--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmSerieHelper.cxx,v $
+ Language: C++
+ Date: $Date: 2005/02/02 15:12:09 $
+ Version: $Revision: 1.1 $
+
+ 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 "gdcmSerieHelper.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 SerieHelper
+ */
+SerieHelper::SerieHelper()
+{
+ // 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.
+ */
+SerieHelper::~SerieHelper()
+{
+ // 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 SerieHelper::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 SerieHelper::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 SerieHelper::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* > *SerieHelper::GetFirstCoherentFileList()
+// Why doesn't it compile ?!?
+//GdcmFileList *SerieHelper::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* > *SerieHelper::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 *SerieHelper::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 SerieHelper::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 SerieHelper::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 SerieHelper::FileNameOrdering(GdcmFileList *)
+{
+ //TODO using the sort
+ //sort(CoherentGdcmFileList.begin(), CoherentGdcmFileList.end());
+ return true;
+}
+
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \brief Canonical printer.
+ */
+void SerieHelper::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: gdcmSerieHelper.h,v $
+ Language: C++
+ Date: $Date: 2005/02/02 15:12:09 $
+ Version: $Revision: 1.1 $
+
+ 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 GDCMSERIEHELPER_H
+#define GDCMSERIEHELPER_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 SerieHelper
+{
+public:
+ typedef std::list<File* > GdcmFileList;
+ typedef std::map<std::string, GdcmFileList *> CoherentFileListmap;
+
+ SerieHelper();
+ ~SerieHelper();
+ 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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