Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/04/04 15:15:24 $
- Version: $Revision: 1.32 $
+ Date: $Date: 2005/11/29 17:21:35 $
+ 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
#include "gdcmDocument.h"
#include "gdcmDebug.h"
#include "gdcmUtil.h"
-#include "gdcmBinEntry.h"
-#include "gdcmValEntry.h"
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
-#include "gdcmContentEntry.h"
+#include "gdcmDataEntry.h"
#include "gdcmFile.h"
#include "gdcmPixelReadConvert.h"
#include "gdcmPixelWriteConvert.h"
#include "gdcmDocEntryArchive.h"
#include "gdcmDictSet.h"
+#include "gdcmOrientation.h"
#include <fstream>
These lines will be moved to the document-to-be 'User's Guide'
// To read an image, user needs a gdcm::File
-gdcm::File *f1 = new gdcm::File(fileName);
+gdcm::File *f = new gdcm::File(fileName);
+// or (advanced) :
+// user may also decide he doesn't want to load some parts of the header
+gdcm::File *f = new gdcm::File();
+f->SetFileName(fileName);
+ f->SetLoadMode(LD_NOSEQ); // or
+ f->SetLoadMode(LD_NOSHADOW); // or
+ f->SetLoadMode(LD_NOSEQ | LD_NOSHADOW); // or
+ f->SetLoadMode(LD_NOSHADOWSEQ);
+f->Load();
+
// user can now check some values
-std::string v = f1->GetEntryValue(groupNb,ElementNb);
+std::string v = f->GetEntryValue(groupNb,ElementNb);
+
// to get the pixels, user needs a gdcm::FileHelper
-gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1);
+gdcm::FileHelper *fh = new gdcm::FileHelper(f);
// user may ask not to convert Palette to RGB
-uint8_t *pixels = fh1->GetImageDataRaw();
-int imageLength = fh1->GetImageDataRawSize();
+uint8_t *pixels = fh->GetImageDataRaw();
+int imageLength = fh->GetImageDataRawSize();
// He can now use the pixels, create a new image, ...
uint8_t *userPixels = ...
To re-write the image, user re-uses the gdcm::FileHelper
-fh1->SetImageData( userPixels, userPixelsLength);
-fh1->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
+fh->SetImageData( userPixels, userPixelsLength);
+fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
// (WriteMode is set)
-fh1->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);)
-->WriteType = ExplicitVR;
-fh1->Write(newFileName); // overwrites the file, if any
+fh->Write(newFileName); // overwrites the file, if any
// or :
-fh1->WriteDcmExplVR(newFileName);
+fh->WriteDcmExplVR(newFileName);
// ----------------------------- WARNING -------------------------
(checks user given pixels length)
FileInternal->Write(fileName,WriteType)
fp = opens file(fileName);
- ComputeGroup0002Length(writetype);
+ 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
/**
* 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
+ * ( GetImageDataSize() + GetImageData() methods)
* \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
* seen as a side effect).
*/
FileHelper::FileHelper( )
-{
- FileInternal = new File( );
- SelfHeader = true;
+{
+ FileInternal = File::New( );
Initialize();
}
* 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
+ * ( GetImageDataSize() + GetImageData() methods)
* \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
*/
FileHelper::FileHelper(File *header)
{
- FileInternal = header;
- SelfHeader = false;
- Initialize();
-}
+ gdcmAssertMacro(header);
-/**
- * \brief 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
- */
-FileHelper::FileHelper(std::string const &filename )
-{
- FileInternal = new File( filename );
- SelfHeader = true;
+ FileInternal = header;
+ FileInternal->Register();
Initialize();
+ if ( FileInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
+ }
}
/**
*/
FileHelper::~FileHelper()
{
- if( PixelReadConverter )
+ if ( PixelReadConverter )
{
delete PixelReadConverter;
}
- if( PixelWriteConverter )
+ if ( PixelWriteConverter )
{
delete PixelWriteConverter;
}
- if( Archive )
+ if ( Archive )
{
delete Archive;
}
- if( SelfHeader )
- {
- delete FileInternal;
- }
- FileInternal = 0;
+ FileInternal->Unregister();
}
//-----------------------------------------------------------------------------
// Public
+
/**
- * \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 Sets the LoadMode of the internal gdcm::File as a boolean string.
+ * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now)
+ * WARNING : before using NO_SHADOW, be sure *all* your files
+ * contain accurate values in the 0x0000 element (if any)
+ * of *each* Shadow Group. The parser will fail if the size is wrong !
+ * @param loadMode Load mode to be used
+ */
+void FileHelper::SetLoadMode(int loadMode)
+{
+ GetFile()->SetLoadMode( loadMode );
+}
+/**
+ * \brief Sets the LoadMode of the internal gdcm::File
+ * @param fileName name of the file to be open
+ */
+void FileHelper::SetFileName(std::string const &fileName)
+{
+ FileInternal->SetFileName( fileName );
+}
+
+/**
+ * \brief Loader
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool FileHelper::Load()
+{
+ if ( !FileInternal->Load() )
+ return false;
+
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
+ return true;
+}
+
+/**
+ * \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::SetValEntry(std::string const &content,
- uint16_t group, uint16_t elem)
+bool FileHelper::SetEntryString(std::string const &content,
+ uint16_t group, uint16_t elem)
{
- return FileInternal->SetValEntry(content, group, 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::SetBinEntry(uint8_t *content, int lgth,
- uint16_t group, uint16_t elem)
+bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
+ uint16_t group, uint16_t elem)
{
- return FileInternal->SetBinEntry(content, lgth, group, 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).
*/
-ValEntry *FileHelper::InsertValEntry(std::string const &content,
- uint16_t group, uint16_t elem)
+DataEntry *FileHelper::InsertEntryString(std::string const &content,
+ uint16_t group, uint16_t elem)
{
- return FileInternal->InsertValEntry(content,group,elem);
+ return FileInternal->InsertEntryString(content, group, elem);
}
/**
- * \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
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
-BinEntry *FileHelper::InsertBinEntry(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
+DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t elem)
{
- return FileInternal->InsertBinEntry(binArea, lgth, group, elem);
+ return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem);
}
/**
- * \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)
{
return PixelWriteConverter->GetUserDataSize();
}
-
return PixelReadConverter->GetRGBSize();
}
/**
- * \brief Get the size of the image data
+ * \brief Get the size of the image data.
* If the image could be converted to RGB using a LUT,
* this transformation is not taken into account by GetImageDataRawSize
* (use GetImageDataSize if you wish)
{
return PixelWriteConverter->GetUserDataSize();
}
-
return PixelReadConverter->GetRawSize();
}
/**
- * \brief - Allocates necessary memory,
+ * \brief brings pixels into memory :
+ * - Allocates necessary memory,
* - Reads the pixels from disk (uncompress if necessary),
* - Transforms YBR pixels, if any, into RGB pixels,
* - Transforms 3 planes R, G, B, if any, into a single RGB Plane
* - 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()
}
/**
- * \brief Allocates necessary memory,
- * Transforms YBR pixels (if any) into RGB pixels
- * Transforms 3 planes R, G, B (if any) into a single RGB Plane
- * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * \brief brings pixels into memory :
+ * - Allocates necessary memory,
+ * - Transforms YBR pixels (if any) into RGB pixels
+ * - Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * - 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.
+ * (uint8_t is just for prototyping. feel free to cast)
* NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
return GetRaw();
}
-/**
- * \brief
- * Read the pixels from disk (uncompress if necessary),
+#ifndef GDCM_LEGACY_REMOVE
+/*
+ * \ 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 3 planes R, G, B, if any, into a single RGB Plane
* 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)
return 0;
}
memcpy( destination,
- (void*)PixelReadConverter->GetRaw(),
+ (void *)PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize() );
return PixelReadConverter->GetRawSize();
}
+#endif
/**
* \brief Points the internal pointer to the callers inData
*/
uint8_t* FileHelper::GetLutRGBA()
{
+ if ( PixelReadConverter->GetLutRGBA() ==0 )
+ PixelReadConverter->BuildLUTRGBA();
return PixelReadConverter->GetLutRGBA();
}
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Number
+ */
+int FileHelper::GetLutItemNumber()
+{
+ return PixelReadConverter->GetLutItemNumber();
+}
+
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Size
+ */
+int FileHelper::GetLutItemSize()
+{
+ return PixelReadConverter->GetLutItemSize();
+}
+
/**
* \brief Writes on disk A SINGLE Dicom file
* NO test is performed on processor "Endiannity".
return false;
}
- if( PixelWriteConverter->GetUserData() )
+ if ( PixelWriteConverter->GetUserData() )
{
- fp1.write( (char*)PixelWriteConverter->GetUserData(),
+ fp1.write( (char *)PixelWriteConverter->GetUserData(),
PixelWriteConverter->GetUserDataSize() );
}
else if ( PixelReadConverter->GetRGB() )
{
- fp1.write( (char*)PixelReadConverter->GetRGB(),
+ fp1.write( (char *)PixelReadConverter->GetRGB(),
PixelReadConverter->GetRGBSize());
}
else if ( PixelReadConverter->GetRaw() )
{
- fp1.write( (char*)PixelReadConverter->GetRaw(),
+ fp1.write( (char *)PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize());
}
else
/**
* \brief Writes on disk A SINGLE Dicom file,
* using the Implicit Value Representation convention
- * NO test is performed on processor "Endiannity".
+ * NO test is performed on processor "Endianity".
* @param fileName name of the file to be created
* (any already existing file is overwritten)
* @return false if write fails
{
case ImplicitVR:
SetWriteFileTypeToImplicitVR();
- CheckMandatoryElements();
break;
case Unknown: // should never happen; ExplicitVR is the default value
case ExplicitVR:
SetWriteFileTypeToExplicitVR();
- CheckMandatoryElements();
break;
case ACR:
case ACR_LIBIDO:
- // Just to avoid further trouble if user create a file ex-nihilo,
+ // NOTHING is done here just for LibIDO.
+ // Just to avoid further trouble if user creates a file ex-nihilo,
// wants to write it as an ACR-NEMA file,
- // and forget to create any Entry belonging to group 0008
+ // and forgets to create any Entry belonging to group 0008
// (shame on him !)
// We add Recognition Code (RET)
- if ( ! FileInternal->GetValEntry(0x0008, 0x0010) )
- FileInternal->InsertValEntry("", 0x0008, 0x0010);
+ if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
+ FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010);
SetWriteFileTypeToACR();
+ // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
+ break;
+ case JPEG:
+ SetWriteFileTypeToJPEG();
+ std::cerr << "Writting as JPEG" << std::endl;
break;
- SetWriteFileTypeToExplicitVR();
- CheckMandatoryElements();
}
+ CheckMandatoryElements();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
/// \todo the best trick would be *change* the recognition code
/// but pb expected if user deals with, e.g. COMPLEX images
- if( WriteType == ACR_LIBIDO )
+ if ( WriteType == ACR_LIBIDO )
{
SetWriteToLibido();
}
}
bool check = CheckWriteIntegrity(); // verifies length
- if(check)
+ if (WriteType == JPEG ) check = true;
+ if (check)
{
check = FileInternal->Write(fileName,WriteType);
}
*/
bool FileHelper::CheckWriteIntegrity()
{
- if(PixelWriteConverter->GetUserData())
+ if ( PixelWriteConverter->GetUserData() )
{
int numberBitsAllocated = FileInternal->GetBitsAllocated();
if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
{
+ gdcmWarningMacro( "numberBitsAllocated changed from "
+ << numberBitsAllocated << " to 16 "
+ << " for consistency purpose" );
numberBitsAllocated = 16;
}
size_t decSize = FileInternal->GetXSize()
- * FileInternal->GetYSize()
- * FileInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * FileInternal->GetSamplesPerPixel();
+ * FileInternal->GetYSize()
+ * FileInternal->GetZSize()
+ * FileInternal->GetSamplesPerPixel()
+ * ( numberBitsAllocated / 8 );
size_t rgbSize = decSize;
- if( FileInternal->HasLUT() )
+ if ( FileInternal->HasLUT() )
rgbSize = decSize * 3;
switch(WriteMode)
{
case WMODE_RAW :
- if( decSize!=PixelWriteConverter->GetUserDataSize() )
+ if ( decSize!=PixelWriteConverter->GetUserDataSize() )
{
gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
<< decSize << " / Found :"
}
break;
case WMODE_RGB :
- if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ if ( rgbSize!=PixelWriteConverter->GetUserDataSize() )
{
gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
<< decSize << " / Found "
break;
}
}
-
+
return true;
}
*/
void FileHelper::SetWriteToRaw()
{
- if( FileInternal->GetNumberOfScalarComponents() == 3
- && !FileInternal->HasLUT())
+ if ( FileInternal->GetNumberOfScalarComponents() == 3
+ && !FileInternal->HasLUT() )
{
SetWriteToRGB();
}
else
{
- ValEntry *photInt = CopyValEntry(0x0028,0x0004);
- if(FileInternal->HasLUT())
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ if (FileInternal->HasLUT() )
{
- photInt->SetValue("PALETTE COLOR ");
+ photInt->SetString("PALETTE COLOR ");
}
else
{
- photInt->SetValue("MONOCHROME2 ");
+ photInt->SetString("MONOCHROME2 ");
}
PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize());
std::string vr = "OB";
- if( FileInternal->GetBitsAllocated()>8 )
+ if ( FileInternal->GetBitsAllocated()>8 )
vr = "OW";
- if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
+ if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
vr = "OB";
- BinEntry *pixel =
- CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
- pixel->SetValue(GDCM_BINLOADED);
+ DataEntry *pixel =
+ CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
+ pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
pixel->SetBinArea(PixelWriteConverter->GetData(),false);
pixel->SetLength(PixelWriteConverter->GetDataSize());
Archive->Push(photInt);
Archive->Push(pixel);
+
+ photInt->Delete();
+ pixel->Delete();
}
}
*/
void FileHelper::SetWriteToRGB()
{
- if(FileInternal->GetNumberOfScalarComponents()==3)
+ if ( FileInternal->GetNumberOfScalarComponents()==3 )
{
PixelReadConverter->BuildRGBImage();
- ValEntry *spp = CopyValEntry(0x0028,0x0002);
- spp->SetValue("3 ");
+ DataEntry *spp = CopyDataEntry(0x0028,0x0002);
+ spp->SetString("3 ");
- ValEntry *planConfig = CopyValEntry(0x0028,0x0006);
- planConfig->SetValue("0 ");
+ DataEntry *planConfig = CopyDataEntry(0x0028,0x0006);
+ planConfig->SetString("0 ");
- ValEntry *photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("RGB ");
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ photInt->SetString("RGB ");
- if(PixelReadConverter->GetRGB())
+ if ( PixelReadConverter->GetRGB() )
{
PixelWriteConverter->SetReadData(PixelReadConverter->GetRGB(),
PixelReadConverter->GetRGBSize());
}
std::string vr = "OB";
- if( FileInternal->GetBitsAllocated()>8 )
+ if ( FileInternal->GetBitsAllocated()>8 )
vr = "OW";
- if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
+ if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
vr = "OB";
- BinEntry *pixel =
- CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
- pixel->SetValue(GDCM_BINLOADED);
+ DataEntry *pixel =
+ CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
+ pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
pixel->SetBinArea(PixelWriteConverter->GetData(),false);
pixel->SetLength(PixelWriteConverter->GetDataSize());
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);
Archive->Push(0x0028,0x1202);
Archive->Push(0x0028,0x1203);
+ // push out Palette Color Lookup Table UID, if any
+ Archive->Push(0x0028,0x1199);
+
// For old '24 Bits' ACR-NEMA
// Thus, we have a RGB image and the bits allocated = 24 and
// samples per pixels = 1 (in the read file)
- if(FileInternal->GetBitsAllocated()==24)
+ if ( FileInternal->GetBitsAllocated()==24 )
{
- ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100);
- bitsAlloc->SetValue("8 ");
+ DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100);
+ bitsAlloc->SetString("8 ");
- ValEntry *bitsStored = CopyValEntry(0x0028,0x0101);
- bitsStored->SetValue("8 ");
+ DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101);
+ bitsStored->SetString("8 ");
- ValEntry *highBit = CopyValEntry(0x0028,0x0102);
- highBit->SetValue("7 ");
+ DataEntry *highBit = CopyDataEntry(0x0028,0x0102);
+ highBit->SetString("7 ");
Archive->Push(bitsAlloc);
Archive->Push(bitsStored);
Archive->Push(highBit);
+
+ bitsAlloc->Delete();
+ bitsStored->Delete();
+ highBit->Delete();
}
}
else
Archive->Restore(0x0028,0x1202);
Archive->Restore(0x0028,0x1203);
+ // 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);
/**
* \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
*/
+void FileHelper::SetWriteFileTypeToJPEG()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
+
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ tss->SetString(ts);
+
+ Archive->Push(tss);
+ tss->Delete();
+}
+
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
- ValEntry *tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ tss->SetString(ts);
Archive->Push(tss);
+ tss->Delete();
}
/**
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
- ValEntry *tss = CopyValEntry(0x0002,0x0010);
- tss->SetValue(ts);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ tss->SetString(ts);
Archive->Push(tss);
+ tss->Delete();
}
*/
void FileHelper::SetWriteToLibido()
{
- ValEntry *oldRow = dynamic_cast<ValEntry *>
- (FileInternal->GetDocEntry(0x0028, 0x0010));
- ValEntry *oldCol = dynamic_cast<ValEntry *>
- (FileInternal->GetDocEntry(0x0028, 0x0011));
+ DataEntry *oldRow = FileInternal->GetDataEntry(0x0028, 0x0010);
+ DataEntry *oldCol = FileInternal->GetDataEntry(0x0028, 0x0011);
- if( oldRow && oldCol )
+ if ( oldRow && oldCol )
{
std::string rows, columns;
- ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
- ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+ DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
+ DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
newRow->Copy(oldCol);
newCol->Copy(oldRow);
- newRow->SetValue(oldCol->GetValue());
- newCol->SetValue(oldRow->GetValue());
+ newRow->SetString(oldCol->GetString());
+ newCol->SetString(oldRow->GetString());
Archive->Push(newRow);
Archive->Push(newCol);
+
+ newRow->Delete();
+ newCol->Delete();
}
- ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
- libidoCode->SetValue("ACRNEMA_LIBIDO_1.1");
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
/**
*/
void FileHelper::SetWriteToNoLibido()
{
- ValEntry *recCode = dynamic_cast<ValEntry *>
- (FileInternal->GetDocEntry(0x0008,0x0010));
- if( recCode )
+ DataEntry *recCode = FileInternal->GetDataEntry(0x0008,0x0010);
+ if ( recCode )
{
- if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
{
- ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
- libidoCode->SetValue("");
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ libidoCode->SetString("");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
}
}
}
/**
- * \brief Duplicates a ValEntry or creates it.
- * @param group Group number of the Entry
- * @param elem Element number of the Entry
- * \return pointer to the new Val Entry (NULL when creation failed).
- */
-ValEntry *FileHelper::CopyValEntry(uint16_t group, uint16_t elem)
-{
- DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
- ValEntry *newE;
-
- if( oldE )
- {
- newE = new ValEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
- }
- else
- {
- newE = GetFile()->NewValEntry(group, elem);
- }
-
- return newE;
-}
-
-/**
- * \brief Duplicates a BinEntry or creates it.
+ * \brief Duplicates a DataEntry or creates it.
* @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).
*/
-BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem,
- const std::string &vr)
+DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
+ const TagName &vr)
{
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
- BinEntry *newE;
+ DataEntry *newE;
- if( oldE )
- if( oldE->GetVR()!=vr )
+ if ( oldE && vr != GDCM_VRUNKNOWN )
+ if ( oldE->GetVR() != vr )
oldE = NULL;
- if( oldE )
+ if ( oldE )
{
- newE = new BinEntry(oldE->GetDictEntry());
+ newE = DataEntry::New(oldE->GetDictEntry());
newE->Copy(oldE);
}
else
{
- newE = GetFile()->NewBinEntry(group, elem, vr);
+ newE = GetFile()->NewDataEntry(group, elem, vr);
}
return newE;
/**
* \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 ?
+
+
+
+-->'Media Storage SOP Class UID' (0x0002,0x0002)
+-->'SOP Class UID' (0x0008,0x0016) are set to
+ [Secondary Capture Image Storage]
+ (Potentialy, the image was modified by user, and post-processed;
+ it's no longer a 'native' image)
+ Except if user told he wants to keep MediaStorageSOPClassUID,
+ when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
+
+--> 'Image Type' (0x0008,0x0008)
+ is forced to "DERIVED\PRIMARY"
+ (The written image is no longer an 'ORIGINAL' one)
+ Except if user told he wants to keep MediaStorageSOPClassUID,
+ when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
+
+--> '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, Study Date, Study Time
+ are force to current Date and Time
+
+--> Conversion Type (0x0008,0x0064)
+ is forced to 'SYN' (Synthetic Image)
+
+--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
+ Image Orientation (Patient) : (0020|0037)
+
+--> 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();
+
// just to remember : 'official' 0002 group
-
+ if ( WriteType != ACR && WriteType != ACR_LIBIDO )
+ {
+ // Group 000002 (Meta Elements) already pushed out
+
//0002 0000 UL 1 Meta Group Length
//0002 0001 OB 1 File Meta Information Version
//0002 0002 UI 1 Media Stored SOP Class UID
// Create them if not found
// Always modify the value
// Push the entries to the archive.
- ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000);
- e_0002_0000->SetValue("0"); // for the moment
- Archive->Push(e_0002_0000);
-
- BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB");
+ CopyMandatoryEntry(0x0002,0x0000,"0");
+
+ 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();
- ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002);
- // [Secondary Capture Image Storage]
- e_0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7");
- Archive->Push(e_0002_0002);
-
- // 'Media Stored SOP Instance UID'
- ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003);
- e_0002_0003->SetValue(Util::CreateUniqueUID());
- Archive->Push(e_0002_0003);
-
+ if ( KeepMediaStorageSOPClassUID)
+ // It up to the use to *know* whether he modified the pixels or not.
+ // he is allowed to keep the original 'Media Storage SOP Class UID'
+ CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
+ else
+ // Potentialy this is a post-processed image
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
+
+ // 'Media Storage SOP Instance UID'
+ CopyMandatoryEntry(0x0002,0x0003,sop);
+
// 'Implementation Class UID'
- ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012);
- e_0002_0012->SetValue(Util::CreateUniqueUID());
- Archive->Push(e_0002_0012);
+ // FIXME : in all examples we have, 0x0002,0x0012 is not so long :
+ // semms to be Root UID + 4 digits (?)
+ CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
// 'Implementation Version Name'
- ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013);
- e_0002_0013->SetValue("GDCM 1.0");
- Archive->Push(e_0002_0013);
-
- //'Source Application Entity Title' Not Mandatory
- //ValEntry *e_0002_0016 = CopyValEntry(0x0002,0x0016);
- // e_0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7");
- // Archive->Push(e_0002_0016);
+ std::string version = "GDCM ";
+ version += Util::GetVersion();
+ CopyMandatoryEntry(0x0002,0x0013,version);
+ }
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
Archive->Push(0x0028,0x0017);
Archive->Push(0x0028,0x00199);
+ // 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");
+ }
+
+ // Check if user wasn't drunk ;-)
+
+ std::ostringstream s;
+ // check 'Bits Allocated' vs decent values
+ int nbBitsAllocated = FileInternal->GetBitsAllocated();
+ if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
+ {
+ CopyMandatoryEntry(0x0028,0x0100,"16");
+ gdcmWarningMacro("(0028,0100) changed from "
+ << nbBitsAllocated << " to 16 for consistency purpose");
+ nbBitsAllocated = 16;
+ }
+ // check 'Bits Stored' vs 'Bits Allocated'
+ int nbBitsStored = FileInternal->GetBitsStored();
+ if ( nbBitsStored == 0 || nbBitsStored > nbBitsAllocated )
+ {
+ s.str("");
+ s << nbBitsAllocated;
+ CopyMandatoryEntry(0x0028,0x0101,s.str());
+ gdcmWarningMacro("(0028,0101) changed from "
+ << nbBitsStored << " to " << nbBitsAllocated
+ << " for consistency purpose" );
+ nbBitsStored = nbBitsAllocated;
+ }
+ // check 'Hight Bit Position' vs 'Bits Allocated' and 'Bits Stored'
+ int highBitPosition = FileInternal->GetHighBitPosition();
+ if ( highBitPosition == 0 ||
+ highBitPosition > nbBitsAllocated-1 ||
+ highBitPosition < nbBitsStored-1 )
+ {
+ s.str("");
+ s << nbBitsStored - 1;
+ CopyMandatoryEntry(0x0028,0x0102,s.str());
+ gdcmWarningMacro("(0028,0102) changed from "
+ << highBitPosition << " to " << nbBitsAllocated-1
+ << " for consistency purpose");
+ }
+
+ std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
+ if ( pixelSpacing == GDCM_UNKNOWN )
+ pixelSpacing = "1.0\\1.0";
+ else
+ // if missing, Pixel Spacing forced to "1.0\1.0"
+ CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
+
+ // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
+ // --> This one is the *legal* one !
+ // FIXME : we should write it only when we are *sure* the image comes from
+ // an imager (see also 0008,0x0064)
+
+ CheckMandatoryEntry(0x0018,0x1164,pixelSpacing);
+
+ // Samples Per Pixel (type 1) : default to grayscale
+ CheckMandatoryEntry(0x0028,0x0002,"1");
+
// --- 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
- ValEntry *e_0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016);
- if ( e_0008_0016 != 0 )
+ DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
+ if ( e_0008_0016 )
{
// Create 'Source Image Sequence' SeqEntry
- SeqEntry *s = new SeqEntry (
+ SeqEntry *sis = SeqEntry::New (
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
- SQItem *sqi = new SQItem(1);
+ SQItem *sqi = SQItem::New(1);
// (we assume 'SOP Instance UID' exists too)
// create 'Referenced SOP Class UID'
- ValEntry *e_0008_1150 = new ValEntry(
+ DataEntry *e_0008_1150 = DataEntry::New(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
- e_0008_1150->SetValue( e_0008_0016->GetValue());
+ e_0008_1150->SetString( e_0008_0016->GetString());
sqi->AddEntry(e_0008_1150);
+ e_0008_1150->Delete();
// create 'Referenced SOP Instance UID'
- ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
- ValEntry *e_0008_1155 = new ValEntry(
+ DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
+ DataEntry *e_0008_1155 = DataEntry::New(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
- e_0008_1155->SetValue( e_0008_0018->GetValue());
+ e_0008_1155->SetString( e_0008_0018->GetString());
sqi->AddEntry(e_0008_1155);
+ e_0008_1155->Delete();
+
+ sis->AddSQItem(sqi,1);
+ sqi->Delete();
- s->AddSQItem(sqi,1);
// temporarily replaces any previous 'Source Image Sequence'
- Archive->Push(s);
+ Archive->Push(sis);
+ sis->Delete();
- // 'Image Type' (The written image is no longer an 'ORIGINAL' one)
- ValEntry *e_0008_0008 = CopyValEntry(0x0008,0x0008);
- e_0008_0008->SetValue("DERIVED\\PRIMARY");
- Archive->Push(e_0008_0008);
- }
- else
- {
- // There was no 'SOP Class UID'.
- // the source image was NOT a true Dicom one.
- // We consider the image is a 'Secondary Capture' one
- // SOP Class UID
- e_0008_0016 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0016) );
- // [Secondary Capture Image Storage]
- e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
- Archive->Push(e_0008_0016);
- }
+ // FIXME : is 'Image Type' *really* depending on the presence of'SOP Class UID'?
+ if ( KeepMediaStorageSOPClassUID)
+ // It up to the use to *know* whether he modified the pixels or not.
+ // he is allowed to keep the original 'Media Storage SOP Class UID'
+ // and 'Image Type' as well
+ CheckMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
+ else
+ // Potentialy this is a post-processed image
+ // (The written image is no longer an 'ORIGINAL' one)
+ CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
-// ---- The user will never have to take any action on the following ----.
+ }
+ // 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);
+
+ // the gdcm written image is a [Secondary Capture Image Storage]
+ // except if user told us he dind't modify the pixels, and, therefore
+ // he want to keep the 'Media Storage SOP Class UID'
+
+ // 'Media Storage SOP Class UID' : [Secondary Capture Image Storage]
+ if ( KeepMediaStorageSOPClassUID)
+ {
+ // It up to the use to *know* whether he modified the pixels or not.
+ // he is allowed to keep the original 'Media Storage SOP Class UID'
+ CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
+ }
+ else
+ {
+ // Potentialy this is a post-processed image
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
+
+ // FIXME : Must we Force Value, or Default value ?
+ // Is it Type 1 for any Modality ?
+ // --> Answer seems to be NO :-(
+ // FIXME : we should write it only when we are *sure* the image
+ // *does not* come from an imager (see also 0018,0x1164)
+
+ // Conversion Type.
+ // Other possible values are :
+ // See PS 3.3, Page 408
+
+ // 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");
+ }
+
+ // ---- The user will never have to take any action on the following ----
+
// new value for 'SOP Instance UID'
- ValEntry *e_0008_0018 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
- e_0008_0018->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e_0008_0018);
+ //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
// Instance Creation Date
- ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012);
- std::string date = Util::GetCurrentDate();
- e_0008_0012->SetValue(date.c_str());
- Archive->Push(e_0008_0012);
+ const std::string &date = Util::GetCurrentDate();
+ CopyMandatoryEntry(0x0008,0x0012,date);
// Instance Creation Time
- ValEntry *e_0008_0013 = CopyValEntry(0x0008,0x0013);
- std::string time = Util::GetCurrentTime();
- e_0008_0013->SetValue(time.c_str());
- Archive->Push(e_0008_0013);
+ const std::string &time = Util::GetCurrentTime();
+ CopyMandatoryEntry(0x0008,0x0013,time);
-// ----- Add Mandatory Entries if missing ---
+ // Study Date
+ CopyMandatoryEntry(0x0008,0x0020,date);
+ // Study Time
+ CopyMandatoryEntry(0x0008,0x0030,time);
-// Entries whose type is 1 are mandatory, with a mandatory value
-// Entries whose type is 1c are mandatory-inside-a-Sequence
-// Entries whose type is 2 are mandatory, with a optional value
-// Entries whose type is 2c are mandatory-inside-a-Sequence
-// Entries whose type is 3 are optional
+ // Accession Number
+ //CopyMandatoryEntry(0x0008,0x0050,"");
+ CheckMandatoryEntry(0x0008,0x0050,"");
+
- // '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
- ValEntry *e_0020_000e = FileInternal->GetValEntry(0x0020, 0x000e);
- if ( !e_0020_000e )
- {
- e_0020_000e = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
- e_0020_000e->SetValue(Util::CreateUniqueUID() );
- Archive->Push(e_0020_000e);
- }
+ // ----- 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
- ValEntry *e_0020_000d = FileInternal->GetValEntry(0x0020, 0x000d);
- if ( !e_0020_000d )
- {
- e_0020_000d = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
- e_0020_000d->SetValue(Util::CreateUniqueUID() );
- Archive->Push(e_0020_000d);
- }
+ // adding new Series to an already existing Study
+ CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID());
+ // '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 prevent him for doing that
+ CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID());
+
+ // Study ID
+ CheckMandatoryEntry(0x0020,0x0010,"");
+
+ // Series Number
+ CheckMandatoryEntry(0x0020,0x0011,"");
+
+ // Instance Number
+ CheckMandatoryEntry(0x0020,0x0013,"");
+
+ // 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 != "\\" )
+ CheckMandatoryEntry(0x0020,0x0020,ori);
+ else
+ CheckMandatoryEntry(0x0020,0x0020,"");
+
// Modality : if missing we set it to 'OTher'
- ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
- if ( !e_0008_0060 )
- {
- e_0008_0060 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) );
- e_0008_0060->SetValue("OT");
- Archive->Push(e_0008_0060);
- }
+ CheckMandatoryEntry(0x0008,0x0060,"OT");
// Manufacturer : if missing we set it to 'GDCM Factory'
- ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
- if ( !e_0008_0070 )
- {
- e_0008_0070 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) );
- e_0008_0070->SetValue("GDCM Factory");
- Archive->Push(e_0008_0070);
- }
+ CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory");
// Institution Name : if missing we set it to 'GDCM Hospital'
- ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
- if ( !e_0008_0080 )
- {
- e_0008_0080 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) );
- e_0008_0080->SetValue("GDCM Hospital");
- Archive->Push(e_0008_0080);
- }
+ CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital");
// Patient's Name : if missing, we set it to 'GDCM^Patient'
- ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
- if ( !e_0010_0010 )
- {
- e_0010_0010 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) );
- e_0010_0010->SetValue("GDCM^Patient");
- Archive->Push(e_0010_0010);
- }
+ CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient");
+
+ // Patient ID
+ CheckMandatoryEntry(0x0010,0x0020,"");
// Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
- ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030);
- if ( !e_0010_0030 )
- {
- e_0010_0030 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0030) );
- e_0010_0030->SetValue("");
- Archive->Push(e_0010_0030);
- }
+ CheckMandatoryEntry(0x0010,0x0030,"");
// Patient's Sex :'type 2' entry -> must exist, value not mandatory
- ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040);
- if ( !e_0010_0040 )
- {
- e_0010_0040 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0040) );
- e_0010_0040->SetValue("");
- Archive->Push(e_0010_0040);
- }
+ CheckMandatoryEntry(0x0010,0x0040,"");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
- ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090);
- if ( !e_0008_0090 )
- {
- e_0008_0090 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) );
- e_0008_0090->SetValue("");
- Archive->Push(e_0008_0090);
- }
-
+ CheckMandatoryEntry(0x0008,0x0090,"");
+
// Remove some inconstencies (probably some more will be added)
// if (0028 0008)Number of Frames exists
// Push out (0020 0052),Frame of Reference UID
// (only meaningfull within a Serie)
- ValEntry *e_0028_0008 = FileInternal->GetValEntry(0x0028, 0x0008);
+ DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008);
if ( !e_0028_0008 )
{
- Archive->Push(0x0020, 0X0052);
+ Archive->Push(0x0020, 0x0052);
}
-}
+ // Deal with element 0x0000 (group length) of each group.
+ // First stage : get all the different Groups
+ /*
+ 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
+*/
+}
+
+void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+{
+ DataEntry *entry = FileInternal->GetDataEntry(group,elem);
+ if ( !entry )
+ {
+ entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ entry->SetString(value);
+ Archive->Push(entry);
+ entry->Delete();
+ }
+}
+
+void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+{
+ DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ entry->SetString(value);
+ Archive->Push(entry);
+ entry->Delete();
+}
+
+void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+{
+ DataEntry *entry = CopyDataEntry(group,elem);
+ entry->SetString(value);
+ Archive->Push(entry);
+ entry->Delete();
+}
+
/**
* \brief Restore in the File the initial group 0002
*/
Archive->Restore(0x0002,0x0001);
Archive->Restore(0x0002,0x0002);
Archive->Restore(0x0002,0x0003);
+ Archive->Restore(0x0002,0x0010);
Archive->Restore(0x0002,0x0012);
Archive->Restore(0x0002,0x0013);
Archive->Restore(0x0002,0x0016);
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(0x0008,0x0018);
+ Archive->Restore(0x0008,0x0060);
+ Archive->Restore(0x0008,0x0070);
+ Archive->Restore(0x0008,0x0080);
+ Archive->Restore(0x0008,0x0090);
+ Archive->Restore(0x0008,0x2112);
+
+ Archive->Restore(0x0010,0x0010);
+ Archive->Restore(0x0010,0x0030);
+ Archive->Restore(0x0010,0x0040);
+
+ Archive->Restore(0x0020,0x000d);
+ Archive->Restore(0x0020,0x000e);
}
//-----------------------------------------------------------------------------
*/
void FileHelper::Initialize()
{
+ UserFunction = 0;
+ KeepMediaStorageSOPClassUID = false;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
Archive = new DocEntryArchive( FileInternal );
-
- if ( FileInternal->IsReadable() )
- {
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
- }
}
/**
- * \brief
+ * \brief Reads/[decompresses] the pixels,
+ * *without* making RGB from Palette Colors
+ * @return the pixels area, whatever its type
+ * (uint8_t is just for prototyping : feel free to Cast it)
*/
uint8_t *FileHelper::GetRaw()
{
+ PixelReadConverter->SetUserFunction( UserFunction );
+
uint8_t *raw = PixelReadConverter->GetRaw();
if ( ! raw )
{
// The Raw image migth not be loaded yet:
std::ifstream *fp = FileInternal->OpenFile();
PixelReadConverter->ReadAndDecompressPixelData( fp );
- if(fp)
+ if ( fp )
FileInternal->CloseFile();
raw = PixelReadConverter->GetRaw();
return 0;
}
}
-
return raw;
}
//-----------------------------------------------------------------------------
-// Print
+/**
+ * \brief Prints the common part of DataEntry, SeqEntry
+ * @param os ostream we want to print in
+ * @param indent (unused)
+ */
void FileHelper::Print(std::ostream &os, std::string const &)
{
FileInternal->SetPrintLevel(PrintLevel);
FileInternal->Print(os);
- PixelReadConverter->SetPrintLevel(PrintLevel);
- PixelReadConverter->Print(os);
+ if ( FileInternal->IsReadable() )
+ {
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
+ }
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff