--- /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://oncora1.lyon.fnclcc.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 "clitkHndImageIO.h"
+#include "clitkCommon.h"
+
+//--------------------------------------------------------------------
+// Read Image Information
+void clitk::HndImageIO::ReadImageInformation()
+{
+ Hnd_header hnd;
+ FILE *fp;
+
+ fp = fopen (m_FileName.c_str(), "rb");
+ if (fp == NULL)
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+
+ fread ((void *) hnd.sFileType, sizeof(char), 32, fp);
+ fread ((void *) &hnd.FileLength, sizeof(uint32_t), 1, fp);
+ fread ((void *) hnd.sChecksumSpec, sizeof(char), 4, fp);
+ fread ((void *) &hnd.nCheckSum, sizeof(uint32_t), 1, fp);
+ fread ((void *) hnd.sCreationDate, sizeof(char), 8, fp);
+ fread ((void *) hnd.sCreationTime, sizeof(char), 8, fp);
+ fread ((void *) hnd.sPatientID, sizeof(char), 16, fp);
+ fread ((void *) &hnd.nPatientSer, sizeof(uint32_t), 1, fp);
+ fread ((void *) hnd.sSeriesID, sizeof(char), 16, fp);
+ fread ((void *) &hnd.nSeriesSer, sizeof(uint32_t), 1, fp);
+ fread ((void *) hnd.sSliceID, sizeof(char), 16, fp);
+ fread ((void *) &hnd.nSliceSer, sizeof(uint32_t), 1, fp);
+ fread ((void *) &hnd.SizeX, sizeof(uint32_t), 1, fp);
+ fread ((void *) &hnd.SizeY, sizeof(uint32_t), 1, fp);
+ fread ((void *) &hnd.dSliceZPos, sizeof(double), 1, fp);
+ fread ((void *) hnd.sModality, sizeof(char), 16, fp);
+ fread ((void *) &hnd.nWindow, sizeof(uint32_t), 1, fp);
+ fread ((void *) &hnd.nLevel, sizeof(uint32_t), 1, fp);
+ fread ((void *) &hnd.nPixelOffset, sizeof(uint32_t), 1, fp);
+ fread ((void *) hnd.sImageType, sizeof(char), 4, fp);
+ fread ((void *) &hnd.dGantryRtn, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dSAD, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dSFD, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCollX1, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCollX2, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCollY1, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCollY2, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCollRtn, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dFieldX, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dFieldY, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dBladeX1, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dBladeX2, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dBladeY1, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dBladeY2, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUPosLng, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUPosLat, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUPosVrt, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUPosRtn, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dPatientSupportAngle, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dTableTopEccentricAngle, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCouchVrt, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCouchLng, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCouchLat, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUResolutionX, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dIDUResolutionY, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dImageResolutionX, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dImageResolutionY, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dEnergy, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dDoseRate, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dXRayKV, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dXRayMA, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dMetersetExposure, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dAcqAdjustment, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCTProjectionAngle, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dCTNormChamber, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dGatingTimeTag, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dGating4DInfoX, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dGating4DInfoY, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dGating4DInfoZ, sizeof(double), 1, fp);
+ fread ((void *) &hnd.dGating4DInfoTime, sizeof(double), 1, fp);
+ fclose (fp);
+
+ /* Convert hnd to ITK image information */
+ SetNumberOfDimensions(2);
+ SetDimensions(0, hnd.SizeX);
+ SetDimensions(1, hnd.SizeY);
+ SetComponentType(itk::ImageIOBase::UINT);
+}
+
+//--------------------------------------------------------------------
+bool clitk::HndImageIO::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::HndImageIO::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 hnd file");
+ free (pt_lut);
+ fclose (fp);
+ return;
+}
+
+//--------------------------------------------------------------------
+bool clitk::HndImageIO::CanWriteFile(const char* FileNameToWrite)
+{
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void clitk::HndImageIO::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://oncora1.lyon.fnclcc.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 CLITKHNDIMAGEIO_H
+#define CLITKHNDIMAGEIO_H
+
+// itk include
+#include "itkImageIOBase.h"
+
+#if defined (_MSC_VER) && (_MSC_VER < 1600)
+#include "msinttypes/stdint.h"
+#else
+#include <stdint.h>
+#endif
+
+namespace clitk {
+
+ //====================================================================
+ // Class for reading Hnd Image file format
+ class HndImageIO: public itk::ImageIOBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef HndImageIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef signed short int PixelType;
+
+ typedef struct hnd_header {
+ char sFileType[32];
+ uint32_t FileLength;
+ char sChecksumSpec[4];
+ uint32_t nCheckSum;
+ char sCreationDate[8];
+ char sCreationTime[8];
+ char sPatientID[16];
+ uint32_t nPatientSer;
+ char sSeriesID[16];
+ uint32_t nSeriesSer;
+ char sSliceID[16];
+ uint32_t nSliceSer;
+ uint32_t SizeX;
+ uint32_t SizeY;
+ double dSliceZPos;
+ char sModality[16];
+ uint32_t nWindow;
+ uint32_t nLevel;
+ uint32_t nPixelOffset;
+ char sImageType[4];
+ double dGantryRtn;
+ double dSAD;
+ double dSFD;
+ double dCollX1;
+ double dCollX2;
+ double dCollY1;
+ double dCollY2;
+ double dCollRtn;
+ double dFieldX;
+ double dFieldY;
+ double dBladeX1;
+ double dBladeX2;
+ double dBladeY1;
+ double dBladeY2;
+ double dIDUPosLng;
+ double dIDUPosLat;
+ double dIDUPosVrt;
+ double dIDUPosRtn;
+ double dPatientSupportAngle;
+ double dTableTopEccentricAngle;
+ double dCouchVrt;
+ double dCouchLng;
+ double dCouchLat;
+ double dIDUResolutionX;
+ double dIDUResolutionY;
+ double dImageResolutionX;
+ double dImageResolutionY;
+ double dEnergy;
+ double dDoseRate;
+ double dXRayKV;
+ double dXRayMA;
+ double dMetersetExposure;
+ double dAcqAdjustment;
+ double dCTProjectionAngle;
+ double dCTNormChamber;
+ double dGatingTimeTag;
+ double dGating4DInfoX;
+ double dGating4DInfoY;
+ double dGating4DInfoZ;
+ double dGating4DInfoTime;
+ } Hnd_header;
+
+ HndImageIO():Superclass() {;}
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(HndImageIO, 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 HndImageIO
+} // end namespace
+
+// explicit template instantiation
+//template class itk::CreateObjectFunction<clitk::HndImageIO>;
+
+#endif /* end #define CLITKHNDIMAGEIO_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://oncora1.lyon.fnclcc.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 CLITKHNDIMAGEIOFACTORY_H
+#define CLITKHNDIMAGEIOFACTORY_H
+
+// clitk include
+#include "clitkHndImageIO.h"
+
+// itk include
+#include "itkImageIOBase.h"
+#include "itkObjectFactoryBase.h"
+#include "itkVersion.h"
+
+namespace clitk {
+
+ //====================================================================
+ // Factory for reading Hnd Image file format
+ class HndImageIOFactory: public itk::ObjectFactoryBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef HndImageIOFactory 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 "Hnd ImageIO Factory, allows the loading of Hnd images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(HndImageIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+ protected:
+ HndImageIOFactory();
+ ~HndImageIOFactory() {};
+ typedef HndImageIOFactory myProductType;
+ const myProductType* m_MyProduct;
+
+ private:
+ HndImageIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+ };
+
+} // end namespace
+
+#endif /* end #define CLITKHNDIMAGEIOFACTORY_H */
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff