Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2006/02/05 23:13:36 $
- Version: $Revision: 1.46 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.47 $
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 <map>
#include <stdio.h> //for sscanf
-namespace gdcm
+namespace gdcm
{
-//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Constructor / Destructor
delete l; // remove the container
l = GetNextSingleSerieUIDFileSet();
}
+ // Need to clear that too:
+ SingleSerieUIDFileSetHT.clear();
}
//-----------------------------------------------------------------------------
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();
* *no* coherence check is performed, but those specified
* by SerieHelper::AddRestriction()
* @param header gdcm::File* of the file to deal with
+ * @return true if file was added, false if file was rejected
*/
-void SerieHelper::AddGdcmFile(File *header)
+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:
- for(SerieRestrictions::iterator it = Restrictions.begin();
- it != Restrictions.end();
- ++it)
+ 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 ( 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 ( 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(id) == 0 )
+ {
+ gdcmDebugMacro(" New 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;
}
/**
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 file from a
+ * 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 if he wants the Rectrictions to be *ored*
- * (and not only *anded*)
* @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)
{
- ExRule r;
- r.group = group;
- r.elem = elem;
- r.value = value;
- r.op = op;
- ExRestrictions.push_back( r );
+ TagKey t(group, elem);
+ AddRestriction(t, value, op);
}
+#endif
/**
* \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
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
-
+/**
+ * \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 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 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 )
if (nb == 0 )
return CoherentFileSet;
float iop[6];
-
std::string strOrient;
- std::ostringstream ossOrient;
+ std::ostringstream ossOrient;
+
FileList::const_iterator it = fileSet->begin();
it ++;
for ( ;
}
strOrient = ossOrient.str();
ossOrient.str("");
- // FIXME : is it a 'cleaner' way to initialize an ostringstream?
-
if ( CoherentFileSet.count(strOrient) == 0 )
{
gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
}
// Current Orientation and DICOM header match; add the file:
CoherentFileSet[strOrient]->push_back( (*it) );
- }
+ }
return CoherentFileSet;
}
}
strPosition = ossPosition.str();
ossPosition.str("");
-
+
if ( CoherentFileSet.count(strPosition) == 0 )
{
gdcmDebugMacro(" New Position :[" << strPosition << "]");
*/
XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t element)
{
XCoherentFileSetmap CoherentFileSet;
// 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 )
{
ipp[0] = (*it)->GetXOrigin();
ipp[1] = (*it)->GetYOrigin();
ipp[2] = (*it)->GetZOrigin();
-
+
dist = 0;
for ( int i = 0; i < 3; ++i )
{
min = (min < dist) ? min : dist;
max = (max > dist) ? max : dist;
}
-
}
// Find out if min/max are coherent
}
// 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)
+ {
+ if (distmultimap.count((*it2).first) != 1)
+ {
+ gdcmErrorMacro("File: "
+ << ((*it2).second->GetFileName())
+ << " Distance: "
+ << (*it2).first
+ << " position is not unique");
+
+ ok = false;
+ }
+ }
+ if (!ok)
+ {
+ return false;
+ }
+
fileList->clear(); // doesn't delete list elements, only nodes
if (DirectOrder)
{
for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
- it3 != distmultimap.end();
- ++it3)
+ it3 != distmultimap.end();
+ ++it3)
{
fileList->push_back( (*it3).second );
}
it4--;
fileList->push_back( (*it4).second );
} 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)
- Sort(fileList,SerieHelper::ImageNumberLessThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::ImageNumberLessThan );
+ if (DirectOrder)
+ Sort(fileList,SerieHelper::ImageNumberLessThan);
else
- Sort(fileList,SerieHelper::ImageNumberGreaterThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::ImageNumberGreaterThan );
+ Sort(fileList,SerieHelper::ImageNumberGreaterThan);
return true;
}
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
if (DirectOrder)
- Sort(fileList,SerieHelper::FileNameLessThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::FileNameLessThan);
+ Sort(fileList,SerieHelper::FileNameLessThan);
else
- Sort(fileList,SerieHelper::FileNameGreaterThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::FileNameGreaterThan);
+ Sort(fileList,SerieHelper::FileNameGreaterThan);
return true;
}
*/
bool SerieHelper::UserOrdering(FileList *fileList)
{
- Sort(fileList,SerieHelper::UserLessThanFunction);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::UserLessThanFunction);
+ Sort(fileList,SerieHelper::UserLessThanFunction);
if (!DirectOrder)
{
std::reverse(fileList->begin(), fileList->end());
return true;
}
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \brief Canonical printer.
+ */
+void SerieHelper::Print(std::ostream &os, std::string const &indent)
+{
+ // For all the Coherent File lists of the gdcm::Serie
+ SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
+ if ( itl == SingleSerieUIDFileSetHT.end() )
+ {
+ gdcmWarningMacro( "No SingleSerieUID File set found" );
+ return;
+ }
+ while (itl != SingleSerieUIDFileSetHT.end())
+ {
+ os << "Serie UID :[" << itl->first << "]" << std::endl;
+
+ // For all the files of a SingleSerieUID File set
+ for (FileList::iterator it = (itl->second)->begin();
+ it != (itl->second)->end();
+ ++it)
+ {
+ os << indent << " --- " << (*it)->GetFileName() << std::endl;
+ }
+ ++itl;
+ }
+}
+
+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.
{
if( inFile->IsReadable() )
{
- // 0020 000e UI REL Series Instance UID
- std::string uid = inFile->GetEntryString (0x0020, 0x000e);
+ // 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 = "";
- }
-
- // You can think on checking Image Orientation (0020,0037), as well.
-
-
- // 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();
-
- // Add a loop, here, to deal with any extra user supplied tag.
- // We allow user to add his own critierions
- // (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] values : ROW/COLUMN
-
- std::string s;
- for(SeriesExDetails::iterator it2 = ExDetails.begin();
- it2 != ExDetails.end();
- ++it2)
{
- const ExDetail &r = *it2;
- s = inFile->GetEntryString( r.group, r.elem );
- num += s.c_str();
+ 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::GDCM_UNFOUND )
+ {
+ s = "";
+ }
+ if( id == uid && !s.empty() )
+ {
+ id += "."; // add separator
+ }
+ id += s;
+ }
}
-
- // Append the new info to the SeriesUID
- id += ".";
- id += num.c_str();
- }
-
- // Eliminate non-alphanum 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] == '-' || 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;
- }
+ // 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;
+ }
}
/**
return id;
}
-//-----------------------------------------------------------------------------
-// Print
-/**
- * \brief Canonical printer.
- */
-void SerieHelper::Print(std::ostream &os, std::string const &indent)
-{
- // For all the Coherent File lists of the gdcm::Serie
- SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
- if ( itl == SingleSerieUIDFileSetHT.end() )
- {
- gdcmWarningMacro( "No SingleSerieUID File set found" );
- return;
- }
- while (itl != SingleSerieUIDFileSetHT.end())
- {
- os << "Serie UID :[" << itl->first << "]" << std::endl;
-
- // For all the files of a SingleSerieUID File set
- for (FileList::iterator it = (itl->second)->begin();
- it != (itl->second)->end();
- ++it)
- {
- os << indent << " --- " << (*it)->GetFileName() << std::endl;
- }
- ++itl;
- }
-}
//-----------------------------------------------------------------------------
// Sort
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff