Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/10/23 15:24:47 $
- Version: $Revision: 1.69 $
+ Date: $Date: 2006/07/06 12:38:06 $
+ Version: $Revision: 1.108 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
#include "gdcmDataEntry.h"
+#include "gdcmDocEntry.h"
#include "gdcmFile.h"
#include "gdcmPixelReadConvert.h"
#include "gdcmPixelWriteConvert.h"
#include "gdcmDocEntryArchive.h"
#include "gdcmDictSet.h"
+#include "gdcmOrientation.h"
+
+#if defined(__BORLANDC__)
+ #include <mem.h> // for memset
+#endif
#include <fstream>
fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
// (WriteMode is set)
-fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
+fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
// Little Endian is the default
// no other value is allowed
(-->SetWriteType(ExplicitVR);)
fp = opens file(fileName);
ComputeGroup0002Length( );
BitsAllocated 12->16
- RemoveEntryNoDestroy(palettes, etc)
+ RemoveEntry(palettes, etc)
Document::WriteContent(fp, writetype);
RestoreWrite();
(moves back to the File all the archived elements)
namespace gdcm
{
+typedef std::map<uint16_t, int> GroupHT; // Hash Table
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
*/
FileHelper::FileHelper( )
{
- FileInternal = new File( );
- SelfHeader = true;
+ FileInternal = File::New( );
Initialize();
}
*/
FileHelper::FileHelper(File *header)
{
- FileInternal = header;
- SelfHeader = false;
- Initialize();
- if ( FileInternal->IsReadable() )
- {
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
- }
-}
+ gdcmAssertMacro(header);
-#ifndef GDCM_LEGACY_REMOVE
-/*
- * brief DEPRECATED : use SetFilename() + SetLoadMode() + Load() methods
- * Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcm::File only deals with the ... header)
- * Opens (in read only and when possible) an existing file and checks
- * for DICOM compliance. Returns NULL on failure.
- * It will be up to the user to load the pixels into memory
- * note the in-memory representation of all available tags found in
- * the DICOM header is post-poned to first header information access.
- * This avoid a double parsing of public part of the header when
- * one sets an a posteriori shadow dictionary (efficiency can be
- * seen as a side effect).
- * param filename file to be opened for parsing
- * deprecated use SetFilename() + Load() methods
- */
-FileHelper::FileHelper(std::string const &filename )
-{
- FileInternal = new File( );
- FileInternal->SetFileName( filename );
- FileInternal->Load();
- SelfHeader = true;
+ FileInternal = header;
+ FileInternal->Register();
Initialize();
if ( FileInternal->IsReadable() )
{
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
}
}
-#endif
/**
* \brief canonical destructor
delete Archive;
}
- if ( SelfHeader )
- {
- delete FileInternal;
- }
- FileInternal = 0;
+ FileInternal->Unregister();
}
//-----------------------------------------------------------------------------
if ( !FileInternal->Load() )
return false;
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
return true;
}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's content with the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param elem element number of the Dicom Element to modify
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryString(std::string const &content,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem)
{
return FileInternal->SetEntryString(content, group, elem);
}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's content with the given value.
* @param content new value (void* -> uint8_t*) to substitute with
* @param lgth new value length
* @param group group number of the Dicom Element to modify
* @param elem element number of the Dicom Element to modify
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem)
{
return FileInternal->SetEntryBinArea(content, lgth, group, elem);
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
- * @param content (string)value to be set
+ * \brief Modifies the value of a given DataEntry when it exists.
+ * Creates it with the given value when unexistant.
+ * @param content (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 Dicom entry (NULL when creation
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryString(std::string const &content,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
- return FileInternal->InsertEntryString(content, group, elem);
+ return FileInternal->InsertEntryString(content, group, elem, vr);
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
+ * \brief Modifies the value of a given DataEntry when it exists.
+ * Creates it with the given value when unexistant.
* A copy of the binArea is made to be kept in the Document.
* @param binArea (binary)value to be set
* @param lgth new value length
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * @param vr Value Represenation of the DataElement to be inserted
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
- return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem);
+ return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr);
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it, empty (?!) when unexistant.
+ * \brief Adds an empty SeqEntry
+ * (remove any existing entry with same group,elem)
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the created SeqEntry (NULL when creation
* failed).
*/
SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
* - Transforms single Grey plane + 3 Palettes into a RGB Plane
* - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* @return Pointer to newly allocated pixel data.
+ * (uint8_t is just for prototyping. feel free to cast)
* NULL if alloc fails
*/
uint8_t *FileHelper::GetImageData()
* - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
- * NULL if alloc fails
+ * (uint8_t is just for prototyping. feel free to cast)
+ * NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
{
return GetRaw();
}
-#ifndef GDCM_LEGACY_REMOVE
+//#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)
{
if ( ! GetRaw() )
PixelReadConverter->GetRawSize() );
return PixelReadConverter->GetRawSize();
}
-#endif
+*/
+//#endif
/**
* \brief Points the internal pointer to the callers inData
*/
bool FileHelper::Write(std::string const &fileName)
{
+
+ CheckMandatoryElements(); //called once, here !
+
+ bool flag = false;
+ DocEntry *e;
switch(WriteType)
{
case ImplicitVR:
SetWriteFileTypeToImplicitVR();
break;
+
case Unknown: // should never happen; ExplicitVR is the default value
case ExplicitVR:
- SetWriteFileTypeToExplicitVR();
+
+ // User should ask gdcm to write an image in Explicit VR mode
+ // only when he is sure *all* the VR of *all* the DataElements is known.
+ // i.e : when there are *only* Public Groups
+ // or *all* the Shadow Groups are fully described in the relevant Shadow
+ // Dictionnary
+ // Let's just *dream* about it; *never* trust a user !
+ // We turn to Implicit VR if at least the VR of one element is unknown.
+
+
+ e = FileInternal->GetFirstEntry();
+ while (e != 0)
+ {
+ if (e->GetVR() == " ")
+ {
+ SetWriteTypeToDcmImplVR();
+ SetWriteFileTypeToImplicitVR();
+ flag = true;
+ break;
+ }
+ e = FileInternal->GetNextEntry();
+ }
+
+ if (!flag)
+ {
+ SetWriteFileTypeToExplicitVR();
+ }
break;
+
+ SetWriteFileTypeToExplicitVR(); // to see JPRx
+ break;
case ACR:
case ACR_LIBIDO:
// NOTHING is done here just for LibIDO.
// (shame on him !)
// We add Recognition Code (RET)
if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
- FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010);
+ FileInternal->InsertEntryString("ACR-NEMA V1.0 ",
+ 0x0008, 0x0010, "LO");
SetWriteFileTypeToACR();
// SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
+
+ /// \todo FIXME : JPEG may be either ExplicitVR or ImplicitVR
case JPEG:
SetWriteFileTypeToJPEG();
- std::cerr << "Writting as JPEG" << std::endl;
+ break;
+
+ case JPEG2000:
+ SetWriteFileTypeToJPEG2000();
break;
}
- CheckMandatoryElements();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
}
bool check = CheckWriteIntegrity(); // verifies length
- if (WriteType == JPEG ) check = true;
+ if (WriteType == JPEG || WriteType == JPEG2000) check = true;
if (check)
{
check = FileInternal->Write(fileName,WriteType);
}
- RestoreWrite();
- RestoreWriteFileType();
- RestoreWriteMandatory();
+ RestoreWrite();
+ // RestoreWriteFileType();
+ // RestoreWriteMandatory();
+
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
size_t decSize = FileInternal->GetXSize()
* FileInternal->GetYSize()
* FileInternal->GetZSize()
+ * FileInternal->GetTSize()
* FileInternal->GetSamplesPerPixel()
* ( numberBitsAllocated / 8 );
size_t rgbSize = decSize;
}
else
{
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
if (FileInternal->HasLUT() )
{
photInt->SetString("PALETTE COLOR ");
vr = "OW";
if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
vr = "OB";
+ // For non RAW data. Mainly JPEG
+ if( WriteType == JPEG || WriteType == JPEG2000)
+ {
+ vr = "OW";
+ }
DataEntry *pixel =
CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
Archive->Push(photInt);
Archive->Push(pixel);
+
+ photInt->Delete();
+ pixel->Delete();
}
}
{
PixelReadConverter->BuildRGBImage();
- DataEntry *spp = CopyDataEntry(0x0028,0x0002);
+ DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
spp->SetString("3 ");
- DataEntry *planConfig = CopyDataEntry(0x0028,0x0006);
+ DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
planConfig->SetString("0 ");
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
photInt->SetString("RGB ");
if ( PixelReadConverter->GetRGB() )
Archive->Push(photInt);
Archive->Push(pixel);
+ spp->Delete();
+ planConfig->Delete();
+ photInt->Delete();
+ pixel->Delete();
+
// Remove any LUT
Archive->Push(0x0028,0x1101);
Archive->Push(0x0028,0x1102);
// samples per pixels = 1 (in the read file)
if ( FileInternal->GetBitsAllocated()==24 )
{
- DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100);
+ DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US");
bitsAlloc->SetString("8 ");
- DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101);
+ DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US");
bitsStored->SetString("8 ");
- DataEntry *highBit = CopyDataEntry(0x0028,0x0102);
+ DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US");
highBit->SetString("7 ");
Archive->Push(bitsAlloc);
Archive->Push(bitsStored);
Archive->Push(highBit);
+
+ bitsAlloc->Delete();
+ bitsStored->Delete();
+ highBit->Delete();
}
}
else
*/
void FileHelper::RestoreWrite()
{
+
Archive->Restore(0x0028,0x0002);
Archive->Restore(0x0028,0x0004);
+
Archive->Restore(0x0028,0x0006);
Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
// For the Palette Color Lookup Table UID
Archive->Restore(0x0028,0x1203);
-
// group 0002 may be pushed out for ACR-NEMA writting purposes
Archive->Restore(0x0002,0x0000);
Archive->Restore(0x0002,0x0001);
Archive->Restore(0x0002,0x0016);
Archive->Restore(0x0002,0x0100);
Archive->Restore(0x0002,0x0102);
+
}
/**
Archive->Push(0x0002,0x0102);
}
+ /**
+ * \brief Sets in the File the TransferSyntax to 'JPEG2000'
+ */
+void FileHelper::SetWriteFileTypeToJPEG2000()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) );
+
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
+ tss->SetString(ts);
+
+ Archive->Push(tss);
+ tss->Delete();
+}
+
/**
- * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ * \brief Sets in the File the TransferSyntax to 'JPEG'
*/
void FileHelper::SetWriteFileTypeToJPEG()
{
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
Archive->Push(tss);
+ tss->Delete();
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ */
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
-
Archive->Push(tss);
+ tss->Delete();
}
/**
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
-
Archive->Push(tss);
+ tss->Delete();
}
{
std::string rows, columns;
- DataEntry *newRow=new DataEntry(oldRow->GetDictEntry());
- DataEntry *newCol=new DataEntry(oldCol->GetDictEntry());
-
+ //DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
+ //DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
+
+ DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US");
+ DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US");
+
newRow->Copy(oldCol);
newCol->Copy(oldRow);
Archive->Push(newRow);
Archive->Push(newCol);
+
+ newRow->Delete();
+ newCol->Delete();
}
- DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
/**
{
if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
{
- DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
libidoCode->SetString("");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
}
}
* @param group Group number of the Entry
* @param elem Element number of the Entry
* @param vr Value Representation of the Entry
- * FIXME : what is it used for?
* \return pointer to the new Bin Entry (NULL when creation failed).
*/
DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
- const TagName &vr)
+ const VRKey &vr)
{
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
DataEntry *newE;
if ( oldE )
{
- newE = new DataEntry(oldE->GetDictEntry());
+ //newE = DataEntry::New(oldE->GetDictEntry());
+ newE = DataEntry::New(group, elem, vr);
newE->Copy(oldE);
}
else
/**
* \brief This method is called automatically, just before writting
- * in order to produce a 'True Dicom V3' image
- * We cannot know *how* the user made the File (reading an old ACR-NEMA
- * file or a not very clean DICOM file ...)
- *
+ * in order to produce a 'True Dicom V3' image.
+ *
+ * We cannot know *how* the user made the File :
+ * (reading an old ACR-NEMA file or a not very clean DICOM file ...)
* Just before writting :
* - we check the Entries
* - we create the mandatory entries if they are missing
* - we push the sensitive entries to the Archive
* The writing process will restore the entries as they where before
* entering FileHelper::CheckMandatoryElements, so the user will always
- * see the entries just as he left them.
+ * see the entries just as they were before he decided to write.
+ *
+ * \note
+ * - Entries whose type is 1 are mandatory, with a mandatory value
+ * - Entries whose type is 1c are mandatory-inside-a-Sequence,
+ * with a mandatory value
+ * - Entries whose type is 2 are mandatory, with an optional value
+ * - Entries whose type is 2c are mandatory-inside-a-Sequence,
+ * with an optional value
+ * - Entries whose type is 3 are optional
*
- * \todo : - warn the user if we had to add some entries :
+ * \todo
+ * - warn the user if we had to add some entries :
* even if a mandatory entry is missing, we add it, with a default value
* (we don't want to give up the writting process if user forgot to
* specify Lena's Patient ID, for instance ...)
* - write a user callable full checker, to allow post reading
* and/or pre writting image consistency check.
*/
+
+/* -------------------------------------------------------------------------------------
+To be moved to User's guide / WIKI ?
+
+We have to deal with 4 *very* different cases :
+-1) user created ex nihilo his own image and wants to write it as a Dicom image.
+ USER_OWN_IMAGE
+-2) user modified the pixels of an existing image.
+ FILTERED_IMAGE
+-3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image)
+ CREATED_IMAGE
+-4) user modified/added some tags *without processing* the pixels (anonymization..
+ UNMODIFIED_PIXELS_IMAGE
+-Probabely some more to be added
+gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
+
+1)2)3)4)
+0008 0012 Instance Creation Date
+0008 0013 Instance Creation Time
+0008 0018 SOP Instance UID
+are *always* created with the current values; user has *no* possible intervention on
+them.
+
+'Serie Instance UID'(0x0020,0x000e)
+'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
+ created if it doesn't.
+ The user is allowed to create his own Series/Studies,
+ keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
+ Warning :
+ The user shouldn't add any image to a 'Manufacturer Serie'
+ but there is no way no to allow him to do that
+
+ None of the 'shadow elements' are droped out.
+
+
+1)
+'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
+
+1)3)
+'Media Storage SOP Class UID' (0x0002,0x0002)
+'SOP Class UID' (0x0008,0x0016) are set to
+ [Secondary Capture Image Storage]
+'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
+Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
+
+2)4)
+If 'SOP Class UID' exists in the native image ('true DICOM' image)
+ we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
+ --> 'Referenced SOP Class UID' (0x0008, 0x1150)
+ whose value is the original 'SOP Class UID'
+ --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
+ whose value is the original 'SOP Class UID'
+
+3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images
+ or the Series, (or the Study ?) he used to created his image
+ (MIP, MPR, cartography image, ...)
+ These info should be stored (?)
+ 0008 1110 SQ 1 Referenced Study Sequence
+ 0008 1115 SQ 1 Referenced Series Sequence
+ 0008 1140 SQ 1 Referenced Image Sequence
+
+4) When user *knows* he didn't modified the pixels, we keep some informations unchanged :
+'Media Storage SOP Class UID' (0x0002,0x0002)
+'SOP Class UID' (0x0008,0x0016)
+'Image Type' (0x0008,0x0008)
+'Conversion Type' (0x0008,0x0064)
+
+
+Bellow follows the full description (hope so !) of the consistency checks performed
+by gdcm::FileHelper::CheckMandatoryElements()
+
+
+-->'Media Storage SOP Class UID' (0x0002,0x0002)
+-->'SOP Class UID' (0x0008,0x0016) are defaulted to
+ [Secondary Capture Image Storage]
+--> 'Image Type' (0x0008,0x0008)
+ is forced to "DERIVED\PRIMARY"
+ (The written image is no longer an 'ORIGINAL' one)
+ Except if user knows he didn't modify the image (e.g. : he just anonymized the file)
+
+ --> Conversion Type (0x0008,0x0064)
+ is defaulted to 'SYN' (Synthetic Image)
+ when *he* knows he created his own image ex nihilo
+
+--> 'Modality' (0x0008,0x0060)
+ is defaulted to "OT" (other) if missing.
+ (a fully user created image belongs to *no* modality)
+
+--> 'Media Storage SOP Instance UID' (0x0002,0x0003)
+--> 'Implementation Class UID' (0x0002,0x0012)
+ are automatically generated; no user intervention possible
+
+--> 'Serie Instance UID'(0x0020,0x000e)
+--> 'Study Instance UID'(0x0020,0x000d) are kept as is if already exist
+ created if it doesn't.
+ The user is allowed to create his own Series/Studies,
+ keeping the same 'Serie Instance UID' / 'Study Instance UID'
+ for various images
+ Warning :
+ The user shouldn't add any image to a 'Manufacturer Serie'
+ but there is no way no to allowed him to do that
+
+--> If 'SOP Class UID' exists in the native image ('true DICOM' image)
+ we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
+
+ --> 'Referenced SOP Class UID' (0x0008, 0x1150)
+ whose value is the original 'SOP Class UID'
+ --> 'Referenced SOP Instance UID' (0x0008, 0x1155)
+ whose value is the original 'SOP Class UID'
+
+--> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
+--> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
+--> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
+
+--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
+
+--> Instance Creation Date, Instance Creation Time are forced to current Date and Time
+
+--> Study Date, Study Time are defaulted to current Date and Time
+ (they remain unchanged if they exist)
+
+--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
+ Image Orientation (Patient) : (0020|0037) or from
+ Image Orientation (RET) : (0020 0035)
+
+--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
+ are created, with empty value if there are missing.
+
+--> Manufacturer, Institution Name, Patient's Name, (Type 2)
+ are defaulted with a 'gdcm' value.
+
+--> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2)
+--> Referring Physician's Name (Type 2)
+ are created, with empty value if there are missing.
+
+ -------------------------------------------------------------------------------------*/
+
void FileHelper::CheckMandatoryElements()
{
std::string sop = Util::CreateUniqueUID();
-
+
+ // --------------------- For Meta Elements ---------------------
// just to remember : 'official' 0002 group
if ( WriteType != ACR && WriteType != ACR_LIBIDO )
{
//0002 0016 AE 1 Source Application Entity Title
//0002 0100 UI 1 Private Information Creator
//0002 0102 OB 1 Private Information
+
+ // Push out 'ACR-NEMA-special' entries, if any
+ Archive->Push(0x0008,0x0001); // Length to End
+ Archive->Push(0x0008,0x0010); // Recognition Code
+ Archive->Push(0x0028,0x0005); // Image Dimension
// Create them if not found
// Always modify the value
// Push the entries to the archive.
- CopyMandatoryEntry(0x0002,0x0000,"0");
-
+ CopyMandatoryEntry(0x0002,0x0000,"0","UL");
+
DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB");
e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
false);
e_0002_0001->SetLength(2);
Archive->Push(e_0002_0001);
+ e_0002_0001->Delete();
- // Potentialy post-processed image --> [Secondary Capture Image Storage]
- // 'Media Storage SOP Class UID'
- CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
-
+ if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
+ {
+ // we keep the original 'Media Storage SOP Class UID', we default it if missing
+ CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
+ else
+ {
+ // It's *not* an image comming straight from a source. We force
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
+
// 'Media Storage SOP Instance UID'
- CopyMandatoryEntry(0x0002,0x0003,sop);
+ CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
// 'Implementation Class UID'
- CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
+ // FIXME : in all examples we have, 0x0002,0x0012 is not so long :
+ // seems to be Root UID + 4 digits (?)
+ CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI");
// 'Implementation Version Name'
std::string version = "GDCM ";
version += Util::GetVersion();
- CopyMandatoryEntry(0x0002,0x0013,version);
+ CopyMandatoryEntry(0x0002,0x0013,version,"SH");
}
+ // --------------------- For DataSet ---------------------
+
+ if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
+ {
+
+ gdcmDebugMacro( "USER_OWN_IMAGE (1)");
+ // If 'SOP Class UID' exists ('true DICOM' image)
+ // we create the 'Source Image Sequence' SeqEntry
+ // to hold informations about the Source Image
+
+ DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
+ if ( e_0008_0016 )
+ {
+ // Create 'Source Image Sequence' SeqEntry
+// SeqEntry *sis = SeqEntry::New (
+// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
+ SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
+ SQItem *sqi = SQItem::New(1);
+ // (we assume 'SOP Instance UID' exists too)
+ // create 'Referenced SOP Class UID'
+// DataEntry *e_0008_1150 = DataEntry::New(
+// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
+ DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
+ e_0008_1150->SetString( e_0008_0016->GetString());
+ sqi->AddEntry(e_0008_1150);
+ e_0008_1150->Delete();
+
+ // create 'Referenced SOP Instance UID'
+ DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
+// DataEntry *e_0008_1155 = DataEntry::New(
+// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
+ DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
+ e_0008_1155->SetString( e_0008_0018->GetString());
+ sqi->AddEntry(e_0008_1155);
+ e_0008_1155->Delete();
+
+ sis->AddSQItem(sqi,1);
+ sqi->Delete();
+
+ // temporarily replaces any previous 'Source Image Sequence'
+ Archive->Push(sis);
+ sis->Delete();
+
+ // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
+ if ( ContentType == FILTERED_IMAGE)
+ // the user *knows* he just modified the pixels
+ // the image is no longer an 'Original' one
+ CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
+ }
+ }
+
+ if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
+ {
+ // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !)
+ CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
+ else
+ {
+ // It's *not* an image comming straight from a source. We force
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI");
+ }
+
+ Archive->Push(0x0028,0x005); // [Image Dimensions (RET)
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
Archive->Push(0x0028,0x0016);
Archive->Push(0x0028,0x0017);
- Archive->Push(0x0028,0x00199);
+ Archive->Push(0x0028,0x0198); // very old versions
+ Archive->Push(0x0028,0x0199);
+
+ // Replace deprecated 0028 0012 US Planes
+ // by new 0028 0008 IS Number of Frames
+
+ ///\todo : find if there is a rule!
+ DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012);
+ if ( e_0028_0012 )
+ {
+ CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS");
+ Archive->Push(0x0028,0x0012);
+ }
// Deal with the pb of (Bits Stored = 12)
// - we're gonna write the image as Bits Stored = 16
if ( FileInternal->GetEntryString(0x0028,0x0100) == "12")
{
- CopyMandatoryEntry(0x0028,0x0100,"16");
+ CopyMandatoryEntry(0x0028,0x0100,"16","US");
}
// Check if user wasn't drunk ;-)
int nbBitsAllocated = FileInternal->GetBitsAllocated();
if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
{
- CopyMandatoryEntry(0x0028,0x0100,"16");
+ CopyMandatoryEntry(0x0028,0x0100,"16","US");
gdcmWarningMacro("(0028,0100) changed from "
<< nbBitsAllocated << " to 16 for consistency purpose");
nbBitsAllocated = 16;
{
s.str("");
s << nbBitsAllocated;
- CopyMandatoryEntry(0x0028,0x0101,s.str());
+ CopyMandatoryEntry(0x0028,0x0101,s.str(),"US");
gdcmWarningMacro("(0028,0101) changed from "
<< nbBitsStored << " to " << nbBitsAllocated
<< " for consistency purpose" );
{
s.str("");
s << nbBitsStored - 1;
- CopyMandatoryEntry(0x0028,0x0102,s.str());
+ CopyMandatoryEntry(0x0028,0x0102,s.str(),"US");
gdcmWarningMacro("(0028,0102) changed from "
<< highBitPosition << " to " << nbBitsAllocated-1
<< " for consistency purpose");
}
- // --- Check UID-related Entries ---
-
- // If 'SOP Class UID' exists ('true DICOM' image)
- // we create the 'Source Image Sequence' SeqEntry
- // to hold informations about the Source Image
- DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
- if ( e_0008_0016 )
+ std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
+ if ( pixelSpacing == GDCM_UNFOUND )
{
- // Create 'Source Image Sequence' SeqEntry
- SeqEntry *sis = new SeqEntry (
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
- SQItem *sqi = new SQItem(1);
- // (we assume 'SOP Instance UID' exists too)
- // create 'Referenced SOP Class UID'
- DataEntry *e_0008_1150 = new DataEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
- e_0008_1150->SetString( e_0008_0016->GetString());
- sqi->AddEntry(e_0008_1150);
-
- // create 'Referenced SOP Instance UID'
- DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
- DataEntry *e_0008_1155 = new DataEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
- e_0008_1155->SetString( e_0008_0018->GetString());
- sqi->AddEntry(e_0008_1155);
+ pixelSpacing = "1.0\\1.0";
+ // if missing, Pixel Spacing forced to "1.0\1.0"
+ CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
+ }
+
+ // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
+ // --> This one is the *legal* one !
+ if ( ContentType != USER_OWN_IMAGE)
+ // we write it only when we are *sure* the image comes from
+ // an imager (see also 0008,0x0064)
+ CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
- sis->AddSQItem(sqi,1);
- // temporarily replaces any previous 'Source Image Sequence'
- Archive->Push(sis);
+
+
+/*
+///Exact meaning of RETired fields
+
+// See page 73 of ACR-NEMA_300-1988.pdf !
+
+// 0020,0020 : Patient Orientation :
+Patient direction of the first row and
+column of the images. The first entry id the direction of the raws, given by the
+direction of the last pixel in the first row from the first pixel in tha row.
+the second entry is the direction of the columns, given by the direction of the
+last pixel in the first column from the first pixel in that column.
+L : Left, F : Feet, A : Anterior, P : Posterior.
+Up to 3 letters can be used in combination to indicate oblique planes.
+
+//0020,0030 Image Position (RET)
+x,y,z coordinates im mm of the first pixel in the image
+
+// 0020,0035 Image Orientation (RET)
+Direction cosines of the R axis of the image system with respect to the
+equipment coordinate axes x,y,z, followed by direction cosines of the C axis of
+the image system with respect to the same axes
+
+//0020,0050 Location
+An image location reference, standard for the modality (such as CT bed
+position), used to indicate position. Calculation of position for other purposes
+is only from (0020,0030) and (0020,0035)
+*/
- // 'Image Type' (The written image is no longer an 'ORIGINAL' one)
- CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
- }
+/*
+// if imagePositionPatient not found, default it with imagePositionRet, if any
+// if imageOrientationPatient not found, default it with imageOrientationRet, if any
+
+ std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030);
+ std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035);
+ std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032);
+ std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037);
+
+ if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND
+ && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND)
+ {
+ CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS");
+ Archive->Push(0x0020,0x0030);
+ CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS");
+ Archive->Push(0x0020,0x0035);
+ }
+*/
+
+ // Samples Per Pixel (type 1) : default to grayscale
+ CheckMandatoryEntry(0x0028,0x0002,"1","US");
+ // --- Check UID-related Entries ---
+
// At the end, not to overwrite the original ones,
// needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
// 'SOP Instance UID'
- CopyMandatoryEntry(0x0008,0x0018,sop);
+ CopyMandatoryEntry(0x0008,0x0018,sop,"UI");
+
+ if ( ContentType == USER_OWN_IMAGE)
+ {
+ gdcmDebugMacro( "USER_OWN_IMAGE (2)");
+ // Conversion Type.
+ // Other possible values are :
+ // See PS 3.3, Page 408
- // whether a 'SOP Class UID' already exists or not in the original image
- // the gdcm written image *is* a [Secondary Capture Image Storage] !
- // 'SOP Class UID' : [Secondary Capture Image Storage]
- CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
-
-// ---- The user will never have to take any action on the following ----.
+ // DV = Digitized Video
+ // DI = Digital Interface
+ // DF = Digitized Film
+ // WSD = Workstation
+ // SD = Scanned Document
+ // SI = Scanned Image
+ // DRW = Drawing
+ // SYN = Synthetic Image
+
+ CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not?
+ }
+/*
+ if ( ContentType == CREATED_IMAGE)
+ {
+ /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image
+
+ }
+*/
+
+ // ---- The user will never have to take any action on the following ----
+
// new value for 'SOP Instance UID'
//SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
// Instance Creation Date
- CopyMandatoryEntry(0x0008,0x0012,Util::GetCurrentDate().c_str());
+ const std::string &date = Util::GetCurrentDate();
+ CopyMandatoryEntry(0x0008,0x0012,date,"DA");
// Instance Creation Time
- CopyMandatoryEntry(0x0008,0x0013,Util::GetCurrentTime().c_str());
+ const std::string &time = Util::GetCurrentTime();
+ CopyMandatoryEntry(0x0008,0x0013,time,"TM");
-// ----- Add Mandatory Entries if missing ---
- // Entries whose type is 1 are mandatory, with a mandatory value
- // Entries whose type is 1c are mandatory-inside-a-Sequence,
- // with a mandatory value
- // Entries whose type is 2 are mandatory, with an optional value
- // Entries whose type is 2c are mandatory-inside-a-Sequence,
- // with an optional value
- // Entries whose type is 3 are optional
+ // Study Date
+ CheckMandatoryEntry(0x0008,0x0020,date,"DA");
+ // Study Time
+ CheckMandatoryEntry(0x0008,0x0030,time,"TM");
+
+ // Accession Number
+ //CopyMandatoryEntry(0x0008,0x0050,"");
+ CheckMandatoryEntry(0x0008,0x0050,"","SH");
+
+
+ // ----- Add Mandatory Entries if missing ---
+ // Entries whose type is 1 are mandatory, with a mandatory value
+ // Entries whose type is 1c are mandatory-inside-a-Sequence,
+ // with a mandatory value
+ // Entries whose type is 2 are mandatory, with an optional value
+ // Entries whose type is 2c are mandatory-inside-a-Sequence,
+ // with an optional value
+ // Entries whose type is 3 are optional
// 'Study Instance UID'
// Keep the value if exists
// The user is allowed to create his own Study,
// keeping the same 'Study Instance UID' for various images
// The user may add images to a 'Manufacturer Study',
- // adding new series to an already existing Study
- CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID());
+ // adding new Series to an already existing Study
+ CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI");
// 'Serie Instance UID'
// Keep the value if exists
// The user is allowed to create his own Series,
// keeping the same 'Serie Instance UID' for various images
// The user shouldn't add any image to a 'Manufacturer Serie'
- // but there is no way no to allowed him to do that
- CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID());
+ // but there is no way no to prevent him for doing that
+ CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI");
+
+ // Study ID
+ CheckMandatoryEntry(0x0020,0x0010,"","SH");
+
+ // Series Number
+ CheckMandatoryEntry(0x0020,0x0011,"","IS");
+
+ // Instance Number
+ CheckMandatoryEntry(0x0020,0x0013,"","IS");
+ // Patient Orientation
+ // Can be computed from (0020|0037) : Image Orientation (Patient)
+ gdcm::Orientation *o = gdcm::Orientation::New();
+ std::string ori = o->GetOrientation ( FileInternal );
+ o->Delete();
+ if (ori != "\\" && ori != GDCM_UNFOUND)
+ CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
+ else
+ CheckMandatoryEntry(0x0020,0x0020,"","CS");
+
+ // Default Patient Position to HFS
+ CheckMandatoryEntry(0x0018,0x5100,"HFS","CS");
+
// Modality : if missing we set it to 'OTher'
- CheckMandatoryEntry(0x0008,0x0060,"OT");
+ CheckMandatoryEntry(0x0008,0x0060,"OT","CS");
// Manufacturer : if missing we set it to 'GDCM Factory'
- CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory");
+ CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO");
// Institution Name : if missing we set it to 'GDCM Hospital'
- CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital");
+ CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO");
// Patient's Name : if missing, we set it to 'GDCM^Patient'
- CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient");
+ CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN");
+
+ // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry.
+ CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO");
// Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0010,0x0030,"");
+ CheckMandatoryEntry(0x0010,0x0030,"","DA");
// Patient's Sex :'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0010,0x0040,"");
+ CheckMandatoryEntry(0x0010,0x0040,"","CS");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0008,0x0090,"");
+ CheckMandatoryEntry(0x0008,0x0090,"","PN");
- // Pixel Spacing : defaulted to 1.0\1.0
- CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
+ /*
+ // Deal with element 0x0000 (group length) of each group.
+ // First stage : get all the different Groups
- // Remove some inconstencies (probably some more will be added)
+ GroupHT grHT;
+ DocEntry *d = FileInternal->GetFirstEntry();
+ while(d)
+ {
+ grHT[d->GetGroup()] = 0;
+ d=FileInternal->GetNextEntry();
+ }
+ // Second stage : add the missing ones (if any)
+ for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
+ {
+ CheckMandatoryEntry(it->first, 0x0000, "0");
+ }
+ // Third stage : update all 'zero level' groups length
+*/
- // if (0028 0008)Number of Frames exists
- // Push out (0020 0052),Frame of Reference UID
- // (only meaningfull within a Serie)
- DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008);
- if ( !e_0028_0008 )
- {
- Archive->Push(0x0020, 0X0052);
- }
}
-void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr )
{
DataEntry *entry = FileInternal->GetDataEntry(group,elem);
if ( !entry )
{
- entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ entry = DataEntry::New(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
- }
+ entry->Delete();
+ }
}
-void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+/// \todo : what is it used for ? (FileHelper::SetMandatoryEntry)
+void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
{
- DataEntry *entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ DataEntry *entry = DataEntry::New(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
+ entry->Delete();
}
-void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
{
- DataEntry *entry = CopyDataEntry(group,elem);
+ DataEntry *entry = CopyDataEntry(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
+ entry->Delete();
}
/**
Archive->Restore(0x0002,0x0100);
Archive->Restore(0x0002,0x0102);
+ // FIXME : Check if none is missing !
+
Archive->Restore(0x0008,0x0012);
Archive->Restore(0x0008,0x0013);
Archive->Restore(0x0008,0x0016);
Archive->Restore(0x0020,0x000d);
Archive->Restore(0x0020,0x000e);
+}
+
+/**
+ * \brief CallStartMethod
+ */
+void FileHelper::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void FileHelper::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void FileHelper::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
}
//-----------------------------------------------------------------------------
void FileHelper::Initialize()
{
UserFunction = 0;
-
+ ContentType = USER_OWN_IMAGE;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
//-----------------------------------------------------------------------------
} // end namespace gdcm
+
+
+/* Probabely something to be added to use Rescale Slope/Intercept
+Have a look ,at ITK code !
+
+// Internal function to rescale pixel according to Rescale Slope/Intercept
+template<class TBuffer, class TSource>
+void RescaleFunction(TBuffer* buffer, TSource *source,
+ double slope, double intercept, size_t size)
+{
+ size /= sizeof(TSource);
+
+ if (slope != 1.0 && intercept != 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]*slope + intercept);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 7: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 6: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 5: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 4: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 3: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 2: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 1: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ } while (--n > 0);
+ }
+ }
+ else if (slope == 1.0 && intercept != 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i] + intercept);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)(*source++ + intercept);
+ case 7: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 6: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 5: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 4: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 3: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 2: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 1: *buffer++ = (TBuffer)(*source++ + intercept);
+ } while (--n > 0);
+ }
+ }
+ else if (slope != 1.0 && intercept == 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]*slope);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)((*source++)*slope);
+ case 7: *buffer++ = (TBuffer)((*source++)*slope);
+ case 6: *buffer++ = (TBuffer)((*source++)*slope);
+ case 5: *buffer++ = (TBuffer)((*source++)*slope);
+ case 4: *buffer++ = (TBuffer)((*source++)*slope);
+ case 3: *buffer++ = (TBuffer)((*source++)*slope);
+ case 2: *buffer++ = (TBuffer)((*source++)*slope);
+ case 1: *buffer++ = (TBuffer)((*source++)*slope);
+ } while (--n > 0);
+ }
+ }
+ else
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)(*source++);
+ case 7: *buffer++ = (TBuffer)(*source++);
+ case 6: *buffer++ = (TBuffer)(*source++);
+ case 5: *buffer++ = (TBuffer)(*source++);
+ case 4: *buffer++ = (TBuffer)(*source++);
+ case 3: *buffer++ = (TBuffer)(*source++);
+ case 2: *buffer++ = (TBuffer)(*source++);
+ case 1: *buffer++ = (TBuffer)(*source++);
+ } while (--n > 0);
+ }
+ }
+
+
+}
+
+
+template<class TSource>
+void RescaleFunction(ImageIOBase::IOComponentType bufferType,
+ void* buffer, TSource *source,
+ double slope, double intercept, size_t size)
+{
+ switch (bufferType)
+ {
+ case ImageIOBase::UCHAR:
+ RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::CHAR:
+ RescaleFunction( (char *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::USHORT:
+ RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size);
+ break;
+ case ImageIOBase::SHORT:
+ RescaleFunction( (short *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::UINT:
+ RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::INT:
+ RescaleFunction( (int *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::FLOAT:
+ RescaleFunction( (float *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::DOUBLE:
+ RescaleFunction( (double *)buffer, source, slope, intercept, size);
+ break;
+ default:
+ ::itk::OStringStream message;
+ message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType;
+ ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);
+ throw e;
+ }
+}
+*/
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff