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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkDCMTKFileReader_h
#define itkDCMTKFileReader_h
#include "ITKIODCMTKExport.h"
#include <stack>
#include <vector>
#include "itkByteSwapper.h"
#include "itkIntTypes.h"
#include "vnl/vnl_vector.h"
#include "dcmtk/dcmdata/dcdict.h" // For DcmDataDictionary
#include "dcmtk/dcmdata/dcdicent.h"
#include "dcmtk/dcmdata/dcxfer.h"
#include "dcmtk/dcmdata/dcvrds.h"
#include "dcmtk/dcmdata/dcstack.h"
#include "dcmtk/dcmdata/dcdatset.h"
#include "dcmtk/dcmdata/dcitem.h"
#include "dcmtk/dcmdata/dcvrobow.h"
#include "dcmtk/dcmdata/dcsequen.h"
#include "itkMacro.h"
#include "itkImageIOBase.h"
class DcmSequenceOfItems;
class DcmFileFormat;
class DcmDictEntry;
// Don't print error messages if you're not throwing
// an exception
// std::cerr body;
#define DCMTKExceptionOrErrorReturn(body) \
{ \
if(throwException) \
{ \
itkGenericExceptionMacro(body); \
} \
else \
{ \
return EXIT_FAILURE; \
} \
}
namespace itk
{
// Forward reference because of circular dependencies
class ITK_FORWARD_EXPORT DCMTKSequence;
class ITKIODCMTK_EXPORT DCMTKItem
{
public:
DCMTKItem() : m_DcmItem(ITK_NULLPTR)
{
}
void SetDcmItem(DcmItem *item);
int GetElementSQ(const unsigned short group,
const unsigned short entry,
DCMTKSequence &sequence,
const bool throwException = true) const;
private:
DcmItem *m_DcmItem;
};
class ITKIODCMTK_EXPORT DCMTKSequence
{
public:
DCMTKSequence() : m_DcmSequenceOfItems(ITK_NULLPTR) {}
void SetDcmSequenceOfItems(DcmSequenceOfItems *seq);
int card() const;
int GetSequence(unsigned long index,
DCMTKSequence &target,const bool throwException = true) const;
int GetStack(const unsigned short group,
const unsigned short element,
DcmStack &resultStack, const bool throwException = true) const;
int GetElementCS(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementOB(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementCSorOB(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
template <typename TType>
int GetElementDSorOB(const unsigned short group,
const unsigned short element,
TType &target,
const bool throwException = true) const
{
if(this->GetElementDS<TType>(group,element,1,&target,false) == EXIT_SUCCESS)
{
return EXIT_SUCCESS;
}
std::string val;
if(this->GetElementOB(group,element,val,throwException) != EXIT_SUCCESS)
{
DCMTKExceptionOrErrorReturn(<< "Cant find DecimalString element " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
const char *data = val.c_str();
const TType *fptr = reinterpret_cast<const TType *>(data);
target = *fptr;
return EXIT_SUCCESS;
}
template <typename TType>
int GetElementDSorOB(const unsigned short group,
const unsigned short element,
int count,
TType *target,
const bool throwException = true) const
{
if(this->GetElementDS<TType>(group,element,count,target,false) == EXIT_SUCCESS)
{
return EXIT_SUCCESS;
}
std::string val;
if(this->GetElementOB(group,element,val,throwException) != EXIT_SUCCESS)
{
DCMTKExceptionOrErrorReturn(<< "Cant find DecimalString element " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
const char *data = val.c_str();
const TType *fptr = reinterpret_cast<const TType *>(data);
for(int i = 0; i < count; ++i)
{
target[i] = fptr[i];
}
return EXIT_SUCCESS;
}
int GetElementFD(const unsigned short group,
const unsigned short element,
int count,
double *target,
const bool throwException = true) const;
int GetElementFD(const unsigned short group,
const unsigned short element,
double &target,
const bool throwException = true) const;
int GetElementDS(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementTM(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
/** Get an array of data values, as contained in a DICOM
* DecimalString Item
*/
template <typename TType>
int GetElementDS(const unsigned short group,
const unsigned short element,
unsigned short count,
TType *target,
const bool throwException = true) const
{
DcmStack resultStack;
if(this->GetStack(group,element,resultStack,throwException) != EXIT_SUCCESS)
{
return EXIT_FAILURE;
}
DcmDecimalString *dsItem =
dynamic_cast<DcmDecimalString *>(resultStack.top());
if(dsItem == ITK_NULLPTR)
{
DCMTKExceptionOrErrorReturn(<< "Can't get DecimalString Element at tag "
<< std::hex << group << " "
<< element << std::dec);
}
OFVector<Float64> doubleVals;
if(dsItem->getFloat64Vector(doubleVals) != EC_Normal)
{
DCMTKExceptionOrErrorReturn(<< "Cant extract Array from DecimalString " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
if(doubleVals.size() != count)
{
DCMTKExceptionOrErrorReturn(<< "DecimalString " << std::hex
<< group << " " << std::hex
<< element << " expected "
<< count << "items, but found "
<< doubleVals.size() << std::dec);
}
for(unsigned i = 0; i < count; i++)
{
target[i] = static_cast<TType>(doubleVals[i]);
}
return EXIT_SUCCESS;
}
int GetElementSQ(const unsigned short group,
const unsigned short element,
DCMTKSequence &target,
const bool throwException = true) const;
int GetElementItem(unsigned short itemIndex,
DCMTKItem &target,
const bool throwException = true) const;
void print(std::ostream &out) const
{
this->m_DcmSequenceOfItems->print(out);
}
private:
DcmSequenceOfItems *m_DcmSequenceOfItems;
};
class ITKIODCMTK_EXPORT DCMTKFileReader
{
public:
typedef DCMTKFileReader Self;
DCMTKFileReader() : m_DFile(ITK_NULLPTR),
m_Dataset(ITK_NULLPTR),
m_Xfer(EXS_Unknown),
m_FrameCount(0),
m_FileNumber(-1L)
{}
~DCMTKFileReader();
void SetFileName(const std::string &fileName);
const std::string &GetFileName() const;
void LoadFile();
int GetElementLO(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementLO(const unsigned short group,
const unsigned short element,
std::vector<std::string> &target,
const bool throwException = true) const;
/** Get an array of data values, as contained in a DICOM
* DecimalString Item
*/
template <typename TType>
int GetElementDS(const unsigned short group,
const unsigned short element,
unsigned short count,
TType *target,
const bool throwException = true) const
{
DcmTagKey tagkey(group,element);
DcmElement *el;
if(this->m_Dataset->findAndGetElement(tagkey,el) != EC_Normal)
{
DCMTKExceptionOrErrorReturn(<< "Cant find tag " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
DcmDecimalString *dsItem = dynamic_cast<DcmDecimalString *>(el);
if(dsItem == ITK_NULLPTR)
{
DCMTKExceptionOrErrorReturn(<< "Cant find DecimalString element " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
OFVector<Float64> doubleVals;
if(dsItem->getFloat64Vector(doubleVals) != EC_Normal)
{
DCMTKExceptionOrErrorReturn(<< "Cant extract Array from DecimalString " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
if(doubleVals.size() != count)
{
DCMTKExceptionOrErrorReturn(<< "DecimalString " << std::hex
<< group << " " << std::hex
<< element << " expected "
<< count << "items, but found "
<< doubleVals.size() << std::dec);
}
for(unsigned i = 0; i < count; i++)
{
target[i] = static_cast<TType>(doubleVals[i]);
}
return EXIT_SUCCESS;
}
template <typename TType>
int GetElementDSorOB(const unsigned short group,
const unsigned short element,
TType &target,
const bool throwException = true) const
{
if(this->GetElementDS<TType>(group,element,1,&target,false) == EXIT_SUCCESS)
{
return EXIT_SUCCESS;
}
std::string val;
if(this->GetElementOB(group,element,val) != EXIT_SUCCESS)
{
DCMTKExceptionOrErrorReturn(<< "Cant find DecimalString element " << std::hex
<< group << " " << std::hex
<< element << std::dec);
}
const char *data = val.c_str();
const TType *fptr = reinterpret_cast<const TType *>(data);
target = *fptr;
switch(this->GetTransferSyntax())
{
case EXS_LittleEndianImplicit:
case EXS_LittleEndianExplicit:
itk::ByteSwapper<TType>::SwapFromSystemToLittleEndian(&target);
break;
case EXS_BigEndianImplicit:
case EXS_BigEndianExplicit:
itk::ByteSwapper<TType>::SwapFromSystemToBigEndian(&target);
break;
default:
break;
}
return EXIT_SUCCESS;
}
/** Get a DecimalString Item as a single string
*/
int GetElementDS(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementFD(const unsigned short group,
const unsigned short element,
double &target,
const bool throwException = true) const;
int GetElementFD(const unsigned short group,
const unsigned short element,
int count,
double * target,
const bool throwException = true) const;
int GetElementFL(const unsigned short group,
const unsigned short element,
float &target,
const bool throwException = true) const;
int GetElementFLorOB(const unsigned short group,
const unsigned short element,
float &target,
const bool throwException = true) const;
int GetElementUS(const unsigned short group,
const unsigned short element,
unsigned short &target,
const bool throwException = true) const;
int GetElementUS(const unsigned short group,
const unsigned short element,
unsigned short *&target,
const bool throwException = true) const;
/** Get a DecimalString Item as a single string
*/
int GetElementCS(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
/** Get a PersonName Item as a single string
*/
int GetElementPN(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
/** get an IS (Integer String Item
*/
int GetElementIS(const unsigned short group,
const unsigned short element,
::itk::int32_t &target,
const bool throwException = true) const;
int GetElementSL(const unsigned short group,
const unsigned short element,
::itk::int32_t &target,
const bool throwException = true) const;
int GetElementISorOB(const unsigned short group,
const unsigned short element,
::itk::int32_t &target,
const bool throwException = true) const;
int GetElementCSorOB(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
/** get an OB OtherByte Item
*/
int GetElementOB(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementSQ(const unsigned short group,
unsigned short entry,
DCMTKSequence &sequence,
const bool throwException = true) const;
int GetElementUI(const unsigned short group,
unsigned short entry,
std::string &target,
const bool throwException = true) const;
int GetElementDA(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetElementTM(const unsigned short group,
const unsigned short element,
std::string &target,
const bool throwException = true) const;
int GetDirCosines(vnl_vector<double> &dir1,
vnl_vector<double> &dir2,
vnl_vector<double> &dir3) const;
int GetDirCosArray(double * const dircos) const;
int GetFrameCount() const;
int GetSlopeIntercept(double &slope, double &intercept) const;
int GetDimensions(unsigned short &rows, unsigned short &columns) const;
ImageIOBase::IOComponentType GetImageDataType() const;
ImageIOBase::IOPixelType GetImagePixelType() const;
int GetSpacing(double * const spacing) const;
int GetOrigin(double * const origin) const;
bool HasPixelData() const;
E_TransferSyntax GetTransferSyntax() const;
long GetFileNumber() const;
static void
AddDictEntry(DcmDictEntry *entry);
static bool CanReadFile(const std::string &filename);
static bool IsImageFile(const std::string &filename);
private:
std::string m_FileName;
DcmFileFormat* m_DFile;
DcmDataset * m_Dataset;
E_TransferSyntax m_Xfer;
Sint32 m_FrameCount;
long m_FileNumber;
};
extern bool CompareDCMTKFileReaders(DCMTKFileReader *a, DCMTKFileReader *b);
}
#endif // itkDCMTKFileReader_h
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