Program: gdcm
Module: $RCSfile: gdcmDicomDir.cxx,v $
Language: C++
- Date: $Date: 2006/01/27 10:01:33 $
- Version: $Revision: 1.185 $
+ Date: $Date: 2006/02/16 20:06:13 $
+ Version: $Revision: 1.186 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#if defined(__BORLANDC__)
#include <mem.h> // for memset
-#endif
+#endif
// ----------------------------------------------------------------------------
// Note for future developpers
NewMeta();
}
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Constructor Parses recursively the directory and creates the DicomDir
+ * or uses an already built DICOMDIR, depending on 'parseDir' value.
+ * @param fileName name
+ * - of the root directory (parseDir = true)
+ * - of the DICOMDIR (parseDir = false)
+ * @param parseDir boolean
+ * - true if user passed an entry point
+ * and wants to explore recursively the directories
+ * - false if user passed an already built DICOMDIR file
+ * and wants to use it
+ * @deprecated use : new DicomDir() + [ SetLoadMode(lm) + ] SetDirectoryName(name)
+ * or : new DicomDir() + SetFileName(name)
+ */
+DicomDir::DicomDir(std::string const &fileName, bool parseDir ):
+ Document( )
+{
+ // At this step, Document constructor is already executed,
+ // whatever user passed (either a root directory or a DICOMDIR)
+ // and whatever the value of parseDir was.
+ // (nothing is cheked in Document constructor, to avoid overhead)
+
+ ParseDir = parseDir;
+ SetLoadMode (LD_ALL); // concerns only dicom files
+ SetFileName( fileName );
+ Load( );
+}
+#endif
+
/**
* \brief Canonical destructor
*/
}
return DoTheLoadingJob( );
}
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : kept not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated use SetFileName(n) + Load() instead
+ */
+bool DicomDir::Load(std::string const &fileName )
+{
+ // We should clean out anything that already exists.
+ Initialize(); // sets all private fields to NULL
+
+ SetFileName( fileName );
+ if (!ParseDir)
+ {
+ if ( ! this->Document::Load( ) )
+ return false;
+ }
+ return DoTheLoadingJob( );
+}
+#endif
/**
* \brief Does the Loading Job (internal use only)
const char *cwd = getcwd(buf, 2048);
if( cwd )
{
- SetFileName( buf ); // will be converted into a string
+ SetFileName( buf ); // will be converted into a string
}
else
{
- gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
+ gdcmErrorMacro( "Path was too long to fit on 2048 bytes" );
}
}
NewMeta();
default:
return;
}
-
+
// FIXME : troubles found when it's a SeqEntry
-
+
// removed all the seems-to-be-useless stuff about Referenced Image Sequence
// to avoid further troubles
// imageElem 0008 1140 "" // Referenced Image Sequence
{
// NULL when we Build Up (ex nihilo) a DICOMDIR
// or when we add the META elems
-
- val = header->GetEntryString(tmpGr, tmpEl);
+ val = header->GetEntryString(tmpGr, tmpEl);
}
else
{
}
if ( val == GDCM_UNFOUND)
- {
+ {
if ( tmpGr == 0x0004 ) // never present in File !
{
switch (tmpEl)
Program: gdcm
Module: $RCSfile: gdcmDicomDir.h,v $
Language: C++
- Date: $Date: 2005/11/29 17:21:34 $
- Version: $Revision: 1.73 $
+ Date: $Date: 2006/02/16 20:06:13 $
+ Version: $Revision: 1.74 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/// \brief Constructs a DicomDir with a RefCounter
static DicomDir *New() {return new DicomDir();}
+ GDCM_LEGACY( bool Load(std::string const &filename) );
bool Load( );
void Print(std::ostream &os = std::cout, std::string const &indent = "" );
protected:
DicomDir();
+ GDCM_LEGACY( DicomDir(std::string const &filename, bool parseDir = false) );
~DicomDir();
void CreateDicomDirChainedList(std::string const &path);
Program: gdcm
Module: $RCSfile: gdcmDicomDirMeta.cxx,v $
Language: C++
- Date: $Date: 2005/11/04 15:33:35 $
- Version: $Revision: 1.34 $
+ Date: $Date: 2006/02/16 20:06:13 $
+ Version: $Revision: 1.35 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* @return
*/
void DicomDirMeta::WriteContent(std::ofstream *fp, FileType filetype)
-{
+{
// 'File Meta Information Version'
uint8_t fmiv[2] = {0x02,0x00};
Program: gdcm
Module: $RCSfile: gdcmDictEntry.cxx,v $
Language: C++
- Date: $Date: 2005/11/30 08:48:17 $
- Version: $Revision: 1.59 $
+ Date: $Date: 2006/02/16 20:06:13 $
+ Version: $Revision: 1.60 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
VRKey const &vr,
TagName const &vm,
TagName const &name)
-
{
Tag.SetGroup(group);
Tag.SetElement(elem);
Program: gdcm
Module: $RCSfile: gdcmDirList.h,v $
Language: C++
- Date: $Date: 2005/11/28 17:24:21 $
- Version: $Revision: 1.30 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.31 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/**
* \brief List containing the file headers of all the 'gdcm readable' files
- * found by exploring (possibely recursively) a root directory.
+ * found by exploring (possibly recursively) a root directory.
*/
class GDCM_EXPORT DirList : public Base
{
Program: gdcm
Module: $RCSfile: gdcmDocEntry.cxx,v $
Language: C++
- Date: $Date: 2005/12/21 14:52:12 $
- Version: $Revision: 1.80 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.81 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
{
uint32_t ffff = 0xffffffff;
uint16_t group = GetGroup();
-
+
///\todo allow skipping Shadow groups
-
+
VRKey vr = GetVR();
uint16_t elem = GetElement();
uint32_t lgth = GetLength();
// we just *always* ignore spurious fffe|0000 tag !
return;
}
-
+
//
// ----------- Writes the common part
//
// Dicom V3 group 0x0002 is *always* Explicit VR !
if ( filetype == ExplicitVR || filetype == JPEG || group == 0x0002 )
{
-
// ----------- Writes the common part : the VR + the length
- // Special case of delimiters:
+ // Special case of delimiters:
if (group == 0xfffe)
{
// Delimiters have NO Value Representation
Program: gdcm
Module: $RCSfile: gdcmDocEntry.h,v $
Language: C++
- Date: $Date: 2005/11/29 12:48:46 $
- Version: $Revision: 1.59 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.60 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/// Dictionnary, of the current Dicom entry
VRKey const &GetVR() const { return DicomDict->GetVR(); }
- /// \brief Returns the 'Value Multiplicity' (e.g. "1", 6", "1-n", "3-n"),
+ /// \brief Returns the 'Value Multiplicity' (e.g. "1", "6", "1-n", "3-n"),
/// found in the Dicom entry or in the Dicom Dictionnary
/// of the current Dicom entry
std::string const &GetVM() const { return DicomDict->GetVM(); }
Program: gdcm
Module: $RCSfile: gdcmDocEntrySet.cxx,v $
Language: C++
- Date: $Date: 2006/01/27 10:01:33 $
- Version: $Revision: 1.69 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.70 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
DocEntry *currentEntry = GetDocEntry(group, elem);
if ( !currentEntry )
return NULL;
-
+
return dynamic_cast<SeqEntry*>(currentEntry);
}
* failed).
*/
DataEntry *DocEntrySet::InsertEntryString(std::string const &value,
- uint16_t group, uint16_t elem,
- VRKey const &vr )
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
DataEntry *dataEntry = 0;
DocEntry *currentEntry = GetDocEntry( group, elem );
* failed).
*/
DataEntry *DocEntrySet::InsertEntryBinArea(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem,
- VRKey const &vr )
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
DataEntry *dataEntry = 0;
DocEntry *currentEntry = GetDocEntry( group, elem );
DictEntry *goodEntry = dictEntry;
VRKey goodVR = vr;
TagName vm;
- if (elem == 0x0000)
+ if (elem == 0x0000)
goodVR="UL";
if ( goodEntry )
{
if ( goodVR != goodEntry->GetVR()
&& goodVR != GDCM_VRUNKNOWN )
- {
+ {
gdcmWarningMacro("For (" << std::hex << group << "|"
<< elem << "), found VR : [" << vr << "]"
<< " expected: [" << goodEntry->GetVR() << "]" ) ;
if (dictEntry)
{
- goodEntry = DictEntry::New(group, elem, goodVR, vm,//"FIXME",
+ goodEntry = DictEntry::New(group, elem, goodVR, vm,
dictEntry->GetName() );
}
else
Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2006/02/09 10:48:04 $
- Version: $Revision: 1.341 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.342 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
return DoTheLoadingDocumentJob( );
}
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : not to break the API)
+ * @param fileName 'Document' (File or DicomDir) to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool Document::Load( std::string const &fileName )
+{
+ Filename = fileName;
+ return DoTheLoadingDocumentJob( );
+}
+#endif
+
/**
* \brief Performs the Loading Job (internal use only)
* @return false if file cannot be open or no swap info was found,
Group0002Parsed = false;
gdcmDebugMacro( "Starting parsing of file: " << Filename.c_str());
-
+
// Computes the total length of the file
Fp->seekg(0, std::ios::end); // Once per Document !
long lgt = Fp->tellg(); // Once per Document !
// -- Neither ACR/No Preamble Dicom nor DICOMV3 file
CloseFile();
- // Don't user Warning nor Error, not to polute the output
+ // Don't user Warning nor Error, not to pollute the output
// while directory recursive parsing ...
gdcmDebugMacro( "Neither ACR/No Preamble Dicom nor DICOMV3 file: "
<< Filename.c_str());
// explicit VR AND (OB, OW, SQ, UT) : 4 more bytes
groupLength += 4;
}
-
groupLength += 2 + 2 + 4 + entry->GetLength();
}
}
// Private
/**
* \brief Loads all the needed Dictionaries
+ * \warning NOT end user intended method !
*/
void Document::Initialize()
{
// but we didn't get it (private Sequence + Implicit VR)
// we have to backtrack.
if ( !first && newDocEntry->IsItemStarter() )
- {
- // Debug message within the method !
- newDocEntry = Backtrack(newDocEntry);
+ {
+ // Debug message within the method !
+ newDocEntry = Backtrack(newDocEntry);
}
else
{
newEntry->SetOffset(offset);
// Move back to the beginning of the Sequence
- // Fp->seekg( 0, std::ios::beg); // JPRx
- // Fp->seekg(offset, std::ios::cur); // JPRx
+
Fp->seekg(offset, std::ios::beg); // Only for Shadow Implicit VR SQ
return newEntry;
}
// (fffe e000) tells us an Element is beginning
// (fffe e00d) tells us an Element just ended
// (fffe e0dd) tells us the current SeQuence just ended
- //
// (fffe 0000) is an 'impossible' tag value,
// found in MR-PHILIPS-16-Multi-Seq.dcm
// The following reserved two bytes (see PS 3.5-2003, section
// "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
-
+
Fp->seekg( 2L, std::ios::cur); // Once per OW,OB,SQ DocEntry
uint32_t length32 = ReadInt32();
// Well ... group 0002 is always coded in 'Explicit VR Litle Endian'
// even if Transfer Syntax is 'Implicit VR ...'
// --> Except for 'Implicit VR Big Endian Transfer Syntax GE Private'
-
+
FixDocEntryFoundLength( entry, ReadInt32() );
return;
}
/**
* \brief Find the Length till the next sequence delimiter
+ * \warning NOT end user intended method !
* @return
*/
uint32_t Document::FindDocEntryLengthOBOrOW()
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
long positionOnEntry = Fp->tellg(); // Only for OB,OW DataElements
-
+
bool foundSequenceDelimiter = false;
uint32_t totalLength = 0;
totalLength += 4;
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- // long filePosition = Fp->tellg(); JPRx
gdcmWarningMacro(
"Neither an Item tag nor a Sequence delimiter tag on :"
<< std::hex << group << " , " << elem
- //<< ") -before- position x(" << filePosition // JPRx
<< ")" );
Fp->seekg(positionOnEntry, std::ios::beg); // Once per fragment (if any) of OB,OW DataElements
// Position the file position indicator at first tag
// (i.e. after the file preamble and the "DICM" string).
- //Fp->seekg(0, std::ios::beg); // JPRx
-
Fp->seekg ( 132L, std::ios::beg); // Once per Document
return true;
} // ------------------------------- End of DicomV3 ----------------
}
// In 'true DICOM' files Group 0002 is always little endian
- if ( HasDCMPreamble )
+ if ( HasDCMPreamble )
{
if ( !Group0002Parsed && CurrentGroup != 0x0002) // avoid calling a function when useless
HandleOutOfGroup0002(CurrentGroup, CurrentElem);
}
}
}
-
+
DocEntry *newEntry;
//if ( Global::GetVR()->IsVROfSequence(realVR) )
if (realVR == "SQ")
group = SwapShort(group);
elem = SwapShort(elem);
}
-
+
/// \todo find a trick to warn user and stop processing
if ( s == TS::DeflatedExplicitVRLittleEndian)
Program: gdcm
Module: $RCSfile: gdcmDocument.h,v $
Language: C++
- Date: $Date: 2006/02/09 10:48:05 $
- Version: $Revision: 1.139 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.140 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// Loading
//Deprecated : use SetFileName() + Load()
- //GDCM_LEGACY( virtual bool Load( std::string const &filename ) );
- //virtual bool Load( std::string const &filename );
+#ifndef GDCM_LEGACY_REMOVE
+ virtual bool Load( std::string const &filename );
+#endif
virtual bool Load( );
// Dictionaries
virtual void LoadEntryBinArea(uint16_t group, uint16_t elem);
virtual void LoadEntryBinArea(DataEntry *entry);
- //void LoadDocEntrySafe(DocEntry *entry);
+ void SetMaxSizeLoadEntry(long);
void AddForceLoadElement(uint16_t group, uint16_t elem);
// Ordering of Documents
private:
// Methods
void Initialize();
- bool DoTheLoadingDocumentJob();
+ bool DoTheLoadingDocumentJob();
// System access (meaning endian related !?)
uint16_t SwapShort(uint16_t);
bool CheckSwap();
void SwitchByteSwapCode();
- void SetMaxSizeLoadEntry(long);
// DocEntry related utilities
DocEntry *ReadNextDocEntry();
Program: gdcm
Module: $RCSfile: gdcmElementSet.cxx,v $
Language: C++
- Date: $Date: 2006/01/31 11:39:47 $
- Version: $Revision: 1.72 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.73 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
entry->SetPrintLevel(PrintLevel);
entry->Print(os);
- if ( dynamic_cast<SeqEntry *>(entry) )
+ if ( dynamic_cast<SeqEntry*>(entry) )
{
// Avoid the newline for a sequence:
continue;
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2006/02/07 12:37:19 $
- Version: $Revision: 1.314 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.315 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/**
* \brief Canonical destructor.
*/
-File::~File ()
+File::~File()
{
if ( RLEInfo )
delete RLEInfo;
* XOrigin, YOrigin, ZOrigin (of the top left image corner)
* of 2 consecutive images, and the Orientation
* Computing ZSpacing on a single image is not really meaningfull !
-
* @return Z dimension of a voxel-to be
*/
float File::GetZSpacing()
{
std::string strImOriPat;
//iop is supposed to be float[6]
+ iop[0] = iop[4] = 1.;
+ iop[1] = iop[2] = iop[3] = iop[5] = 0.;
// 0020 0037 DS REL Image Orientation (Patient)
if ( (strImOriPat = GetEntryString(0x0020,0x0037)) != GDCM_UNFOUND )
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- iop[0] = iop[4] = 1.;
- iop[1] = iop[2] = iop[3] = iop[5] = 0.;
gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037)."
<< " Less than 6 values were found." );
return false;
}
- else
- return true;
+ return true;
}
//For ACR-NEMA
// 0020 0035 DS REL Image Orientation (RET)
if ( sscanf( strImOriPat.c_str(), "%f \\ %f \\%f \\%f \\%f \\%f ",
&iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
{
- iop[0] = iop[4] = 1.;
- iop[1] = iop[2] = iop[3] = iop[5] = 0.;
gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). "
<< "Less than 6 values were found." );
return false;
}
- else
- return true;
+ return true;
}
return false;
}
/**
*\brief gets the info from 0028,1053 : Rescale Slope
- * @return Rescale Slope. defaulted to 0.0 is not found or empty
+ * @return Rescale Slope. defaulted to 1.0 is not found or empty
*/
float File::GetRescaleSlope()
{
return true;
}
-
//-----------------------------------------------------------------------------
// Protected
long fragmentLength;
int i=0;
uint32_t sum = 0;
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) != 0 )
{
// Since we have read the basic offset table, let's check the value were correct
// or else produce a warning:
return false;
}
if ( itemTagGroup != testGroup || itemTagElem != testElem )
- {
+ {
// in order not to pollute output we don't warn on 'delimitors'
if (itemTagGroup != 0xfffe || testGroup != 0xfffe )
gdcmWarningMacro( "Wrong Item Tag found:"
// These are the deprecated method that one day should be removed (after the next release)
-//#ifndef GDCM_LEGACY_REMOVE
+#ifndef GDCM_LEGACY_REMOVE
/*
* \ brief Loader. (DEPRECATED : temporaryly kept not to break the API)
* @ param fileName file to be open for parsing
* @ return false if file cannot be open or no swap info was found,
* or no tag was found.
- * @ deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
+ * @deprecated Use the Load() [ + SetLoadMode() ] + SetFileName() functions instead
*/
- /*
bool File::Load( std::string const &fileName )
{
GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
return DoTheLoadingJob( );
}
-*/
-//#endif
+#endif
//-----------------------------------------------------------------------------
// Print
Program: gdcm
Module: $RCSfile: gdcmFile.h,v $
Language: C++
- Date: $Date: 2005/12/21 14:52:13 $
- Version: $Revision: 1.123 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.124 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
static File *New() {return new File();}
// Loading
- //GDCM_LEGACY(bool Load( std::string const &filename ));
+ GDCM_LEGACY(bool Load( std::string const &filename ));
bool Load();
// Standard values and informations contained in the header
bool IsReadable();
void AnonymizeNoLoad();
/// Replace patient's own information by info from the Anonymization list
bool AnonymizeFile();
-
+
bool Write(std::string fileName, FileType filetype);
-
protected:
File();
- ~File();
+ virtual ~File();
/// \brief Protect the Writer from writing illegal groups
bool MayIWrite(uint16_t group)
{ if (group < 8 && group !=2 ) return false; else return true; }
Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2006/02/15 21:58:54 $
- Version: $Revision: 1.92 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.93 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* (uint8_t is just for prototyping. feel free to cast)
- * NULL if alloc fails
+ * NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
{
#ifndef GDCM_LEGACY_REMOVE
/*
- * \ brief Useless function, since PixelReadConverter forces us
+ * \brief Useless function, since PixelReadConverter forces us
* copy the Pixels anyway.
* Reads the pixels from disk (uncompress if necessary),
* Transforms YBR pixels, if any, into RGB pixels
* Transforms single Grey plane + 3 Palettes into a RGB Plane
* Copies at most MaxSize bytes of pixel data to caller allocated
* memory space.
- * \ warning This function allows people that want to build a volume
+ * \warning This function allows people that want to build a volume
* from an image stack *not to* have, first to get the image pixels,
* and then move them to the volume area.
* It's absolutely useless for any VTK user since vtk chooses
* to load the image line by line, starting from the end.
* VTK users have to call GetImageData
*
- * @ param destination Address (in caller's memory space) at which the
+ * @param destination Address (in caller's memory space) at which the
* pixel data should be copied
- * @ param maxSize Maximum number of bytes to be copied. When MaxSize
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
* is not sufficient to hold the pixel data the copy is not
* executed (i.e. no partial copy).
- * @ return On success, the number of bytes actually copied. Zero on
+ * @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
break;
case JPEG:
SetWriteFileTypeToJPEG();
- std::cerr << "Writting as JPEG" << std::endl;
break;
}
CheckMandatoryElements();
}
/**
- * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ * \brief Sets in the File the TransferSyntax to 'JPEG'
*/
void FileHelper::SetWriteFileTypeToJPEG()
{
tss->Delete();
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ */
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
Program: gdcm
Module: $RCSfile: gdcmFileHelper.h,v $
Language: C++
- Date: $Date: 2005/11/30 13:42:19 $
- Version: $Revision: 1.37 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.38 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// Write variables
/// \brief (WMODE_RAW, WMODE_RGB)
FileMode WriteMode;
-
+
/// \brief (ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO)
FileType WriteType;
Program: gdcm
Module: $RCSfile: gdcmOrientation.h,v $
Language: C++
- Date: $Date: 2005/11/28 16:31:23 $
- Version: $Revision: 1.17 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.18 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#define GDCMORIENTATION_H
#include "gdcmRefCounter.h"
-
#include <map>
namespace gdcm
std::string GetOrientation ( File *file );
static const char* GetOrientationTypeString(OrientationType const o);
-
+
protected:
/// \brief Constructor
Orientation() {}
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.cxx,v $
Language: C++
- Date: $Date: 2006/01/27 10:01:34 $
- Version: $Revision: 1.109 $
+ Date: $Date: 2006/02/16 20:06:14 $
+ Version: $Revision: 1.110 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* \brief Gets various usefull informations from the file header
* @param file gdcm::File pointer
*/
-void PixelReadConvert::GrabInformationsFromFile( File *file,
+void PixelReadConvert::GrabInformationsFromFile( File *file,
FileHelper *fileHelper )
{
// Number of Bits Allocated for storing a Pixel is defaulted to 16
//PixelSize = file->GetPixelSize(); Useless
PixelSign = file->IsSignedPixelData();
SwapCode = file->GetSwapCode();
-
+
IsPrivateGETransferSyntax = IsMPEG
= IsJPEG2000 = IsJPEGLS = IsJPEGLossy
= IsJPEGLossless = IsRLELossless
= false;
-
+
if (! file->IsDicomV3() ) // Should be ACR-NEMA file
{
IsRaw = true;
if ( PixelDataLength != RawSize )
{
gdcmWarningMacro( "Mismatch between PixelReadConvert : "
- << PixelDataLength << " and RawSize : " << RawSize );
+ << PixelDataLength << " and RawSize : " << RawSize );
}
//todo : is it the right patch?
if (remainingLength !=0 )
fp->read( raw, remainingLength);
- //if ( PixelDataLength > RawSize )
- //{
- // fp->read( (char*)Raw, RawSize); // Read all the frames with a single fread
- //}
- //else
- //{
- // fp->read( (char*)Raw, PixelDataLength); // Read all the frames with a single fread
- //}
-
if ( fp->fail() || fp->eof())
{
gdcmWarningMacro( "Reading of Raw pixel data failed." );
* and
* - (0028,1101),(0028,1102),(0028,1102)
* xxx Palette Color Lookup Table Descriptor are found
- * and
+ * and
* - (0028,1201),(0028,1202),(0028,1202)
* xxx Palette Color Lookup Table Data - are found
* \warning does NOT deal with :
void PixelReadConvert::ConvertSwapZone()
{
unsigned int i;
-
+
// If this file is 'ImplicitVR BigEndian PrivateGE Transfer Syntax',
// then the header is in little endian format and the pixel data is in
// big endian format. When reading the header, GDCM has already established
Program: gdcm
Module: $RCSfile: gdcmPixelReadConvert.h,v $
Language: C++
- Date: $Date: 2005/11/29 17:21:35 $
- Version: $Revision: 1.28 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.29 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/**
* \brief Utility container for gathering the various forms the pixel data
* migth take during the user demanded processes.
- * WARNING : *none* of these functions may be invoked by gdm user
+ * WARNING : *none* of these functions may be invoked by gdcm user
* (internal use only)
*/
class GDCM_EXPORT PixelReadConvert : public Base
//int PixelSize; // useless
bool PixelSign;
int SwapCode;
-
+
// cache whether this is a strange GE transfer syntax (which has
// one transfer syntax for the header and another for the pixel data).
bool IsPrivateGETransferSyntax;
-
+
bool IsRaw;
bool IsJPEG2000;
bool IsJPEGLS;
Program: gdcm
Module: $RCSfile: gdcmPixelWriteConvert.h,v $
Language: C++
- Date: $Date: 2005/10/23 15:09:19 $
- Version: $Revision: 1.7 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.8 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
virtual ~PixelWriteConvert();
// Set/Get of images and their size
-
void SetReadData(uint8_t *data, size_t size);
/// \brief returns ReadData
uint8_t *GetReadData() { return ReadData; }
/// \brief returns ReadDataSize
size_t GetReadDataSize() { return ReadDataSize; }
+ /// \brief Set UserData
void SetUserData(uint8_t *data, size_t size);
/// \brief returns UserData
uint8_t *GetUserData() { return UserData; }
uint8_t *GetData();
size_t GetDataSize();
-
// Variables
/// Pixel data represented as RGB after LUT color interpretation.
uint8_t *ReadData;
Program: gdcm
Module: $RCSfile: gdcmRLEFrame.h,v $
Language: C++
- Date: $Date: 2005/11/28 17:24:21 $
- Version: $Revision: 1.19 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.20 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
* - the offsets of each segment of the frame,
* - the (corresponding) lengths of each segment of the frame.
*/
- class GDCM_EXPORT RLEFrame : public Base
+class GDCM_EXPORT RLEFrame : public Base
{
friend class File;
friend class RLEFramesInfo;
bool ReadAndDecompressRLEFragment( uint8_t *subRaw, long fragmentSize,
long rawSegmentSize, std::ifstream *fp );
-//private:
unsigned int NumberOfFragments;
long Offset[15];
long Length[15];
Program: gdcm
Module: $RCSfile: gdcmRLEFramesInfo.h,v $
Language: C++
- Date: $Date: 2005/11/18 14:33:24 $
- Version: $Revision: 1.20 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.21 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
RLEFrame *GetFirstFrame();
RLEFrame *GetNextFrame();
-//private::
typedef std::list<RLEFrame *> RLEFrameList;
RLEFrameList Frames;
Program: gdcm
Module: $RCSfile: gdcmSQItem.cxx,v $
Language: C++
- Date: $Date: 2005/12/13 09:22:05 $
- Version: $Revision: 1.83 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.84 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// because we wrote the Item as a 'no Length' item
for(j=0;j<4;++j)
{
- binary_write( *fp, itemt[j]); // fffe e000 0000 0000
+ binary_write( *fp, itemt[j]); // fffe e000 0000 0000
}
}
Program: gdcm
Module: $RCSfile: gdcmSQItem.h,v $
Language: C++
- Date: $Date: 2005/11/29 17:11:52 $
- Version: $Revision: 1.50 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.51 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
static SQItem *New(int depthLevel) {return new SQItem(depthLevel);}
virtual void Print(std::ostream &os = std::cout,
- std::string const &indent = "" );
+ std::string const &indent = "" );
void WriteContent(std::ofstream *fp, FileType filetype);
uint32_t ComputeFullLength();
Program: gdcm
Module: $RCSfile: gdcmSeqEntry.cxx,v $
Language: C++
- Date: $Date: 2005/12/01 09:12:21 $
- Version: $Revision: 1.64 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.65 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// ignore 'Zero length' Sequences
if ( GetReadLength() == 0 )
return;
-
+
DocEntry::WriteContent(fp, filetype);
for(ListSQItem::iterator cc = Items.begin();
cc != Items.end();
Program: gdcm
Module: $RCSfile: gdcmSeqEntry.h,v $
Language: C++
- Date: $Date: 2005/11/29 12:48:47 $
- Version: $Revision: 1.39 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.40 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
void Print(std::ostream &os = std::cout, std::string const &indent = "" );
void WriteContent(std::ofstream *fp, FileType filetype);
uint32_t ComputeFullLength();
-
+
void AddSQItem(SQItem *it, int itemNumber);
void ClearSQItem();
SQItem *GetFirstSQItem();
/// Sets the delimitor mode
void SetDelimitorMode(bool dm) { DelimitorMode = dm; }
+ /// Sets the Sequence Delimitation Item
void SetDelimitationItem(DocEntry *e);
+
/// Gets the Sequence Delimitation Item
DocEntry *GetDelimitationItem() { return SeqTerm;}
Program: gdcm
Module: $RCSfile: gdcmSerieHelper.cxx,v $
Language: C++
- Date: $Date: 2006/02/05 23:13:36 $
- Version: $Revision: 1.46 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.47 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <math.h>
#include <vector>
-#include <map>
#include <algorithm>
+#include <map>
#include <stdio.h> //for sscanf
-namespace gdcm
+namespace gdcm
{
-//-----------------------------------------------------------------------------
//-----------------------------------------------------------------------------
// Constructor / Destructor
delete l; // remove the container
l = GetNextSingleSerieUIDFileSet();
}
+ // Need to clear that too:
+ SingleSerieUIDFileSetHT.clear();
}
//-----------------------------------------------------------------------------
if ( header->IsReadable() )
{
- int allrules = 1;
- // First step : the user defined a set of rules for the DICOM file
- // he is looking for.
- // Make sure the file corresponds to his set of rules:
-
- std::string s;
- for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
- it2 != ExRestrictions.end();
- ++it2)
- {
- const ExRule &r = *it2;
- s = header->GetEntryString( r.group, r.elem );
- if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
- {
- // Argh ! This rule is unmatched; let's just quit
-
- allrules = 0;
- break;
- }
- }
-
- if ( allrules ) // all rules are respected:
- {
- // Allright! we have a found a DICOM that matches the user expectation.
- // Let's add it!
-
- // 0020 000e UI REL Series Instance UID
- const std::string &uid = header->GetEntryString(0x0020, 0x000e);
- // if uid == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
- // no need here to do anything special
-
-
- if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- SingleSerieUIDFileSetHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- SingleSerieUIDFileSetHT[uid]->push_back( header );
- }
- else
+ if ( !AddFile( header ) )
{
// at least one rule was unmatched we need to deallocate the file:
header->Delete();
* *no* coherence check is performed, but those specified
* by SerieHelper::AddRestriction()
* @param header gdcm::File* of the file to deal with
+ * @return true if file was added, false if file was rejected
*/
-void SerieHelper::AddGdcmFile(File *header)
+bool SerieHelper::AddFile(File *header)
{
- int allrules = 1;
- // First step the user has defined a set of rules for the DICOM
- // he is looking for.
- // make sure the file correspond to his set of rules:
- for(SerieRestrictions::iterator it = Restrictions.begin();
- it != Restrictions.end();
- ++it)
+ int allrules = 1;
+ // First step the user has defined a set of rules for the DICOM
+ // he is looking for.
+ // make sure the file correspond to his set of rules:
+
+ std::string s;
+ for(SerieExRestrictions::iterator it2 = ExRestrictions.begin();
+ it2 != ExRestrictions.end();
+ ++it2)
+ {
+ const ExRule &r = *it2;
+ s = header->GetEntryString( r.group, r.elem );
+ if ( !Util::CompareDicomString(s, r.value.c_str(), r.op) )
{
- const Rule &r = *it;
- const std::string s;// = header->GetEntryString( r.first );
- if ( !Util::DicomStringEqual(s, r.second.c_str()) )
- {
- // Argh ! This rule is unmatch let's just quit
- allrules = 0;
- break;
- }
+ // Argh ! This rule is unmatched; let's just quit
+ allrules = 0;
+ break;
}
- if ( allrules ) // all rules are respected:
- {
- // Allright ! we have a found a DICOM that match the user expectation.
- // Let's add it !
-
- const std::string &uid = "0";
- // Serie UID of the gdcm::File* may be different.
- // User is supposed to know what he wants
+ }
- if ( SingleSerieUIDFileSetHT.count(uid) == 0 )
- {
- gdcmDebugMacro(" New Serie UID :[" << uid << "]");
- // create a std::list in 'uid' position
- SingleSerieUIDFileSetHT[uid] = new FileList;
- }
- // Current Serie UID and DICOM header seems to match; add the file:
- SingleSerieUIDFileSetHT[uid]->push_back( header );
+ if ( allrules ) // all rules are respected:
+ {
+ // Allright! we have a found a DICOM that matches the user expectation.
+ // Let's add it to the specific 'id' which by default is uid (Serie UID)
+ // but can be `refined` by user with more paramater (see AddRestriction(g,e))
+
+ std::string id = CreateUniqueSeriesIdentifier( header );
+ // if id == GDCM_UNFOUND then consistently we should find GDCM_UNFOUND
+ // no need here to do anything special
+
+ if ( SingleSerieUIDFileSetHT.count(id) == 0 )
+ {
+ gdcmDebugMacro(" New Serie UID :[" << id << "]");
+ // create a std::list in 'id' position
+ SingleSerieUIDFileSetHT[id] = new FileList;
}
- // Even if a rule was unmatch we don't deallocate the gdcm::File:
+ // Current Serie UID and DICOM header seems to match add the file:
+ SingleSerieUIDFileSetHT[id]->push_back( header );
+ }
+ else
+ {
+ // one rule not matched, tell user:
+ return false;
+ }
+ return true;
}
/**
ExRestrictions.push_back( r );
}
+void SerieHelper::AddRestriction(TagKey const &key)
+{
+ ExRule r;
+ r.group = key[0];
+ r.elem = key[1];
+ ExRefine.push_back( r );
+}
+
+#ifndef GDCM_LEGACY_REMOVE
/**
* \brief add a rule for restricting a DICOM file to be in the serie we are
- * trying to find. For example you can select only the DICOM file from a
+ * trying to find. For example you can select only the DICOM files from a
* directory which would have a particular EchoTime==4.0.
* This method is a user level, value is not required to be formatted as a DICOM
* string
- * \todo find a trick to allow user if he wants the Rectrictions to be *ored*
- * (and not only *anded*)
* @param group tag group number we want restrict on a given value
* @param elem tag element number we want restrict on a given value
* @param value value to be checked to exclude File
* @param op operator we want to use to check
+ * @deprecated use : AddRestriction(TagKey const &key,
+ * std::string const &value, int op);
*/
void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
std::string const &value, int op)
{
- ExRule r;
- r.group = group;
- r.elem = elem;
- r.value = value;
- r.op = op;
- ExRestrictions.push_back( r );
+ TagKey t(group, elem);
+ AddRestriction(t, value, op);
}
+#endif
/**
* \brief add an extra 'SerieDetail' for building a 'Serie Identifier'
return false;
if ( (*it)->IsSignedPixelData() != signedPixelData )
return false;
- // probabely more is to be checked (?)
+ // probabely more is to be checked (?)
}
return true;
}
#ifndef GDCM_LEGACY_REMOVE
-
+/**
+ * \brief accessor (DEPRECATED : use GetFirstSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * @return The first FileList if found, otherwhise NULL
+ */
FileList *SerieHelper::GetFirstCoherentFileList()
{
ItFileSetHt = SingleSerieUIDFileSetHT.begin();
return NULL;
}
-
+/**
+ * \brief accessor (DEPRECATED : use GetNextSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * \note : meaningfull only if GetFirstCoherentFileList() already called
+ * @return The next FileList if found, otherwhise NULL
+ */
FileList *SerieHelper::GetNextCoherentFileList()
{
gdcmAssertMacro (ItFileSetHt != SingleSerieUIDFileSetHT.end());
return NULL;
}
-
+/**
+ * \brief accessor (DEPRECATED : use GetSingleSerieUIDFileSet )
+ * Warning : 'coherent' means here they have the same Serie UID
+ * @param SerieUID SerieUID
+ * \return pointer to the FileList if found, otherwhise NULL
+ */
FileList *SerieHelper::GetCoherentFileList(std::string SerieUID)
{
if ( SingleSerieUIDFileSetHT.count(SerieUID) == 0 )
if (nb == 0 )
return CoherentFileSet;
float iop[6];
-
std::string strOrient;
- std::ostringstream ossOrient;
+ std::ostringstream ossOrient;
+
FileList::const_iterator it = fileSet->begin();
it ++;
for ( ;
}
strOrient = ossOrient.str();
ossOrient.str("");
- // FIXME : is it a 'cleaner' way to initialize an ostringstream?
-
if ( CoherentFileSet.count(strOrient) == 0 )
{
gdcmDebugMacro(" New Orientation :[" << strOrient << "]");
}
// Current Orientation and DICOM header match; add the file:
CoherentFileSet[strOrient]->push_back( (*it) );
- }
+ }
return CoherentFileSet;
}
}
strPosition = ossPosition.str();
ossPosition.str("");
-
+
if ( CoherentFileSet.count(strPosition) == 0 )
{
gdcmDebugMacro(" New Position :[" << strPosition << "]");
*/
XCoherentFileSetmap SerieHelper::SplitOnTagValue(FileList *fileSet,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t element)
{
XCoherentFileSetmap CoherentFileSet;
// 0020,0032 : Image Position Patient
// 0020,0030 : Image Position (RET)
- strTagValue = (*it)->GetEntryString(group,elem);
+ strTagValue = (*it)->GetEntryString(group,element);
if ( CoherentFileSet.count(strTagValue) == 0 )
{
ipp[0] = (*it)->GetXOrigin();
ipp[1] = (*it)->GetYOrigin();
ipp[2] = (*it)->GetZOrigin();
-
+
dist = 0;
for ( int i = 0; i < 3; ++i )
{
min = (min < dist) ? min : dist;
max = (max > dist) ? max : dist;
}
-
}
// Find out if min/max are coherent
}
// Check to see if image shares a common position
- bool ok = true;
- for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
- it2 != distmultimap.end();
- ++it2)
- {
- if (distmultimap.count((*it2).first) != 1)
- {
- gdcmErrorMacro("File: "
- << ((*it2).second->GetFileName())
- << " Distance: "
- << (*it2).first
- << " position is not unique");
- ok = false;
- }
- }
- if (!ok)
- {
- return false;
- }
-
+ bool ok = true;
+ for (std::multimap<double, File *>::iterator it2 = distmultimap.begin();
+ it2 != distmultimap.end();
+ ++it2)
+ {
+ if (distmultimap.count((*it2).first) != 1)
+ {
+ gdcmErrorMacro("File: "
+ << ((*it2).second->GetFileName())
+ << " Distance: "
+ << (*it2).first
+ << " position is not unique");
+
+ ok = false;
+ }
+ }
+ if (!ok)
+ {
+ return false;
+ }
+
fileList->clear(); // doesn't delete list elements, only nodes
if (DirectOrder)
{
for (std::multimap<double, File *>::iterator it3 = distmultimap.begin();
- it3 != distmultimap.end();
- ++it3)
+ it3 != distmultimap.end();
+ ++it3)
{
fileList->push_back( (*it3).second );
}
it4--;
fileList->push_back( (*it4).second );
} while (it4 != distmultimap.begin() );
- }
+ }
distmultimap.clear();
* \note Works only on bona fide files (i.e image number is a character string
* corresponding to an integer)
* within a bona fide serie (i.e image numbers are consecutive)
- * @param fileList File set (same Serie UID) to sort
+ * @param fileList File set (same Serie UID) to sort
* @return false if non bona fide stuff encountered
*/
bool SerieHelper::ImageNumberOrdering(FileList *fileList)
<< " No ImageNumberOrdering sort performed.");
return false;
}
- if (DirectOrder)
- Sort(fileList,SerieHelper::ImageNumberLessThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::ImageNumberLessThan );
+ if (DirectOrder)
+ Sort(fileList,SerieHelper::ImageNumberLessThan);
else
- Sort(fileList,SerieHelper::ImageNumberGreaterThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::ImageNumberGreaterThan );
+ Sort(fileList,SerieHelper::ImageNumberGreaterThan);
return true;
}
bool SerieHelper::FileNameOrdering(FileList *fileList)
{
if (DirectOrder)
- Sort(fileList,SerieHelper::FileNameLessThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::FileNameLessThan);
+ Sort(fileList,SerieHelper::FileNameLessThan);
else
- Sort(fileList,SerieHelper::FileNameGreaterThan);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::FileNameGreaterThan);
+ Sort(fileList,SerieHelper::FileNameGreaterThan);
return true;
}
*/
bool SerieHelper::UserOrdering(FileList *fileList)
{
- Sort(fileList,SerieHelper::UserLessThanFunction);
-// std::sort(fileList->begin(), fileList->end(),
-// SerieHelper::UserLessThanFunction);
+ Sort(fileList,SerieHelper::UserLessThanFunction);
if (!DirectOrder)
{
std::reverse(fileList->begin(), fileList->end());
return true;
}
+//-----------------------------------------------------------------------------
+// Print
+/**
+ * \brief Canonical printer.
+ */
+void SerieHelper::Print(std::ostream &os, std::string const &indent)
+{
+ // For all the Coherent File lists of the gdcm::Serie
+ SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
+ if ( itl == SingleSerieUIDFileSetHT.end() )
+ {
+ gdcmWarningMacro( "No SingleSerieUID File set found" );
+ return;
+ }
+ while (itl != SingleSerieUIDFileSetHT.end())
+ {
+ os << "Serie UID :[" << itl->first << "]" << std::endl;
+
+ // For all the files of a SingleSerieUID File set
+ for (FileList::iterator it = (itl->second)->begin();
+ it != (itl->second)->end();
+ ++it)
+ {
+ os << indent << " --- " << (*it)->GetFileName() << std::endl;
+ }
+ ++itl;
+ }
+}
+
+void SerieHelper::CreateDefaultUniqueSeriesIdentifier()
+{
+ // If the user requests, additional information can be appended
+ // to the SeriesUID to further differentiate volumes in the DICOM
+ // objects being processed.
+
+ // 0020 0011 Series Number
+ // A scout scan prior to a CT volume scan can share the same
+ // SeriesUID, but they will sometimes have a different Series Number
+ AddRestriction( TagKey(0x0020, 0x0011) );
+ // 0018 0024 Sequence Name
+ // For T1-map and phase-contrast MRA, the different flip angles and
+ // directions are only distinguished by the Sequence Name
+ AddRestriction( TagKey(0x0018, 0x0024) );
+ // 0018 0050 Slice Thickness
+ // On some CT systems, scout scans and subsequence volume scans will
+ // have the same SeriesUID and Series Number - YET the slice
+ // thickness will differ from the scout slice and the volume slices.
+ AddRestriction( TagKey(0x0018, 0x0050));
+ // 0028 0010 Rows
+ // If the 2D images in a sequence don't have the same number of rows,
+ // then it is difficult to reconstruct them into a 3D volume.
+ AddRestriction( TagKey(0x0028, 0x0010));
+ // 0028 0011 Columns
+ // If the 2D images in a sequence don't have the same number of columns,
+ // then it is difficult to reconstruct them into a 3D volume.
+ AddRestriction( TagKey(0x0028, 0x0011));
+}
+
/**
* \brief Heuristics to *try* to build a Serie Identifier that would ensure
* all the images are coherent.
{
if( inFile->IsReadable() )
{
- // 0020 000e UI REL Series Instance UID
- std::string uid = inFile->GetEntryString (0x0020, 0x000e);
+ // 0020 000e UI REL Series Instance UID
+ std::string uid = inFile->GetEntryString (0x0020, 0x000e);
std::string id = uid.c_str();
if(m_UseSeriesDetails)
- {
- // If the user requests, additional information can be appended
- // to the SeriesUID to further differentiate volumes in the DICOM
- // objects being processed.
-
- // 0020 0011 Series Number
- // A scout scan prior to a CT volume scan can share the same
- // SeriesUID, but they will sometimes have a different Series Number
- std::string sNum = inFile->GetEntryString(0x0020, 0x0011);
- if( sNum == gdcm::GDCM_UNFOUND )
- {
- sNum = "";
- }
- // 0018 0024 Sequence Name
- // For T1-map and phase-contrast MRA, the different flip angles and
- // directions are only distinguished by the Sequence Name
- std::string sName = inFile->GetEntryString(0x0018, 0x0024);
- if( sName == gdcm::GDCM_UNFOUND )
- {
- sName = "";
- }
-
- // You can think on checking Image Orientation (0020,0037), as well.
-
-
- // 0018 0050 Slice Thickness
- // On some CT systems, scout scans and subsequence volume scans will
- // have the same SeriesUID and Series Number - YET the slice
- // thickness will differ from the scout slice and the volume slices.
- std::string sThick = inFile->GetEntryString (0x0018, 0x0050);
- if( sThick == gdcm::GDCM_UNFOUND )
- {
- sThick = "";
- }
- // 0028 0010 Rows
- // If the 2D images in a sequence don't have the same number of rows,
- // then it is difficult to reconstruct them into a 3D volume.
- std::string sRows = inFile->GetEntryString (0x0028, 0x0010);
- if( sRows == gdcm::GDCM_UNFOUND )
- {
- sRows = "";
- }
- // 0028 0011 Columns
- // If the 2D images in a sequence don't have the same number of columns,
- // then it is difficult to reconstruct them into a 3D volume.
- std::string sColumns = inFile->GetEntryString (0x0028, 0x0011);
- if( sColumns == gdcm::GDCM_UNFOUND )
- {
- sColumns = "";
- }
-
- // Concat the new info
- std::string num = sNum.c_str();
- num += sName.c_str();
- num += sThick.c_str();
- num += sRows.c_str();
- num += sColumns.c_str();
-
- // Add a loop, here, to deal with any extra user supplied tag.
- // We allow user to add his own critierions
- // (he knows more than we do about his images!)
- // ex : in tagging series, the only pertinent tag is
- // 0018|1312 [In-plane Phase Encoding Direction] values : ROW/COLUMN
-
- std::string s;
- for(SeriesExDetails::iterator it2 = ExDetails.begin();
- it2 != ExDetails.end();
- ++it2)
{
- const ExDetail &r = *it2;
- s = inFile->GetEntryString( r.group, r.elem );
- num += s.c_str();
+ for(SerieExRestrictions::iterator it2 = ExRefine.begin();
+ it2 != ExRefine.end();
+ ++it2)
+ {
+ const ExRule &r = *it2;
+ std::string s = inFile->GetEntryString( r.group, r.elem );
+ if( s == gdcm::GDCM_UNFOUND )
+ {
+ s = "";
+ }
+ if( id == uid && !s.empty() )
+ {
+ id += "."; // add separator
+ }
+ id += s;
+ }
}
-
- // Append the new info to the SeriesUID
- id += ".";
- id += num.c_str();
- }
-
- // Eliminate non-alphanum characters, including whitespace...
- // that may have been introduced by concats.
- for(unsigned int i=0; i<id.size(); i++)
- {
- while(i<id.size()
- && !( id[i] == '.' || id[i] == '-' || id[i] == '_'
- || (id[i] >= 'a' && id[i] <= 'z')
- || (id[i] >= '0' && id[i] <= '9')
- || (id[i] >= 'A' && id[i] <= 'Z')))
- {
- id.erase(i, 1);
- }
- }
- return id;
- }
- else // Could not open inFile
- {
- gdcmWarningMacro("Could not parse series info.");
- std::string id = gdcm::GDCM_UNFOUND;
- return id;
- }
+ // Eliminate non-alnum characters, including whitespace...
+ // that may have been introduced by concats.
+ for(unsigned int i=0; i<id.size(); i++)
+ {
+ while(i<id.size()
+ && !( id[i] == '.'
+ || (id[i] >= 'a' && id[i] <= 'z')
+ || (id[i] >= '0' && id[i] <= '9')
+ || (id[i] >= 'A' && id[i] <= 'Z')))
+ {
+ id.erase(i, 1);
+ }
+ }
+ return id;
+ }
+ else // Could not open inFile
+ {
+ gdcmWarningMacro("Could not parse series info.");
+ std::string id = gdcm::GDCM_UNFOUND;
+ return id;
+ }
}
/**
return id;
}
-//-----------------------------------------------------------------------------
-// Print
-/**
- * \brief Canonical printer.
- */
-void SerieHelper::Print(std::ostream &os, std::string const &indent)
-{
- // For all the Coherent File lists of the gdcm::Serie
- SingleSerieUIDFileSetmap::iterator itl = SingleSerieUIDFileSetHT.begin();
- if ( itl == SingleSerieUIDFileSetHT.end() )
- {
- gdcmWarningMacro( "No SingleSerieUID File set found" );
- return;
- }
- while (itl != SingleSerieUIDFileSetHT.end())
- {
- os << "Serie UID :[" << itl->first << "]" << std::endl;
-
- // For all the files of a SingleSerieUID File set
- for (FileList::iterator it = (itl->second)->begin();
- it != (itl->second)->end();
- ++it)
- {
- os << indent << " --- " << (*it)->GetFileName() << std::endl;
- }
- ++itl;
- }
-}
//-----------------------------------------------------------------------------
// Sort
Program: gdcm
Module: $RCSfile: gdcmSerieHelper.h,v $
Language: C++
- Date: $Date: 2006/01/18 15:25:07 $
- Version: $Revision: 1.36 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.37 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
class File;
typedef std::vector<File* > FileList;
-
- /// \brief XCoherent stands for 'Extra Coherent',
+#ifndef GDCM_LEGACY_REMOVE
+typedef std::vector<File* > GdcmFileList;
+#endif
+
+ /// \brief XCoherent stands for 'Extra Coherent',
/// (The name 'Coherent' would be enough but it was used before;
/// I don't want to put a bomb in the code)
/// Any 'better name' is welcome !
- typedef std::map<std::string, FileList *> XCoherentFileSetmap;
-
+ typedef std::map<std::string, FileList *> XCoherentFileSetmap;
+
typedef bool (*BOOL_FUNCTION_PFILE_PFILE_POINTER)(File *, File *);
//-----------------------------------------------------------------------------
/// \todo should return bool or throw error ?
void AddFileName(std::string const &filename);
- void AddGdcmFile(File *header);
+ bool AddFile(File *header);
+#ifndef GDCM_LEGACY_REMOVE
+ bool AddGdcmFile(File* header) { return AddFile(header); }
+#endif
void SetDirectory(std::string const &dir, bool recursive=false);
bool IsCoherent(FileList *fileSet);
void OrderFileList(FileList *fileSet);
-
+ void Clear() { ClearAll(); }
+
/// \brief Gets the FIRST Single SerieUID Fileset.
/// Deprecated; kept not to break the API
/// \note Caller must call OrderFileList first
/// \todo : find a trick to allow user to say the retrictetons are ored
/// (not only anded)
/// ex : keep the images whose SerieNumber is 101 or 102 or 103.
+ void AddRestriction(TagKey const &key);
void AddRestriction(TagKey const &key, std::string const &value, int op);
void AddRestriction(uint16_t group, uint16_t elem, std::string const &value,
int op);
/// and SeriesName to identify when a single SeriesUID contains
/// multiple 3D volumes - as can occur with perfusion and DTI imaging
void SetUseSeriesDetails( bool useSeriesDetails )
- { m_UseSeriesDetails = useSeriesDetails;}
- bool GetUseSeriesDetails( ){ return m_UseSeriesDetails; }
-
+ {
+ m_UseSeriesDetails = useSeriesDetails;
+ }
+ bool GetUseSeriesDetails()
+ {
+ return m_UseSeriesDetails;
+ }
+ /// \brief This function will add the following DICOM tag as being part of a
+ /// 'fake' uid. This is usefull when the Serie UID is not enough to disseminate
+ /// into multiple sub serie when needed:
+ /// 0020 0011 Series Number
+ /// 0018 0024 Sequence Name
+ /// 0018 0050 Slice Thickness
+ /// 0028 0010 Rows
+ /// 0028 0011 Columns
+ void CreateDefaultUniqueSeriesIdentifier();
+
void AddSeriesDetail(uint16_t group, uint16_t elem, bool convert);
-
- std::string CreateUniqueSeriesIdentifier( File * inFile );
-
+
std::string CreateUserDefinedFileIdentifier( File * inFile );
+
+ /// \brief Create a string that uniquely identifies a series. By default
+ // uses the SeriesUID. If UseSeriesDetails(true) has been called,
+ // then additional identifying information is used.
+ std::string CreateUniqueSeriesIdentifier( File * inFile );
/**
* \brief Sets the LoadMode as a boolean string.
XCoherentFileSetmap SplitOnOrientation(FileList *fileSet);
XCoherentFileSetmap SplitOnPosition(FileList *fileSet);
XCoherentFileSetmap SplitOnTagValue(FileList *fileSet,
- uint16_t group, uint16_t elem);
+ uint16_t group, uint16_t element);
protected :
SerieHelper();
SingleSerieUIDFileSetmap SingleSerieUIDFileSetHT;
SingleSerieUIDFileSetmap::iterator ItFileSetHt;
-
+
+#ifndef GDCM_LEGACY_REMOVE
typedef std::pair<TagKey, std::string> Rule;
typedef std::vector<Rule> SerieRestrictions;
SerieRestrictions Restrictions;
-
+#endif
+
// New style for (extented) Rules
typedef struct {
uint16_t group;
} ExRule;
typedef std::vector<ExRule> SerieExRestrictions;
SerieExRestrictions ExRestrictions;
-
+ SerieExRestrictions ExRefine;
+
typedef struct {
uint16_t group;
uint16_t elem;
typedef std::vector<ExDetail> SeriesExDetails;
SeriesExDetails ExDetails;
- bool m_UseSeriesDetails;
/// \brief Bit string integer (each one considered as a boolean)
/// Bit 0 : Skip Sequences, if possible
/// \brief If user knows more about his images than gdcm does,
/// he may supply his own comparison function.
- BOOL_FUNCTION_PFILE_PFILE_POINTER UserLessThanFunction;
+ BOOL_FUNCTION_PFILE_PFILE_POINTER UserLessThanFunction;
+
+ void Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) );
- void Sort(FileList *fileList, bool (*pt2Func)( File *file1, File *file2) );
+ bool m_UseSeriesDetails;
};
} // end namespace gdcm
Program: gdcm
Module: $RCSfile: gdcmUtil.cxx,v $
Language: C++
- Date: $Date: 2006/01/10 15:54:03 $
- Version: $Revision: 1.182 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.183 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
/**
* \brief Safely check the equality of two Dicom String:
* - Both strings should be of even length
- * - We allow padding of even length string by either
- * a null character of a space
+ * - We allow padding of even length string by either
+ * a null character of a space
*/
bool Util::DicomStringEqual(const std::string &s1, const char *s2)
{
/**
* \brief Safely compare two Dicom String:
* - Both strings should be of even length
- * - We allow padding of even length string by either
+ * - We allow padding of even length string by either
* a null character of a space
*/
bool Util::CompareDicomString(const std::string &s1, const char *s2, int op)
OUT AsnObjectIdentifier * supportedView);
#endif //_WIN32
+#ifdef __sgi
+static int SGIGetMacAddress(unsigned char *addr)
+{
+ FILE *f = popen("/etc/nvram eaddr","r");
+ if(f == 0)
+ {
+ return -1;
+ }
+ unsigned int x[6];
+ if(fscanf(f,"%02x:%02x:%02x:%02x:%02x:%02x",
+ x,x+1,x+2,x+3,x+4,x+5) != 6)
+ {
+ pclose(f);
+ return -1;
+ }
+ for(unsigned int i = 0; i < 6; i++)
+ {
+ addr[i] = static_cast<unsigned char>(x[i]);
+ }
+ return 0;
+}
+#endif
+
/// \brief gets current M.A.C adress (for internal use only)
int GetMacAddrSys ( unsigned char *addr );
int GetMacAddrSys ( unsigned char *addr )
return 0;
#endif //Win32 version
+#if defined(__sgi)
+ return SGIGetMacAddress(addr);
+#endif // __sgi
+
// implementation for POSIX system
#if defined(CMAKE_HAVE_NET_IF_ARP_H) && defined(__sun)
#endif //GDCM_WORDS_BIGENDIAN
}
-
/**
* \brief binary_write binary_write
* @param os ostream to write to
#endif //GDCM_WORDS_BIGENDIAN
}
-
/**
* \brief binary_write binary_write
* @param os ostream to write to
Program: gdcm
Module: $RCSfile: gdcmValidator.cxx,v $
Language: C++
- Date: $Date: 2005/11/21 09:43:43 $
- Version: $Revision: 1.13 $
+ Date: $Date: 2006/02/16 20:06:15 $
+ Version: $Revision: 1.14 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmElementSet.h"
#include "gdcmDataEntry.h"
#include "gdcmUtil.h"
+#include "gdcmDebug.h" // hidden way to include sstream
#include <map>
-#include <sstream>
namespace gdcm
{
bool CheckVM(DataEntry *entry)
{
// Don't waste time checking tags where VM is OB and OW, since we know
- // it's allways 1, whatever the actual length (found on disc)
+ // it's always 1, whatever the actual length (found on disc)
if ( entry->GetVR() == "OB" || entry->GetVR() == "OW" )
return true;
-
+
const std::string &s = entry->GetString();
unsigned int n = Util::CountSubstring( s , "\\");
projects / gdcm.git / commitdiff