clitkXdrImageIOFactory.cxx
clitkHndImageIO.cxx
clitkHndImageIOFactory.cxx
+ clitkGateAsciiImageIO.cxx
+ clitkGateAsciiImageIOFactory.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
+===========================================================================**/
+
+// std include
+#include <stdio.h>
+
+// clitk include
+#include "clitkGateAsciiImageIO.h"
+#include "clitkCommon.h"
+
+// itk include
+#include <itkMetaDataObject.h>
+
+//--------------------------------------------------------------------
+// Read Image Information
+void clitk::GateAsciiImageIO::ReadImageInformation()
+{
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+
+
+ /* Convert hnd to ITK image information */
+ SetNumberOfDimensions(2);
+ //SetDimensions(0, hnd.SizeX);
+ //SetDimensions(1, hnd.SizeY);
+ //SetSpacing(0, hnd.dIDUResolutionX);
+ //SetSpacing(1, hnd.dIDUResolutionY);
+ //SetOrigin(0, -0.5*(hnd.SizeX-1)*hnd.dIDUResolutionX); //SR: assumed centered
+ //SetOrigin(1, -0.5*(hnd.SizeY-1)*hnd.dIDUResolutionY); //SR: assumed centered
+ //SetComponentType(itk::ImageIOBase::UINT);
+
+ /* Store important meta information in the meta data dictionary */
+ //itk::EncapsulateMetaData<double>(this->GetMetaDataDictionary(), "dCTProjectionAngle", hnd.dCTProjectionAngle);
+ //itk::ExposeMetaData<double>( this->GetMetaDataDictionary(), &(hnd.dCTProjectionAngle), "dCTProjectionAngle");
+}
+
+//--------------------------------------------------------------------
+bool clitk::GateAsciiImageIO::CanReadFile(const char* FileNameToRead)
+{
+ std::string filename(FileNameToRead);
+ std::string filenameext = GetExtension(filename);
+ if (filenameext != std::string("hnd")) return false;
+ return true;
+}
+
+//--------------------------------------------------------------------
+// Read Image Content
+void clitk::GateAsciiImageIO::Read(void * buffer)
+{
+ FILE *fp;
+
+ uint32_t* buf = (uint32_t*)buffer;
+ unsigned char *pt_lut;
+ uint32_t a;
+ float b;
+ unsigned char v;
+ int lut_idx, lut_off;
+ size_t num_read;
+ char dc;
+ short ds;
+ long dl, diff=0;
+ uint32_t i;
+
+ fp = fopen (m_FileName.c_str(), "rb");
+ if (fp == NULL)
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+
+ pt_lut = (unsigned char*) malloc (sizeof (unsigned char) * GetDimensions(0) * GetDimensions(1));
+
+ /* Read LUT */
+ fseek (fp, 1024, SEEK_SET);
+ fread (pt_lut, sizeof(unsigned char), (GetDimensions(1)-1)*GetDimensions(0) / 4, fp);
+
+ /* Read first row */
+ for (i = 0; i < GetDimensions(0); i++) {
+ fread (&a, sizeof(uint32_t), 1, fp);
+ buf[i] = a;
+ b = a;
+ }
+
+ /* Read first pixel of second row */
+ fread (&a, sizeof(uint32_t), 1, fp);
+ buf[i++] = a;
+ b = a;
+
+ /* Decompress the rest */
+ lut_idx = 0;
+ lut_off = 0;
+ while (i < GetDimensions(0) * GetDimensions(1)) {
+ uint32_t r11, r12, r21;
+
+ r11 = buf[i-GetDimensions(0)-1];
+ r12 = buf[i-GetDimensions(0)];
+ r21 = buf[i-1];
+ v = pt_lut[lut_idx];
+ switch (lut_off) {
+ case 0:
+ v = v & 0x03;
+ lut_off ++;
+ break;
+ case 1:
+ v = (v & 0x0C) >> 2;
+ lut_off ++;
+ break;
+ case 2:
+ v = (v & 0x30) >> 4;
+ lut_off ++;
+ break;
+ case 3:
+ v = (v & 0xC0) >> 6;
+ lut_off = 0;
+ lut_idx ++;
+ break;
+ }
+ switch (v) {
+ case 0:
+ num_read = fread (&dc, sizeof(unsigned char), 1, fp);
+ if (num_read != 1) goto read_error;
+ diff = dc;
+ break;
+ case 1:
+ num_read = fread (&ds, sizeof(unsigned short), 1, fp);
+ if (num_read != 1) goto read_error;
+ diff = ds;
+ break;
+ case 2:
+ num_read = fread (&dl, sizeof(uint32_t), 1, fp);
+ if (num_read != 1) goto read_error;
+ diff = dl;
+ break;
+ }
+
+ buf[i] = r21 + r12 + diff - r11;
+ b = buf[i];
+ i++;
+ }
+
+ /* Clean up */
+ free (pt_lut);
+ fclose (fp);
+ return;
+
+read_error:
+
+ itkGenericExceptionMacro(<< "Error reading gate ascii file");
+ free (pt_lut);
+ fclose (fp);
+ return;
+}
+
+//--------------------------------------------------------------------
+bool clitk::GateAsciiImageIO::CanWriteFile(const char* FileNameToWrite)
+{
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void clitk::GateAsciiImageIO::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 CLITKGATEASCIIIMAGEIO_H
+#define CLITKGATEASCIIIMAGEIO_H
+
+// itk include
+#include "itkImageIOBase.h"
+
+#if defined (_MSC_VER) && (_MSC_VER < 1600)
+//SR: taken from
+//#include "msinttypes/stdint.h"
+typedef unsigned int uint32_t;
+#else
+#include <stdint.h>
+#endif
+
+namespace clitk {
+
+ //====================================================================
+ // Class for reading gate ascii Image file format
+ class GateAsciiImageIO: public itk::ImageIOBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef signed short int PixelType;
+
+ struct GateAsciiHeader {
+ double matrix_size[3];
+ int resolution[3];
+ double voxel_size[3];
+ int nb_value;
+ };
+
+ GateAsciiImageIO():Superclass() {;}
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIO, 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:
+ int m_HeaderSize;
+
+ }; // end class GateAsciiImageIO
+} // end namespace
+
+// explicit template instantiation
+//template class itk::CreateObjectFunction<clitk::GateAsciiImageIO>;
+
+#endif /* end #define CLITKGATEASCIIIMAGEIO_H */
+
--- /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 "clitkGateAsciiImageIOFactory.h"
+
+//====================================================================
+clitk::GateAsciiImageIOFactory::GateAsciiImageIOFactory()
+{
+ this->RegisterOverride("itkImageIOBase",
+ "GateAsciiImageIO",
+ "GateAscii Image IO",
+ 1,
+ itk::CreateObjectFunction<GateAsciiImageIO>::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 CLITKGATEASCIIIMAGEIOFACTORY_H
+#define CLITKGATEASCIIIMAGEIOFACTORY_H
+
+// clitk include
+#include "clitkGateAsciiImageIO.h"
+
+// itk include
+#include "itkImageIOBase.h"
+#include "itkObjectFactoryBase.h"
+#include "itkVersion.h"
+
+namespace clitk {
+
+ //====================================================================
+ // Factory for reading GateAscii Image file format
+ class GateAsciiImageIOFactory: public itk::ObjectFactoryBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIOFactory 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 "GateAscii ImageIO Factory, allows the loading of gate ascii images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+ protected:
+ GateAsciiImageIOFactory();
+ ~GateAsciiImageIOFactory() {};
+ typedef GateAsciiImageIOFactory myProductType;
+ const myProductType* m_MyProduct;
+
+ private:
+ GateAsciiImageIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+ };
+
+} // end namespace
+
+#endif /* end #define CLITKGATEASCIIIMAGEIOFACTORY_H */
+
#include "clitkVfImageIOFactory.h"
#include "clitkXdrImageIOFactory.h"
#include "clitkHndImageIOFactory.h"
+#include "clitkGateAsciiImageIOFactory.h"
//--------------------------------------------------------------------
// Register factories
void clitk::RegisterClitkFactories()
{
+ clitk::GateAsciiImageIOFactory::RegisterOneFactory();
clitk::DicomRTDoseIOFactory::RegisterOneFactory();
#if ITK_VERSION_MAJOR <= 3
itk::ImageIOFactory::RegisterBuiltInFactories();
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff