+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: gdcmSerieHeader.cxx,v $
- Language: C++
- Date: $Date: 2005/02/01 19:05:53 $
- Version: $Revision: 1.21 $
-
- 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.html 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 "gdcmSerieHeader.h"
-#include "gdcmDirList.h"
-#include "gdcmFile.h"
-#include "gdcmDebug.h"
-
-#include <math.h>
-#include <algorithm>
-#include <vector>
-
-namespace gdcm
-{
-typedef std::list<File* > GdcmFileList;
-typedef std::vector<File* > GdcmFileVector;
-
-//-----------------------------------------------------------------------------
-// Constructor / Destructor
-/**
- * \brief Constructor from a given SerieHeader
- */
-SerieHeader::SerieHeader()
-{
- // For all the File lists of the gdcm::Serie
- GdcmFileList *l = GetFirstCoherentFileList();
- while (l)
- {
- // For all the files of a File list
- for (GdcmFileList::iterator it = l->begin();
- it != l->end();
- ++it)
- {
- delete *it;
- }
- l->clear();
- delete l;;
- l = GetNextCoherentFileList();
- }
-}
-
-/**
- * \brief Canonical destructor.
- */
-SerieHeader::~SerieHeader()
-{
- // For all the Coherent File lists of the gdcm::Serie
- GdcmFileList *l = GetFirstCoherentFileList();
- while (l)
- {
- // For all the files of a Coherent File list
- for (GdcmFileList::iterator it = l->begin();
- it != l->end();
- ++it)
- {
- delete *it;
- }
- l->clear();
- delete l;
- l = GetNextCoherentFileList();
- }
-}
-
-//-----------------------------------------------------------------------------
-
-//-----------------------------------------------------------------------------
-
-// Public
-/**
- * \brief add a gdcm::File to the list corresponding to its Serie UID
- * @param filename Name of the file to deal with
- */
-void SerieHeader::AddFileName(std::string const &filename)
-{
- //directly use string and not const char*:
- File *header = new File( filename );
- if( header->IsReadable() )
- {
- // 0020 000e UI REL Series Instance UID
- std::string uid = header->GetEntryValue (0x0020, 0x000e);
- // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
- // no need here to do anything special
-
- if ( CoherentGdcmFileListHT.count(uid) == 0 )
- {
- gdcmVerboseMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- CoherentGdcmFileListHT[uid] = new GdcmFileList;
- }
- // Current Serie UID and DICOM header seems to match add the file:
- CoherentGdcmFileListHT[uid]->push_back( header );
- }
- else
- {
- gdcmVerboseMacro("Could not read file: " << filename );
- delete header;
- }
-}
-
-/**
- * \brief Sets the root Directory
- * @param dir Name of the directory to deal with
- * @param recursive whether we want explore recursively the Directory
- */
-void SerieHeader::SetDirectory(std::string const &dir, bool recursive)
-{
- DirList dirList(dir, recursive); // OS specific
-
- DirListType filenames_list = dirList.GetFilenames();
- for( DirListType::const_iterator it = filenames_list.begin();
- it != filenames_list.end(); ++it)
- {
- AddFileName( *it );
- }
-}
-
-/**
- * \brief Sorts the given 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 SerieHeader::OrderGdcmFileList(GdcmFileList *CoherentGdcmFileList)
-{
- if( ImagePositionPatientOrdering( CoherentGdcmFileList ) )
- {
- return ;
- }
- else if( ImageNumberOrdering(CoherentGdcmFileList ) )
- {
- return ;
- }
- else
- {
- FileNameOrdering(CoherentGdcmFileList );
- }
-}
-
-/**
- * \brief Get the first List while visiting the CoherentFileListHT
- * @return The first GdcmFileList if found, otherwhise NULL
- */
- std::list<File* > *SerieHeader::GetFirstCoherentFileList()
-// Why doesn't it compile ?!?
-//GdcmFileList *SerieHeader::GetFirstCoherentFileList()
-{
- ItListHt = CoherentGdcmFileListHT.begin();
- if( ItListHt != CoherentGdcmFileListHT.end() )
- return ItListHt->second;
- return NULL;
-}
-
-/**
- * \brief Get the next List while visiting the CoherentFileListHT
- * \note : meaningfull only if GetFirstCoherentFileList already called
- * @return The next GdcmFileList if found, otherwhise NULL
- */
-std::list<File* > *SerieHeader::GetNextCoherentFileList()
-{
- gdcmAssertMacro (ItListHt != CoherentGdcmFileListHT.end());
-
- ++ItListHt;
- if ( ItListHt != CoherentGdcmFileListHT.end() )
- return ItListHt->second;
- return NULL;
-}
-
-/**
- * \brief Get the Coherent Files list according to its Serie UID
- * @param SerieUID SerieUID
- * \return pointer to the Coherent Filseslist if found, otherwhise NULL
- */
-GdcmFileList *SerieHeader::GetCoherentFileList(std::string SerieUID)
-{
- if ( CoherentGdcmFileListHT.count(SerieUID) == 0 )
- return 0;
- return CoherentGdcmFileListHT[SerieUID];
-}
-
-//-----------------------------------------------------------------------------
-// Protected
-
-//-----------------------------------------------------------------------------
-// Private
-/**
- * \brief sorts the images, according to their Patient Position
- * We may order, considering :
- * -# Image Position Patient
- * -# Image Number
- * -# More to come :-)
- * @param CoherentGdcmFileList Coherent File list (same Serie UID) to sort
- * @return false only if the header is bugged !
- */
-bool SerieHeader::ImagePositionPatientOrdering(
- GdcmFileList *CoherentGdcmFileList )
-//based on Jolinda's algorithm
-{
- //iop is calculated based on the file file
- float cosines[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 ( GdcmFileList::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];
-
- 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 )
- {
- return false;
- }
-
- distlist.push_back( dist );
-
- 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];
- }
-
- if( dist == 0 )
- {
- return false;
- }
-
- 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.
- GdcmFileVector CoherentGdcmFileVector(n);
- // CoherentGdcmFileVector.reserve( n );
- CoherentGdcmFileVector.resize( n );
- // gdcmAssertMacro( CoherentGdcmFileVector.capacity() >= n );
-
- float step = (max - min)/(n - 1);
- int pos;
- n = 0;
-
- //VC++ don't understand what scope is !! it -> it2
- for (GdcmFileList::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 );
-
- // a Dicom 'Serie' may contain scout views
- // and images may have differents directions
- // -> More than one may have the same 'pos'
- // Sorting has then NO meaning !
- if (CoherentGdcmFileVector[pos]==NULL)
- CoherentGdcmFileVector[pos] = *it2;
- else
- {
- gdcmVerboseMacro( "2 files same position");
- return false;
- }
- }
-
- CoherentGdcmFileList->clear(); // doesn't delete list elements, only node
-
- //VC++ don't understand what scope is !! it -> it3
- for (GdcmFileVector::const_iterator it3 = CoherentGdcmFileVector.begin();
- it3 != CoherentGdcmFileVector.end(); ++it3)
- {
- CoherentGdcmFileList->push_back( *it3 );
- }
-
- distlist.clear();
- CoherentGdcmFileVector.clear();
-
- return true;
-}
-
-/**
- * \brief sorts the images, according to their Image Number
- * \note Works only on bona fide files (i.e image number is a character string
- * corresponding to an integer)
- * within a bona fide serie (i.e image numbers are consecutive)
- * @param CoherentGdcmFileList Coherent File list (same Serie UID) to sort
- * @return false if non nona fide stuff encountered
- */
-bool SerieHeader::ImageNumberOrdering(GdcmFileList *CoherentGdcmFileList)
-{
- int min, max, pos;
- int n = 0;//CoherentGdcmFileList.size() is a O(N) operation
-
- GdcmFileList::const_iterator it = CoherentGdcmFileList->begin();
- min = max = (*it)->GetImageNumber();
-
- for (; it != CoherentGdcmFileList->end(); ++it, ++n)
- {
- pos = (*it)->GetImageNumber();
- min = (min < pos) ? min : pos;
- max = (max > pos) ? max : pos;
- }
-
- // Find out if image numbers are coherent (consecutive)
- if( min == max || max == 0 || max >= (n+min))
- return false;
-
- unsigned char *partition = new unsigned char[n];
- memset(partition, 0, n);
-
- GdcmFileVector CoherentGdcmFileVector(n);
-
- for (it = CoherentGdcmFileList->begin();
- it != CoherentGdcmFileList->end(); ++it)
- {
- pos = (*it)->GetImageNumber();
- CoherentGdcmFileVector[pos - min] = *it;
- partition[pos - min]++;
- }
-
- //VC++ doesn't understand what scope is, it -> it3
- CoherentGdcmFileList->clear(); // doesn't delete list elements, only nodes
- for ( GdcmFileVector::const_iterator it3 = CoherentGdcmFileVector.begin();
- it3 != CoherentGdcmFileVector.end(); ++it3 )
- {
- CoherentGdcmFileList->push_back( *it3 );
- }
- CoherentGdcmFileVector.clear();
- delete[] partition;
-
- return true;
-}
-
-/**
- * \brief sorts the images, according to their File Name
- * @param CoherentGdcmFileList Coherent File list (same Serie UID) to sort
- * @return false only if the header is bugged !
- */
-bool SerieHeader::FileNameOrdering(GdcmFileList *)
-{
- //TODO using the sort
- //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
- return true;
-}
-
-//-----------------------------------------------------------------------------
-// Print
-/**
- * \brief Canonical printer.
- */
-void SerieHeader::Print()
-{
- // For all the Coherent File lists of the gdcm::Serie
- CoherentFileListmap::iterator itl = CoherentGdcmFileListHT.begin();
- if ( itl == CoherentGdcmFileListHT.end() )
- {
- gdcmVerboseMacro( "No Coherent File list found" );
- return;
- }
- while (itl != CoherentGdcmFileListHT.end())
- {
- std::cout << "Serie UID :[" << itl->first << "]" << std::endl;
-
- // For all the files of a Coherent File list
- for (GdcmFileList::iterator it = (itl->second)->begin();
- it != (itl->second)->end();
- ++it)
- {
- std::cout << " --- " << (*it)->GetFileName() << std::endl;
- }
- ++itl;
- }
-}
-
-//-----------------------------------------------------------------------------
-} // end namespace gdcm
+++ /dev/null
-/*=========================================================================
-
- Program: gdcm
- Module: $RCSfile: gdcmSerieHeader.h,v $
- Language: C++
- Date: $Date: 2005/01/30 17:22:55 $
- Version: $Revision: 1.9 $
-
- 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.html 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.
-
-=========================================================================*/
-
-#ifndef GDCMSERIEHEADER_H
-#define GDCMSERIEHEADER_H
-
-#include "gdcmCommon.h"
-#include <list>
-#include <map>
-namespace gdcm
-{
-class File;
-
-//-----------------------------------------------------------------------------
-/**
- * \brief
- * - This class should be used for a stack of 2D dicom images.
- * It allows to explore (recursively or not) a directory and
- * makes a set of 'Coherent Files' list (coherent : same Serie UID)
- * It allows to sort any of the Coherent File list on the image postion
- */
-class GDCM_EXPORT SerieHeader
-{
-public:
- typedef std::list<File* > GdcmFileList;
- typedef std::map<std::string, GdcmFileList *> CoherentFileListmap;
-
- SerieHeader();
- ~SerieHeader();
- void Print();
-
- /// \todo should return bool or throw error ?
- void AddFileName(std::string const &filename);
- void SetDirectory(std::string const &dir, bool recursive=false);
- void OrderGdcmFileList(GdcmFileList *CoherentGdcmFileList);
-
- /// \brief Gets the FIRST *coherent* File List.
- /// Deprecated; kept not to break the API
- /// \note Caller must call OrderGdcmFileList first
- /// @return the (first) *coherent* File List
- const GdcmFileList &GetGdcmFileList() { return
- *CoherentGdcmFileListHT.begin()->second; }
-
- GdcmFileList *GetFirstCoherentFileList();
- GdcmFileList *GetNextCoherentFileList();
- GdcmFileList *GetCoherentFileList(std::string SerieUID);
-
-private:
- bool ImagePositionPatientOrdering(GdcmFileList *CoherentGdcmFileList);
- bool ImageNumberOrdering(GdcmFileList *CoherentGdcmFileList);
- bool FileNameOrdering(GdcmFileList *CoherentGdcmFileList);
-
- CoherentFileListmap CoherentGdcmFileListHT;
- CoherentFileListmap::iterator ItListHt;
-};
-
-} // end namespace gdcm
-
-//-----------------------------------------------------------------------------
-#endif
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