instance creation date and time
OFString s;
if (result.good()) result = DcmDate::getCurrentDate(s);
if (result.good()) result = dataset->putAndInsertOFStringArray(DCM_InstanceCreationDate, s);
if (result.good()) result = DcmTime::getCurrentTime(s);
if (result.good()) result = dataset->putAndInsertOFStringArray(DCM_InstanceCreationTime, s);
//--- Write image-data ---
std::vector<Uint16> uint16_data;
float val=0;
float min_val;
float max_val = *std::max_element(data.begin(),data.end());
for(unsigned int i=0; i<data.size(); ++i)
{
val = (data[i]/max_val)*65535;
uint16_data.push_back(Uint16(val));
}
max_val = *std::max_element(uint16_data.begin(),uint16_data.end());
min_val = *std::min_element(uint16_data.begin(),uint16_data.end());
std::cout<<"\n max-val: "<<max_val;
std::cout<<"\n min-val: "<<min_val;
unsigned bits=16;
Uint16 bitsAllocated=((bits-1)/8+1)*8;
Uint16 bitsStored=bits;
Uint16 highBit=bits-1;
if (result.good()) result = dataset->putAndInsertUint16(DCM_BitsAllocated, bitsAllocated);
if (result.good()) result = dataset->putAndInsertUint16(DCM_BitsStored, bitsStored);
if (result.good()) result = dataset->putAndInsertUint16(DCM_HighBit, highBit);
if (result.good()) result = dataset->putAndInsertUint16(DCM_Rows, rows);
if (result.good()) result = dataset->putAndInsertUint16(DCM_Columns, cols);
if (result.good()) result = dataset->putAndInsertUint16(DCM_PixelRepresentation, 0); // 1 signed, 0 unsigned
if (result.good()) result = dataset->putAndInsertOFStringArray(DCM_PhotometricInterpretation, "MONOCHROME2");
if (result.good()) result = dataset->putAndInsertUint16(DCM_SamplesPerPixel, 1);
if (result.good()) result = dataset->putAndInsertUint16(DCM_SmallestImagePixelValue, min_val);
if (result.good()) result = dataset->putAndInsertUint16(DCM_LargestImagePixelValue, max_val);
Uint8* pixelData = (Uint8*)&uint16_data[0];
Uint32 pixelLength;
pixelLength = uint16_data.size()*2; //number of elements in vector * 2bytes (for Uint16)
dataset->putAndInsertUint8Array(DCM_PixelData, pixelData, pixelLength);
OFCondition status = fileformat.saveFile(file_name, EXS_LittleEndianExplicit);
if (result.bad())
std::cerr << "Error: cannot write DICOM file (" << result.text() << ")" << std::endl;
if (status.bad())
std::cerr << "Error: cannot write DICOM file (" << status.text() << ")" << std::endl;
return 0;
}
