rtkHndImageIOFactory.cxx
rtkEdfImageIO.cxx
rtkEdfImageIOFactory.cxx
+ clitkEsrfHstImageIO.cxx
+ clitkEsrfHstImageIOFactory.cxx
+ clitkEsrfHstXMLFileReader.cxx
clitkDicomRTDoseIO.cxx
clitkDicomRTDoseIOFactory.cxx
clitkOrientation.cxx
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#include "clitkEsrfHstImageIO.h"
+#include "clitkEsrfHstXMLFileReader.h"
+#include "clitkDD.h"
+
+// itk include (for itkReadRawBytesAfterSwappingMacro)
+#include <itkRawImageIO.h>
+#include <itksys/SystemTools.hxx>
+#include <itkMetaDataObject.h>
+
+//--------------------------------------------------------------------
+// Read Image Information
+void clitk::EsrfHstImageIO::ReadImageInformation()
+{
+ clitk::EsrfHstXMLFileReader::Pointer hstXmlReader;
+ hstXmlReader = clitk::EsrfHstXMLFileReader::New();
+ hstXmlReader->SetFilename(m_XmlFileName);
+ hstXmlReader->GenerateOutputInformation();
+ itk::MetaDataDictionary &dic = *(hstXmlReader->GetOutputObject() );
+
+ typedef itk::MetaDataObject< double > MetaDataDoubleType;
+ typedef itk::MetaDataObject< std::string > MetaDataStringType;
+ typedef itk::MetaDataObject< int > MetaDataIntType;
+ SetComponentType(itk::ImageIOBase::FLOAT);
+ SetNumberOfDimensions(3);
+ SetDimensions(0, dynamic_cast<MetaDataIntType *>(dic["SIZEX"].GetPointer() )->GetMetaDataObjectValue());
+ SetDimensions(1, dynamic_cast<MetaDataIntType *>(dic["SIZEY"].GetPointer() )->GetMetaDataObjectValue());
+ SetDimensions(2, dynamic_cast<MetaDataIntType *>(dic["SIZEZ"].GetPointer() )->GetMetaDataObjectValue());
+ SetSpacing(0, dynamic_cast<MetaDataDoubleType *>(dic["voxelsize"].GetPointer() )->GetMetaDataObjectValue());
+ SetSpacing(1, GetSpacing(0));
+ SetSpacing(2, GetSpacing(0));
+ SetOrigin(0, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINX"].GetPointer() )->GetMetaDataObjectValue()-1));
+ SetOrigin(1, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINY"].GetPointer() )->GetMetaDataObjectValue()-1));
+ SetOrigin(2, GetSpacing(0)*(dynamic_cast<MetaDataIntType *>(dic["ORIGINZ"].GetPointer() )->GetMetaDataObjectValue()-1));
+ if(std::string("LOWBYTEFIRST") == dynamic_cast<MetaDataStringType*>(dic["SUBVOLUME_NAME"].GetPointer() )->GetMetaDataObjectValue())
+ this->SetByteOrder(BigEndian);
+ else
+ this->SetByteOrder(LittleEndian);
+
+ // Prepare raw file name
+ m_RawFileName = itksys::SystemTools::GetFilenamePath(m_XmlFileName);
+ if(m_RawFileName != "")
+ m_RawFileName += std::string("/");
+ m_RawFileName += dynamic_cast<MetaDataStringType*>(dic["SUBVOLUME_NAME"].GetPointer() )->GetMetaDataObjectValue();
+} ////
+
+//--------------------------------------------------------------------
+// Read Image Information
+bool clitk::EsrfHstImageIO::CanReadFile(const char* FileNameToRead)
+{
+ std::string ext = itksys::SystemTools::GetFilenameLastExtension(FileNameToRead);
+ if( ext!=std::string(".xml") && ext!=std::string(".vol") )
+ return false;
+
+ m_XmlFileName = std::string(FileNameToRead);
+ if( ext==std::string(".vol") )
+ m_XmlFileName += std::string(".xml");
+
+ std::ifstream is(m_XmlFileName.c_str());
+ if(! is.is_open() )
+ return false;
+
+ std::string firstLine;
+ std::getline(is, firstLine);
+ if(firstLine != std::string("<!-- PyHST VOLUME XML FILE -->") )
+ return false;
+
+ return true;
+} ////
+
+//--------------------------------------------------------------------
+// Read Image Content
+void clitk::EsrfHstImageIO::Read(void * buffer)
+{
+ // Adapted from itkRawImageIO
+ std::ifstream is(m_RawFileName.c_str(), std::ios::binary);
+ if(! is.is_open() )
+ itkExceptionMacro(<<"Could not open file " << m_RawFileName);
+
+ unsigned long numberOfBytesToBeRead = GetComponentSize();
+ for(unsigned int i=0; i<GetNumberOfDimensions(); i++) numberOfBytesToBeRead *= GetDimensions(i);
+
+ if(!this->ReadBufferAsBinary(is, buffer, numberOfBytesToBeRead)) {
+ itkExceptionMacro(<<"Read failed: Wanted "
+ << numberOfBytesToBeRead
+ << " bytes, but read "
+ << is.gcount() << " bytes.");
+ }
+ itkDebugMacro(<< "Reading Done");
+
+ // Adapted from itkRawImageIO
+ {
+ using namespace itk;
+ // Swap bytes if necessary
+ if itkReadRawBytesAfterSwappingMacro( unsigned short, USHORT )
+ else if itkReadRawBytesAfterSwappingMacro( short, SHORT )
+ else if itkReadRawBytesAfterSwappingMacro( char, CHAR )
+ else if itkReadRawBytesAfterSwappingMacro( unsigned char, UCHAR )
+ else if itkReadRawBytesAfterSwappingMacro( unsigned int, UINT )
+ else if itkReadRawBytesAfterSwappingMacro( int, INT )
+ else if itkReadRawBytesAfterSwappingMacro( unsigned int, ULONG )
+ else if itkReadRawBytesAfterSwappingMacro( int, LONG )
+ else if itkReadRawBytesAfterSwappingMacro( float, FLOAT )
+ else if itkReadRawBytesAfterSwappingMacro( double, DOUBLE );
+ }
+}
+
+//--------------------------------------------------------------------
+// Write Image Information
+void clitk::EsrfHstImageIO::WriteImageInformation(bool keepOfStream)
+{
+}
+
+//--------------------------------------------------------------------
+// Write Image Information
+bool clitk::EsrfHstImageIO::CanWriteFile(const char* FileNameToWrite)
+{
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void clitk::EsrfHstImageIO::Write(const void * buffer)
+{
+} ////
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#ifndef __clitkEsrfHstImageIO_h
+#define __clitkEsrfHstImageIO_h
+
+#include <itkImageIOBase.h>
+#include <fstream>
+#include <string.h>
+
+namespace clitk
+{
+
+//====================================================================
+// Class for reading Esrf Hst Image file format
+class EsrfHstImageIO: public itk::ImageIOBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef EsrfHstImageIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+
+ EsrfHstImageIO():Superclass() { }
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(EsrfHstImageIO, ImageIOBase);
+
+ /*-------- This part of the interface deals with reading data. ------ */
+ virtual void ReadImageInformation();
+ virtual bool CanReadFile( const char* FileNameToRead );
+ virtual void Read(void * buffer);
+
+ /*-------- This part of the interfaces deals with writing data. ----- */
+ virtual void WriteImageInformation(bool keepOfStream);
+ virtual void WriteImageInformation() { WriteImageInformation(false); }
+ virtual bool CanWriteFile(const char* filename);
+ virtual void Write(const void* buffer);
+
+protected:
+ std::string m_XmlFileName;
+ std::string m_RawFileName;
+};
+
+} // end namespace
+
+#endif
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#include "clitkEsrfHstImageIOFactory.h"
+
+//====================================================================
+clitk::EsrfHstImageIOFactory::EsrfHstImageIOFactory()
+{
+ this->RegisterOverride("itkImageIOBase",
+ "EsrfHstImageIO",
+ "Esrf Hst Image IO",
+ 1,
+ itk::CreateObjectFunction<EsrfHstImageIO>::New());
+}
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#ifndef __clitkEsrfHstImageIOFactory_h
+#define __clitkEsrfHstImageIOFactory_h
+
+#include "clitkEsrfHstImageIO.h"
+#include <itkImageIOBase.h>
+#include <itkObjectFactoryBase.h>
+#include <itkVersion.h>
+
+namespace clitk
+{
+
+//====================================================================
+// Factory for reading Esrf Hst Image file format
+class EsrfHstImageIOFactory: public itk::ObjectFactoryBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef EsrfHstImageIOFactory Self;
+ typedef itk::ObjectFactoryBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Class methods used to interface with the registered factories. */
+ const char* GetITKSourceVersion(void) const {
+ return ITK_SOURCE_VERSION;
+ }
+
+ const char* GetDescription(void) const {
+ return "Esrf Hst ImageIO Factory, allows the loading of Esrf Hst images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(EsrfHstImageIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+protected:
+ EsrfHstImageIOFactory();
+ ~EsrfHstImageIOFactory() {};
+ typedef EsrfHstImageIOFactory myProductType;
+ const myProductType* m_MyProduct;
+
+private:
+ EsrfHstImageIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+};
+
+} // end namespace
+
+#endif
+
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#include "clitkEsrfHstXMLFileReader.h"
+#include "itkMacro.h"
+
+#include <itksys/SystemTools.hxx>
+#include <itkMetaDataObject.h>
+
+namespace clitk
+{
+
+int
+EsrfHstXMLFileReader::
+CanReadFile(const char *name)
+{
+ if(!itksys::SystemTools::FileExists(name) ||
+ itksys::SystemTools::FileIsDirectory(name) ||
+ itksys::SystemTools::FileLength(name) == 0)
+ return 0;
+ return 1;
+}
+
+void
+EsrfHstXMLFileReader::
+StartElement(const char * itkNotUsed(name),const char ** itkNotUsed(atts))
+{
+ m_CurCharacterData = "";
+}
+
+void
+EsrfHstXMLFileReader::
+EndElement(const char *name)
+{
+#define ENCAPLULATE_META_DATA_DOUBLE(metaName) \
+ if(itksys::SystemTools::Strucmp(name, metaName) == 0) { \
+ double d = atof(m_CurCharacterData.c_str() ); \
+ itk::EncapsulateMetaData<double>(m_Dictionary, metaName, d); \
+ }
+
+#define ENCAPLULATE_META_DATA_INT(metaName) \
+ if(itksys::SystemTools::Strucmp(name, metaName) == 0) { \
+ double d = atof(m_CurCharacterData.c_str() ); \
+ itk::EncapsulateMetaData<int>(m_Dictionary, metaName, d); \
+ }
+
+#define ENCAPLULATE_META_DATA_STRING(metaName) \
+ if(itksys::SystemTools::Strucmp(name, metaName) == 0) { \
+ itk::EncapsulateMetaData<std::string>(m_Dictionary, metaName, m_CurCharacterData); \
+ }
+
+ ENCAPLULATE_META_DATA_INT("idAc");
+ ENCAPLULATE_META_DATA_STRING("SUBVOLUME_NAME");
+ ENCAPLULATE_META_DATA_INT("SIZEX");
+ ENCAPLULATE_META_DATA_INT("SIZEY");
+ ENCAPLULATE_META_DATA_INT("SIZEZ");
+ ENCAPLULATE_META_DATA_INT("ORIGINX");
+ ENCAPLULATE_META_DATA_INT("ORIGINY");
+ ENCAPLULATE_META_DATA_INT("ORIGINZ");
+ ENCAPLULATE_META_DATA_INT("DIM_REC");
+ ENCAPLULATE_META_DATA_DOUBLE("voxelsize");
+ ENCAPLULATE_META_DATA_STRING("BYTE_ORDER");
+}
+
+void
+EsrfHstXMLFileReader::
+CharacterDataHandler(const char *inData, int inLength)
+{
+ for(int i = 0; i < inLength; i++)
+ m_CurCharacterData = m_CurCharacterData + inData[i];
+}
+
+}
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#ifndef __clitkEsrfHstXMLFileReader_h
+#define __clitkEsrfHstXMLFileReader_h
+
+#ifdef _MSC_VER
+#pragma warning ( disable : 4786 )
+#endif
+
+#include <itkXMLFile.h>
+#include <itkMetaDataDictionary.h>
+
+#include <map>
+
+namespace clitk
+{
+
+/** \class EsrfHstXMLFileReader
+ *
+ * Reads the XML-format file written by the software High Speed Tomography
+ * at the European Synchrotron Radiation Facility
+ */
+class EsrfHstXMLFileReader : public itk::XMLReader<itk::MetaDataDictionary>
+{
+public:
+ /** Standard typedefs */
+ typedef EsrfHstXMLFileReader Self;
+ typedef itk::XMLReader<itk::MetaDataDictionary> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(EsrfHstXMLFileReader, itk::XMLReader);
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Determine if a file can be read */
+ int CanReadFile(const char* name);
+
+protected:
+ EsrfHstXMLFileReader() {m_OutputObject = &m_Dictionary;};
+ virtual ~EsrfHstXMLFileReader() {};
+
+ virtual void StartElement(const char * name,const char **atts);
+
+ virtual void EndElement(const char *name);
+
+ void CharacterDataHandler(const char *inData, int inLength);
+
+private:
+ EsrfHstXMLFileReader(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ itk::MetaDataDictionary m_Dictionary;
+ std::string m_CurCharacterData;
+};
+
+}
+#endif
#include "rtkHisImageIOFactory.h"
#include "rtkHndImageIOFactory.h"
#include "rtkEdfImageIOFactory.h"
+#include "clitkEsrfHstImageIOFactory.h"
#include "clitkGateAsciiImageIOFactory.h"
#include "clitkConfiguration.h"
#if CLITK_PRIVATE_FEATURES
rtk::HisImageIOFactory::RegisterOneFactory();
rtk::HndImageIOFactory::RegisterOneFactory();
rtk::EdfImageIOFactory::RegisterOneFactory();
+ clitk::EsrfHstImageIOFactory::RegisterOneFactory();
} ////
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff