Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2005/10/17 15:05:44 $
- Version: $Revision: 1.22 $
+ Date: $Date: 2006/01/18 15:25:07 $
+ Version: $Revision: 1.42 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
*/
SerieHelper::SerieHelper()
{
+ m_UseSeriesDetails = false;
ClearAll();
UserLessThanFunction = 0;
DirectOrder = true;
}
/**
- * \brief - Preventively, clear everything at constructor time.
- * - use it at destructor time.
+ * \brief Preventively, clear everything at constructor time.
+ * ( use it at destructor time.)
*/
void SerieHelper::ClearAll()
{
it != l->end();
++it)
{
- delete *it; // remove each entry
+ (*it)->Delete(); // remove each entry
}
l->clear();
delete l; // remove the container
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();
++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 unmatched; let's just quit
+
allrules = 0;
break;
}
// 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 ( SingleSerieUIDFileSetHT.count(uid) == 0 )
{
gdcmDebugMacro(" New Serie UID :[" << uid << "]");
else
{
// at least one rule was unmatched we need to deallocate the file:
- delete header;
+ header->Delete();
}
}
else
{
gdcmWarningMacro("Could not read file: " << filename );
- delete header;
+ header->Delete();
}
}
* 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)!
+ * \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
++it)
{
const Rule &r = *it;
- const std::string s;// = header->GetEntryValue( r.first );
+ 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
}
/**
- * \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
- * @param group Group number of the target tag.
- * @param elem Element number of the target tag.
+ * \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
*/
-void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+void SerieHelper::AddRestriction(TagKey const &key,
std::string const &value, int op)
{
ExRule r;
- r.group = group;
- r.elem = elem;
+ r.group = key[0];
+ r.elem = key[1];
r.value = value;
r.op = op;
ExRestrictions.push_back( r );
}
-#ifndef GDCM_LEGACY_REMOVE
/**
- * \brief add a rules for restricting a DICOM file to be in the serie we are
+ * \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
* 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
- * @deprecated use : AddRestriction(uint16_t group, uint16_t elem,
- * std::string const &value, int op);
+ * \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
*/
-void SerieHelper::AddRestriction(TagKey const &key, std::string const &value)
+void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+ std::string const &value, int op)
{
- Rule r;
- r.first = key;
- r.second = value;
- Restrictions.push_back( r );
+ ExRule r;
+ r.group = group;
+ r.elem = elem;
+ r.value = value;
+ r.op = op;
+ ExRestrictions.push_back( r );
}
-#endif
+/**
+ * \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
+ * that ensures (hope so) File constistency (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
FileList::const_iterator it = fileSet->begin();
- int nX = (*it)->GetXSize();
- int nY = (*it)->GetYSize();
- int pixelSize = (*it)->GetPixelSize();
-
+ int nX = (*it)->GetXSize();
+ int nY = (*it)->GetYSize();
+ int pixelSize = (*it)->GetPixelSize();
+ bool signedPixelData = (*it)->IsSignedPixelData();
it ++;
for ( ;
it != fileSet->end();
return false;
if ( (*it)->GetPixelSize() != pixelSize )
return false;
- // probabely more is to be checked (?)
+ if ( (*it)->IsSignedPixelData() != signedPixelData )
+ return false;
+ // 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::ostringstream ossOrient;
+
std::string strOrient;
-
+ std::ostringstream ossOrient;
FileList::const_iterator it = fileSet->begin();
it ++;
for ( ;
// 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 << 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 << "]");
}
// 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
+ * \brief Splits a 'Single SerieUID' Fileset according to the Positions
* @param fileSet File Set to be splitted
* \return std::map of 'Xcoherent' File sets
*/
// 0020,0032 : Image Position Patient
// 0020,0030 : Image Position (RET)
- std::string strImPos = (*it)->GetEntryValue(0x0020,0x0032);
+ strImPos = (*it)->GetEntryString(0x0020,0x0032);
if ( strImPos == GDCM_UNFOUND)
{
gdcmWarningMacro( "Unfound Image Position Patient (0020,0032)");
- strImPos = (*it)->GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ strImPos = (*it)->GetEntryString(0x0020,0x0030); // For ACR-NEMA images
if ( strImPos == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
ossPosition << pos[i];
}
strPosition = ossPosition.str();
-
+ ossPosition.str("");
+
if ( CoherentFileSet.count(strPosition) == 0 )
{
gdcmDebugMacro(" New Position :[" << strPosition << "]");
}
/**
- * \brief Splits a SingleSerieUID File set Coherent according to the
+ * \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 element)
+ uint16_t group, uint16_t elem)
{
XCoherentFileSetmap CoherentFileSet;
// 0020,0032 : Image Position Patient
// 0020,0030 : Image Position (RET)
- std::string strTagValue = (*it)->GetEntryValue(group,element);
+ strTagValue = (*it)->GetEntryString(group,elem);
if ( CoherentFileSet.count(strTagValue) == 0 )
{
}
// Current Tag value and DICOM header match; add the file:
CoherentFileSet[strTagValue]->push_back( (*it) );
- }
+ }
return CoherentFileSet;
}
//-----------------------------------------------------------------------------
// Private
/**
- * \brief sorts the images, according to their Patient Position
+ * \brief sorts the images, according to their Patient Position.
+ *
* 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 !
*/
{
//iop is calculated based on the file file
float cosines[6];
- float normal[3];
- float ipp[3];
- float dist;
- float min = 0, max = 0;
+ double normal[3];
+ double ipp[3];
+ double dist;
+ double min = 0, max = 0;
bool first = true;
- int n=0;
- std::vector<float> distlist;
- //!\todo rewrite this for loop.
+ 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 )
dist += normal[i]*ipp[i];
}
- distlist.push_back( dist );
+ distmultimap.insert(std::pair<const double,File *>(dist, *it));
max = min = dist;
first = false;
dist += normal[i]*ipp[i];
}
- distlist.push_back( dist );
+ distmultimap.insert(std::pair<const double,File *>(dist, *it));
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.
- FileVector CoherentFileVector(n);
- // CoherentFileVector.reserve( n );
- CoherentFileVector.resize( n );
- // gdcmAssertMacro( CoherentFileVector.capacity() >= n );
+ }
// Find out if min/max are coherent
if ( min == max )
return false;
}
- float step = (max - min)/(n - 1);
- int pos;
- n = 0;
-
- //VC++ don't understand what scope is !! it -> it2
- for (FileList::const_iterator it2 = fileList->begin();
- it2 != fileList->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 (CoherentFileVector[pos]==NULL)
- CoherentFileVector[pos] = *it2;
- else
- {
- gdcmWarningMacro( "At least 2 files with same position."
- << " No PositionPatientOrdering sort performed");
- 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;
+ }
+
fileList->clear(); // doesn't delete list elements, only nodes
if (DirectOrder)
{
- //VC++ don't understand what scope is !! it -> it3
- for (FileVector::const_iterator it3 = CoherentFileVector.begin();
- it3 != CoherentFileVector.end(); ++it3)
+ for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
+ it3 != distmultimap.end();
+ ++it3)
{
- fileList->push_back( *it3 );
+ fileList->push_back( (*it3).second );
}
}
else // user asked for reverse order
{
- FileVector::const_iterator it4;
- it4 = CoherentFileVector.end();
+ std::multimap<double, File *>::const_iterator it4;
+ it4 = distmultimap.end();
do
{
it4--;
- fileList->push_back( *it4 );
- } while (it4 != CoherentFileVector.begin() );
+ fileList->push_back( (*it4).second );
+ } while (it4 != distmultimap.begin() );
}
- distlist.clear();
- CoherentFileVector.clear();
+ distmultimap.clear();
return true;
}
* \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)
return false;
}
if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::ImageNumberLessThan );
+ Sort(fileList,SerieHelper::ImageNumberLessThan);
+// std::sort(fileList->begin(), fileList->end(),
+// SerieHelper::ImageNumberLessThan );
else
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::ImageNumberGreaterThan );
+ Sort(fileList,SerieHelper::ImageNumberGreaterThan);
+// std::sort(fileList->begin(), fileList->end(),
+// SerieHelper::ImageNumberGreaterThan );
return true;
}
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
if (DirectOrder)
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::FileNameLessThan);
+ Sort(fileList,SerieHelper::FileNameLessThan);
+// std::sort(fileList->begin(), fileList->end(),
+// SerieHelper::FileNameLessThan);
else
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::FileNameGreaterThan);
+ Sort(fileList,SerieHelper::FileNameGreaterThan);
+// std::sort(fileList->begin(), fileList->end(),
+// SerieHelper::FileNameGreaterThan);
return true;
}
*/
bool SerieHelper::UserOrdering(FileList *fileList)
{
- std::sort(fileList->begin(), fileList->end(),
- SerieHelper::UserLessThanFunction);
+ Sort(fileList,SerieHelper::UserLessThanFunction);
+// std::sort(fileList->begin(), fileList->end(),
+// SerieHelper::UserLessThanFunction);
if (!DirectOrder)
{
std::reverse(fileList->begin(), fileList->end());
return true;
}
+/**
+ * \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 pertnent tag is
+ * 0018|1312 [In-plane Phase Encoding Direction] value : ROW/COLUMN
+ * @param inFile gdcm::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)
+ {
+ // 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();
+ }
+
+ // 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;
+ }
+}
+
+/**
+ * \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 '_')
+ */
+std::string SerieHelper::CreateUserDefinedFileIdentifier( File * inFile )
+{
+ // Deal with all user supplied tags.
+ // (user knows more than we do about his images!)
+
+ float 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 );
+
+ // User is allowed to ask 'convertion', to allow further ordering
+ // e.g : 100 would be *before* 20; 000020.00 vs 00100.00 : OK
+ if (it2->convert)
+ {
+ 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.
+ for(unsigned int i=0; i<s.size(); i++)
+ {
+ while(i<s.size()
+ && !( s[i] == '.' || s[i] == '-'
+ || (s[i] >= 'a' && s[i] <= 'z')
+ || (s[i] >= '0' && s[i] <= '9')
+ || (s[i] >= 'A' && s[i] <= 'Z')))
+ {
+ s.erase(i, 1);
+ }
+ }
+
+ id += s.c_str();
+ id += "_"; // make the FileIdentifier Tokenizable
+ }
+
+ return id;
+}
//-----------------------------------------------------------------------------
// Print
/**
}
}
+//-----------------------------------------------------------------------------
+// Sort
+/**
+ * \brief Sort FileList.
+ */
+void SerieHelper::Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) )
+{
+ std::sort(fileList->begin(), fileList->end(), pt2Func );
+}
+
//-----------------------------------------------------------------------------
} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff