-// gdcmDocument.cxx
-//-----------------------------------------------------------------------------
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: gdcmDocument.cxx,v $
+ Language: C++
+ Date: $Date: 2004/06/20 18:08:47 $
+ Version: $Revision: 1.19 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+
+ 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 "gdcmDocument.h"
#include "gdcmValEntry.h"
# include <iomanip>
+// Implicit VR Little Endian
#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
+// Explicit VR Little Endian
#define UI1_2_840_10008_1_2_1 "1.2.840.10008.1.2.1"
-#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
+// Deflated Explicit VR Little Endian
#define UI1_2_840_10008_1_2_1_99 "1.2.840.10008.1.2.1.99"
-#define UI1_1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
+// Explicit VR Big Endian
+#define UI1_2_840_10008_1_2_2 "1.2.840.10008.1.2.2"
+// JPEG Baseline (Process 1)
+#define UI1_2_840_10008_1_2_4_50 "1.2.840.10008.1.2.4.50"
+// JPEG Extended (Process 2 & 4)
+#define UI1_2_840_10008_1_2_4_51 "1.2.840.10008.1.2.4.51"
+// JPEG Extended (Process 3 & 5)
+#define UI1_2_840_10008_1_2_4_52 "1.2.840.10008.1.2.4.52"
+// JPEG Spectral Selection, Non-Hierarchical (Process 6 & 8)
+#define UI1_2_840_10008_1_2_4_53 "1.2.840.10008.1.2.4.53"
+// JPEG Full Progression, Non-Hierarchical (Process 10 & 12)
+#define UI1_2_840_10008_1_2_4_55 "1.2.840.10008.1.2.4.55"
+// JPEG Lossless, Non-Hierarchical (Process 14)
+#define UI1_2_840_10008_1_2_4_57 "1.2.840.10008.1.2.4.57"
+// JPEG Lossless, Hierarchical, First-Order Prediction (Process 14,
+// [Selection Value 1])
+#define UI1_2_840_10008_1_2_4_70 "1.2.840.10008.1.2.4.70"
+// JPEG 2000 Lossless
+#define UI1_2_840_10008_1_2_4_90 "1.2.840.10008.1.2.4.90"
+// JPEG 2000
+#define UI1_2_840_10008_1_2_4_91 "1.2.840.10008.1.2.4.91"
+// RLE Lossless
+#define UI1_2_840_10008_1_2_5 "1.2.840.10008.1.2.5"
#define str2num(str, typeNum) *((typeNum *)(str))
if ( !OpenFile(exception_on_error))
return;
+ dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
+ filename.c_str());
rewind(fp);
- //if (!CheckSwap())
- // return false; // to go on compiling
fseek(fp,0L,SEEK_END);
long lgt = ftell(fp);
gdcmDocument::~gdcmDocument (void) {
RefPubDict = NULL;
RefShaDict = NULL;
+
+ // Recursive clean up of sequences
+ for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it )
+ {
+ delete (it->second);
+ }
+ tagHT.clear();
}
//-----------------------------------------------------------------------------
// Print
-/**
-
/**
* \brief Prints The Dict Entries of THE public Dicom Dictionary
*/
bool gdcmDocument::IsReadable(void) {
if(filetype==gdcmUnknown) {
- std::cout << "wrong filetype" <<std::endl;
+ dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
return(false);
}
if(!tagHT.empty()<=0) {
- std::cout << "wrong tagHT size "<< tagHT.size() <<std::endl;
+ dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal"
+ " hash table.");
return(false);
}
}
/**
- * \brief Determines if the Transfer Syntax was already encountered
- * and if it corresponds to a ImplicitVRLittleEndian one.
- * @return True when ImplicitVRLittleEndian found. False in all other cases.
+ * \brief Internal function that checks whether the Transfer Syntax given
+ * as argument is the one present in the current document.
+ * @param SyntaxToCheck The transfert syntax we need to check against.
+ * @return True when SyntaxToCheck corresponds to the Transfer Syntax of
+ * the current document. False either when the document contains
+ * no Transfer Syntax, or when the Tranfer Syntaxes don't match.
*/
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry *Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
+bool gdcmDocument::IsGivenTransferSyntax(const std::string & SyntaxToCheck)
+{
+ gdcmDocEntry *Entry = GetDocEntryByNumber(0x0002, 0x0010);
+ if ( !Entry )
return false;
- LoadDocEntrySafe(Element);
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2 )
- return true;
+ // The entry might be present but not loaded (parsing and loading
+ // happen at differente stages): try loading and proceed with check...
+ LoadDocEntrySafe(Entry);
+ if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(Entry) )
+ {
+ std::string Transfer = ValEntry->GetValue();
+ // The actual transfer (as read from disk) might be padded. We
+ // first need to remove the potential padding. We can make the
+ // weak assumption that padding was not executed with digits...
+ while ( ! isdigit(Transfer[Transfer.length()-1]) )
+ {
+ Transfer.erase(Transfer.length()-1, 1);
+ }
+ if ( Transfer == SyntaxToCheck )
+ return true;
+ }
return false;
}
+/**
+ * \brief Determines if the Transfer Syntax of the present document
+ * corresponds to a Implicit Value Representation of
+ * Little Endian.
+ * \sa \ref gdcmDocument::IsGivenTransferSyntax.
+ * @return True when ImplicitVRLittleEndian found. False in all other cases.
+ */
+bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
+}
+
/**
* \brief Determines if the Transfer Syntax was already encountered
* and if it corresponds to a ExplicitVRLittleEndian one.
* @return True when ExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
-
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1 )
- return true;
- return false;
+bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1);
}
/**
* and if it corresponds to a DeflatedExplicitVRLittleEndian one.
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
-
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_1_99 )
- return true;
- return false;
+bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99);
}
/**
* and if it corresponds to a Explicit VR Big Endian one.
* @return True when big endian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void) {
- gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !Element )
- return false;
- LoadDocEntrySafe(Element);
+bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
+}
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
- return true;
- return false;
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGBaseLineProcess1 one.
+ * @return True when JPEGBaseLineProcess1found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendedProcess2-4 one.
+ * @return True when JPEGExtendedProcess2-4 found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGExtendeProcess3-5 one.
+ * @return True when JPEGExtendedProcess3-5 found. False in all other cases.
+ */
+bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEGSpectralSelectionProcess6-8 one.
+ * @return True when JPEGSpectralSelectionProcess6-8 found. False in all
+ * other cases.
+ */
+bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a RLE Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmDocument::IsRLELossLessTransferSyntax(void)
+{
+ return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
+}
+
+/**
+ * \brief Determines if Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG Lossless one.
+ * @return True when RLE Lossless found. False in all
+ * other cases.
+ */
+bool gdcmDocument::IsJPEGLossless(void)
+{
+ return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90) );
+}
+
+/**
+ * \brief Determines if the Transfer Syntax was already encountered
+ * and if it corresponds to a JPEG2000 one
+ * @return True when JPEG2000 (Lossly or LossLess) found. False in all
+ * other cases.
+ */
+bool gdcmDocument::IsJPEG2000(void)
+{
+ return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90)
+ || IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
+}
+
+/**
+ * \brief Predicate for dicom version 3 file.
+ * @return True when the file is a dicom version 3.
+ */
+bool gdcmDocument::IsDicomV3(void) {
+ // Checking if Transfert Syntax exists is enough
+ // Anyway, it's to late check if the 'Preamble' was found ...
+ // And ... would it be a rich idea to check ?
+ // (some 'no Preamble' DICOM images exist !)
+ return (GetDocEntryByNumber(0x0002, 0x0010) != NULL);
}
/**
throw(gdcmFileError)
{
fp=fopen(filename.c_str(),"rb");
- if(exception_on_error)
+
+ if(!fp)
{
- if(!fp)
- throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
+ if(exception_on_error)
+ throw gdcmFileError("gdcmDocument::gdcmDocument(const char *, bool)");
+ else
+ {
+ std::cout <<"gdcmDocument::OpenFile cannot open file: "
+ << filename.c_str() << std::endl;
+ dbg.Verbose(0, "gdcmDocument::OpenFile cannot open file: ",
+ filename.c_str());
+ return (NULL);
+ }
}
if ( fp )
/**
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
- * \warning Adds the Header Entry to the HTable, NOT to the chained List
- * @param Value Value to be set
- * @param Group Group of the Entry
- * @param Elem Element of the Entry
+ * @param Value (string) Value to be set
+ * @param Group Group number of the Entry
+ * @param Elem Element number of the Entry
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-
-
-gdcmDocEntry * gdcmDocument::ReplaceOrCreateByNumber(
+
+gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
std::string Value,
guint16 Group,
guint16 Elem ){
+ gdcmDocEntry* CurrentEntry;
+ gdcmValEntry* ValEntry;
+
+ CurrentEntry = GetDocEntryByNumber( Group, Elem);
+ if (!CurrentEntry)
+ {
+ // The entry wasn't present and we simply create the required ValEntry:
+ CurrentEntry = NewDocEntryByNumber(Group, Elem);
+ if (!CurrentEntry)
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
+ " NewDocEntryByNumber failed.");
+ return (gdcmValEntry *)0;
+ }
+ ValEntry = new gdcmValEntry(CurrentEntry);
+ if ( !AddEntry(ValEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
+ " failed allthough this is a creation.");
+ }
+ }
+ else
+ {
+ ValEntry = dynamic_cast< gdcmValEntry* >(CurrentEntry);
+ if ( !ValEntry )
+ {
+ // We need to promote the gdcmDocEntry to a gdcmValEntry:
+ ValEntry = new gdcmValEntry(CurrentEntry);
+ if (!RemoveEntry(CurrentEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
+ " of previous DocEntry failed.");
+ return (gdcmValEntry *)0;
+ }
+ if ( !AddEntry(ValEntry))
+ {
+ dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
+ " promoted ValEntry failed.");
+ return (gdcmValEntry *)0;
+ }
+ }
+ }
+
+ SetEntryByNumber(Value, Group, Elem);
+
+ return ValEntry;
+}
+
+/*
+ * \brief Modifies the value of a given Header Entry (Dicom Element)
+ * when it exists. Create it with the given value when unexistant.
+ * @param voidArea (binary) value to be set
+ * @param Group Group number of the Entry
+ * @param Elem Element number of the Entry
+ * \return pointer to the modified/created Header Entry (NULL when creation
+ * failed).
+ */
+gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
+ void *voidArea,
+ int lgth,
+ guint16 Group,
+ guint16 Elem)
+{
gdcmDocEntry* a;
+ gdcmBinEntry* b;
a = GetDocEntryByNumber( Group, Elem);
if (a == NULL) {
- a =NewDocEntryByNumber(Group, Elem);
+ a =NewBinEntryByNumber(Group, Elem);
if (a == NULL)
return NULL;
- AddEntry(a);
+ b = new gdcmBinEntry(a);
+ AddEntry(b);
}
- SetEntryByNumber(Value, Group, Elem);
- //a->SetValue(Value);
- return(a);
-}
+ SetEntryByNumber(voidArea, lgth, Group, Elem);
+ b->SetVoidArea(voidArea);
+ return (gdcmBinEntry*)b;
+}
+
+
/**
* \brief Set a new value if the invoked element exists
* Seems to be useless !!!
* @param Value new element value
- * @param Group group of the Entry
- * @param Elem element of the Entry
+ * @param Group group number of the Entry
+ * @param Elem element number of the Entry
* \return boolean
*/
bool gdcmDocument::ReplaceIfExistByNumber(char* Value, guint16 Group, guint16 Elem )
// Protected
/**
- * \brief Checks if a given Dicom Element exists
- * within the H table
- * @param group Group number of the searched Dicom Element
+ * \brief Checks if a given Dicom Element exists within the H table
+ * @param group Group number of the searched Dicom Element
* @param element Element number of the searched Dicom Element
* @return number of occurences
*/
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the element value representation of a given tag.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
+ * @param group Group number of the searched tag.
+ * @param element Element number of the searched tag.
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
* to convert the string typed content to caller's native type
* (think of C++ vs Python). The VR is actually of a higher level
* of semantics than just the native C++ type.
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
+ * @param group Group number of the searched tag.
+ * @param element Element number of the searched tag.
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
* \brief Searches within Header Entries (Dicom Elements) parsed with
* the public and private dictionaries
* for the value length of a given tag..
- * @param group Group of the searched tag.
- * @param element Element of the searched tag.
+ * @param group Group number of the searched tag.
+ * @param element Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
int gdcmDocument::GetEntryLengthByNumber(guint16 group, guint16 element) {
* \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
- * @param content new value to substitute with
- * @param group group of the Dicom Element to modify
- * @param element element of the Dicom Element to modify
+ * @param content new value (string) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
*/
bool gdcmDocument::SetEntryByNumber(std::string content,
guint16 group,
guint16 element)
{
- TagKey key = gdcmDictEntry::TranslateToKey(group, element);
- if ( ! tagHT.count(key))
+ gdcmValEntry* ValEntry = GetValEntryByNumber(group, element);
+ if (!ValEntry)
+ {
+ dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding",
+ " ValEntry (try promotion first).");
return false;
- int l = content.length();
- if(l%2) // Non even length are padded with a space (020H).
- {
- l++;
- content = content + '\0';
}
+
+ // Non even content must be padded with a space (020H).
+ if((content.length())%2)
+ content = content + '\0';
- gdcmDocEntry * a;
- a = tagHT[key];
-
- ((gdcmValEntry*)a)->SetValue(content);
-
- std::string vr = a->GetVR();
+ ValEntry->SetValue(content);
- guint32 lgr;
+ // Integers have a special treatement for their length:
+ VRKey vr = ValEntry->GetVR();
if( (vr == "US") || (vr == "SS") )
- lgr = 2;
+ ValEntry->SetLength(2);
else if( (vr == "UL") || (vr == "SL") )
- lgr = 4;
+ ValEntry->SetLength(4);
else
- lgr = l;
+ ValEntry->SetLength(content.length());
- a->SetLength(lgr);
return true;
-}
+}
+
+/**
+ * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * through it's (group, element) and modifies it's content with
+ * the given value.
+ * @param content new value (void *) to substitute with
+ * @param group group number of the Dicom Element to modify
+ * @param element element number of the Dicom Element to modify
+ */
+bool gdcmDocument::SetEntryByNumber(void *content,
+ int lgth,
+ guint16 group,
+ guint16 element)
+{
+ TagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ if ( ! tagHT.count(key))
+ return false;
+
+/* Hope Binray field length is never wrong
+ if(lgth%2) // Non even length are padded with a space (020H).
+ {
+ lgth++;
+ //content = content + '\0'; // fing a trick to enlarge a binary field?
+ }
+*/
+ gdcmBinEntry * a;
+ a = (gdcmBinEntry *)tagHT[key];
+ a->SetVoidArea(content);
+ //a->SetLength(lgth); // ???
+ return true;
+}
/**
* \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
* the given value.
* \warning Use with extreme caution.
* @param l new length to substitute with
- * @param group group of the Entry to modify
- * @param element element of the Entry to modify
+ * @param group group number of the Entry to modify
+ * @param element element number of the Entry to modify
* @return true on success, false otherwise.
*/
bool gdcmDocument::SetEntryLengthByNumber(guint32 l,
/**
* \brief Gets (from Header) the offset of a 'non string' element value
* (LoadElementValues has already be executed)
- * @param Group group of the Entry
- * @param Elem element of the Entry
+ * @param Group group number of the Entry
+ * @param Elem element number of the Entry
* @return File Offset of the Element Value
*/
size_t gdcmDocument::GetEntryOffsetByNumber(guint16 Group, guint16 Elem)
/**
* \brief Gets (from Header) a 'non string' element value
* (LoadElementValues has already be executed)
- * @param Group group of the Entry
- * @param Elem element of the Entry
+ * @param Group group number of the Entry
+ * @param Elem element number of the Entry
* @return Pointer to the 'non string' area
*/
void * gdcmDocument::GetEntryVoidAreaByNumber(guint16 Group, guint16 Elem)
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param Group group of the Entry
- * @param Elem element of the Entry
+ * @param Group group number of the Entry
+ * @param Elem element number of the Entry
*/
void *gdcmDocument::LoadEntryVoidArea(guint16 Group, guint16 Elem)
{
/**
* \brief Sets a 'non string' value to a given Dicom Element
* @param area
- * @param group Group number of the searched Dicom Element
+ * @param group Group number of the searched Dicom Element
* @param element Element number of the searched Dicom Element
* @return
*/
gdcmDictEntry *entry;
std::string vr;
- // TODO : if still any use (?) explore recursively the whole structure
+ /// \todo TODO : still any use to explore recursively the whole structure?
/*
for(ListTag::iterator it=listEntries.begin();
it!=listEntries.end();
CheckDocEntryVR(*it,vr);
(*it)->SetValue(GetDocEntryValue(*it)); // to go on compiling
-
+
}
else
{
return tagHT.find(key)->second;
}
+/**
+ * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only
+ * returns a result when the corresponding entry is of type
+ * ValEntry.
+ * @return When present, the corresponding ValEntry.
+ */
+gdcmValEntry* gdcmDocument::GetValEntryByNumber(guint16 group, guint16 element)
+{
+ gdcmDocEntry* CurrentEntry = GetDocEntryByNumber(group, element);
+ if (! CurrentEntry)
+ return (gdcmValEntry*)0;
+ if ( gdcmValEntry* ValEntry = dynamic_cast<gdcmValEntry*>(CurrentEntry) )
+ {
+ return ValEntry;
+ }
+ dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
+ return (gdcmValEntry*)0;
+}
+
/**
* \brief Loads the element while preserving the current
* underlying file position indicator as opposed to
FileType type)
{
guint16 group = tag->GetGroup();
- std::string vr = tag->GetVR();
+ VRKey vr = tag->GetVR();
guint16 el = tag->GetElement();
guint32 lgr = tag->GetReadLength();
* @param type type of the File to be written
*/
- // TODO : to be re -written recursively !
-
+// \todo TODO : to be re -written recursively !
void gdcmDocument::WriteEntryValue(gdcmDocEntry *tag, FILE *_fp,FileType type)
{
(void)type;
guint16 group = tag->GetGroup();
- std::string vr = tag->GetVR();
+ VRKey vr = tag->GetVR();
guint32 lgr = tag->GetReadLength();
if (vr == "SQ")
if (group == 0xfffe)
// Delimiters have no associated value:
return;
-
- void *voidArea;
- // voidArea = tag->GetVoidArea(); // to go on compiling
- if (voidArea != NULL)
- { // there is a 'non string' LUT, overlay, etc
- fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
- return;
- }
-
+
+ //--------------------------------
+ //
+ // FIXME :right now, both value and voidArea belong to gdcmValue
+ //
+ // -------------------------------
+
+// if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) ) {
+ void *voidArea;
+ gdcmBinEntry *BinEntry= (gdcmBinEntry *)tag;;
+ voidArea = BinEntry->GetVoidArea();
+ if (voidArea != NULL)
+ { // there is a 'non string' LUT, overlay, etc
+ fwrite ( voidArea,(size_t)lgr ,(size_t)1 ,_fp); // Elem value
+ return;
+ }
+// }
+
if (vr == "US" || vr == "SS")
{
// some 'Short integer' fields may be mulivaluated
tokens.clear();
return;
}
- // some 'Integer' fields may be mulivaluated
- // each single value is separated from the next one by '\'
- // we split the string and write each value as an int
if (vr == "UL" || vr == "SL")
{
+ // Some 'Integer' fields may be multivaluated (multiple instances
+ // of integers). But each single integer value is separated from the
+ // next one by '\' (backslash character). Hence we split the string
+ // along the '\' and write each value as an int:
std::vector<std::string> tokens;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
Tokenize (((gdcmValEntry *)tag)->GetValue(), tokens, "\\");
tokens.clear();
return;
}
- fwrite (((gdcmValEntry *)tag)->GetValue().c_str(), (size_t)lgr ,(size_t)1, _fp); // Elem value
+ fwrite (((gdcmValEntry *)tag)->GetValue().c_str(),
+ (size_t)lgr ,(size_t)1, _fp); // Elem value
}
/**
{
guint32 length = tag->GetLength();
- // The value of a tag MUST (see the DICOM norm) be an odd number of
- // bytes. When this is not the case, pad with an additional byte:
- if(length%2==1)
- {
-// tag->SetValue(tag->GetValue()+"\0"); // to go on compiling
- tag->SetLength(tag->GetReadLength()+1);
+ if (gdcmValEntry* ValEntry = dynamic_cast< gdcmValEntry* >(tag) )
+ {
+ // The value of a tag MUST (see the DICOM norm) be an odd number of
+ // bytes. When this is not the case, pad with an additional byte:
+ if(length%2==1) {
+ ValEntry->SetValue(ValEntry->GetValue()+"\0");
+ ValEntry->SetLength(ValEntry->GetReadLength()+1);
+ }
+ WriteEntryTagVRLength(ValEntry, _fp, type);
+ WriteEntryValue(ValEntry, _fp, type);
+ return true;
}
- WriteEntryTagVRLength(tag, _fp, type);
- WriteEntryValue(tag, _fp, type);
- return true;
+ if (gdcmBinEntry* BinEntry = dynamic_cast< gdcmBinEntry* >(tag) )
+ {
+ /// \todo FIXME : when voidArea belong to gdcmBinEntry only, fix
+ /// voidArea length
+ //
+ // The value of a tag MUST (see the DICOM norm) be an odd number of
+ // bytes. When this is not the case, pad with an additional byte:
+/*
+ if(length%2==1) {
+ tag->SetValue(tag->GetValue()+"\0");
+ tag->SetLength(tag->GetReadLength()+1);
+ }
+*/
+ WriteEntryTagVRLength(tag, _fp, type);
+ WriteEntryValue(tag, _fp, type);
+ return true;
+ }
}
/**
* (function CheckHeaderCoherence to be written)
* \warning DON'T try, right now, to write a DICOM image
* from an ACR Header (meta elements will be missing!)
- * \sa WriteEntriesDeprecated (Special temporary method for Theralys)
* @param type type of the File to be written
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* @param _fp already open file pointer
bool gdcmDocument::WriteEntries(FILE *_fp,FileType type)
{
-
-// FIXME : explore recursively the whole structure...
-
+ /// \todo FIXME : explore recursively the whole structure...
/// \todo (?) check write failures (after *each* fwrite)
-
- for (TagDocEntryHT::iterator tag2=tagHT.begin();
- tag2 != tagHT.end();
- ++tag2)
+
+ dbg.Verbose(0, "gdcmDocument::WriteEntries: entering.");
+ for (TagDocEntryHT::iterator it = tagHT.begin(); it != tagHT.end(); ++it )
{
+ gdcmDocEntry * entry = it->second;
+
if ( type == gdcmACR ){
- if ((*tag2).second->GetGroup() < 0x0008)
+ if (entry->GetGroup() < 0x0008)
// Ignore pure DICOM V3 groups
continue;
- if ((*tag2).second->GetElement() %2)
+ if (entry->GetGroup() %2)
// Ignore the "shadow" groups
continue;
- if ((*tag2).second->GetVR() == "SQ" ) // ignore Sequences
- continue;
- if ((*tag2).second->GetSQDepthLevel() != 0) // Not only ignore the SQ element
- continue;
+ if (entry->GetVR() == "SQ" ) // ignore Sequences
+ continue;
}
- if (! WriteEntry((*tag2).second,_fp,type) )
+ if (! WriteEntry(entry, _fp, type) ) {
+ dbg.Verbose(0, "gdcmDocument::WriteEntries: write failure.");
return false;
+ }
}
return true;
}
long gdcmDocument::ParseDES(gdcmDocEntrySet *set, long offset, long l_max, bool delim_mode) {
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
- gdcmValEntry *vl;
+ gdcmValEntry *NewValEntry = (gdcmValEntry *)0;
gdcmBinEntry *bn;
gdcmSeqEntry *sq;
- string vr;
+ VRKey vr;
long l;
int depth;
NewDocEntry = ReadNextDocEntry( );
if (!NewDocEntry)
break;
-
- vr = NewDocEntry->GetVR();
- if (vr!="SQ") {
+
+ vr = NewDocEntry->GetVR();
+ if (vr!="SQ")
+ {
- if (vr == "AE" || vr == "AS" || vr == "DA" || vr == "PN" ||
- vr == "UI" || vr == "TM" || vr == "SH" || vr == "LO" ||
- vr == "CS" || vr == "IS" || vr == "LO" || vr == "LT" ||
- vr == "SH" || vr == "ST" || vr == "DS" ||
- vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
- ) {
- // --- ValEntry
- vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- vl->SetDepthLevel(depth),
- set->AddEntry(vl);
- LoadDocEntry(vl);
- if (/*!delim_mode && */vl->isItemDelimitor())
+ if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ {
+ /////// ValEntry
+ NewValEntry = new gdcmValEntry(NewDocEntry->GetDictEntry());
+ NewValEntry->Copy(NewDocEntry);
+ NewValEntry->SetDepthLevel(depth);
+ set->AddEntry(NewValEntry);
+ LoadDocEntry(NewValEntry);
+ if (/*!delim_mode && */NewValEntry->isItemDelimitor())
break;
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ {
break;
- }
- } else { // BinEntry
-
- // Hope the following VR *do* correspond to a BinEntry
-
- //AT Attribute Tag; // 2 16-bit unsigned short integers
- //FL Floating Point Single; // 32-bit IEEE 754:1985 float
- //FD Floating Point Double; // 64-bit IEEE 754:1985 double
- //UN Unknown; // Any length of bytes
- //UT Unlimited Text; // At most 2^32 -1 chars
- //OB Other Byte String; // String of bytes (VR independant)
- //OW Other Word String; // String of 16-bit words (VR dependant)
-
+ }
+ }
+ else
+ {
+ if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
+ "nor BinEntry. Probably unknown VR.");
+ }
+
+ ////// BinEntry or UNKOWN VR:
bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
- bn->Copy(NewDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
- }
- if (NewDocEntry->GetGroup() == 0x7fe0 &&
- NewDocEntry->GetElement() == 0x0010 ) {
- if (NewDocEntry->GetLength()==0xffffffff)
- // Broke US.3405.1.dcm
-
+ bn->Copy(NewDocEntry);
+ set->AddEntry(bn);
+ LoadDocEntry(bn);
+ }
+
+ if (NewDocEntry->GetGroup() == 0x7fe0 &&
+ NewDocEntry->GetElement() == 0x0010 )
+ {
+ if (NewDocEntry->GetLength()==0xffffffff)
+ // Broken US.3405.1.dcm
Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
- } else {
- SkipToNextDocEntry(NewDocEntry); // to be sure we are at the beginning
- l = NewDocEntry->GetFullLength();
- }
- } else { // VR = "SQ"
+ // (multipart JPEG/RLE are trouble makers)
+ }
+ else
+ {
+ // to be sure we are at the beginning
+ SkipToNextDocEntry(NewDocEntry);
+ l = NewDocEntry->GetFullLength();
+ }
+ }
+ else
+ { // VR = "SQ"
l=NewDocEntry->GetReadLength();
if (l != 0) // don't mess the delim_mode for zero-length sequence
delim_mode = true;
else
delim_mode = false;
- // no other way to create it ...
- sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),set->GetDepthLevel());
+ // no other way to create it ...
+ sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),
+ set->GetDepthLevel());
sq->Copy(NewDocEntry);
- sq->SetDelimitorMode(delim_mode);
- sq->SetDepthLevel(depth);
+ sq->SetDelimitorMode(delim_mode);
+ sq->SetDepthLevel(depth);
- if (l != 0) { // Don't try to parse zero-length sequences
-
+ if (l != 0)
+ { // Don't try to parse zero-length sequences
long lgt = ParseSQ( sq,
NewDocEntry->GetOffset(),
l, delim_mode);
- }
- // FIXME : on en fait quoi, de lgt ?
+ }
+ // FIXME : on en fait quoi, de lgt ?
set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ {
break;
- }
- }
+ }
+ }
+ delete NewDocEntry;
}
- delete NewDocEntry;
return l; // ??
}
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-long gdcmDocument::ParseSQ(gdcmSeqEntry *set, long offset, long l_max, bool delim_mode) {
+long gdcmDocument::ParseSQ(gdcmSeqEntry *set,
+ long offset, long l_max, bool delim_mode)
+{
int SQItemNumber = 0;
+
gdcmDocEntry *NewDocEntry = (gdcmDocEntry *)0;
gdcmSQItem *itemSQ;
bool dlm_mod;
int lgr, l, lgth;
int depth = set->GetDepthLevel();
+
while (true) {
-
NewDocEntry = ReadNextDocEntry();
if(delim_mode) {
- if (NewDocEntry->isSequenceDelimitor()) {
- //add the Sequence Delimitor // TODO : find the trick to put it properly !
- set->SetSequenceDelimitationItem(NewDocEntry);
- break;
- }
- }
+ if (NewDocEntry->isSequenceDelimitor()) {
+ /// \todo add the Sequence Delimitor
+ /// \todo find the trick to put it properly !
+ set->SetSequenceDelimitationItem(NewDocEntry);
+ break;
+ }
+ }
if (!delim_mode && (ftell(fp)-offset) >= l_max) {
- break;
+ break;
}
+
itemSQ = new gdcmSQItem(set->GetDepthLevel());
- itemSQ->AddEntry(NewDocEntry); // no value, no voidArea. Think of it while printing !
+ itemSQ->AddEntry(NewDocEntry);
+ /// \todo no value, no voidArea. Think of it while printing !
l= NewDocEntry->GetReadLength();
- if (l ==0xffffffff)
+ if (l == 0xffffffff)
dlm_mod = true;
else
dlm_mod=false;
-
+
lgr=ParseDES(itemSQ, NewDocEntry->GetOffset(), l, dlm_mod);
- set->AddEntry(itemSQ);
- SQItemNumber ++; // a voir
+ set->AddEntry(itemSQ,SQItemNumber);
+ SQItemNumber ++;
if (!delim_mode && (ftell(fp)-offset) >= l_max) {
break;
- }
+ }
}
lgth = ftell(fp) - offset;
return(lgth);
* the value specified with gdcmDocument::SetMaxSizeLoadEntry()
* @param Entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry) {
+void gdcmDocument::LoadDocEntry(gdcmDocEntry *Entry)
+{
size_t item_read;
guint16 group = Entry->GetGroup();
std::string vr= Entry->GetVR();
// are not loaded. Instead we leave a short notice of the offset of
// the element content and it's length.
if (length > MaxSizeLoadEntry) {
- std::ostringstream s;
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+ if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) )
+ {
+ std::ostringstream s;
+ s << "gdcm::NotLoaded.";
+ s << " Address:" << (long)Entry->GetOffset();
+ s << " Length:" << Entry->GetLength();
+ s << " x(" << std::hex << Entry->GetLength() << ")";
+ ValEntryPtr->SetValue(s.str());
+ }
// to be sure we are at the end of the value ...
fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
/**
* \brief When the length of an element value is obviously wrong (because
* the parser went Jabberwocky) one can hope improving things by
- * applying this heuristic.
+ * applying some heuristics.
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry, guint32 FoundLength)
+void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *Entry,
+ guint32 FoundLength)
{
Entry->SetReadLength(FoundLength); // will be updated only if a bug is found
if ( FoundLength == 0xffffffff) {
if (FoundLength%2) {
std::ostringstream s;
- s << "Warning : Tag with uneven length " << FoundLength
- << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
- dbg.Verbose(0,s.str().c_str());
+ s << "Warning : Tag with uneven length "
+ << FoundLength
+ << " in x(" << std::hex << gr << "," << el <<")" << std::dec;
+ dbg.Verbose(0, s.str().c_str());
}
- // Sorry for the patch!
- // XMedCom did the trick to read some naughty GE images ...
- if (FoundLength == 13) {
- // The following 'if' will be removed when there is no more
- // images on Creatis HDs with a 13 length for Manufacturer...
- if ( (Entry->GetGroup() != 0x0008) ||
- ( (Entry->GetElement() != 0x0070) && (Entry->GetElement() != 0x0080) ) ){
- // end of remove area
- FoundLength =10;
- Entry->SetReadLength(10); // a bug is to be fixed
+ //////// Fix for some naughty General Electric images.
+ // Allthough not recent many such GE corrupted images are still present
+ // on Creatis hard disks. Hence this fix shall remain when such images
+ // are no longer in user (we are talking a few years, here)...
+ // Note: XMedCom probably uses such a trick since it is able to read
+ // those pesky GE images ...
+ if (FoundLength == 13) { // Only happens for this length !
+ if ( (Entry->GetGroup() != 0x0008)
+ || ( (Entry->GetElement() != 0x0070)
+ && (Entry->GetElement() != 0x0080) ) )
+ {
+ FoundLength = 10;
+ Entry->SetReadLength(10); /// \todo a bug is to be fixed !?
}
}
- // to fix some garbage 'Leonardo' Siemens images
- // May be commented out to avoid overhead
- else if ( (Entry->GetGroup() == 0x0009) &&
- ( (Entry->GetElement() == 0x1113) || (Entry->GetElement() == 0x1114) ) ){
- FoundLength =4;
- Entry->SetReadLength(4); // a bug is to be fixed
+ //////// Fix for some brain-dead 'Leonardo' Siemens images.
+ // Occurence of such images is quite low (unless one leaves close to a
+ // 'Leonardo' source. Hence, one might consider commenting out the
+ // following fix on efficiency reasons.
+ else
+ if ( (Entry->GetGroup() == 0x0009)
+ && ( (Entry->GetElement() == 0x1113)
+ || (Entry->GetElement() == 0x1114) ) )
+ {
+ FoundLength = 4;
+ Entry->SetReadLength(4); /// \todo a bug is to be fixed !?
}
- // end of fix
- // to try to 'go inside' SeQuences (with length), and not to skip them
- else if ( Entry->GetVR() == "SQ")
- {
- if (enableSequences) // only if the user does want to !
- FoundLength =0; // ReadLength is unchanged
+ //////// Deal with sequences, but only on users request:
+ else
+ if ( ( Entry->GetVR() == "SQ") && enableSequences)
+ {
+ FoundLength = 0; // ReadLength is unchanged
}
- // we found a 'delimiter' element
- // fffe|xxxx is just a marker, we don't take its length into account
- else if(Entry->GetGroup() == 0xfffe)
+ //////// We encountered a 'delimiter' element i.e. a tag of the form
+ // "fffe|xxxx" which is just a marker. Delimiters length should not be
+ // taken into account.
+ else
+ if(Entry->GetGroup() == 0xfffe)
{
- // *normally, fffe|0000 doesn't exist !
- if( Entry->GetElement() != 0x0000 ) // gdcm-MR-PHILIPS-16-Multi-Seq.dcm
- // causes extra troubles :-(
- FoundLength =0;
+ // According to the norm, fffe|0000 shouldn't exist. BUT the Philips
+ // image gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm happens to
+ // causes extra troubles...
+ if( Entry->GetElement() != 0x0000 )
+ {
+ FoundLength = 0;
+ }
}
Entry->SetUsableLength(FoundLength);
guint16 group = Entry->GetGroup();
std::string vr = Entry->GetVR();
guint32 length = Entry->GetLength();
+
// When we have some semantics on the element we just read, and if we
// a priori know we are dealing with an integer, then we shall be
// able to swap it's element value properly.
return true;
else
{
+ // Allthough this should never happen, still some images have a
+ // corrupted group length [e.g. have a glance at offset x(8336) of
+ // gdcmData/gdcm-MR-PHILIPS-16-Multi-Seq.dcm].
+ // Since for dicom compliant and well behaved headers, the present
+ // test is useless (and might even look a bit paranoid), when we
+ // encounter such an ill-formed image, we simply display a warning
+ // message and proceed on parsing (while crossing fingers).
std::ostringstream s;
int filePosition = ftell(fp);
s << "Erroneous Group Length element length on : (" \
<< std::hex << group << " , " << element
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length;
- // These 2 lines commented out : a *very dirty* patch
- // to go on PrintHeader'ing gdcm-MR-PHILIPS-16-Multi-Seq.dcm.
- // have a glance at offset x(8336) ...
- // For *regular* headers, the test is useless..
- // lets's print a warning message and go on,
- // instead of giving up with an error message
-
- //std::cout << s.str().c_str() << std::endl;
- // dbg.Error("gdcmDocument::IsDocEntryAnInteger",
- // s.str().c_str());
+ dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() );
}
}
+
if ( (vr == "UL") || (vr == "US") || (vr == "SL") || (vr == "SS") )
return true;
return false;
}
+
/**
* \brief Find the Length till the next sequence delimiter
* \warning NOT end user intended method !
// header parsing has to be considered as finished.
return (gdcmDocEntry *)0;
-// Pb : how to propagate the element length (used in SkipDocEntry)
-// direct call to SkipBytes ?
-
-// if (ignoreShadow == 1 && g%2 ==1)
- // if user wants to skip shadow groups
- // and current element *is* a shadow element
- // we don't create anything
-// return (gdcmDocEntry *)1; // to tell caller it's NOT finished
-
NewEntry = NewDocEntryByNumber(g, n);
FindDocEntryVR(NewEntry);
FindDocEntryLength(NewEntry);
/**
* \brief Request a new virtual dict entry to the dict set
- * @param group group of the underlying DictEntry
- * @param element element of the underlying DictEntry
+ * @param group group number of the underlying DictEntry
+ * @param element element number of the underlying DictEntry
* @param vr VR of the underlying DictEntry
* @param fourth owner group
* @param name english name
* \brief Build a new Element Value from all the low level arguments.
* Check for existence of dictionary entry, and build
* a default one when absent.
- * @param Group group of the underlying DictEntry
- * @param Elem element of the underlying DictEntry
+ * @param Group group number of the underlying DictEntry
+ * @param Elem element number of the underlying DictEntry
*/
-gdcmDocEntry *gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem)
+gdcmDocEntry* gdcmDocument::NewDocEntryByNumber(guint16 Group, guint16 Elem)
{
// Find out if the tag we encountered is in the dictionaries:
gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
{
dbg.Verbose(1, "gdcmDocument::NewDocEntryByNumber",
"failed to allocate gdcmDocEntry");
+ return (gdcmDocEntry*)0;
+ }
+ return NewEntry;
+}
+
+
+/**
+ * \brief Build a new Element Value from all the low level arguments.
+ * Check for existence of dictionary entry, and build
+ * a default one when absent.
+ * @param Group group number of the underlying DictEntry
+ * @param Elem element number of the underlying DictEntry
+ */
+gdcmValEntry *gdcmDocument::NewValEntryByNumber(guint16 Group, guint16 Elem)
+{
+ // Find out if the tag we encountered is in the dictionaries:
+ gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
+ if (!DictEntry)
+ DictEntry = NewVirtualDictEntry(Group, Elem);
+
+ gdcmValEntry *NewEntry = new gdcmValEntry(DictEntry);
+ if (!NewEntry)
+ {
+ dbg.Verbose(1, "gdcmDocument::NewValEntryByNumber",
+ "failed to allocate gdcmValEntry");
return NULL;
}
return NewEntry;
}
-/// \todo Never used; commented out, waiting for removal.
-/**
- * \brief Small utility function that creates a new manually crafted
- * (as opposed as read from the file) gdcmDocEntry with user
- * specified name and adds it to the public tag hash table.
- * \note A fake TagKey is generated so the PubDict can keep it's coherence.
- * @param NewTagName The name to be given to this new tag.
- * @param VR The Value Representation to be given to this new tag.
- * @return The newly hand crafted Element Value.
- */
-//gdcmDocEntry *gdcmDocument::NewManualDocEntryToPubDict(std::string NewTagName,
-// std::string VR)
-//{
-// gdcmDocEntry *NewEntry = NULL;
-// guint32 StuffGroup = 0xffff; // Group to be stuffed with additional info
-// guint32 FreeElem = 0;
-// gdcmDictEntry *DictEntry = NULL;
-//
-// FreeElem = GenerateFreeTagKeyInGroup(StuffGroup);
-// if (FreeElem == UINT32_MAX)
-// {
-// dbg.Verbose(1, "gdcmHeader::NewManualDocEntryToPubDict",
-// "Group 0xffff in Public Dict is full");
-// return NULL;
-// }
-//
-// DictEntry = NewVirtualDictEntry(StuffGroup, FreeElem,
-// VR, "GDCM", NewTagName);
-// NewEntry = new gdcmDocEntry(DictEntry);
-// AddEntry(NewEntry);
-// return NewEntry;
-//}
+
+/**
+ * \brief Build a new Element Value from all the low level arguments.
+ * Check for existence of dictionary entry, and build
+ * a default one when absent.
+ * @param Group group number of the underlying DictEntry
+ * @param Elem element number of the underlying DictEntry
+ */
+gdcmBinEntry *gdcmDocument::NewBinEntryByNumber(guint16 Group, guint16 Elem)
+{
+ // Find out if the tag we encountered is in the dictionaries:
+ gdcmDictEntry *DictEntry = GetDictEntryByNumber(Group, Elem);
+ if (!DictEntry)
+ DictEntry = NewVirtualDictEntry(Group, Elem);
+
+ gdcmBinEntry *NewEntry = new gdcmBinEntry(DictEntry);
+ if (!NewEntry)
+ {
+ dbg.Verbose(1, "gdcmDocument::NewBinEntryByNumber",
+ "failed to allocate gdcmBinEntry");
+ return NULL;
+ }
+ return NewEntry;
+}
/**
* \brief Generate a free TagKey i.e. a TagKey that is not present
* exist) for the presence of the DictEntry with given
* group and element. The public dictionary has precedence on the
* shadow one.
- * @param group group of the searched DictEntry
- * @param element element of the searched DictEntry
+ * @param group group number of the searched DictEntry
+ * @param element element number of the searched DictEntry
* @return Corresponding DictEntry when it exists, NULL otherwise.
*/
gdcmDictEntry *gdcmDocument::GetDictEntryByNumber(guint16 group,guint16 element)
return found;
}
+/**
+ * \brief Assuming the internal file pointer \ref gdcmDocument::fp
+ * is placed at the beginning of a tag (TestGroup, TestElement),
+ * read the length associated to the Tag.
+ * \warning On success the internal file pointer \ref gdcmDocument::fp
+ * is modified to point after the tag and it's length.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref gdcmDocument::fp is restored to it's original position.
+ * @param TestGroup The expected group of the tag.
+ * @param TestElement The expected Element of the tag.
+ * @return On success returns the length associated to the tag. On failure
+ * returns 0.
+ */
+guint32 gdcmDocument::ReadTagLength(guint16 TestGroup, guint16 TestElement)
+{
+ guint16 ItemTagGroup;
+ guint16 ItemTagElement;
+ long PositionOnEntry = ftell(fp);
+ long CurrentPosition = ftell(fp); // On debugging purposes
+
+ //// Read the Item Tag group and element, and make
+ // sure they are respectively 0xfffe and 0xe000:
+ ItemTagGroup = ReadInt16();
+ ItemTagElement = ReadInt16();
+ if ( (ItemTagGroup != TestGroup) || (ItemTagElement != TestElement ) )
+ {
+ std::ostringstream s;
+ s << " We should have found tag (";
+ s << std::hex << TestGroup << "," << TestElement << ")" << std::endl;
+ s << " but instead we encountered tag (";
+ s << std::hex << ItemTagGroup << "," << ItemTagElement << ")"
+ << std::endl;
+ s << " at address: " << (unsigned)CurrentPosition << std::endl;
+ dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
+ dbg.Verbose(0, s.str().c_str());
+ fseek(fp, PositionOnEntry, SEEK_SET);
+ return 0;
+ }
+
+ //// Then read the associated Item Length
+ CurrentPosition=ftell(fp);
+ guint32 ItemLength;
+ ItemLength = ReadInt32();
+ {
+ std::ostringstream s;
+ s << "Basic Item Length is: "
+ << ItemLength << std::endl;
+ s << " at address: " << (unsigned)CurrentPosition << std::endl;
+ dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str());
+ }
+ return ItemLength;
+}
+
+/**
+ * \brief Read the length of an exptected Item tag i.e. (0xfffe, 0xe000).
+ * \sa \ref gdcmDocument::ReadTagLength
+ * \warning See warning of \ref gdcmDocument::ReadTagLength
+ * @return On success returns the length associated to the item tag.
+ * On failure returns 0.
+ */
+guint32 gdcmDocument::ReadItemTagLength(void)
+{
+ return ReadTagLength(0xfffe, 0xe000);
+}
+
+/**
+ * \brief Read the length of an exptected Sequence Delimiter tag i.e.
+ * (0xfffe, 0xe0dd).
+ * \sa \ref gdcmDocument::ReadTagLength
+ * \warning See warning of \ref gdcmDocument::ReadTagLength
+ * @return On success returns the length associated to the Sequence
+ * Delimiter tag. On failure returns 0.
+ */
+guint32 gdcmDocument::ReadSequenceDelimiterTagLength(void)
+{
+ return ReadTagLength(0xfffe, 0xe0dd);
+}
+
/**
- * \ingroup gdcmDocument
* \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * \ No other way so 'skip' the Data
+ * No other way so 'skip' the Data
*
*/
-void gdcmDocument::Parse7FE0 (void) {
-
+void gdcmDocument::Parse7FE0 (void)
+{
gdcmDocEntry* Element = GetDocEntryByNumber(0x0002, 0x0010);
if ( !Element )
return;
- std::string Transfer = ((gdcmValEntry *)Element)->GetValue();
- if (Transfer == UI1_2_840_10008_1_2 )
- return;
- if ( Transfer == UI1_2_840_10008_1_2_1 )
- return;
- if ( Transfer == UI1_2_840_10008_1_2_2 ) //1.2.2 ??? A verifier !
- return;
- if ( Transfer == UI1_2_840_10008_1_2_1_99 )
+ if ( IsImplicitVRLittleEndianTransferSyntax()
+ || IsExplicitVRLittleEndianTransferSyntax()
+ || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
+ || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
return;
- int nb;
- std::string str_nb=GetEntryByNumber(0x0028,0x0100);
- if (str_nb == GDCM_UNFOUND ) {
- nb = 16;
- } else {
- nb = atoi(str_nb.c_str() );
- if (nb == 12) nb =16;
+ // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
+
+ //// Read the Basic Offset Table Item Tag length...
+ guint32 ItemLength = ReadItemTagLength();
+
+ //// ... and then read length[s] itself[themselves]. We don't use
+ // the values read (BTW what is the purpous of those lengths ?)
+ if (ItemLength != 0) {
+ // BTW, what is the purpous of those length anyhow !?
+ char * BasicOffsetTableItemValue = new char[ItemLength + 1];
+ fread(BasicOffsetTableItemValue, ItemLength, 1, fp);
+ for (int i=0; i < ItemLength; i += 4){
+ guint32 IndividualLength;
+ IndividualLength = str2num(&BasicOffsetTableItemValue[i],guint32);
+ std::ostringstream s;
+ s << " Read one length: ";
+ s << std::hex << IndividualLength << std::endl;
+ dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
+ }
}
-
- guint16 ItemTagGr,ItemTagEl;
- int ln;
- long ftellRes;
- // -------------------- for Parsing : Position on begining of Jpeg/RLE Pixels
-
- if ( Transfer != UI1_1_2_840_10008_1_2_5 ) { // !RLELossLessTransferSyntax
+ if ( ! IsRLELossLessTransferSyntax() )
+ {
// JPEG Image
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
- fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item Length
- printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
- (unsigned)ftellRes,ln,ln);
- if (ln != 0) {
- // What is it used for ??
- char * BasicOffsetTableItemValue= new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- guint32 a;
- for (int i=0;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
- }
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- while ( ( ItemTagGr==0xfffe) && (ItemTagEl!=0xe0dd) ) { // Parse fragments
-
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // length
- printf(" at %x : fragment length %d x(%08x)\n",
- (unsigned)ftellRes, ln,ln);
-
- // ------------------------
- fseek(fp,ln,SEEK_CUR); // skipping (not reading) fragment pixels
- // ------------------------
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ //// We then skip (not reading them) all the fragments of images:
+ while ( ItemLength = ReadItemTagLength() )
+ {
+ SkipBytes(ItemLength);
}
- } else {
-
+ }
+ else
+ {
// RLE Image
- long RleSegmentLength[15],fragmentLength;
- guint32 nbRleSegments;
- guint32 RleSegmentOffsetTable[15];
- ftellRes=ftell(fp);
- // Basic Offset Table with Item Value
- // Item Tag
- fread(&ItemTagGr,2,1,fp); //Reading (fffe):Basic Offset Table Item Tag Gr
- fread(&ItemTagEl,2,1,fp); //Reading (e000):Basic Offset Table Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
- // Item Length
- ftellRes=ftell(fp);
- fread(&ln,4,1,fp);
- if(GetSwapCode())
- ln=SwapLong(ln); // Basic Offset Table Item Length
- printf("at %x : Basic Offset Table Item Length (\?\?) %d x(%08x)\n",
- (unsigned)ftellRes,ln,ln);
- if (ln != 0) {
- // What is it used for ??
- char * BasicOffsetTableItemValue= new char[ln+1];
- fread(BasicOffsetTableItemValue,ln,1,fp);
- guint32 a;
- for (int i=0;i<ln;i+=4){
- a=str2num(&BasicOffsetTableItemValue[i],guint32);
- printf(" x(%08x) %d\n",a,a);
- }
- }
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ long ftellRes;
+ long RleSegmentLength[15], fragmentLength;
// while 'Sequence Delimiter Item' (fffe,e0dd) not found
- while ( ( ItemTagGr == 0xfffe) && (ItemTagEl != 0xe0dd) ) {
- // Parse fragments of the current Fragment (Frame)
- ftellRes=ftell(fp);
- fread(&fragmentLength,4,1,fp);
- if(GetSwapCode())
- fragmentLength=SwapLong(fragmentLength); // length
- printf(" at %x : 'fragment' length %d x(%08x)\n",
- (unsigned)ftellRes, (unsigned)fragmentLength,(unsigned)fragmentLength);
-
- //------------------ scanning (not reading) fragment pixels
-
- fread(&nbRleSegments,4,1,fp); // Reading : Number of RLE Segments
- if(GetSwapCode())
- nbRleSegments=SwapLong(nbRleSegments);
- printf(" Nb of RLE Segments : %d\n",nbRleSegments);
+ while ( fragmentLength = ReadSequenceDelimiterTagLength() )
+ {
+ // Parse fragments of the current Fragment (Frame)
+ //------------------ scanning (not reading) fragment pixels
+ guint32 nbRleSegments = ReadInt32();
+ printf(" Nb of RLE Segments : %d\n",nbRleSegments);
- for(int k=1; k<=15; k++) { // Reading RLE Segments Offset Table
+ //// Reading RLE Segments Offset Table
+ guint32 RleSegmentOffsetTable[15];
+ for(int k=1; k<=15; k++) {
ftellRes=ftell(fp);
- fread(&RleSegmentOffsetTable[k],4,1,fp);
- if(GetSwapCode())
- RleSegmentOffsetTable[k]=SwapLong(RleSegmentOffsetTable[k]);
+ RleSegmentOffsetTable[k] = ReadInt32();
printf(" at : %x Offset Segment %d : %d (%x)\n",
(unsigned)ftellRes,k,RleSegmentOffsetTable[k],
RleSegmentOffsetTable[k]);
}
- if (nbRleSegments>1) { // skipping (not reading) RLE Segments
- for(unsigned int k=1; k<=nbRleSegments-1; k++) {
+ // skipping (not reading) RLE Segments
+ if (nbRleSegments>1) {
+ for(unsigned int k=1; k<=nbRleSegments-1; k++) {
RleSegmentLength[k]= RleSegmentOffsetTable[k+1]
- RleSegmentOffsetTable[k];
ftellRes=ftell(fp);
printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- k,(unsigned)RleSegmentLength[k],(unsigned)RleSegmentLength[k], (unsigned)ftellRes);
- fseek(fp,RleSegmentLength[k],SEEK_CUR);
+ k,(unsigned)RleSegmentLength[k],
+ (unsigned)RleSegmentLength[k], (unsigned)ftellRes);
+ SkipBytes(RleSegmentLength[k]);
}
}
+
RleSegmentLength[nbRleSegments]= fragmentLength
- RleSegmentOffsetTable[nbRleSegments];
ftellRes=ftell(fp);
printf (" Segment %d : Length = %d x(%x) Start at %x\n",
- nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments],
- (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes);
-
- fseek(fp,RleSegmentLength[nbRleSegments],SEEK_CUR);
-
- // ------------------ end of scanning fragment pixels
-
- ftellRes=ftell(fp);
- fread(&ItemTagGr,2,1,fp); // Reading (fffe) : Item Tag Gr
- fread(&ItemTagEl,2,1,fp); // Reading (e000) : Item Tag El
- if(GetSwapCode()) {
- ItemTagGr=SwapShort(ItemTagGr);
- ItemTagEl=SwapShort(ItemTagEl);
- }
- printf ("at %x : ItemTag (should be fffe,e000 or e0dd): %04x,%04x\n",
- (unsigned)ftellRes,ItemTagGr,ItemTagEl );
+ nbRleSegments,(unsigned)RleSegmentLength[nbRleSegments],
+ (unsigned)RleSegmentLength[nbRleSegments],(unsigned)ftellRes);
+ SkipBytes(RleSegmentLength[nbRleSegments]);
}
}
return;
}
+/**
+ * \brief Compares two documents, according to \ref gdcmDicomDir rules
+ * \warning Does NOT work with ACR-NEMA files
+ * \todo Find a trick to solve the pb (use RET fields ?)
+ * @param document
+ * @return true if 'smaller'
+ */
+ bool gdcmDocument::operator<(gdcmDocument &document){
+ std::string s1,s2;
+
+ // Patient Name
+ s1=this->GetEntryByNumber(0x0010,0x0010);
+ s2=document.GetEntryByNumber(0x0010,0x0010);
+ if(s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Patient ID
+ s1=this->GetEntryByNumber(0x0010,0x0020);
+ s2=document.GetEntryByNumber(0x0010,0x0020);
+ if (s1 < s2)
+ return(true);
+ else if (s1 > s2)
+ return(1);
+ else
+ {
+ // Study Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000d);
+ s2=document.GetEntryByNumber(0x0020,0x000d);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ else
+ {
+ // Serie Instance UID
+ s1=this->GetEntryByNumber(0x0020,0x000e);
+ s2=document.GetEntryByNumber(0x0020,0x000e);
+ if (s1 < s2)
+ return(true);
+ else if(s1 > s2)
+ return(false);
+ }
+ }
+ }
+ return(false);
+}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff