Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2005/11/25 13:56:32 $
- Version: $Revision: 1.36 $
+ Date: $Date: 2011/04/04 17:33:58 $
+ Version: $Revision: 1.73 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
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 "gdcmDictEntry.h" // for TranslateToKey
+//#include "gdcmDictEntry.h" // for TranslateToKey : no more !
#include "gdcmDebug.h"
#include "gdcmUtil.h"
#include <math.h>
#include <vector>
-#include <map>
#include <algorithm>
+#include <map>
#include <stdio.h> //for sscanf
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
-//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Constructor / Destructor
ClearAll();
UserLessThanFunction = 0;
DirectOrder = true;
+ DropDuplicatePositions = false;
}
/**
FileList *l = GetFirstSingleSerieUIDFileSet();
while (l)
{
- // For all the gdcm::File of a File set
- for (gdcm::FileList::iterator it = l->begin();
+ // For all the GDCM_NAME_SPACE::File of a File set
+ for (GDCM_NAME_SPACE::FileList::iterator it = l->begin();
it != l->end();
++it)
{
delete l; // remove the container
l = GetNextSingleSerieUIDFileSet();
}
+ // Need to clear that too:
+ SingleSerieUIDFileSetHT.clear();
}
//-----------------------------------------------------------------------------
// Public
/**
- * \brief add a gdcm::File to the Fileset corresponding to its Serie UID
+ * \brief add a GDCM_NAME_SPACE::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)
if ( header->IsReadable() )
{
- int allrules = 1;
- // First step : the user defined a set of rules for the DICOM file
- // he is looking for.
- // Make sure the file corresponds to his set of rules:
-
- std::string s;
- for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
- it2 != ExRestrictions.end();
- ++it2)
- {
- const ExRule &r = *it2;
- s = header->GetEntryString( r.group, r.elem );
- if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
- {
- // 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 matches the user expectation.
- // Let's add it!
-
- // 0020 000e UI REL Series Instance UID
- 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 ( SingleSerieUIDFileSetHT.count(uid) == 0 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- SingleSerieUIDFileSetHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- SingleSerieUIDFileSetHT[uid]->push_back( header );
- }
- else
+ if ( !AddFile( header ) )
{
// at least one rule was unmatched we need to deallocate the file:
header->Delete();
}
/**
- * \brief add a gdcm::File to the first (and supposed to be unique) file set
- * of the gdcm::SerieHelper.
+ * \brief add a GDCM_NAME_SPACE::File to the first (and supposed to be unique) file set
+ * of the GDCM_NAME_SPACE::SerieHelper.
* \warning : this method should be used by aware users only!
- * Passing a gdcm::File* has the same effect than passing a file name!
+ * Passing a GDCM_NAME_SPACE::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
* vtkGdcmReader parsing twice the same files.
* *no* coherence check is performed, but those specified
* by SerieHelper::AddRestriction()
- * @param header gdcm::File* of the file to deal with
+ * @param header GDCM_NAME_SPACE::File* of the file to deal with
+ * @return true if file was added, false if file was rejected
*/
-void SerieHelper::AddGdcmFile(File *header)
-{
- int allrules = 1;
- // 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)
+bool SerieHelper::AddFile(File *header)
+{
+ int allrules = 1;
+ // 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:
+
+ std::string s;
+ for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
+ it2 != ExRestrictions.end();
+ ++it2)
+ {
+ const ExRule &r = *it2;
+ s = header->GetEntryString( r.group, r.elem );
+ if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
{
- const Rule &r = *it;
- const std::string s;// = header->GetEntryString( r.first );
- if ( !Util::DicomStringEqual(s, r.second.c_str()) )
- {
- // Argh ! This rule is unmatch let's just quit
- allrules = 0;
- break;
- }
+ // 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 !
+ }
- const std::string &uid = "0";
- // Serie UID of the gdcm::File* may be different.
- // User is supposed to know what he wants
+ if ( allrules ) // all rules are respected:
+ {
+ // Allright! we have a found a DICOM that matches the user expectation.
+ // Let's add it to the specific 'id' which by default is uid (Serie UID)
+ // but can be `refined` by user with more paramater (see AddRestriction(g,e))
+
+ std::string id = CreateUniqueSeriesIdentifier( header );
+ // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
+ // no need here to do anything special
- if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- SingleSerieUIDFileSetHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- SingleSerieUIDFileSetHT[uid]->push_back( header );
+ if ( SingleSerieUIDFileSetHT.count(id) == 0 )
+ {
+ gdcmDebugMacro(" New/gdcmSerieHelper.cxx Serie UID :[" << id << "]");
+ // create a std::list in 'id' position
+ SingleSerieUIDFileSetHT[id] = new FileList;
}
- // Even if a rule was unmatch we don't deallocate the gdcm::File:
+ // Current Serie UID and DICOM header seems to match add the file:
+ SingleSerieUIDFileSetHT[id]->push_back( header );
+ }
+ else
+ {
+ // one rule not matched, tell user:
+ return false;
+ }
+ return true;
}
/**
- * \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
+ * \brief add a rule for restricting a DICOM file to be in the serie we are
+ * trying to find. For example you can select only the DICOM files 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
+ * \todo find a trick to allow user to say if he wants the Rectrictions
+ * to be *ored* (and not only *anded*)
* @param key Target tag we want restrict on a given value
* @param value value to be checked to exclude File
* @param op operator we want to use to check
ExRestrictions.push_back( r );
}
+void SerieHelper::AddRestriction(TagKey const &key)
+{
+ ExRule r;
+ r.group = key[0];
+ r.elem = key[1];
+ ExRefine.push_back( r );
+}
+
+//#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief add a rule for restricting a DICOM file to be in the serie we are
+ * trying to find. For example you can select only the DICOM files 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
+ * @param group tag group number we want restrict on a given value
+ * @param elem tag element number we want restrict on a given value
+ * @param value value to be checked to exclude File
+ * @param op operator we want to use to check
+ * @deprecated use : AddRestriction(TagKey const &key,
+ * std::string const &value, int op);
+ */
+
+void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+ std::string const &value, int op)
+{
+ TagKey t(group, elem);
+ AddRestriction(t, value, op);
+}
+
+//#endif
+
+/**
+ * \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
+ * that ensures (hope so) File consistency (Series Instance UID doesn't)
+ * @param group tag group number we want restrict on a given value
+ * @param elem tag element number we want restrict on a given value
+ * @param convert wether we want 'convertion', to allow further ordering
+ * e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
+ */
+void SerieHelper::AddSeriesDetail(uint16_t group, uint16_t elem, bool convert)
+{
+ ExDetail d;
+ d.group = group;
+ d.elem = elem;
+ d.convert = convert;
+ ExDetails.push_back( d );
+}
/**
* \brief Sets the root Directory
* @param dir Name of the directory to deal with
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)
+ {
+ // std::cout << "-----------------------------filename [" << *it << "]"
+ // << std::endl;
+ gdcmDebugMacro("filename [" << *it << "]" );
+ AddFileName( *it );
+ }
+}
+
+/**
+ * \brief Sets the DicomDirSerie
+ * @param se DicomDirSerie to deal with
+ */
+void SerieHelper::SetDicomDirSerie(DicomDirSerie *se)
+{
+ DirList dirList(se);
DirListType filenames_list = dirList.GetFilenames();
for( DirListType::const_iterator it = filenames_list.begin();
*/
void SerieHelper::OrderFileList(FileList *fileSet)
{
-
+ // Only computed during ImagePositionPatientOrdering
+ // (need to sort the FileList using IPP and IOP !)
+ ZSpacing = -1.0;
+
if ( SerieHelper::UserLessThanFunction )
{
+ gdcmDebugMacro("Use UserLessThanFunction");
UserOrdering( fileSet );
return;
}
else if ( ImagePositionPatientOrdering( fileSet ) )
- {
+ {
+ gdcmDebugMacro("ImagePositionPatientOrdering succeeded");
return ;
}
else if ( ImageNumberOrdering(fileSet ) )
{
+ gdcmDebugMacro("ImageNumberOrdering succeeded");
return ;
}
else
{
+ gdcmDebugMacro("Use FileNameOrdering");
FileNameOrdering(fileSet );
}
}
return false;
if ( (*it)->IsSignedPixelData() != signedPixelData )
return false;
- // probabely more is to be checked (?)
+ // probabely more is to be checked (?)
}
return true;
}
-#ifndef GDCM_LEGACY_REMOVE
-
+//#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * @return The first FileList if found, otherwhise NULL
+ */
+ /*
FileList *SerieHelper::GetFirstCoherentFileList()
{
ItFileSetHt = SingleSerieUIDFileSetHT.begin();
return ItFileSetHt->second;
return NULL;
}
-
-
+*/
+/**
+ * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * \note : meaningfull only if GetFirstCoherentFileList() already called
+ * @return The next FileList if found, otherwhise NULL
+ */
+ /*
FileList *SerieHelper::GetNextCoherentFileList()
{
gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
return ItFileSetHt->second;
return NULL;
}
+*/
-
+/**
+ * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * @param SerieUID SerieUID
+ * \return pointer to the FileList if found, otherwhise NULL
+ */
+ /*
FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
{
if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
return 0;
return SingleSerieUIDFileSetHT[SerieUID];
}
-#endif
+*/
+//#endif
/**
XCoherentFileSetmap CoherentFileSet;
int nb = fileSet->size();
- if (nb == 0 )
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnOrientation");
return CoherentFileSet;
- double iop[6];
+ }
+ float iop[6];
std::string strOrient;
- std::ostringstream ossOrient;
+ std::ostringstream ossOrient;
+
FileList::const_iterator it = fileSet->begin();
- it ++;
for ( ;
it != fileSet->end();
++it)
// 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
+ // Let's build again the 'cosines' string, to be sure of its format
(*it)->GetImageOrientationPatient(iop);
ossOrient << iop[0];
}
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;
+ gdcmDebugMacro(" CoherentFileSet[strOrient]" << strOrient << "created");
}
// Current Orientation and DICOM header match; add the file:
CoherentFileSet[strOrient]->push_back( (*it) );
- }
+ gdcmDebugMacro(" CoherentFileSet[strOrient]" << "pushed back")
+ }
return CoherentFileSet;
}
XCoherentFileSetmap CoherentFileSet;
int nb = fileSet->size();
- if (nb == 0 )
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnPosition");
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)
{
gdcmWarningMacro( "Wrong number for Position : ["
<< strImPos << "]" );
- return CoherentFileSet;
+ return CoherentFileSet;
}
// Let's build again the 'position' string, to be sure of it's format
}
strPosition = ossPosition.str();
ossPosition.str("");
-
+
if ( CoherentFileSet.count(strPosition) == 0 )
{
gdcmDebugMacro(" New Position :[" << strPosition << "]");
* 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
+ * @param element 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 SerieHelper::SplitOnTagValue(FileList *fileSet,
+ uint16_t group, uint16_t element)
{
XCoherentFileSetmap CoherentFileSet;
int nb = fileSet->size();
- if (nb == 0 )
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnTagValue");
return CoherentFileSet;
+ }
std::string strTagValue; // read on disc
FileList::const_iterator it = fileSet->begin();
- it ++;
+ //it ++;
for ( ;
it != fileSet->end();
++it)
// 0020,0032 : Image Position Patient
// 0020,0030 : Image Position (RET)
- strTagValue = (*it)->GetEntryString(group,elem);
+ strTagValue = (*it)->GetEntryString(group,element);
+
+ if ( CoherentFileSet.count(strTagValue) == 0 )
+ {
+ gdcmDebugMacro(" :[" << 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;
+}
+
+
+/**
+ * \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 element element number of the target Element
+ * \return std::map of 'Xcoherent' File sets
+ */
+
+XCoherentFileSetmap SerieHelper::SplitOnTagValueConvertToFloat(FileList *fileSet,
+ uint16_t group, uint16_t element)
+{
+ XCoherentFileSetmap CoherentFileSet;
+
+ int nb = fileSet->size();
+ if (nb == 0 ) {
+ gdcmWarningMacro("Empty FileList passed to SplitOnTagValue");
+ return CoherentFileSet;
+ }
+
+ std::string strTagValue; // read on disc
+
+ double dTagValue;
+ int iTagValue;
+ char cTagValue[11];
+ std::string sTagValue;
+
+ FileList::const_iterator it = fileSet->begin();
+ //it ++;
+ for ( ;
+ it != fileSet->end();
+ ++it)
+ {
+ /// \TODO : find a trick to create a string whose value follows lexicographical order
+
+ strTagValue = (*it)->GetEntryString(group,element);
+ dTagValue = atof( strTagValue.c_str());
+ iTagValue = dTagValue*10000.;
+ sprintf(cTagValue, "%010d", iTagValue);
+ strTagValue = cTagValue;
if ( CoherentFileSet.count(strTagValue) == 0 )
{
- gdcmDebugMacro(" New Tag Value :[" << strTagValue << "]");
+ gdcmDebugMacro(" :[" << strTagValue << "]");
// create a File set in 'position' position
CoherentFileSet[strTagValue] = new FileList;
}
// Private
/**
* \brief sorts the images, according to their Patient Position.
- *
+ * As a side effect, it computes the ZSpacing, according to Jolinda Smith's
+ * algorithm. (get it with double GetZSpacing() !)
* We may order, considering :
* -# Image Position Patient
* -# Image Number
bool SerieHelper::ImagePositionPatientOrdering( FileList *fileList )
//based on Jolinda Smith's algorithm
{
+//Tags always use the same coordinate system, where "x" is left
+//to right, "y" is posterior to anterior, and "z" is foot to head (RAH).
+
//iop is calculated based on the file file
- double cosines[6];
+ float cosines[6];
double normal[3];
double ipp[3];
double dist;
double min = 0, max = 0;
bool first = true;
+ ZSpacing = -1.0; // will be updated if process doesn't fail
+ gdcmDebugMacro("============================================DropDuplicatePositions : " << DropDuplicatePositions );
+
std::multimap<double,File *> distmultimap;
// Use a multimap to sort the distances from 0,0,0
for ( FileList::const_iterator
it = fileList->begin();
it != fileList->end(); ++it )
{
+ gdcmDebugMacro("deal with " << (*it)->GetFileName() );
if ( first )
{
(*it)->GetImageOrientationPatient( cosines );
-
+
+ // The "Image Orientation Patient" tag gives the direction cosines
+ // for the rows and columns for the three axes defined above.
+ // Typical axial slices will have a value 1/0/0/0/1/0:
+ // rows increase from left to right,
+ // columns increase from posterior to anterior. This is your everyday
+ // "looking up from the bottom of the head with the eyeballs up" image.
+
+ // The "Image Position Patient" tag gives the coordinates of the first
+ // voxel in the image in the "RAH" coordinate system, relative to some
+ // origin.
+
+ // First, calculate the slice normal from IOP :
+
// 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 ("Image Position Patient") tag.
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];
-
+
+ // For each slice (here : the first), calculate the distance along
+ // the slice normal using the IPP tag
+
ipp[0] = (*it)->GetXOrigin();
ipp[1] = (*it)->GetYOrigin();
ipp[2] = (*it)->GetZOrigin();
dist += normal[i]*ipp[i];
}
+ gdcmDebugMacro("dist : " << dist);
distmultimap.insert(std::pair<const double,File *>(dist, *it));
max = min = dist;
}
else
{
+ // Next, for each slice, calculate the distance along the slice normal
+ // using the IPP tag
ipp[0] = (*it)->GetXOrigin();
ipp[1] = (*it)->GetYOrigin();
ipp[2] = (*it)->GetZOrigin();
-
+
dist = 0;
for ( int i = 0; i < 3; ++i )
{
}
distmultimap.insert(std::pair<const double,File *>(dist, *it));
-
+ gdcmDebugMacro("dist : " << dist);
min = (min < dist) ? min : dist;
max = (max > dist) ? max : dist;
}
-
}
+ gdcmDebugMacro("After parsing vector, nb of elements : " << fileList->size() );
+
// 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. "
+ << "No 'ZSpacing' calculated! ");
return false;
}
// Check to see if image shares a common position
- bool ok = true;
- for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
- it2 != distmultimap.end();
- ++it2)
- {
- if (distmultimap.count((*it2).first) != 1)
- {
- gdcmErrorMacro("File: "
- << ((*it2).second->GetFileName())
- << " Distance: "
- << (*it2).first
- << " position is not unique");
- ok = false;
- }
- }
- if (!ok)
- {
- return false;
- }
-
+ bool ok = true;
+ for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
+ it2 != distmultimap.end();
+ ++it2)
+ {
+
+ gdcmDebugMacro("Check if image shares a common position : " << (*it2).second->GetFileName() );
+
+ if (distmultimap.count((*it2).first) != 1)
+ {
+ gdcmWarningMacro("File: ["
+ << ((*it2).second->GetFileName())
+ << "] : more than ONE file at distance: '"
+ << (*it2).first
+ << " (position is not unique!) "
+ << "No PositionPatientOrdering sort performed. "
+ << "No 'ZSpacing' calculated! ");
+
+ ok = false;
+ }
+ }
+ if (!ok)
+ {
+ if (! DropDuplicatePositions)
+ return false;
+ }
+
+// Now, we can calculate Z Spacing as the difference
+// between the "dist" values for the first two slices.
+
+// The following (un)-commented out code is let here
+// to be re-used by whomsoever is interested...
+
+ std::multimap<double, File *>::iterator it5 = distmultimap.begin();
+ double d1 = (*it5).first;
+ it5++;
+ double d2 = (*it5).first;
+ ZSpacing = d1-d2;
+ if (ZSpacing < 0.0)
+ ZSpacing = - ZSpacing;
+
fileList->clear(); // doesn't delete list elements, only nodes
+// Acording to user requierement, we sort direct order or reverse order.
if (DirectOrder)
{
for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
- it3 != distmultimap.end();
- ++it3)
+ it3 != distmultimap.end();
+ ++it3)
{
fileList->push_back( (*it3).second );
+ if (DropDuplicatePositions)
+ {
+ // ImagePositionPatientOrdering wrong duplicates are found ???
+ // --> fixed. See comment
+
+ it3 = distmultimap.upper_bound((*it3).first); // skip all duplicates
+ // the upper_bound function increments the iterator to the next non-duplicate entry
+ // The for loop iteration also increments the iterator, which causes the code to skip every other image
+ // --> decrement the iterator after the upper_bound function call
+ it3--;
+ if (it3 == distmultimap.end() ) // if last image, stop iterate
+ break;
+ }
}
}
else // user asked for reverse order
{
it4--;
fileList->push_back( (*it4).second );
+ if (DropDuplicatePositions) // skip all duplicates
+ {
+ // lower_bound finds the next element that is
+ // less than or *equal to* the current value!
+ //it4 = distmultimap.lower_bound((*it4).first);
+
+ // David Feng's fix
+ std::multimap<double, File *>::const_iterator itPrev = it4;
+ while (itPrev->first == it4->first)
+ --itPrev;
+ it4 = itPrev;
+
+ if (it4 == distmultimap.begin() ) // if first image, stop iterate
+ break;
+ }
} while (it4 != distmultimap.begin() );
- }
+ }
distmultimap.clear();
* \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 File set (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)
<< " No ImageNumberOrdering sort performed.");
return false;
}
- if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::ImageNumberLessThan );
+ if (DirectOrder)
+ Sort(fileList,SerieHelper::ImageNumberLessThan);
else
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::ImageNumberGreaterThan );
+ Sort(fileList,SerieHelper::ImageNumberGreaterThan);
return true;
}
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::FileNameLessThan);
+ Sort(fileList,SerieHelper::FileNameLessThan);
else
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::FileNameGreaterThan);
+ Sort(fileList,SerieHelper::FileNameGreaterThan);
return true;
}
*/
bool SerieHelper::UserOrdering(FileList *fileList)
{
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::UserLessThanFunction);
+ Sort(fileList,SerieHelper::UserLessThanFunction);
if (!DirectOrder)
{
std::reverse(fileList->begin(), fileList->end());
return true;
}
-std::string SerieHelper::CreateUniqueSeriesIdentifier( File * inFile )
-{
- if( inFile->IsReadable() )
- {
- // 0020 000e UI REL Series Instance UID
- std::string uid = inFile->GetEntryString (0x0020, 0x000e);
- std::string id = uid.c_str();
- if(m_UseSeriesDetails)
- {
- // If the user requests, additional information can be appended
- // to the SeriesUID to further differentiate volumes in the DICOM
- // objects being processed.
-
- // 0020 0011 Series Number
- // A scout scan prior to a CT volume scan can share the same
- // SeriesUID, but they will sometimes have a different Series Number
- std::string sNum = inFile->GetEntryString(0x0020, 0x0011);
- if( sNum == gdcm::GDCM_UNFOUND )
- {
- sNum = "";
- }
- // 0018 0024 Sequence Name
- // For T1-map and phase-contrast MRA, the different flip angles and
- // directions are only distinguished by the Sequence Name
- std::string sName = inFile->GetEntryString(0x0018, 0x0024);
- if( sName == gdcm::GDCM_UNFOUND )
- {
- sName = "";
- }
- // 0018 0050 Slice Thickness
- // On some CT systems, scout scans and subsequence volume scans will
- // have the same SeriesUID and Series Number - YET the slice
- // thickness will differ from the scout slice and the volume slices.
- std::string sThick = inFile->GetEntryString (0x0018, 0x0050);
- if( sThick == gdcm::GDCM_UNFOUND )
- {
- sThick = "";
- }
- // 0028 0010 Rows
- // If the 2D images in a sequence don't have the same number of rows,
- // then it is difficult to reconstruct them into a 3D volume.
- std::string sRows = inFile->GetEntryString (0x0028, 0x0010);
- if( sRows == gdcm::GDCM_UNFOUND )
- {
- sRows = "";
- }
- // 0028 0011 Columns
- // If the 2D images in a sequence don't have the same number of columns,
- // then it is difficult to reconstruct them into a 3D volume.
- std::string sColumns = inFile->GetEntryString (0x0028, 0x0011);
- if( sColumns == gdcm::GDCM_UNFOUND )
- {
- sColumns = "";
- }
-
- // Concat the new info
- std::string num = sNum.c_str();
- num += sName.c_str();
- num += sThick.c_str();
- num += sRows.c_str();
- num += sColumns.c_str();
-
- // Append the new info to the SeriesUID
- id += ".";
- id += num.c_str();
- }
-
- // Eliminate non-alnum characters, including whitespace...
- // that may have been introduced by concats.
- for(unsigned int i=0; i<id.size(); i++)
- {
- while(i<id.size()
- && !( id[i] == '.'
- || (id[i] >= 'a' && id[i] <= 'z')
- || (id[i] >= '0' && id[i] <= '9')
- || (id[i] >= 'A' && id[i] <= 'Z')))
- {
- id.erase(i, 1);
- }
- }
- return id;
- }
- else // Could not open inFile
- {
- gdcmWarningMacro("Could not parse series info.");
- std::string id = gdcm::GDCM_UNFOUND;
- return id;
- }
-}
-
-
//-----------------------------------------------------------------------------
// Print
/**
*/
void SerieHelper::Print(std::ostream &os, std::string const &indent)
{
- // For all the Coherent File lists of the gdcm::Serie
+ // For all the Coherent File lists of the GDCM_NAME_SPACE::Serie
SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
if ( itl == SingleSerieUIDFileSetHT.end() )
{
// For all the files of a SingleSerieUID File set
for (FileList::iterator it = (itl->second)->begin();
- it != (itl->second)->end();
- ++it)
+ it != (itl->second)->end();
+ ++it)
{
os << indent << " --- " << (*it)->GetFileName() << std::endl;
}
}
}
+void SerieHelper::CreateDefaultUniqueSeriesIdentifier()
+{
+ // If the user requests, additional information can be appended
+ // to the SeriesUID to further differentiate volumes in the DICOM
+ // objects being processed.
+
+ // 0020 0011 Series Number
+ // A scout scan prior to a CT volume scan can share the same
+ // SeriesUID, but they will sometimes have a different Series Number
+ AddRestriction( TagKey(0x0020, 0x0011) );
+
+ // 0018 0024 Sequence Name
+ // For T1-map and phase-contrast MRA, the different flip angles and
+ // directions are only distinguished by the Sequence Name
+ AddRestriction( TagKey(0x0018, 0x0024) );
+
+ // 0018 0050 Slice Thickness
+ // On some CT systems, scout scans and subsequence volume scans will
+ // have the same SeriesUID and Series Number - YET the slice
+ // thickness will differ from the scout slice and the volume slices.
+ AddRestriction( TagKey(0x0018, 0x0050));
+
+ // 0028 0010 Rows
+ // If the 2D images in a sequence don't have the same number of rows,
+ // then it is difficult to reconstruct them into a 3D volume.
+ AddRestriction( TagKey(0x0028, 0x0010));
+
+ // 0028 0011 Columns
+ // If the 2D images in a sequence don't have the same number of columns,
+ // then it is difficult to reconstruct them into a 3D volume.
+ AddRestriction( TagKey(0x0028, 0x0011));
+}
+
+/**
+ * \brief Heuristics to *try* to build a Serie Identifier that would ensure
+ * all the images are coherent.
+ *
+ * By default, uses the SeriesUID. If UseSeriesDetails(true) has been called,
+ * then additional identifying information is used.
+ * We allow user to add his own critierions, using AddSeriesDetail
+ * (he knows more than we do about his images!)
+ * ex : in tagging series, the only pertinent tag is
+ * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
+ * @param inFile GDCM_NAME_SPACE::File we want to build a Serie Identifier for.
+ * @return the SeriesIdentifier
+ */
+std::string SerieHelper::CreateUniqueSeriesIdentifier( File *inFile )
+{
+ if( inFile->IsReadable() )
+ {
+ // 0020 000e UI REL Series Instance UID
+ std::string uid = inFile->GetEntryString (0x0020, 0x000e);
+ std::string id = uid.c_str();
+ if(m_UseSeriesDetails)
+ {
+ for(SerieExRestrictions::iterator it2 = ExRefine.begin();
+ it2 != ExRefine.end();
+ ++it2)
+ {
+ const ExRule &r = *it2;
+ std::string s = inFile->GetEntryString( r.group, r.elem );
+ if( s == GDCM_UNFOUND )
+ {
+ s = "";
+ }
+ if( id == uid && !s.empty() )
+ {
+ id += "."; // add separator
+ }
+ id += s;
+ }
+ }
+ // Eliminate non-alnum characters, including whitespace...
+ // that may have been introduced by concats.
+ unsigned int s_size = id.size();
+ for(unsigned int i=0; i<s_size; i++)
+ {
+ while(i<s_size
+ && !( id[i] == '.' || id[i] == '%' || id[i] == '_'
+ || (id[i] >= '+' && id[i] <= '-')
+ || (id[i] >= 'a' && id[i] <= 'z')
+ || (id[i] >= '0' && id[i] <= '9')
+ || (id[i] >= 'A' && id[i] <= 'Z')))
+ {
+ id.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable
+ }
+ }
+ // deal with Dicom strings trailing '\0'
+ if(s_size && id[s_size-1] == '_')
+ id.erase(s_size-1, 1);
+ return id;
+ }
+ else // Could not open inFile
+ {
+ gdcmWarningMacro("Could not parse series info.");
+ std::string id = GDCM_UNFOUND;
+ return id;
+ }
+}
+
+/**
+ * \brief Allow user to build is own File Identifier (to be able to sort
+ * temporal series just as he wants)
+ * Criterions will be set with AddSeriesDetail.
+ * (Maybe the method should be moved elsewhere
+ * -File class? FileHelper class?-
+ * @return FileIdentifier (Tokenizable on '%%%'. Hope it's enough !)
+ */
+std::string SerieHelper::CreateUserDefinedFileIdentifier( File *inFile )
+{
+ // Deal with all user supplied tags.
+ // (user knows more than we do about his images!)
+
+ double converted;
+ std::string id;
+ std::string s;
+ char charConverted[17];
+
+ for(SeriesExDetails::iterator it2 = ExDetails.begin();
+ it2 != ExDetails.end();
+ ++it2)
+ {
+ const ExDetail &r = *it2;
+ s = inFile->GetEntryString( r.group, r.elem );
+ if (s == "") // avoid troubles when empty string is found
+ s = "-";
+
+ // User is allowed to ask for 'convertion', to allow further ordering
+ // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
+ if (it2->convert)
+ {
+ if ( s != GDCM_UNFOUND) // Don't convert unfound fields !
+ {
+ converted = atof(s.c_str());
+ // probabely something much more complicated is possible,
+ // using C++ features
+ /// \todo check the behaviour when there are >0 and <0 numbers
+ sprintf(charConverted, "%016.6f",converted);
+ s = charConverted;
+ }
+ }
+ // Eliminate non-alphanum characters, including whitespace.
+ unsigned int s_size = s.size();
+ if(s_size == 0)
+ { // to avoid further troubles when wild anonymization was performed
+ s = "a";
+ }
+ else
+ {
+ for(unsigned int i=0; i<s_size; i++)
+ {
+ while(i<s_size
+ && !( s[i] == '.' || s[i] == '%' || s[i] == '_'
+ || (s[i] >= '+' && s[i] <= '-')
+ || (s[i] >= 'a' && s[i] <= 'z')
+ || (s[i] >= '0' && s[i] <= '9')
+ || (s[i] >= 'A' && s[i] <= 'Z')))
+ {
+ s.replace(i, 1, "_"); // ImagePositionPatient related stuff will be more human readable
+ }
+ }
+ // deal with Dicom strings trailing '\0'
+ if(s[s_size-1] == '_')
+ s.erase(s_size-1, 1);
+ }
+ id += s.c_str();
+ id += "%%%"; // make the FileIdentifier Tokenizable
+ }
+ id += inFile->GetFileName();
+ id += "%%%";
+ return id;
+}
+
+//-----------------------------------------------------------------------------
+// Sort
+/**
+ * \brief Sort FileList.
+ */
+void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
+{
+ std::sort(fileList->begin(), fileList->end(), pt2Func );
+}
+
+/*
+#ifndef GDCM_LEGACY_REMOVE
+bool SerieHelper::AddGdcmFile(File* header)
+{
+ return AddFile(header);
+}
+#endif
+*/
+
//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff