Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.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
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
// std include
#include <stdio.h>
#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);
- SetComponentType(itk::ImageIOBase::UINT);
+ 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");
}
//--------------------------------------------------------------------
// 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 */
+ 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;
- 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++;
+ 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;
+ /* Clean up */
+ free (pt_lut);
+ fclose (fp);
+ return;
- read_error:
+read_error:
- itkGenericExceptionMacro(<< "Error reading hnd file");
- free (pt_lut);
- fclose (fp);
- return;
+ itkGenericExceptionMacro(<< "Error reading hnd file");
+ free (pt_lut);
+ fclose (fp);
+ return;
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff