clitkXdrImageIOReader.cxx
clitkXdrImageIOWriter.cxx
clitkXdrImageIOFactory.cxx
- clitkHndImageIO.cxx
- clitkHndImageIOFactory.cxx
+ rtkHndImageIO.cxx
+ rtkHndImageIOFactory.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 "clitkHndImageIO.h"
-#include "clitkCommon.h"
-
-// itk include
-#include <itkMetaDataObject.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);
- 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::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;
- 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;
- }
-
- /* Read first pixel of second row */
- fread (&a, sizeof(uint32_t), 1, fp);
- buf[i++] = 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;
- 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://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 CLITKHNDIMAGEIO_H
-#define CLITKHNDIMAGEIO_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 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://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 "clitkHndImageIOFactory.h"
-
-//====================================================================
-clitk::HndImageIOFactory::HndImageIOFactory()
-{
- this->RegisterOverride("itkImageIOBase",
- "HndImageIO",
- "Hnd Image IO",
- 1,
- itk::CreateObjectFunction<HndImageIO>::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 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 */
-
#include "clitkHisImageIOFactory.h"
#include "clitkVfImageIOFactory.h"
#include "clitkXdrImageIOFactory.h"
-#include "clitkHndImageIOFactory.h"
+#include "rtkHndImageIOFactory.h"
#include "clitkGateAsciiImageIOFactory.h"
#include "clitkConfiguration.h"
#if CLITK_PRIVATE_FEATURES
clitk::VfImageIOFactory::RegisterOneFactory();
clitk::HisImageIOFactory::RegisterOneFactory();
clitk::XdrImageIOFactory::RegisterOneFactory();
- clitk::HndImageIOFactory::RegisterOneFactory();
+ rtk::HndImageIOFactory::RegisterOneFactory();
} ////
--- /dev/null
+/*=========================================================================
+ *
+ * Copyright RTK 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.
+ *
+ *=========================================================================*/
+
+// std include
+#include <stdio.h>
+
+#include "rtkHndImageIO.h"
+#include <itkMetaDataObject.h>
+
+//--------------------------------------------------------------------
+// Read Image Information
+void rtk::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);
+
+ size_t nelements = 0;
+ nelements += fread ( (void *) hnd.sFileType, sizeof(char), 32, fp);
+ nelements += fread ( (void *) &hnd.FileLength, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) hnd.sChecksumSpec, sizeof(char), 4, fp);
+ nelements += fread ( (void *) &hnd.nCheckSum, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) hnd.sCreationDate, sizeof(char), 8, fp);
+ nelements += fread ( (void *) hnd.sCreationTime, sizeof(char), 8, fp);
+ nelements += fread ( (void *) hnd.sPatientID, sizeof(char), 16, fp);
+ nelements += fread ( (void *) &hnd.nPatientSer, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) hnd.sSeriesID, sizeof(char), 16, fp);
+ nelements += fread ( (void *) &hnd.nSeriesSer, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) hnd.sSliceID, sizeof(char), 16, fp);
+ nelements += fread ( (void *) &hnd.nSliceSer, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) &hnd.SizeX, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) &hnd.SizeY, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) &hnd.dSliceZPos, sizeof(double), 1, fp);
+ nelements += fread ( (void *) hnd.sModality, sizeof(char), 16, fp);
+ nelements += fread ( (void *) &hnd.nWindow, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) &hnd.nLevel, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) &hnd.nPixelOffset, sizeof(uint32_t), 1, fp);
+ nelements += fread ( (void *) hnd.sImageType, sizeof(char), 4, fp);
+ nelements += fread ( (void *) &hnd.dGantryRtn, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dSAD, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dSFD, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCollX1, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCollX2, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCollY1, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCollY2, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCollRtn, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dFieldX, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dFieldY, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dBladeX1, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dBladeX2, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dBladeY1, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dBladeY2, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUPosLng, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUPosLat, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUPosVrt, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUPosRtn, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dPatientSupportAngle, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dTableTopEccentricAngle, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCouchVrt, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCouchLng, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCouchLat, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUResolutionX, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dIDUResolutionY, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dImageResolutionX, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dImageResolutionY, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dEnergy, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dDoseRate, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dXRayKV, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dXRayMA, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dMetersetExposure, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dAcqAdjustment, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCTProjectionAngle, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dCTNormChamber, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dGatingTimeTag, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dGating4DInfoX, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dGating4DInfoY, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dGating4DInfoZ, sizeof(double), 1, fp);
+ nelements += fread ( (void *) &hnd.dGating4DInfoTime, sizeof(double), 1, fp);
+
+ if(nelements != /*char*/120 + /*uint32_t*/10 + /*double*/41)
+ itkGenericExceptionMacro(<< "Could not read header data in " << m_FileName);
+
+ if(fclose (fp) != 0)
+ itkGenericExceptionMacro(<< "Could not close file: " << 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);
+}
+
+//--------------------------------------------------------------------
+bool rtk::HndImageIO::CanReadFile(const char* FileNameToRead)
+{
+ std::string filename(FileNameToRead);
+ const std::string::size_type it = filename.find_last_of( "." );
+ std::string fileExt( filename, it+1, filename.length() );
+
+ if (fileExt != std::string("hnd") )
+ return false;
+ return true;
+}
+
+//--------------------------------------------------------------------
+// Read Image Content
+void rtk::HndImageIO::Read(void * buffer)
+{
+ FILE *fp;
+
+ uint32_t* buf = (uint32_t*)buffer;
+ unsigned char *pt_lut;
+ uint32_t a;
+ 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 */
+ if(fseek (fp, 1024, SEEK_SET) != 0)
+ itkGenericExceptionMacro(<< "Could not seek to image data in: " << m_FileName);
+
+ size_t nbytes = (GetDimensions(1)-1)*GetDimensions(0) / 4;
+ if(nbytes != fread (pt_lut, sizeof(unsigned char), nbytes, fp))
+ itkGenericExceptionMacro(<< "Could not read image LUT in: " << m_FileName);
+
+ /* Read first row */
+ for (i = 0; i < GetDimensions(0); i++) {
+ if(1 != fread (&a, sizeof(uint32_t), 1, fp))
+ itkGenericExceptionMacro(<< "Could not read first row in: " << m_FileName);
+ buf[i] = a;
+ }
+
+ /* Read first pixel of second row */
+ if(1 != fread (&a, sizeof(uint32_t), 1, fp))
+ itkGenericExceptionMacro(<< "Could not read first pixel of second row");
+ buf[i++] = 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;
+ i++;
+ }
+
+ /* Clean up */
+ free (pt_lut);
+ if(fclose (fp) != 0)
+ itkGenericExceptionMacro(<< "Could not close file: " << m_FileName);
+ return;
+
+read_error:
+
+ itkGenericExceptionMacro(<< "Error reading hnd file");
+ free (pt_lut);
+ if(fclose (fp) != 0)
+ itkGenericExceptionMacro(<< "Could not close file: " << m_FileName);
+ return;
+}
+
+//--------------------------------------------------------------------
+bool rtk::HndImageIO::CanWriteFile(const char* itkNotUsed(FileNameToWrite))
+{
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void rtk::HndImageIO::Write(const void* itkNotUsed(buffer))
+{
+ //TODO?
+}
--- /dev/null
+/*=========================================================================
+ *
+ * Copyright RTK 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 __rtkHndImageIO_h
+#define __rtkHndImageIO_h
+
+// itk include
+#include <itkImageIOBase.h>
+
+#if defined (_MSC_VER) && (_MSC_VER < 1600)
+//SR: taken from
+//#include "msinttypes/stdint.h"
+#else
+#include <stdint.h>
+#endif
+
+namespace rtk {
+
+/** \class HndImageIO
+ * \brief Class for reading Hnd Image file format
+ *
+ * Reads Hnd files (file format used by Varian for Obi raw data).
+ *
+ * \author Simon Rit
+ *
+ * \ingroup IOFilters
+ */
+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];
+ unsigned int FileLength;
+ char sChecksumSpec[4];
+ unsigned int nCheckSum;
+ char sCreationDate[8];
+ char sCreationTime[8];
+ char sPatientID[16];
+ unsigned int nPatientSer;
+ char sSeriesID[16];
+ unsigned int nSeriesSer;
+ char sSliceID[16];
+ unsigned int nSliceSer;
+ unsigned int SizeX;
+ unsigned int SizeY;
+ double dSliceZPos;
+ char sModality[16];
+ unsigned int nWindow;
+ unsigned int nLevel;
+ unsigned int 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, itk::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);
+
+}; // end class HndImageIO
+
+} // end namespace
+
+#endif /* end #define __rtkHndImageIO_h */
--- /dev/null
+/*=========================================================================
+ *
+ * Copyright RTK 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.
+ *
+ *=========================================================================*/
+
+#include "rtkHndImageIOFactory.h"
+
+#include <fstream>
+
+//====================================================================
+rtk::HndImageIOFactory::HndImageIOFactory()
+{
+ this->RegisterOverride("itkImageIOBase",
+ "HndImageIO",
+ "Hnd Image IO",
+ 1,
+ itk::CreateObjectFunction<HndImageIO>::New() );
+}
--- /dev/null
+/*=========================================================================
+ *
+ * Copyright RTK 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 ITKHNDIMAGEIOFACTORY_H
+//#define ITKHNDIMAGEIOFACTORY_H
+
+#ifndef __rtkHndImageIOFactory_h
+#define __rtkHndImageIOFactory_h
+
+#include "rtkHndImageIO.h"
+
+// itk include
+#include <itkImageIOBase.h>
+#include <itkObjectFactoryBase.h>
+#include <itkVersion.h>
+
+namespace rtk
+{
+
+/** \class HndImageIOFactory
+ * \brief ITK factory for Hnd file I/O.
+ *
+ * \author Simon Rit
+ */
+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 "His ImageIO Factory, allows the loading of His images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(HndImageIOFactory, itk::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 // __rtkHndImageIOFactory_h
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff