Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2005/07/29 15:07:16 $
- Version: $Revision: 1.16 $
+ Date: $Date: 2005/10/26 06:23:37 $
+ Version: $Revision: 1.31 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <math.h>
#include <vector>
+#include <map>
#include <algorithm>
+#include <stdio.h> //for sscanf
namespace gdcm
{
+//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Constructor / Destructor
*/
SerieHelper::SerieHelper()
{
- // For all the File lists of the gdcm::Serie
- FileList *l = GetFirstCoherentFileList();
- while (l)
- {
- // For all the files of a File list
- for (gdcm::FileList::iterator it = l->begin();
- it != l->end();
- ++it)
- {
- delete *it;
- }
- l->clear();
- delete l;;
- l = GetNextCoherentFileList();
- }
+ ClearAll();
+ UserLessThanFunction = 0;
DirectOrder = true;
}
*/
SerieHelper::~SerieHelper()
{
- // For all the Coherent File lists of the gdcm::Serie
- FileList *l = GetFirstCoherentFileList();
+ ClearAll();
+}
+
+/**
+ * \brief Preventively, clear everything at constructor time.
+ * ( use it at destructor time.)
+ */
+void SerieHelper::ClearAll()
+{
+ // For all the 'Single SerieUID' Filesets that may already exist
+ FileList *l = GetFirstSingleSerieUIDFileSet();
while (l)
{
- // For all the files of a Coherent File list
- for (FileList::iterator it = l->begin();
- it != l->end();
- ++it)
+ // For all the gdcm::File of a File set
+ for (gdcm::FileList::iterator it = l->begin();
+ it != l->end();
+ ++it)
{
- delete *it;
+ (*it)->Delete(); // remove each entry
}
l->clear();
- delete l;
- l = GetNextCoherentFileList();
+ delete l; // remove the container
+ l = GetNextSingleSerieUIDFileSet();
}
}
// Public
/**
- * \brief add a gdcm::File to the list corresponding to its Serie UID
+ * \brief add a gdcm::File to the Fileset corresponding to its Serie UID
* @param filename Name of the file to deal with
*/
void SerieHelper::AddFileName(std::string const &filename)
{
// Create a DICOM file
- File *header = new File ();
+ File *header = File::New();
header->SetLoadMode(LoadMode);
header->SetFileName( filename );
header->Load();
if ( header->IsReadable() )
{
int allrules = 1;
- // First step the user has defined a set of rules for the DICOM file
+ // First step : the user defined a set of rules for the DICOM file
// he is looking for.
- // make sure the file correspond to his set of rules:
+ // Make sure the file corresponds to his set of rules:
-/*
- for(SerieRestrictions::iterator it = Restrictions.begin();
- it != Restrictions.end();
- ++it)
- {
- const Rule &r = *it;
- // doesn't compile (no matching function...).
- const std::string s;// = header->GetEntryValue( r.first );
- if ( !Util::DicomStringEqual(s, r.second.c_str()) )
- {
- // Argh ! This rule is unmatch let's just quit
- allrules = 0;
- break;
- }
- }
-*/
- // Just keep 'new style' for Rules
std::string s;
for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
it2 != ExRestrictions.end();
++it2)
{
const ExRule &r = *it2;
- s = header->GetEntryValue( r.group, r.elem );
+ s = header->GetEntryString( r.group, r.elem );
if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
{
- // Argh ! This rule is unmatch let's just quit
+ // Argh ! This rule is unmatched; let's just quit
+
allrules = 0;
break;
}
if ( allrules ) // all rules are respected:
{
- // Allright ! we have a found a DICOM that match the user expectation.
- // Let's add it !
+ // Allright! we have a found a DICOM that matches the user expectation.
+ // Let's add it!
// 0020 000e UI REL Series Instance UID
- const std::string &uid = header->GetEntryValue (0x0020, 0x000e);
+ const std::string &uid = header->GetEntryString(0x0020, 0x000e);
// if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
// no need here to do anything special
- if ( CoherentFileListHT.count(uid) == 0 )
+
+ if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
{
gdcmDebugMacro(" New Serie UID :[" << uid << "]");
// create a std::list in 'uid' position
- CoherentFileListHT[uid] = new FileList;
+ SingleSerieUIDFileSetHT[uid] = new FileList;
}
// Current Serie UID and DICOM header seems to match; add the file:
- CoherentFileListHT[uid]->push_back( header );
+ SingleSerieUIDFileSetHT[uid]->push_back( header );
}
else
{
- // at least one rule was unmatch we need to deallocate the file:
- delete header;
+ // at least one rule was unmatched we need to deallocate the file:
+ header->Delete();
}
}
else
{
gdcmWarningMacro("Could not read file: " << filename );
- delete header;
+ header->Delete();
}
}
/**
- * \brief add a gdcm::File to the first (and supposed to be unique) list
+ * \brief add a gdcm::File to the first (and supposed to be unique) file set
* of the gdcm::SerieHelper.
* \warning : this method should be used by aware users only!
+ * Passing a gdcm::File* has the same effect than passing a file name!
+ * \todo : decide which one is wrong (the method, or the commentary)!
+ * the following comment doesn't match the method :-(
* User is supposed to know the files he want to deal with
* and consider them they belong to the same Serie
* (even if their Serie UID is different)
// First step the user has defined a set of rules for the DICOM
// he is looking for.
// make sure the file correspond to his set of rules:
- for(SerieRestrictions::iterator it = Restrictions.begin();
- it != Restrictions.end();
- ++it)
+ for(SerieRestrictions::iterator it = Restrictions.begin();
+ it != Restrictions.end();
+ ++it)
{
const Rule &r = *it;
const std::string s;// = header->GetEntryValue( r.first );
// Serie UID of the gdcm::File* may be different.
// User is supposed to know what he wants
- if ( CoherentFileListHT.count(uid) == 0 )
+ if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
{
gdcmDebugMacro(" New Serie UID :[" << uid << "]");
// create a std::list in 'uid' position
- CoherentFileListHT[uid] = new FileList;
+ SingleSerieUIDFileSetHT[uid] = new FileList;
}
// Current Serie UID and DICOM header seems to match; add the file:
- CoherentFileListHT[uid]->push_back( header );
+ SingleSerieUIDFileSetHT[uid]->push_back( header );
}
// Even if a rule was unmatch we don't deallocate the gdcm::File:
}
* directory which would have a particular EchoTime==4.0.
* This method is a user level, value is not required to be formatted as a DICOM
* string
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value value to be checked to exclude File
+ * @param op operator we want to use to check
*/
void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
std::string const &value, int op)
}
#ifndef GDCM_LEGACY_REMOVE
-/**
- * \brief add a rules for restricting a DICOM file to be in the serie we are
- * trying to find. For example you can select only the DICOM file from a
- * directory which would have a particular EchoTime==4.0.
- * This method is a user level, value is not required to be formatted as a DICOM
- * string
- * @deprecated use : AddRestriction(uint16_t group, uint16_t elem,
- * std::string const &value, int op);
- */
void SerieHelper::AddRestriction(TagKey const &key, std::string const &value)
{
Rule r;
/**
* \brief Sets the root Directory
* @param dir Name of the directory to deal with
- * @param recursive whether we want explore recursively the Directory
+ * @param recursive whether we want explore recursively the root Directory
*/
void SerieHelper::SetDirectory(std::string const &dir, bool recursive)
{
}
/**
- * \brief Sorts the given File List
+ * \brief Sorts the given Fileset
* \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 :)
+ * BTW, this is also a Strategy, I don't know this is
+ * the best approach :)
*/
-void SerieHelper::OrderFileList(FileList *coherentFileList)
+void SerieHelper::OrderFileList(FileList *fileSet)
{
- if ( ImagePositionPatientOrdering( coherentFileList ) )
+
+ if ( SerieHelper::UserLessThanFunction )
+ {
+ UserOrdering( fileSet );
+ return;
+ }
+ else if ( ImagePositionPatientOrdering( fileSet ) )
{
return ;
}
- else if ( ImageNumberOrdering(coherentFileList ) )
+ else if ( ImageNumberOrdering(fileSet ) )
{
return ;
}
else
{
- FileNameOrdering(coherentFileList );
+ FileNameOrdering(fileSet );
}
}
/**
- * \brief Get the first List while visiting the CoherentFileListHT
- * @return The first FileList if found, otherwhise NULL
- */
+ * \brief Elementary coherence checking of the files with the same Serie UID
+ * Only sizes and pixel type are checked right now ...
+ */
+bool SerieHelper::IsCoherent(FileList *fileSet)
+{
+ if(fileSet->size() == 1)
+ return true;
+
+ FileList::const_iterator it = fileSet->begin();
+
+ int nX = (*it)->GetXSize();
+ int nY = (*it)->GetYSize();
+ int pixelSize = (*it)->GetPixelSize();
+
+ it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ if ( (*it)->GetXSize() != nX )
+ return false;
+ if ( (*it)->GetYSize() != nY )
+ return false;
+ if ( (*it)->GetPixelSize() != pixelSize )
+ return false;
+ // probabely more is to be checked (?)
+ }
+ return true;
+}
+
+#ifndef GDCM_LEGACY_REMOVE
+
FileList *SerieHelper::GetFirstCoherentFileList()
{
- ItListHt = CoherentFileListHT.begin();
- if ( ItListHt != CoherentFileListHT.end() )
- return ItListHt->second;
+ ItFileSetHt = SingleSerieUIDFileSetHT.begin();
+ if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
+ return ItFileSetHt->second;
return NULL;
}
+
+FileList *SerieHelper::GetNextCoherentFileList()
+{
+ gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
+
+ ++ItFileSetHt;
+ if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
+ return ItFileSetHt->second;
+ return NULL;
+}
+
+
+FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
+{
+ if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
+ return 0;
+ return SingleSerieUIDFileSetHT[SerieUID];
+}
+#endif
+
+
/**
- * \brief Get the next List while visiting the CoherentFileListHT
- * \note : meaningfull only if GetFirstCoherentFileList() already called
- * @return The next FileList if found, otherwhise NULL
+ * \brief Get the first Fileset while visiting the SingleSerieUIDFileSetmap
+ * @return The first FileList (SingleSerieUIDFileSet) if found, otherwhise 0
*/
-FileList *SerieHelper::GetNextCoherentFileList()
+FileList *SerieHelper::GetFirstSingleSerieUIDFileSet()
{
- gdcmAssertMacro (ItListHt != CoherentFileListHT.end());
+ ItFileSetHt = SingleSerieUIDFileSetHT.begin();
+ if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
+ return ItFileSetHt->second;
+ return NULL;
+}
+
+/**
+ * \brief Get the next Fileset while visiting the SingleSerieUIDFileSetmap
+ * \note : meaningfull only if GetNextSingleSerieUIDFileSet() already called
+ * @return The next FileList (SingleSerieUIDFileSet) if found, otherwhise 0
+ */
+FileList *SerieHelper::GetNextSingleSerieUIDFileSet()
+{
+ gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
- ++ItListHt;
- if ( ItListHt != CoherentFileListHT.end() )
- return ItListHt->second;
+ ++ItFileSetHt;
+ if ( ItFileSetHt != SingleSerieUIDFileSetHT.end() )
+ return ItFileSetHt->second;
return NULL;
}
/**
- * \brief Get the Coherent Files list according to its Serie UID
- * @param SerieUID SerieUID
- * \return pointer to the Coherent Files list if found, otherwhise NULL
+ * \brief Get the SingleSerieUIDFileSet according to its Serie UID
+ * @param SerieUID SerieUID to retrieve
+ * \return pointer to the FileList (SingleSerieUIDFileSet) if found, otherwhise 0
*/
-FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
+FileList *SerieHelper::GetSingleSerieUIDFileSet(std::string SerieUID)
{
- if ( CoherentFileListHT.count(SerieUID) == 0 )
+ if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
return 0;
- return CoherentFileListHT[SerieUID];
+ return SingleSerieUIDFileSetHT[SerieUID];
+}
+
+/**
+ * \brief Splits a Single SerieUID Fileset according to the Orientations
+ * @param fileSet File Set to be splitted
+ * \return std::map of 'Xcoherent' File sets
+ */
+
+XCoherentFileSetmap SerieHelper::SplitOnOrientation(FileList *fileSet)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 )
+ return CoherentFileSet;
+ float iop[6];
+
+ std::string strOrient;
+ std::ostringstream ossOrient;
+ FileList::const_iterator it = fileSet->begin();
+ it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ // Information is in :
+ // 0020 0037 : Image Orientation (Patient) or
+ // 0020 0035 : Image Orientation (RET)
+
+ // Let's build again the 'cosines' string, to be sure of it's format
+ (*it)->GetImageOrientationPatient(iop);
+
+ ossOrient << iop[0];
+ for (int i = 1; i < 6; i++)
+ {
+ ossOrient << "\\";
+ ossOrient << iop[i];
+ }
+ strOrient = ossOrient.str();
+ ossOrient.str("");
+ // FIXME : is it a 'cleaner' way to initialize an ostringstream?
+
+ if ( CoherentFileSet.count(strOrient) == 0 )
+ {
+ gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
+ // create a File set in 'orientation' position
+ CoherentFileSet[strOrient] = new FileList;
+ }
+ // Current Orientation and DICOM header match; add the file:
+ CoherentFileSet[strOrient]->push_back( (*it) );
+ }
+ return CoherentFileSet;
+}
+
+/**
+ * \brief Splits a 'Single SerieUID' Fileset according to the Positions
+ * @param fileSet File Set to be splitted
+ * \return std::map of 'Xcoherent' File sets
+ */
+
+XCoherentFileSetmap SerieHelper::SplitOnPosition(FileList *fileSet)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 )
+ return CoherentFileSet;
+ float pos[3];
+ std::string strImPos; // read on disc
+ std::ostringstream ossPosition;
+ std::string strPosition; // re computed
+ FileList::const_iterator it = fileSet->begin();
+ it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ // Information is in :
+ // 0020,0032 : Image Position Patient
+ // 0020,0030 : Image Position (RET)
+
+ strImPos = (*it)->GetEntryString(0x0020,0x0032);
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
+ // User wants to split on the 'Position'
+ // No 'Position' info found.
+ // We return an empty Htable !
+ return CoherentFileSet;
+ }
+ }
+
+ if ( sscanf( strImPos.c_str(), "%f \\%f \\%f ",
+ &pos[0], &pos[1], &pos[2]) != 3 )
+ {
+ gdcmWarningMacro( "Wrong number for Position : ["
+ << strImPos << "]" );
+ return CoherentFileSet;
+ }
+
+ // Let's build again the 'position' string, to be sure of it's format
+
+ ossPosition << pos[0];
+ for (int i = 1; i < 3; i++)
+ {
+ ossPosition << "\\";
+ ossPosition << pos[i];
+ }
+ strPosition = ossPosition.str();
+
+ if ( CoherentFileSet.count(strPosition) == 0 )
+ {
+ gdcmDebugMacro(" New Position :[" << strPosition << "]");
+ // create a File set in 'position' position
+ CoherentFileSet[strPosition] = new FileList;
+ }
+ // Current Position and DICOM header match; add the file:
+ CoherentFileSet[strPosition]->push_back( (*it) );
+ }
+ return CoherentFileSet;
+}
+
+/**
+ * \brief Splits a 'Single SerieUID' File set Coherent according to the
+ * value of a given Tag
+ * @param fileSet File Set to be splitted
+ * @param group group number of the target Element
+ * @param elem element number of the target Element
+ * \return std::map of 'Xcoherent' File sets
+ */
+
+XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
+ uint16_t group, uint16_t elem)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 )
+ return CoherentFileSet;
+
+ std::string strTagValue; // read on disc
+
+ FileList::const_iterator it = fileSet->begin();
+ it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ // Information is in :
+ // 0020,0032 : Image Position Patient
+ // 0020,0030 : Image Position (RET)
+
+ strTagValue = (*it)->GetEntryString(group,elem);
+
+ if ( CoherentFileSet.count(strTagValue) == 0 )
+ {
+ gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
+ // create a File set in 'position' position
+ CoherentFileSet[strTagValue] = new FileList;
+ }
+ // Current Tag value and DICOM header match; add the file:
+ CoherentFileSet[strTagValue]->push_back( (*it) );
+ }
+ return CoherentFileSet;
}
//-----------------------------------------------------------------------------
* We may order, considering :
* -# Image Position Patient
* -# Image Number
+ * -# File Name
* -# More to come :-)
- * WARNING : FileList = std::vector<File* >
+ * \note : FileList = std::vector<File* >
* @param fileList Coherent File list (same Serie UID) to sort
* @return false only if the header is bugged !
*/
// 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) :
+ // using the IPP ("Image Position Patient") 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];
// Find out if min/max are coherent
if ( min == max )
- {
- gdcmWarningMacro( "Looks like all images have the exact same image position."
- << "No PositionPatientOrdering sort performed" );
+ {
+ gdcmWarningMacro("Looks like all images have the exact same image position"
+ << ". No PositionPatientOrdering sort performed" );
return false;
- }
+ }
float step = (max - min)/(n - 1);
int pos;
CoherentFileVector[pos] = *it2;
else
{
- gdcmWarningMacro( "At least 2 files with same position. No PositionPatientOrdering sort performed");
+ gdcmWarningMacro( "At least 2 files with same position."
+ << " No PositionPatientOrdering sort performed");
return false;
}
}
{
return file1->GetImageNumber() > file2->GetImageNumber();
}
+
/**
* \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 fileList Coherent File list (same Serie UID) to sort
+ * @param fileList File set (same Serie UID) to sort
* @return false if non bona fide stuff encountered
*/
bool SerieHelper::ImageNumberOrdering(FileList *fileList)
// Find out if image numbers are coherent (consecutive)
if ( min == max || max == 0 || max >= (n+min) )
{
- gdcmWarningMacro( " 'Image numbers' not coherent. No ImageNumberOrdering sort performed.");
+ gdcmWarningMacro( " 'Image numbers' not coherent. "
+ << " No ImageNumberOrdering sort performed.");
return false;
}
if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberLessThan );
+ std::sort(fileList->begin(), fileList->end(),
+ SerieHelper::ImageNumberLessThan );
else
- std::sort(fileList->begin(), fileList->end(), SerieHelper::ImageNumberGreaterThan );
+ std::sort(fileList->begin(), fileList->end(),
+ SerieHelper::ImageNumberGreaterThan );
return true;
}
bool SerieHelper::FileNameLessThan(File *file1, File *file2)
{
- return file1->GetFileName() < file2->GetFileName();
+ return file1->GetFileName() < file2->GetFileName();
}
bool SerieHelper::FileNameGreaterThan(File *file1, File *file2)
{
- return file1->GetFileName() > file2->GetFileName();
+ return file1->GetFileName() > file2->GetFileName();
}
/**
* \brief sorts the images, according to their File Name
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameLessThan);
+ std::sort(fileList->begin(), fileList->end(),
+ SerieHelper::FileNameLessThan);
else
- std::sort(fileList->begin(), fileList->end(), SerieHelper::FileNameGreaterThan);
+ std::sort(fileList->begin(), fileList->end(),
+ SerieHelper::FileNameGreaterThan);
+
+ return true;
+}
+/**
+ * \brief sorts the images, according to user supplied function
+ * @param fileList Coherent File list (same Serie UID) to sort
+ * @return false only if the header is bugged !
+ */
+bool SerieHelper::UserOrdering(FileList *fileList)
+{
+ std::sort(fileList->begin(), fileList->end(),
+ SerieHelper::UserLessThanFunction);
+ if (!DirectOrder)
+ {
+ std::reverse(fileList->begin(), fileList->end());
+ }
return true;
}
void SerieHelper::Print(std::ostream &os, std::string const &indent)
{
// For all the Coherent File lists of the gdcm::Serie
- CoherentFileListmap::iterator itl = CoherentFileListHT.begin();
- if ( itl == CoherentFileListHT.end() )
+ SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
+ if ( itl == SingleSerieUIDFileSetHT.end() )
{
- gdcmWarningMacro( "No Coherent File list found" );
+ gdcmWarningMacro( "No SingleSerieUID File set found" );
return;
}
- while (itl != CoherentFileListHT.end())
+ while (itl != SingleSerieUIDFileSetHT.end())
{
os << "Serie UID :[" << itl->first << "]" << std::endl;
- // For all the files of a Coherent File list
+ // For all the files of a SingleSerieUID File set
for (FileList::iterator it = (itl->second)->begin();
it != (itl->second)->end();
++it)
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff