X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmElValSet.cxx;h=58302b3d37979d44641b114cb86b393bbbbc85a6;hb=add2c91a1dff06ba91f44543642e7cda0db7d9e0;hp=7e15c037bf33cf07cbbff3fa2b79a43cd7d4bf9d;hpb=0fa193d8b312b90f2ee822e1ee87f6e2fbd1dcb5;p=gdcm.git

diff --git a/src/gdcmElValSet.cxx b/src/gdcmElValSet.cxx
index 7e15c037..58302b3d 100644
--- a/src/gdcmElValSet.cxx
+++ b/src/gdcmElValSet.cxx
@@ -3,6 +3,7 @@
 #include <sstream>
 #include "gdcmUtil.h"
 #include "gdcmElValSet.h"
+#include "gdcmTS.h"
 using namespace std;
 
 gdcmElValSet::~gdcmElValSet() {
@@ -13,7 +14,7 @@ gdcmElValSet::~gdcmElValSet() {
    }
    tagHt.clear();
    // Since Add() adds symetrical in both tagHt and NameHt we can
-   // assume all the pointed gdcmElValues are allready cleaned-up when
+   // assume all the pointed gdcmElValues are already cleaned-up when
    // we cleaned tagHt.
    NameHt.clear();
 }
@@ -22,101 +23,195 @@ TagElValueHT & gdcmElValSet::GetTagHt(void) {
 	return tagHt;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   newElValue
+ * @return  
+ */
 void gdcmElValSet::Add(gdcmElValue * newElValue) {
 	tagHt [newElValue->GetKey()]  = newElValue;
 	NameHt[newElValue->GetName()] = newElValue;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   Checks if a given Dicom element exists
+ * \        within a ElValSet
+ * @param   Group
+ * @param   Elem
+ * @return  
+ */
+int gdcmElValSet::CheckIfExistByNumber(guint16 Group, guint16 Elem ) {
+	string key = TranslateToKey(Group, Elem );
+	return (tagHt.count(key));
+}
+
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ */
 void gdcmElValSet::Print(ostream & os) {
-	for (TagElValueHT::iterator tag = tagHt.begin();
-		  tag != tagHt.end();
-		  ++tag){
-		os << tag->first << ": ";
-		os << "[" << tag->second->GetValue() << "]";
-		os << "[" << tag->second->GetName()  << "]";
-		os << "[" << tag->second->GetVR()    << "]"; 
-		os << " lgr : " << tag->second->GetLength();
-		os << endl;
-	}
+
+   size_t o;
+   short int g, e;
+   TSKey v;
+   char * d;
+   string d2;
+   gdcmTS * ts = gdcmGlobal::GetTS();
+   
+   for (TagElValueHT::iterator tag = tagHt.begin();
+	   tag != tagHt.end();
+	   ++tag){
+      g = tag->second->GetGroup();
+      e = tag->second->GetElement();
+      v = tag->second->GetValue();
+      o = tag->second->GetOffset();
+      d = _CreateCleanString(v);  // replace non printable characters by '.'
+      d2=d;
+		 
+      os << tag->first << ": ";
+      os << " lgr : " << tag->second->GetLength();
+      os << ", Offset : " << o;
+      os << " x(" << hex << o << dec << ") ";
+      os << "\t[" << tag->second->GetVR()    << "]";
+      os << "\t[" << tag->second->GetName()  << "]";       
+      os << "\t[" << d2 << "]";
+      
+      // Display the UID value (instead of displaying the rough code)  
+      if (g == 0x0002) {  // Some more to be displayed ?
+         if ( (e == 0x0010) || (e == 0x0002) ) 	   
+            os << "  ==>\t[" << ts->GetValue(v) << "]";   
+      } else {
+         if (g == 0x0008) {
+            if ( (e == 0x0016) || (e == 0x1150)  ) 	   
+               os << "  ==>\t[" << ts->GetValue(v) << "]"; 
+         }
+      }              
+      free(d);     
+      os << endl;
+   }
 } 
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ */
 void gdcmElValSet::PrintByName(ostream & os) {
-	for (TagElValueNameHT::iterator tag = NameHt.begin();
-		  tag != NameHt.end();
-		  ++tag){
-		os << tag->first << ": ";
-		os << "[" << tag->second->GetValue() << "]";
-		os << "[" << tag->second->GetKey()   << "]";
-		os << "[" << tag->second->GetVR()    << "]" << endl;
-	}
+   for (TagElValueNameHT::iterator tag = NameHt.begin();
+          tag != NameHt.end();
+          ++tag){
+      os << tag->first << ": ";
+      os << "[" << tag->second->GetValue() << "]";
+      os << "[" << tag->second->GetKey()   << "]";
+      os << "[" << tag->second->GetVR()    << "]" << endl;
+   }
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   group 
+ * @param   element 
+ * @return  
+ */
 gdcmElValue* gdcmElValSet::GetElementByNumber(guint16 group, guint16 element) {
-	TagKey key = gdcmDictEntry::TranslateToKey(group, element);
-	if ( ! tagHt.count(key))
-		return (gdcmElValue*)0;
-	return tagHt.find(key)->second;
+   TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+   if ( ! tagHt.count(key))
+      return (gdcmElValue*)0;
+   return tagHt.find(key)->second;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @return  
+ */
 gdcmElValue* gdcmElValSet::GetElementByName(string TagName) {
    if ( ! NameHt.count(TagName))
       return (gdcmElValue*)0;
    return NameHt.find(TagName)->second;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   group 
+ * @param   element 
+ * @return  
+ */
 string gdcmElValSet::GetElValueByNumber(guint16 group, guint16 element) {
-	TagKey key = gdcmDictEntry::TranslateToKey(group, element);
-	if ( ! tagHt.count(key))
-		return "gdcm::Unfound";
-	return tagHt.find(key)->second->GetValue();
+   TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+   if ( ! tagHt.count(key))
+      return "gdcm::Unfound";
+   return tagHt.find(key)->second->GetValue();
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @return  
+ */
 string gdcmElValSet::GetElValueByName(string TagName) {
-	if ( ! NameHt.count(TagName))
-		return "gdcm::Unfound";
-	return NameHt.find(TagName)->second->GetValue();
+   if ( ! NameHt.count(TagName))
+      return "gdcm::Unfound";
+   return NameHt.find(TagName)->second->GetValue();
 }
 
-
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   content
+ * @param   group 
+ * @param   element 
+ * @return  
+ */
 int gdcmElValSet::SetElValueByNumber(string content,
                                      guint16 group, guint16 element) {
-	TagKey key = gdcmDictEntry::TranslateToKey(group, element);
-	if ( ! tagHt.count(key))
-		return 0;
-	tagHt[key]->SetValue(content);	
-	string vr = tagHt[key]->GetVR();
-	guint32 lgr;
-
-	if( (vr == "US") || (vr == "SS") ) 
-	   lgr = 2;
-	else if( (vr == "UL") || (vr == "SL") )
-	   lgr = 4;
-	else
-	   lgr = content.length();	   
-	tagHt[key]->SetLength(lgr); 
-	return 1;
+   TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+   if ( ! tagHt.count(key))
+      return 0;
+   tagHt[key]->SetValue(content);	
+   string vr = tagHt[key]->GetVR();
+   guint32 lgr;
+
+   if( (vr == "US") || (vr == "SS") ) 
+      lgr = 2;
+   else if( (vr == "UL") || (vr == "SL") )
+      lgr = 4;
+   else
+      lgr = content.length();	   
+   tagHt[key]->SetLength(lgr); 
+   return 1;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   content
+ * @param   TagName
+ * @return  
+ */
 int gdcmElValSet::SetElValueByName(string content, string TagName) {
-	if ( ! NameHt.count(TagName))
-		return 0;
-	NameHt[TagName]->SetValue(content);
-	string vr = NameHt[TagName]->GetVR();
-	guint32 lgr;
-
-	if( (vr == "US") || (vr == "SS") ) 
-	   lgr = 2;
-	else if( (vr == "UL") || (vr == "SL") )
-	   lgr = 4;	   
-	else 
-	   lgr = content.length();
+   if ( ! NameHt.count(TagName))
+      return 0;
+   NameHt[TagName]->SetValue(content);
+   string vr = NameHt[TagName]->GetVR();
+   guint32 lgr;
+
+   if( (vr == "US") || (vr == "SS") ) 
+      lgr = 2;
+   else if( (vr == "UL") || (vr == "SL") )
+      lgr = 4;	   
+   else 
+      lgr = content.length();
 	   
 // TODO : WARNING: le cas de l'element des pixels (7fe0,0010) n'est pas traite
 // par SetElValueByName
 // il faudra utiliser SetElValueByNumber
 	   
-	NameHt[TagName]->SetLength(lgr);
-	return 1;		
+   NameHt[TagName]->SetLength(lgr);
+   return 1;		
 }
 
 /**
@@ -135,25 +230,59 @@ guint32 gdcmElValSet::GenerateFreeTagKeyInGroup(guint16 group) {
    return UINT32_MAX;
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   area
+ * @param   group 
+ * @param   element 
+ * @return  
+ */
+int gdcmElValSet::SetVoidAreaByNumber(void * area,
+                                      guint16 group, guint16 element) {
+   TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+   if ( ! tagHt.count(key))
+      return 0;
+   tagHt[key]->SetVoidArea(area);	 
+   return 1 ;		
+}
+
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   length
+ * @param   group 
+ * @param   element 
+ * @return  int acts as a boolean
+ */
 int gdcmElValSet::SetElValueLengthByNumber(guint32 length,
                                            guint16 group, guint16 element) {
-	TagKey key = gdcmDictEntry::TranslateToKey(group, element);
-	if ( ! tagHt.count(key))
-		return 0;
-	tagHt[key]->SetLength(length);	 
-	return 1 ;		
+   TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+   if ( ! tagHt.count(key))
+      return 0;
+   tagHt[key]->SetLength(length);	 
+   return 1 ;		
 }
-
-
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   length
+ * @param   TagName
+ * @return  
+ */
 int gdcmElValSet::SetElValueLengthByName(guint32 length, string TagName) {
-	if ( ! NameHt.count(TagName))
-		return 0;
-	NameHt.find(TagName)->second->SetLength(length);	 
-	return 1 ;		
+   if ( ! NameHt.count(TagName))
+      return 0;
+   NameHt.find(TagName)->second->SetLength(length);	 
+   return 1 ;		
 }
 
-
-
+/**
+ * \ingroup gdcmElValSet
+ * \brief   Re-computes the length of a ACR-NEMA/Dicom group from a DcmHeader
+ * @param   SkipSequence TRUE if we don't want to write Sequences (ACR-NEMA Files)
+ * @param   type
+ */
 void gdcmElValSet::UpdateGroupLength(bool SkipSequence, FileType type) {
    guint16 gr, el;
    string vr;
@@ -161,12 +290,18 @@ void gdcmElValSet::UpdateGroupLength(bool SkipSequence, FileType type) {
    gdcmElValue *elem;
    char trash[10];
    string str_trash;
+   
    GroupKey key;
-   GroupHT groupHt;
+   GroupHT groupHt;  // to hold the length of each group
    TagKey tk;
+   // remember :
+   // typedef std::map<GroupKey, int> GroupHT;
+   
    gdcmElValue *elemZ;
+  
+   // for each Tag in the DCM Header
    
-   for (TagElValueHT::iterator tag2 = tagHt.begin();
+   for (TagElValueHT::iterator tag2 = tagHt.begin(); 
         tag2 != tagHt.end();
         ++tag2){
 
@@ -176,55 +311,54 @@ void gdcmElValSet::UpdateGroupLength(bool SkipSequence, FileType type) {
       vr = elem->GetVR(); 
                  
       sprintf(trash, "%04x", gr);
-      key = trash;
-                  
+      key = trash;		// generate 'group tag'
+      
+      // if the caller decided not to take SEQUENCEs into account 
+      // e.g : he wants to write an ACR-NEMA File 
+                
       if (SkipSequence && vr == "SQ") continue;
+      
+         // Still unsolved problem :
+         // we cannot find the 'Sequence Delimitation Item'
+         // since it's at the end of the Hash Table
+         // (fffe,e0dd) 
+             
          // pas SEQUENCE en ACR-NEMA
-         // WARNING : pb CERTAIN
-         //           si on est descendu 'a l'interieur' des SQ 
-         //
+         // WARNING : 
          // --> la descente a l'interieur' des SQ 
-         // devra etre faite avec une liste chainee, pas avec une HTable...
-             
-      if ( groupHt.count(key) == 0) { 
-         if (el ==0x0000) {
-            groupHt[key] = 0;
+         // devrait etre faite avec une liste chainee, pas avec une HTable...
+            
+      if ( groupHt.count(key) == 0) { // we just read the first elem of a given group
+         if (el == 0x0000) {	      // the first elem is 0x0000
+            groupHt[key] = 0;	      // initialize group length 
          } else {
-            groupHt[key] =2 + 2 + 4 + elem->GetLength();
+            groupHt[key] = 2 + 2 + 4 + elem->GetLength(); // non 0x0000 first group elem
          } 
-      } else {       
-         if (type = ExplicitVR) {
+      } else {   // any elem but the first    
+         if (type == ExplicitVR) {
             if ( (vr == "OB") || (vr == "OW") || (vr == "SQ") ) {
-               groupHt[key] +=  4;
+               groupHt[key] +=  4; // explicit VR AND OB, OW, SQ : 4 more bytes
             }
          }
          groupHt[key] += 2 + 2 + 4 + elem->GetLength(); 
       } 
    }
-  
-     if(0)
-     for (GroupHT::iterator g = groupHt.begin();
-        g != groupHt.end();
-        ++g){        
-        printf("groupKey %s : %d\n",g->first.c_str(),g->second);
-     }
-       
-  
+
    unsigned short int gr_bid;
   
-   for (GroupHT::iterator g = groupHt.begin();
+   for (GroupHT::iterator g = groupHt.begin(); // for each group we found
         g != groupHt.end();
         ++g){ 
       // FIXME: g++ -Wall -Wstrict-prototypes reports on following line:
       //        warning: unsigned int format, different type arg
       sscanf(g->first.c_str(),"%x",&gr_bid);
-      tk = g->first + "|0000";
+      tk = g->first + "|0000";			// generate the element full tag
                      
-      if ( tagHt.count(tk) == 0) { 
+      if ( tagHt.count(tk) == 0) { 		// if element 0x0000 not found
          gdcmDictEntry * tagZ = new gdcmDictEntry(gr_bid, 0x0000, "UL");       
          elemZ = new gdcmElValue(tagZ);
          elemZ->SetLength(4);
-         Add(elemZ);
+         Add(elemZ);				// create it
       } else {
          elemZ=GetElementByNumber(gr_bid, 0x0000);
       }     
@@ -234,6 +368,13 @@ void gdcmElValSet::UpdateGroupLength(bool SkipSequence, FileType type) {
    }   
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   type
+ * @param   _fp 
+ * @return  
+ */
 void gdcmElValSet::WriteElements(FileType type, FILE * _fp) {
    guint16 gr, el;
    guint32 lgr;
@@ -258,18 +399,21 @@ void gdcmElValSet::WriteElements(FileType type, FILE * _fp) {
       lgr = tag2->second->GetLength();
       val = tag2->second->GetValue().c_str();
       vr =  tag2->second->GetVR();
+      
+     // cout << "Tag "<< hex << gr << " " << el << "\n";
 
       if ( type == ACR ) { 
-         if (gr < 0x0008) continue;
-         if (gr %2)   continue;
-         if (vr == "SQ" ) continue;
+         if (gr < 0x0008)   continue; // ignore pure DICOM V3 groups
+         if (gr %2)         continue; // ignore shadow groups
+         if (vr == "SQ" )   continue; // ignore Sequences
+         if (gr == 0xfffe ) continue; // ignore delimiters
       } 
 
       fwrite ( &gr,(size_t)2 ,(size_t)1 ,_fp);  //group
       fwrite ( &el,(size_t)2 ,(size_t)1 ,_fp);  //element
 
       if ( (type == ExplicitVR) && (gr <= 0x0002) ) {
-         // On est en EXPLICIT VR
+         // EXPLICIT VR
          guint16 z=0, shortLgr;
          fwrite (vr.c_str(),(size_t)2 ,(size_t)1 ,_fp);
 
@@ -281,38 +425,46 @@ void gdcmElValSet::WriteElements(FileType type, FILE * _fp) {
             shortLgr=lgr;
             fwrite ( &shortLgr,(size_t)2 ,(size_t)1 ,_fp);
          }
-      } else {
+      } else { // IMPLICIT VR
          fwrite ( &lgr,(size_t)4 ,(size_t)1 ,_fp);
       }
 
-      tokens.erase(tokens.begin(),tokens.end());
-      Tokenize (tag2->second->GetValue(), tokens, "\\");
-
       if (vr == "US" || vr == "SS") {
+         tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+         Tokenize (tag2->second->GetValue(), tokens, "\\");
          for (unsigned int i=0; i<tokens.size();i++) {
             val_uint16 = atoi(tokens[i].c_str());
             ptr = &val_uint16;
             fwrite ( ptr,(size_t)2 ,(size_t)1 ,_fp);
          }
+         tokens.clear();
          continue;
       }
       if (vr == "UL" || vr == "SL") {
+         tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
+         Tokenize (tag2->second->GetValue(), tokens, "\\");
          for (unsigned int i=0; i<tokens.size();i++) {
             val_uint32 = atoi(tokens[i].c_str());
             ptr = &val_uint32;
             fwrite ( ptr,(size_t)4 ,(size_t)1 ,_fp);
          }
+         tokens.clear();
          continue;
-      }
-      tokens.clear();
-
-      // Les pixels ne sont pas chargés dans l'element !
+      }     
+      // Pixels are never loaded in the element !
       if ((gr == 0x7fe0) && (el == 0x0010) ) break;
 
-      fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); //valeur Elem
+      fwrite ( val,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
    }
 }
 
+/**
+ * \ingroup gdcmElValSet
+ * \brief   
+ * @param   _fp
+ * @param   type
+ * @return  
+ */
 int gdcmElValSet::Write(FILE * _fp, FileType type) {
 
    if (type == ImplicitVR) {
@@ -324,15 +476,13 @@ int gdcmElValSet::Write(FILE * _fp, FileType type) {
       //      Dans le cas suivant on doit pader manuellement avec un 0
       
       SetElValueLengthByNumber(18, 0x0002, 0x0010);
-   }
-   
+   }  
    	// Question :
 	// Comment pourrait-on savoir si le DcmHeader vient d'un fichier DicomV3 ou non ,
 	// (FileType est un champ de gdcmHeader ...)
 	// WARNING : Si on veut ecrire du DICOM V3 a partir d'un DcmHeader ACR-NEMA
 	// no way
 	
-	
    if (type == ExplicitVR) {
       string explicitVRTransfertSyntax = "1.2.840.10008.1.2.1";
       SetElValueByNumber(explicitVRTransfertSyntax, 0x0002, 0x0010);
@@ -346,6 +496,5 @@ int gdcmElValSet::Write(FILE * _fp, FileType type) {
       UpdateGroupLength(true,ACR);
 
    WriteElements(type, _fp);
-
    return(1);
 }