-// gdcmHeaderHelper.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmHeaderHelper.cxx,v $
+ Language: C++
+ Date: $Date: 2004/08/01 00:59:21 $
+ Version: $Revision: 1.41 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
#include "gdcmHeaderHelper.h"
#include "gdcmDirList.h"
-#include "gdcmUtil.h" //for debug
+#include "gdcmDebug.h"
#include <math.h>
#include <algorithm>
+#include <vector>
-/*#ifdef _MSC_VER
- #include <windows.h>
-
- int GetDir(std::string dPath, std::list<std::string> &filenames)
- {
- //For now dPath should have an ending "\"
- WIN32_FIND_DATA FileData;
- HANDLE hFile;
- hFile = FindFirstFile((dPath+"*").c_str(), &FileData);
- if ( hFile == INVALID_HANDLE_VALUE )
- {
- //No files !
- return false;
- }
-
- if( strncmp(FileData.cFileName, ".", 1) != 0 )
- filenames.push_back( dPath+FileData.cFileName );
- while( FindNextFile(hFile, &FileData ) != 0)
- {
- if( strncmp(FileData.cFileName, ".", 1) != 0 )
- filenames.push_back( dPath+FileData.cFileName );
- }
- return true;
- }
-
-#else
- #include <dirent.h>
-
- int GetDir(std::string dPath, std::list<std::string> &filenames)
- {
- DIR *dir = opendir( dPath.c_str() );
- if (dir == NULL)
- return false;
- struct dirent *entry;
- while((entry = readdir(dir)) != NULL)
- {
- // if( strncmp(entry->d_name, ".", 1) != 0 && strncmp(entry->d_name, "..", 2) != 0)
- if( strncmp(entry->d_name, ".", 1) != 0 )
- {
- filenames.push_back( dPath + "/" + entry->d_name );
- }
- }
- closedir(dir);
- return true;
- }
-
-#endif*/
-
-//-----------------------------------------------------------------------------
-// gdcmHeaderHelper
+typedef std::vector<gdcmHeader* > GdcmHeaderVector;
//-----------------------------------------------------------------------------
// Constructor / Destructor
-/**
- * \ingroup gdcmHeaderHelper
- * \brief cstor
- */
-gdcmHeaderHelper::gdcmHeaderHelper() : gdcmHeader( ) {
-
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief cstor
- */
-gdcmHeaderHelper::gdcmHeaderHelper(const char *InFilename,
- bool exception_on_error,
- bool enable_sequences,
- bool ignore_shadow)
- : gdcmHeader( InFilename,
- exception_on_error,
- enable_sequences,
- ignore_shadow)
+gdcmSerieHeader::gdcmSerieHeader()
{
+ CoherentGdcmFileList.clear();
}
-//-----------------------------------------------------------------------------
-// Print
-
-//-----------------------------------------------------------------------------
-// Public
-/**
- * \ingroup gdcmHeaderHelper
- * \brief Return the size (in bytes) of a single pixel of data.
- * @return The size in bytes of a single pixel of data.
- *
- */
-int gdcmHeaderHelper::GetPixelSize() {
-
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
- return 3;
-
- std::string PixelType = GetPixelType();
- if (PixelType == "8U" || PixelType == "8S")
- return 1;
- if (PixelType == "16U" || PixelType == "16S")
- return 2;
- if (PixelType == "32U" || PixelType == "32S")
- return 4;
- if (PixelType == "FD") // to help unfortunate users to manage DOUBLE
- return 8;
- dbg.Verbose(0, "gdcmHeader::GetPixelSize: Unknown pixel type");
- return 0;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief Build the Pixel Type of the image.
- * Possible values are:
- * - 8U unsigned 8 bit,
- * - 8S signed 8 bit,
- * - 16U unsigned 16 bit,
- * - 16S signed 16 bit,
- * - 32U unsigned 32 bit,
- * - 32S signed 32 bit,
- * - FD Double,
- * \warning 12 bit images appear as 16 bit.
- * \ 24 bit images appear as 8 bit
- * \ 64 bit means 'DOUBLE' images
- * \ (no DOUBLE images in kosher DICOM,
- * \ but so usefull for people that miss them ;-)
- * @return
- */
-std::string gdcmHeaderHelper::GetPixelType() {
- std::string BitsAlloc;
- BitsAlloc = GetEntryByNumber(0x0028, 0x0100);
- if (BitsAlloc == GDCM_UNFOUND) { // Bits Allocated
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Bits Allocated");
- BitsAlloc = std::string("16");
- }
- if (BitsAlloc == "12") // It will be unpacked
- BitsAlloc = std::string("16");
- else if (BitsAlloc == "24") // (in order no to be messed up
- BitsAlloc = std::string("8"); // by old RGB images)
-
- std::string Signed;
- Signed = GetEntryByNumber(0x0028, 0x0103);
- if (Signed == GDCM_UNFOUND) { // "Pixel Representation"
- dbg.Verbose(0, "gdcmHeader::GetPixelType: unfound Pixel Representation");
- BitsAlloc = std::string("0");
- }
- if (BitsAlloc == "64") // to help users that want to deal with DOUBLE
- return("FD");
-
- if (Signed == "0")
- Signed = std::string("U");
- else
- Signed = std::string("S");
-
- return( BitsAlloc + Signed);
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * \ else 1.
- * @return X dimension of a pixel
- */
-float gdcmHeaderHelper::GetXSpacing() {
- float xspacing, yspacing;
- std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
-
- if (StrSpacing == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetXSpacing: unfound Pixel Spacing (0028,0030)");
- return 1.;
- }
- if( sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2)
- return 0.;
- if (xspacing == 0.) {
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
- // seems to be a bug in the header ...
- sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
- }
- return xspacing;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * \ else 1.
- * @return Y dimension of a pixel
- */
-float gdcmHeaderHelper::GetYSpacing() {
- float xspacing, yspacing;
- std::string StrSpacing = GetEntryByNumber(0x0028,0x0030);
-
- if (StrSpacing == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: unfound Pixel Spacing (0028,0030)");
- return 1.;
- }
- if( sscanf( StrSpacing.c_str(), "%f\\%f", &yspacing, &xspacing) != 2)
- return 0.;
- if (xspacing == 0.) {
- dbg.Verbose(0, "gdcmHeader::GetYSpacing: gdcmData/CT-MONO2-8-abdo.dcm problem");
- // seems to be a bug in the header ...
- sscanf( StrSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
- }
- return yspacing;
-}
-
-/**
- *\ingroup gdcmHeaderHelper
- *\brief gets the info from 0018,0088 : Space Between Slices
- *\ else from 0018,0050 : Slice Thickness
- *\ else 1.
- * @return Z dimension of a voxel-to be
- */
-float gdcmHeaderHelper::GetZSpacing() {
- // Spacing Between Slices : distance entre le milieu de chaque coupe
- // Les coupes peuvent etre :
- // jointives (Spacing between Slices = Slice Thickness)
- // chevauchantes (Spacing between Slices < Slice Thickness)
- // disjointes (Spacing between Slices > Slice Thickness)
- // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
- // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
- // Si le Spacing Between Slices est absent,
- // on suppose que les coupes sont jointives
-
- std::string StrSpacingBSlices = GetEntryByNumber(0x0018,0x0088);
-
- if (StrSpacingBSlices == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetZSpacing: unfound StrSpacingBSlices");
- std::string StrSliceThickness = GetEntryByNumber(0x0018,0x0050);
- if (StrSliceThickness == GDCM_UNFOUND)
- return 1.;
- else
- // if no 'Spacing Between Slices' is found,
- // we assume slices join together
- // (no overlapping, no interslice gap)
- // if they don't, we're fucked up
- return atof(StrSliceThickness.c_str());
- } else {
- return atof(StrSpacingBSlices.c_str());
- }
-}
-
-float gdcmHeaderHelper::GetRescaleIntercept() {
- float resInter = 0.;
- std::string StrRescInter = GetEntryByNumber(0x0028,0x1052); //0028 1052 DS IMG Rescale Intercept
- if (StrRescInter != GDCM_UNFOUND) {
- if( sscanf( StrRescInter.c_str(), "%f", &resInter) != 1) {
- dbg.Verbose(0, "gdcmHeader::GetRescaleIntercept: Rescale Slope is empty");
- // bug in the element 0x0028,0x1052
- }
- }
- return resInter;
-}
-
-float gdcmHeaderHelper::GetRescaleSlope() {
- float resSlope = 1.;
- std::string StrRescSlope = GetEntryByNumber(0x0028,0x1053); //0028 1053 DS IMG Rescale Slope
- if (StrRescSlope != GDCM_UNFOUND) {
- if( sscanf( StrRescSlope.c_str(), "%f", &resSlope) != 1) {
- dbg.Verbose(0, "gdcmHeader::GetRescaleSlope: Rescale Slope is empty");
- // bug in the element 0x0028,0x1053
- }
- }
- return resSlope;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief This function is intended to user who doesn't whan
- * \ to have to manage a LUT and expects to get an RBG Pixel image
- * \ (or a monochrome one ...)
- * \warning to be used with GetImagePixels()
- * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
- */
-int gdcmHeaderHelper::GetNumberOfScalarComponents() {
-
- if (GetSamplesPerPixel() ==3)
- return 3;
-
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
- return 3;
-
- std::string PhotometricInterpretation =
- gdcmHeader::GetEntryByNumber(0x0028,0x0004);
-
- if ( ( PhotometricInterpretation == "PALETTE COLOR ") ) {
- if (HasLUT()) // PALETTE COLOR is NOT enough
- return 3;
- else
- return 1;
- }
-
- //beware of trailing space at end of string
- if (PhotometricInterpretation.find(GDCM_UNFOUND) <
- PhotometricInterpretation.length() ||
- PhotometricInterpretation.find("MONOCHROME1") <
- PhotometricInterpretation.length() ||
- PhotometricInterpretation.find("MONOCHROME2") <
- PhotometricInterpretation.length() )
- return 1;
- else
- // we assume that *all* kinds of YBR are dealt with
- return 3;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief This function is intended to user that DOESN'T want
- * \to get RGB pixels image when it's stored as a PALETTE COLOR image
- * \ - the (vtk) user is supposed to know how deal with LUTs -
- * \warning to be used with GetImagePixelsRaw()
- * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
- */
-int gdcmHeaderHelper::GetNumberOfScalarComponentsRaw() {
-
- // 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
- if (gdcmHeader::GetEntryByNumber(0x0028,0x0100) == "24")
- return 3;
-
- // we assume that *all* kinds of YBR are dealt with
- return GetSamplesPerPixel();
-}
-
-std::string gdcmHeaderHelper::GetStudyUID(){
- return GetEntryByNumber(0x0020,0x000d); //0020 000d UI REL Study Instance UID
-}
-
-std::string gdcmHeaderHelper::GetSeriesUID(){
- return GetEntryByNumber(0x0020,0x000e); //0020 000e UI REL Series Instance UID
-}
-
-std::string gdcmHeaderHelper::GetClassUID(){
- return GetEntryByNumber(0x0008,0x0016); //0008 0016 UI ID SOP Class UID
-}
-
-std::string gdcmHeaderHelper::GetInstanceUID(){
- return GetEntryByNumber(0x0008,0x0018); //0008 0018 UI ID SOP Instance UID
-}
-
-// Image Position Patient (0020,0032):
-// If not found (ACR_NEMA) we try Image Position (0020,0030)
-// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
-// or Location (0020,0050)
-// as the Z coordinate,
-// 0. for all the coordinates if nothing is found
-
-// TODO : find a way to inform the caller nothing was found
-// TODO : How to tell the caller a wrong number of values was found?
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0020,0032 : Image Position Patient
- *\ else from 0020,0030 : Image Position (RET)
- *\ else 0.
- * @return up-left image corner position
- */
-float gdcmHeaderHelper::GetXOrigin() {
- float xImPos, yImPos, zImPos;
- std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
-
- if (StrImPos == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position Patient (0020,0032)");
- StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetXImagePosition: unfound Image Position (RET) (0020,0030)");
- // How to tell the caller nothing was found ?
- return 0.;
- }
- }
- if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
- return 0.;
- return xImPos;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0020,0032 : Image Position Patient
- * \ else from 0020,0030 : Image Position (RET)
- * \ else 0.
- * @return up-left image corner position
- */
-float gdcmHeaderHelper::GetYOrigin() {
- float xImPos, yImPos, zImPos;
- std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
-
- if (StrImPos == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position Patient (0020,0032)");
- StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos == GDCM_UNFOUND) {
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Image Position (RET) (0020,0030)");
- // How to tell the caller nothing was found ?
- return 0.;
- }
- }
- if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
- return 0.;
- return yImPos;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0020,0032 : Image Position Patient
- * \ else from 0020,0030 : Image Position (RET)
- * \ else from 0020,1041 : Slice Location
- * \ else from 0020,0050 : Location
- * \ else 0.
- * @return up-left image corner position
- */
-float gdcmHeaderHelper::GetZOrigin() {
- float xImPos, yImPos, zImPos;
- std::string StrImPos = GetEntryByNumber(0x0020,0x0032);
- if (StrImPos != GDCM_UNFOUND) {
- if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position Patient (0020,0032)");
- return 0.; // bug in the element 0x0020,0x0032
- } else {
- return zImPos;
- }
- }
- StrImPos = GetEntryByNumber(0x0020,0x0030); // For ACR-NEMA images
- if (StrImPos != GDCM_UNFOUND) {
- if( sscanf( StrImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Image Position (RET) (0020,0030)");
- return 0.; // bug in the element 0x0020,0x0032
- } else {
- return zImPos;
- }
- }
- std::string StrSliceLocation = GetEntryByNumber(0x0020,0x1041);// for *very* old ACR-NEMA images
- if (StrSliceLocation != GDCM_UNFOUND) {
- if( sscanf( StrSliceLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Slice Location (0020,1041)");
- return 0.; // bug in the element 0x0020,0x1041
- } else {
- return zImPos;
- }
- }
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: unfound Slice Location (0020,1041)");
- std::string StrLocation = GetEntryByNumber(0x0020,0x0050);
- if (StrLocation != GDCM_UNFOUND) {
- if( sscanf( StrLocation.c_str(), "%f", &zImPos) !=1) {
- dbg.Verbose(0, "gdcmHeader::GetZImagePosition: wrong Location (0020,0050)");
- return 0.; // bug in the element 0x0020,0x0050
- } else {
- return zImPos;
- }
+gdcmSerieHeader::~gdcmSerieHeader()
+{
+ /// \todo
+ for ( GdcmHeaderList::const_iterator it = CoherentGdcmFileList.begin();
+ it != CoherentGdcmFileList.end(); ++it)
+ {
+ delete *it;
}
- dbg.Verbose(0, "gdcmHeader::GetYImagePosition: unfound Location (0020,0050)");
- return 0.; // Hopeless
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0020,0013 : Image Number
- * \ else 0.
- * @return image number
- */
-int gdcmHeaderHelper::GetImageNumber() {
- //The function i atoi() takes the address of an area of memory as parameter and converts
- //the string stored at that location to an integer using the external decimal to internal
- //binary conversion rules. This may be preferable to sscanf() since atoi() is a much smaller,
- // simpler and faster function. sscanf() can do all possible conversions whereas atoi() can
- //only do single decimal integer conversions.
- std::string StrImNumber = GetEntryByNumber(0x0020,0x0013); //0020 0013 IS REL Image Number
- if (StrImNumber != GDCM_UNFOUND) {
- return atoi( StrImNumber.c_str() );
- }
- return 0; //Hopeless
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0008,0060 : Modality
- * @return ModalityType
- */
-ModalityType gdcmHeaderHelper::GetModality(void) {
- std::string StrModality = GetEntryByNumber(0x0008,0x0060); //0008 0060 CS ID Modality
- if (StrModality != GDCM_UNFOUND) {
- if ( StrModality.find("AU") < StrModality.length()) return AU;
- else if ( StrModality.find("AS") < StrModality.length()) return AS;
- else if ( StrModality.find("BI") < StrModality.length()) return BI;
- else if ( StrModality.find("CF") < StrModality.length()) return CF;
- else if ( StrModality.find("CP") < StrModality.length()) return CP;
- else if ( StrModality.find("CR") < StrModality.length()) return CR;
- else if ( StrModality.find("CT") < StrModality.length()) return CT;
- else if ( StrModality.find("CS") < StrModality.length()) return CS;
- else if ( StrModality.find("DD") < StrModality.length()) return DD;
- else if ( StrModality.find("DF") < StrModality.length()) return DF;
- else if ( StrModality.find("DG") < StrModality.length()) return DG;
- else if ( StrModality.find("DM") < StrModality.length()) return DM;
- else if ( StrModality.find("DS") < StrModality.length()) return DS;
- else if ( StrModality.find("DX") < StrModality.length()) return DX;
- else if ( StrModality.find("ECG") < StrModality.length()) return ECG;
- else if ( StrModality.find("EPS") < StrModality.length()) return EPS;
- else if ( StrModality.find("FA") < StrModality.length()) return FA;
- else if ( StrModality.find("FS") < StrModality.length()) return FS;
- else if ( StrModality.find("HC") < StrModality.length()) return HC;
- else if ( StrModality.find("HD") < StrModality.length()) return HD;
- else if ( StrModality.find("LP") < StrModality.length()) return LP;
- else if ( StrModality.find("LS") < StrModality.length()) return LS;
- else if ( StrModality.find("MA") < StrModality.length()) return MA;
- else if ( StrModality.find("MR") < StrModality.length()) return MR;
- else if ( StrModality.find("NM") < StrModality.length()) return NM;
- else if ( StrModality.find("OT") < StrModality.length()) return OT;
- else if ( StrModality.find("PT") < StrModality.length()) return PT;
- else if ( StrModality.find("RF") < StrModality.length()) return RF;
- else if ( StrModality.find("RG") < StrModality.length()) return RG;
- else if ( StrModality.find("RTDOSE") < StrModality.length()) return RTDOSE;
- else if ( StrModality.find("RTIMAGE") < StrModality.length()) return RTIMAGE;
- else if ( StrModality.find("RTPLAN") < StrModality.length()) return RTPLAN;
- else if ( StrModality.find("RTSTRUCT")< StrModality.length()) return RTSTRUCT;
- else if ( StrModality.find("SM") < StrModality.length()) return SM;
- else if ( StrModality.find("ST") < StrModality.length()) return ST;
- else if ( StrModality.find("TG") < StrModality.length()) return TG;
- else if ( StrModality.find("US") < StrModality.length()) return US;
- else if ( StrModality.find("VF") < StrModality.length()) return VF;
- else if ( StrModality.find("XA") < StrModality.length()) return XA;
- else if ( StrModality.find("XC") < StrModality.length()) return XC;
-
- else
- {
- //throw error return value ???
- // specified <> unknow in our database
- return Unknow;
- }
- }
- return Unknow;
-}
-
-/**
- * \ingroup gdcmHeaderHelper
- * \brief gets the info from 0020,0037 : Image Orientation Patient
- * @return cosines of image orientation patient
- */
-void gdcmHeaderHelper::GetImageOrientationPatient( float* iop ) {
-
- //iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0;
-
- std::string StrImOriPat = GetEntryByNumber(0x0020,0x0037); // 0020 0037 DS REL Image Orientation (Patient)
- if (StrImOriPat != GDCM_UNFOUND) {
- if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
- dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0037)");
- return ; // bug in the element 0x0020,0x0037
- }
- else
- return ;
- }
-
- //For ACR-NEMA
- StrImOriPat = GetEntryByNumber(0x0020,0x0035); //0020 0035 DS REL Image Orientation (RET)
- if (StrImOriPat != GDCM_UNFOUND) {
- if( sscanf( StrImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6) {
- dbg.Verbose(0, "gdcmHeader::GetImageOrientationPatient: wrong Image Orientation Patient (0020,0035)");
- return ; // bug in the element 0x0020,0x0035
- }
- else
- return ;
- }
-}
-
-//-----------------------------------------------------------------------------
-// Protected
-
-//-----------------------------------------------------------------------------
-// Private
-
-//-----------------------------------------------------------------------------
-
-
-
-//-----------------------------------------------------------------------------
-// gdcmSerieHeaderHelper
-//-----------------------------------------------------------------------------
-// Constructor / Destructor
-gdcmSerieHeaderHelper::~gdcmSerieHeaderHelper(){
- //! \todo
- for (std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
- it != CoherentGdcmFileList.end(); it++)
- {
- delete *it;
- }
- CoherentGdcmFileList.clear();
+ CoherentGdcmFileList.clear();
}
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmHeaderHelper
* \brief add a gdcmFile to the list based on file name
+ * @param filename Name of the file to deal with
*/
-void gdcmSerieHeaderHelper::AddFileName(std::string filename) {
- gdcmHeaderHelper *GdcmFile = new gdcmHeaderHelper( filename.c_str() );
- this->CoherentGdcmFileList.push_back( GdcmFile );
+void gdcmSerieHeader::AddFileName(std::string const & filename)
+{
+ gdcmHeader *header = new gdcmHeader( filename );
+ CoherentGdcmFileList.push_back( header );
}
/**
- * \ingroup gdcmHeaderHelper
* \brief add a gdcmFile to the list
+ * @param file gdcmHeader to add
*/
-void gdcmSerieHeaderHelper::AddGdcmFile(gdcmHeaderHelper *file){
- this->CoherentGdcmFileList.push_back( file );
+void gdcmSerieHeader::AddGdcmFile(gdcmHeader *file)
+{
+ CoherentGdcmFileList.push_back( file );
}
/**
- * \ingroup gdcmHeaderHelper
- * \brief \todo
+ * \brief Sets the Directory
+ * @param dir Name of the directory to deal with
*/
-void gdcmSerieHeaderHelper::SetDirectory(std::string dir){
- gdcmDirList filenames_list(dir); //OS specific
+void gdcmSerieHeader::SetDirectory(std::string const & dir)
+{
+ gdcmDirList filenames_list(dir); //OS specific
- for(gdcmDirList::iterator it = filenames_list.begin();
- it !=filenames_list.end(); it++)
- {
- gdcmHeaderHelper *file = new gdcmHeaderHelper( it->c_str() );
- this->CoherentGdcmFileList.push_back( file );
- }
-}
-
-//This could be implemented in a 'Strategy Pattern' approach
-//But as I don't know how to do it, I leave it this way
-//BTW, this is also a Strategy, I don't know this is the best approach :)
-void gdcmSerieHeaderHelper::OrderGdcmFileList(){
- if( ImagePositionPatientOrdering() )
- {
- return ;
- }
- else if( ImageNumberOrdering() )
- {
- return ;
- }
- else
- {
- FileNameOrdering();
- }
+ for( gdcmDirList::const_iterator it = filenames_list.begin();
+ it != filenames_list.end(); ++it)
+ {
+ //use string and not const char*:
+ gdcmHeader *header = new gdcmHeader( *it );
+ CoherentGdcmFileList.push_back( header );
+ }
}
-std::list<gdcmHeaderHelper*> &gdcmSerieHeaderHelper::GetGdcmFileList() {
- return CoherentGdcmFileList;
+/**
+ * \brief Sorts the File List
+ * \warning This could be implemented in a 'Strategy Pattern' approach
+ * But as I don't know how to do it, I leave it this way
+ * BTW, this is also a Strategy, I don't know this is the best approach :)
+ */
+void gdcmSerieHeader::OrderGdcmFileList()
+{
+ if( ImagePositionPatientOrdering() )
+ {
+ return ;
+ }
+ else if( ImageNumberOrdering() )
+ {
+ return ;
+ }
+ else
+ {
+ FileNameOrdering();
+ }
}
//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Private
/**
- * \ingroup gdcmHeaderHelper
- * \brief
+ * \ingroup gdcmHeader
+ * \brief sorts the images, according to their Patient Position
* We may order, considering :
* -# Image Number
* -# Image Position Patient
* -# More to come :)
+ * @return false only if the header is bugged !
*/
-bool gdcmSerieHeaderHelper::ImagePositionPatientOrdering()
+bool gdcmSerieHeader::ImagePositionPatientOrdering()
//based on Jolinda's algorithm
{
- //iop is calculated based on the file file
- float *cosines = new float[6];
- float normal[3];
- float ipp[3];
- float dist;
- float min, max;
- bool first = true;
- int n=0;
- std::vector<float> distlist;
-
- //!\todo rewrite this for loop.
- for (std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
- it != CoherentGdcmFileList.end(); it++)
- {
- if(first) {
- (*it)->GetImageOrientationPatient(cosines);
+ //iop is calculated based on the file file
+ float *cosines = new float[6];
+ float normal[3];
+ float ipp[3];
+ float dist;
+ float min = 0, max = 0;
+ bool first = true;
+ int n=0;
+ std::vector<float> distlist;
+
+ //!\todo rewrite this for loop.
+ for ( GdcmHeaderList::const_iterator
+ it = CoherentGdcmFileList.begin();
+ it != CoherentGdcmFileList.end(); ++it )
+ {
+ if( first )
+ {
+ (*it)->GetImageOrientationPatient( cosines );
- //You only have to do this once for all slices in the volume. Next, for
- //each slice, calculate the distance along the slice normal using the IPP
- //tag ("dist" is initialized to zero before reading the first slice) :
- normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
- normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
- normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
+ //You only have to do this once for all slices in the volume. Next,
+ // for each slice, calculate the distance along the slice normal
+ // using the IPP tag ("dist" is initialized to zero before reading
+ // the first slice) :
+ normal[0] = cosines[1]*cosines[5] - cosines[2]*cosines[4];
+ normal[1] = cosines[2]*cosines[3] - cosines[0]*cosines[5];
+ normal[2] = cosines[0]*cosines[4] - cosines[1]*cosines[3];
- ipp[0] = (*it)->GetXOrigin();
- ipp[1] = (*it)->GetYOrigin();
- ipp[2] = (*it)->GetZOrigin();
-
- dist = 0;
- for (int i = 0; i < 3; ++i)
- dist += normal[i]*ipp[i];
+ ipp[0] = (*it)->GetXOrigin();
+ ipp[1] = (*it)->GetYOrigin();
+ ipp[2] = (*it)->GetZOrigin();
+
+ dist = 0;
+ for ( int i = 0; i < 3; ++i )
+ {
+ dist += normal[i]*ipp[i];
+ }
- if( dist == 0 )
- {
- delete[] cosines;
- return false;
- }
+ if( dist == 0 )
+ {
+ delete[] cosines;
+ return false;
+ }
- distlist.push_back( dist );
+ distlist.push_back( dist );
- max = min = dist;
- first = false;
- }
- else {
- ipp[0] = (*it)->GetXOrigin();
- ipp[1] = (*it)->GetYOrigin();
- ipp[2] = (*it)->GetZOrigin();
+ max = min = dist;
+ first = false;
+ }
+ else
+ {
+ ipp[0] = (*it)->GetXOrigin();
+ ipp[1] = (*it)->GetYOrigin();
+ ipp[2] = (*it)->GetZOrigin();
- dist = 0;
- for (int i = 0; i < 3; ++i)
- dist += normal[i]*ipp[i];
+ dist = 0;
+ for ( int i = 0; i < 3; ++i )
+ {
+ dist += normal[i]*ipp[i];
+ }
+
+ if( dist == 0 )
+ {
+ delete[] cosines;
+ return false;
+ }
+
+ distlist.push_back( dist );
- if( dist == 0 )
- {
- delete[] cosines;
- return false;
+ min = (min < dist) ? min : dist;
+ max = (max > dist) ? max : dist;
}
+ ++n;
+ }
-
- distlist.push_back( dist );
-
- min = (min < dist) ? min : dist;
- max = (max > dist) ? max : dist;
- }
- n++;
- }
-
- //Then I order the slices according to the value "dist". Finally, once
- //I've read in all the slices, I calculate the z-spacing as the difference
- //between the "dist" values for the first two slices.
- std::vector<gdcmHeaderHelper*> CoherentGdcmFileVector(n);
- //CoherentGdcmFileVector.reserve( n );
- CoherentGdcmFileVector.resize( n );
- //assert( CoherentGdcmFileVector.capacity() >= n );
-
- float step = (max - min)/(n - 1);
- int pos;
- n = 0;
+ // Then I order the slices according to the value "dist". Finally, once
+ // I've read in all the slices, I calculate the z-spacing as the difference
+ // between the "dist" values for the first two slices.
+ GdcmHeaderVector CoherentGdcmFileVector(n);
+ // CoherentGdcmFileVector.reserve( n );
+ CoherentGdcmFileVector.resize( n );
+ // assert( CoherentGdcmFileVector.capacity() >= n );
+
+ float step = (max - min)/(n - 1);
+ int pos;
+ n = 0;
- //VC++ don't understand what scope is !! it -> it2
- for (std::list<gdcmHeaderHelper*>::iterator it2 = CoherentGdcmFileList.begin();
- it2 != CoherentGdcmFileList.end(); it2++, n++)
- {
+ //VC++ don't understand what scope is !! it -> it2
+ for (GdcmHeaderList::const_iterator it2 = CoherentGdcmFileList.begin();
+ it2 != CoherentGdcmFileList.end(); ++it2, ++n)
+ {
//2*n sort algo !!
//Assumption: all files are present (no one missing)
pos = (int)( fabs( (distlist[n]-min)/step) + .5 );
CoherentGdcmFileVector[pos] = *it2;
- }
+ }
- CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
-
- //VC++ don't understand what scope is !! it -> it3
- for (std::vector<gdcmHeaderHelper*>::iterator it3 = CoherentGdcmFileVector.begin();
- it3 != CoherentGdcmFileVector.end(); it3++)
- {
- CoherentGdcmFileList.push_back( *it3 );
- }
-
- distlist.clear();
- CoherentGdcmFileVector.clear();
- delete[] cosines;
+ CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
- return true;
+ //VC++ don't understand what scope is !! it -> it3
+ for (GdcmHeaderVector::const_iterator it3 = CoherentGdcmFileVector.begin();
+ it3 != CoherentGdcmFileVector.end(); ++it3)
+ {
+ CoherentGdcmFileList.push_back( *it3 );
+ }
+
+ distlist.clear();
+ CoherentGdcmFileVector.clear();
+ delete[] cosines;
+
+ return true;
}
-//Based on Image Number
+/**
+ * \ingroup gdcmHeader
+ * \brief sorts the images, according to their Image Number
+ * @return false only if the header is bugged !
+ */
-bool gdcmSerieHeaderHelper::ImageNumberOrdering() {
- int min, max, pos;
- int n = 0;//CoherentGdcmFileList.size(); //O(N) operation !!
- unsigned char *partition;
+bool gdcmSerieHeader::ImageNumberOrdering()
+{
+ int min, max, pos;
+ int n = 0;//CoherentGdcmFileList.size() is a O(N) operation !!
+ unsigned char *partition;
- std::list<gdcmHeaderHelper*>::iterator it = CoherentGdcmFileList.begin();
- min = max = (*it)->GetImageNumber();
-
- for (; it != CoherentGdcmFileList.end(); it++, n++)
- {
- pos = (*it)->GetImageNumber();
-
- //else
- min = (min < pos) ? min : pos;
- }
-
- //bzeros(partition, n); //Cette fonction est déconseillée, utilisez plutôt memset.
- partition = new unsigned char[n];
- memset(partition, 0, n);
-
- std::vector<gdcmHeaderHelper*> CoherentGdcmFileVector(n);
-
- //VC++ don't understand what scope is !! it -> it2
- for (std::list<gdcmHeaderHelper*>::iterator it2 = CoherentGdcmFileList.begin();
- it2 != CoherentGdcmFileList.end(); it2++)
- {
- pos = (*it2)->GetImageNumber();
- CoherentGdcmFileVector[pos - min] = *it2;
- partition[pos - min]++;
- }
+ GdcmHeaderList::const_iterator it = CoherentGdcmFileList.begin();
+ min = max = (*it)->GetImageNumber();
+
+ for (; it != CoherentGdcmFileList.end(); ++it, ++n)
+ {
+ pos = (*it)->GetImageNumber();
+
+ //else
+ min = (min < pos) ? min : pos;
+ }
+
+ //bzeros(partition, n); //Cette fonction est déconseillée, utilisez plutôt memset.
+ partition = new unsigned char[n];
+ memset(partition, 0, n);
+
+ GdcmHeaderVector CoherentGdcmFileVector(n);
+
+ //VC++ don't understand what scope is !! it -> it2
+ for (GdcmHeaderList::const_iterator it2 = CoherentGdcmFileList.begin();
+ it2 != CoherentGdcmFileList.end(); ++it2)
+ {
+ pos = (*it2)->GetImageNumber();
+ CoherentGdcmFileVector[pos - min] = *it2;
+ partition[pos - min]++;
+ }
- unsigned char mult = 1;
- for(int i=0; i<n ; i++)
- {
- mult *= partition[i];
- }
-
- //VC++ don't understand what scope is !! it -> it3
- CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
- for (std::vector<gdcmHeaderHelper*>::iterator it3 = CoherentGdcmFileVector.begin();
- it3 != CoherentGdcmFileVector.end(); it3++)
- {
- CoherentGdcmFileList.push_back( *it3 );
- }
- CoherentGdcmFileVector.clear();
+ unsigned char mult = 1;
+ for( int i=0; i<n ; i++ )
+ {
+ mult *= partition[i];
+ }
+
+ //VC++ don't understand what scope is !! it -> it3
+ CoherentGdcmFileList.clear(); //this doesn't delete list's element, node only
+ for ( GdcmHeaderVector::const_iterator it3 = CoherentGdcmFileVector.begin();
+ it3 != CoherentGdcmFileVector.end(); ++it3 )
+ {
+ CoherentGdcmFileList.push_back( *it3 );
+ }
+ CoherentGdcmFileVector.clear();
- delete[] partition;
- return (mult!=0);
+ delete[] partition;
+
+ return (mult != 0);
}
-bool gdcmSerieHeaderHelper::FileNameOrdering() {
- //using the sort
- //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
- return true;
+
+/**
+ * \ingroup gdcmHeader
+ * \brief sorts the images, according to their File Name
+ * @return false only if the header is bugged !
+ */
+bool gdcmSerieHeader::FileNameOrdering()
+{
+ //using the sort
+ //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
+ return true;
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff