X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkHndImageIO.cxx;h=bd8e51855c848605ec4a45111503077645852ef4;hb=573d80d0f7a17607d2ee883c21c940c0ba020282;hp=85602bcf0ad48bffa6c986c855c9d951ab73d6b6;hpb=3451be2e38ff6603113fb95f7498e127707de370;p=clitk.git

diff --git a/common/clitkHndImageIO.cxx b/common/clitkHndImageIO.cxx
index 85602bc..bd8e518 100644
--- a/common/clitkHndImageIO.cxx
+++ b/common/clitkHndImageIO.cxx
@@ -3,7 +3,7 @@
 
   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
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 
 // std include
 #include <stdio.h>
@@ -23,84 +23,95 @@
 #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");
 }
 
 //--------------------------------------------------------------------
@@ -116,105 +127,105 @@ bool clitk::HndImageIO::CanReadFile(const char* FileNameToRead)
 // 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;
+  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;
+    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++;
+  }
+
+  /* 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;
     }
 
-    /* Clean up */
-    free (pt_lut);
-    fclose (fp);
-    return;
+    buf[i] = r21 + r12 + diff - r11;
+    b = buf[i];
+    i++;
+  }
+
+  /* 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;
 }
 
 //--------------------------------------------------------------------