Program: gdcm
Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/01/20 16:22:52 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2005/02/23 09:54:59 $
+ Version: $Revision: 1.20 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDebug.h"
#include "gdcmUtil.h"
#include "gdcmBinEntry.h"
-#include "gdcmHeader.h"
+#include "gdcmValEntry.h"
+#include "gdcmSeqEntry.h"
+#include "gdcmSQItem.h"
+#include "gdcmContentEntry.h"
+#include "gdcmFile.h"
#include "gdcmPixelReadConvert.h"
#include "gdcmPixelWriteConvert.h"
#include "gdcmDocEntryArchive.h"
+#include "gdcmDictSet.h"
#include <fstream>
namespace gdcm
{
-typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header only deals with the ... header)
+ * 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
- * (see GetImageData, GetImageDataRaw)
* \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( )
{
- HeaderInternal = new Header( );
+ FileInternal = new File( );
SelfHeader = true;
- Initialise();
+ Initialize();
}
/**
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header only deals with the ... header)
+ * file (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
- * (see GetImageData, GetImageDataRaw)
* \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).
* @param header already built Header
*/
-FileHelper::FileHelper(Header *header)
+FileHelper::FileHelper(File *header)
{
- HeaderInternal = header;
+ FileInternal = header;
SelfHeader = false;
- Initialise();
+ Initialize();
}
/**
* \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header only deals with the ... header)
+ * 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
- * (see GetImageData, GetImageDataRaw)
* \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).
* @param filename file to be opened for parsing
*/
-FileHelper::FileHelper(std::string const & filename )
+FileHelper::FileHelper(std::string const &filename )
{
- HeaderInternal = new Header( filename );
+ FileInternal = new File( filename );
SelfHeader = true;
- Initialise();
+ Initialize();
}
/**
if( SelfHeader )
{
- delete HeaderInternal;
+ delete FileInternal;
}
- HeaderInternal = 0;
+ FileInternal = 0;
}
//-----------------------------------------------------------------------------
-// Print
-void FileHelper::Print(std::ostream &os, std::string const &)
+// 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.
+ * @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
+ */
+bool FileHelper::SetValEntry(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return FileInternal->SetValEntry(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.
+ * @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
+ */
+bool FileHelper::SetBinEntry(uint8_t *content, int lgth,
+ uint16_t group, uint16_t elem)
{
- HeaderInternal->SetPrintLevel(PrintLevel);
- HeaderInternal->Print(os);
+ return FileInternal->SetBinEntry(content, lgth, group, elem);
+}
- PixelReadConverter->SetPrintLevel(PrintLevel);
- PixelReadConverter->Print(os);
+/**
+ * \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
+ * @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
+ * failed).
+ */
+ValEntry *FileHelper::InsertValEntry(std::string const &content,
+ uint16_t group, uint16_t elem)
+{
+ return FileInternal->InsertValEntry(content,group,elem);
+}
+
+/**
+ * \brief Modifies the value of a given DocEntry (Dicom entry)
+ * 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
+ * failed).
+ */
+BinEntry *FileHelper::InsertBinEntry(uint8_t *binArea, int lgth,
+ uint16_t group, uint16_t elem)
+{
+ return FileInternal->InsertBinEntry(binArea, lgth, group, elem);
+}
+
+/**
+ * \brief Modifies the value of a given DocEntry (Dicom entry)
+ * when it exists. Creates it, empty (?!) when unexistant.
+ * @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
+ * failed).
+ */
+SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
+{
+ return FileInternal->InsertSeqEntry(group, elem);
}
-//-----------------------------------------------------------------------------
-// Public
/**
* \brief Get the size of the image data
* If the image can be RGB (with a lut or by default), the size
}
/**
- * \brief - Allocates necessary memory,
+ * \brief - Allocates necessary memory,
* - Reads the pixels from disk (uncompress if necessary),
- * - Transforms YBR pixels, if any, into RGB pixels
+ * - 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 0;
}
- if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
return PixelReadConverter->GetRGB();
}
* 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
+ * NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
{
return 0;
}
- if ( HeaderInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
+ if ( FileInternal->HasLUT() && PixelReadConverter->BuildRGBImage() )
{
if ( PixelReadConverter->GetRGBSize() > maxSize )
{
- gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
return 0;
}
memcpy( destination,
// Either no LUT conversion necessary or LUT conversion failed
if ( PixelReadConverter->GetRawSize() > maxSize )
{
- gdcmVerboseMacro( "Pixel data bigger than caller's expected MaxSize");
+ gdcmWarningMacro( "Pixel data bigger than caller's expected MaxSize");
return 0;
}
memcpy( destination,
}
/**
- * \brief Points the internal pointer to the callers inData
- * image representation, BUT WITHOUT COPYING THE DATA.
- * 'image' Pixels are presented as C-like 2D arrays : line per line.
- * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
* \warning Since the pixels are not copied, it is the caller's responsability
- * not to deallocate it's data before gdcm uses them (e.g. with
- * the Write() method.
- * @param inData user supplied pixel area
- * @param expectedSize total image size, in Bytes
- *
- * @return boolean
+ * not to deallocate its data before gdcm uses them (e.g. with
+ * the Write() method )
+ * @param inData user supplied pixel area (uint8_t* is just for the compiler.
+ * user is allowed to pass any kind of pixelsn since the size is
+ * given in bytes)
+ * @param expectedSize total image size, *in Bytes*
*/
void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
{
- SetUserData(inData,expectedSize);
+ SetUserData(inData, expectedSize);
}
/**
- * \brief Set the image datas defined by the user
- * \warning When writting the file, this datas are get as default datas to write
+ * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
+ * \warning When writting the file, this data are get as default data to write
+ * \warning Since the pixels are not copied, it is the caller's responsability
+ * not to deallocate its data before gdcm uses them (e.g. with
+ * the Write() method )
+ * @param inData user supplied pixel area (uint8_t* is just for the compiler.
+ * user is allowed to pass any kind of pixels since the size is
+ * given in bytes)
+ * @param expectedSize total image size, *in Bytes*
*/
-void FileHelper::SetUserData(uint8_t *data, size_t expectedSize)
+void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
{
- PixelWriteConverter->SetUserData(data,expectedSize);
+ PixelWriteConverter->SetUserData(inData, expectedSize);
}
/**
- * \brief Get the image datas defined by the user
- * \warning When writting the file, this datas are get as default data to write
+ * \brief Get the image data defined by the user
+ * \warning When writting the file, this data are get as default data to write
*/
uint8_t *FileHelper::GetUserData()
{
/**
* \brief Get the image data size defined by the user
- * \warning When writting the file, this datas are get as default data to write
+ * \warning When writting the file, this data are get as default data to write
*/
size_t FileHelper::GetUserDataSize()
{
}
/**
- * \brief Get the image datas from the file.
+ * \brief Get the image data from the file.
* If a LUT is found, the data are expanded to be RGB
*/
uint8_t *FileHelper::GetRGBData()
}
/**
- * \brief Get the image datas from the file.
- * If a LUT is found, the datas are not expanded !
+ * \brief Get the image data from the file.
+ * Even when a LUT is found, the data are not expanded to RGB!
*/
uint8_t *FileHelper::GetRawData()
{
/**
* \brief Get the image data size from the file.
- * If a LUT is found, the data are not expanded !
+ * Even when a LUT is found, the data are not expanded to RGB!
*/
size_t FileHelper::GetRawDataSize()
{
return PixelReadConverter->GetRawSize();
}
+/**
+ * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ */
+uint8_t* FileHelper::GetLutRGBA()
+{
+ return PixelReadConverter->GetLutRGBA();
+}
+
/**
* \brief Writes on disk A SINGLE Dicom file
* NO test is performed on processor "Endiannity".
* (any already existing file is over written)
* @return false if write fails
*/
-
bool FileHelper::WriteRawData(std::string const &fileName)
{
std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
if (!fp1)
{
- gdcmVerboseMacro( "Fail to open (write) file:" << fileName.c_str());
+ gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str());
return false;
}
{
case ImplicitVR:
SetWriteFileTypeToImplicitVR();
+ CheckMandatoryElements();
break;
case ExplicitVR:
SetWriteFileTypeToExplicitVR();
+ CheckMandatoryElements();
break;
case ACR:
case ACR_LIBIDO:
break;
default:
SetWriteFileTypeToExplicitVR();
+ CheckMandatoryElements();
}
// --------------------------------------------------------------
switch(WriteMode)
{
case WMODE_RAW :
- SetWriteToRaw();
+ SetWriteToRaw(); // modifies and pushes to the archive, when necessary
break;
case WMODE_RGB :
- SetWriteToRGB();
+ SetWriteToRGB(); // modifies and pushes to the archive, when necessary
break;
}
- bool check = CheckWriteIntegrity();
+ bool check = CheckWriteIntegrity(); // verifies length
if(check)
{
- check = HeaderInternal->Write(fileName,WriteType);
+ check = FileInternal->Write(fileName,WriteType);
}
RestoreWrite();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//
- // ...and we restore the Header to be Dicom Compliant again
+ // ...and we restore the header to be Dicom Compliant again
// just after writting
RestoreWriteOfLibido();
// ----------------- End of Special Patch ----------------
return check;
}
-/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * 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
- */
-bool FileHelper::SetEntry(std::string const &content,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->SetEntry(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.
- * @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
- */
-bool FileHelper::SetEntry(uint8_t *content, int lgth,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->SetEntry(content,lgth,group,elem);
-}
-
-/**
- * \brief Modifies the value of a given Doc Entry (Dicom Element)
- * when it exists. Create 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 Header Entry (NULL when creation
- * failed).
- */
-bool FileHelper::ReplaceOrCreate(std::string const &content,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->ReplaceOrCreate(content,group,elem) != NULL;
-}
-
-/*
- * \brief Modifies the value of a given Header Entry (Dicom Element)
- * when it exists. Create 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 group Group number of the Entry
- * @param elem Element number of the Entry
- * \return pointer to the modified/created Header Entry (NULL when creation
- * failed).
- */
-bool FileHelper::ReplaceOrCreate(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
-{
- return HeaderInternal->ReplaceOrCreate(binArea,lgth,group,elem) != NULL;
-}
-
-/**
- * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
- */
-uint8_t* FileHelper::GetLutRGBA()
-{
- return PixelReadConverter->GetLutRGBA();
-}
-
//-----------------------------------------------------------------------------
// Protected
-
/**
- * \brief Check the write integrity
+ * \brief Checks the write integrity
*
* The tests made are :
* - verify the size of the image to write with the possible write
* when the user set an image data
- * @return true if the check successfulls
+ * @return true if check is successfull
*/
bool FileHelper::CheckWriteIntegrity()
{
if(PixelWriteConverter->GetUserData())
{
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ int numberBitsAllocated = FileInternal->GetBitsAllocated();
if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
{
numberBitsAllocated = 16;
}
- size_t decSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
+ size_t decSize = FileInternal->GetXSize()
+ * FileInternal->GetYSize()
+ * FileInternal->GetZSize()
* ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
+ * FileInternal->GetSamplesPerPixel();
size_t rgbSize = decSize;
- if( HeaderInternal->HasLUT() )
+ if( FileInternal->HasLUT() )
rgbSize = decSize * 3;
switch(WriteMode)
case WMODE_RAW :
if( decSize!=PixelWriteConverter->GetUserDataSize() )
{
- gdcmVerboseMacro( "Data size is incorrect (Raw)" << decSize
- << " / " << PixelWriteConverter->GetUserDataSize() );
+ gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
+ << decSize << " / Found :"
+ << PixelWriteConverter->GetUserDataSize() );
return false;
}
break;
case WMODE_RGB :
if( rgbSize!=PixelWriteConverter->GetUserDataSize() )
{
- gdcmVerboseMacro( "Data size is incorrect (RGB)" << decSize
- << " / " << PixelWriteConverter->GetUserDataSize() );
+ gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
+ << decSize << " / Found "
+ << PixelWriteConverter->GetUserDataSize() );
return false;
}
break;
}
/**
- * \brief
+ * \brief Updates the File to write RAW data (as opposed to RGB data)
+ * (modifies, when necessary, photochromatic interpretation,
+ * bits allocated, Pixels element VR)
*/
void FileHelper::SetWriteToRaw()
{
- if( HeaderInternal->GetNumberOfScalarComponents() == 3
- && !HeaderInternal->HasLUT())
+ if( FileInternal->GetNumberOfScalarComponents() == 3
+ && !FileInternal->HasLUT())
{
SetWriteToRGB();
}
else
{
ValEntry *photInt = CopyValEntry(0x0028,0x0004);
- if(HeaderInternal->HasLUT())
+ if(FileInternal->HasLUT())
{
photInt->SetValue("PALETTE COLOR ");
}
else
{
- photInt->SetValue("MONOCHROME1 ");
+ photInt->SetValue("MONOCHROME2 ");
}
PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize());
+ std::string vr = "OB";
+ if( FileInternal->GetBitsAllocated()>8 )
+ vr = "OW";
+ if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
+ vr = "OB";
BinEntry *pixel =
- CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
pixel->SetValue(GDCM_BINLOADED);
pixel->SetBinArea(PixelWriteConverter->GetData(),false);
pixel->SetLength(PixelWriteConverter->GetDataSize());
}
}
-
/**
- * \brief
+ * \brief Updates the File to write RGB data (as opposed to RAW data)
+ * (modifies, when necessary, photochromatic interpretation,
+ * samples per pixel, Planar configuration,
+ * bits allocated, bits stored, high bit -ACR 24 bits-
+ * Pixels element VR, pushes out the LUT, )
*/
void FileHelper::SetWriteToRGB()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3)
+ if(FileInternal->GetNumberOfScalarComponents()==3)
{
PixelReadConverter->BuildRGBImage();
PixelReadConverter->GetRawSize());
}
+ std::string vr = "OB";
+ if( FileInternal->GetBitsAllocated()>8 )
+ vr = "OW";
+ if( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
+ vr = "OB";
BinEntry *pixel =
- CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ CopyBinEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
pixel->SetValue(GDCM_BINLOADED);
pixel->SetBinArea(PixelWriteConverter->GetData(),false);
pixel->SetLength(PixelWriteConverter->GetDataSize());
Archive->Push(0x0028,0x1202);
Archive->Push(0x0028,0x1203);
- // For old ACR-NEMA
+ // 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(HeaderInternal->GetBitsAllocated()==24)
+ if(FileInternal->GetBitsAllocated()==24)
{
ValEntry *bitsAlloc = CopyValEntry(0x0028,0x0100);
bitsAlloc->SetValue("8 ");
}
/**
- * \brief
+ * \brief Restore the File write mode
*/
void FileHelper::RestoreWrite()
{
Archive->Restore(0x0028,0x0002);
Archive->Restore(0x0028,0x0004);
Archive->Restore(0x0028,0x0006);
- Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
+ Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
// For old ACR-NEMA (24 bits problem)
Archive->Restore(0x0028,0x0100);
Archive->Restore(0x0028,0x1201);
Archive->Restore(0x0028,0x1202);
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(0x0002,0x0002);
+ 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);
}
/**
- * \brief
+ * \brief Pushes out the whole group 0002
+ * FIXME : better, set a flag to tell the writer not to write it ...
+ * FIXME : method should probably have an other name !
+ * SetWriteFileTypeToACR is NOT opposed to
+ * SetWriteFileTypeToExplicitVR and SetWriteFileTypeToImplicitVR
*/
void FileHelper::SetWriteFileTypeToACR()
{
- Archive->Push(0x0002,0x0010);
+ Archive->Push(0x0002,0x0000);
+ Archive->Push(0x0002,0x0001);
+ Archive->Push(0x0002,0x0002);
+ Archive->Push(0x0002,0x0003);
+ Archive->Push(0x0002,0x0010);// Only TransferSyntax was pushed out !
+ Archive->Push(0x0002,0x0012);
+ Archive->Push(0x0002,0x0013);
+ Archive->Push(0x0002,0x0016);
+ Archive->Push(0x0002,0x0100);
+ Archive->Push(0x0002,0x0102);
}
/**
- * \brief
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
*/
void FileHelper::SetWriteFileTypeToExplicitVR()
{
}
/**
- * \brief
+ * \brief Sets in the File the TransferSyntax to 'Implicit VR Little Endian"
*/
void FileHelper::SetWriteFileTypeToImplicitVR()
{
/**
- * \brief
+ * \brief Restore in the File the initial group 0002
*/
void FileHelper::RestoreWriteFileType()
{
- Archive->Restore(0x0002,0x0010);
+ // group 0002 may be pushed out for ACR-NEMA writting purposes
+ Archive->Restore(0x0002,0x0000);
+ Archive->Restore(0x0002,0x0001);
+ Archive->Restore(0x0002,0x0002);
+ Archive->Restore(0x0002,0x0003);
+ Archive->Restore(0x0002,0x0010);//only TransferSyntax was pushed out/restored
+ Archive->Restore(0x0002,0x0012);
+ Archive->Restore(0x0002,0x0013);
+ Archive->Restore(0x0002,0x0016);
+ Archive->Restore(0x0002,0x0100);
+ Archive->Restore(0x0002,0x0102);
}
+/**
+ * \brief Set the Write not to Libido format
+ */
void FileHelper::SetWriteToLibido()
{
ValEntry *oldRow = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0028, 0x0010));
+ (FileInternal->GetDocEntry(0x0028, 0x0010));
ValEntry *oldCol = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0028, 0x0011));
+ (FileInternal->GetDocEntry(0x0028, 0x0011));
if( oldRow && oldCol )
{
}
/**
- * \brief
+ * \brief Set the Write not to No Libido format
*/
void FileHelper::SetWriteToNoLibido()
{
ValEntry *recCode = dynamic_cast<ValEntry *>
- (HeaderInternal->GetDocEntry(0x0008,0x0010));
+ (FileInternal->GetDocEntry(0x0008,0x0010));
if( recCode )
{
if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
}
/**
- * \brief
+ * \brief Restore the Write format
*/
void FileHelper::RestoreWriteOfLibido()
{
Archive->Restore(0x0008,0x0010);
}
-ValEntry *FileHelper::CopyValEntry(uint16_t group,uint16_t elem)
+/**
+ * \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 = HeaderInternal->GetDocEntry(group, elem);
+ DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
ValEntry *newE;
- if(oldE)
+ if( oldE )
{
newE = new ValEntry(oldE->GetDictEntry());
newE->Copy(oldE);
}
else
{
- newE = GetHeader()->NewValEntry(group,elem);
+ newE = GetFile()->NewValEntry(group, elem);
}
return newE;
}
/**
- * \brief Modifies the value of a given Bin Entry (Dicom Element)
- * when it exists. Create it with the given value when unexistant.
- * @param content (string) Value to be set
+ * \brief Duplicates a BinEntry or creates it.
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Bin Entry (NULL when creation
- * failed).
+ * @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)
+BinEntry *FileHelper::CopyBinEntry(uint16_t group, uint16_t elem,
+ const std::string &vr)
{
- DocEntry *oldE = HeaderInternal->GetDocEntry(group, elem);
+ DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
BinEntry *newE;
- if(oldE)
+ if( oldE )
+ if( oldE->GetVR()!=vr )
+ oldE = NULL;
+
+ if( oldE )
{
newE = new BinEntry(oldE->GetDictEntry());
newE->Copy(oldE);
}
else
{
- newE = GetHeader()->NewBinEntry(group,elem);
+ newE = GetFile()->NewBinEntry(group, elem, vr);
}
return newE;
}
+/**
+ * \brief Checks the Mandatory Elements
+ * adds the mandatory Entries if not found
+ * (when user asks to write as a DICOM file, an ACR-NEMA file
+ * he read before)
+ */
+void FileHelper::CheckMandatoryElements()
+{
+ // just to remember : 'official' 0002 group
+
+ //0002 0000 UL 1 Meta Group Length
+ //0002 0001 OB 1 File Meta Information Version
+ //0002 0002 UI 1 Media Stored SOP Class UID
+ //0002 0003 UI 1 Media Stored SOP Instance UID
+ //0002 0010 UI 1 Transfer Syntax UID
+ //0002 0012 UI 1 Implementation Class UID
+ //0002 0013 SH 1 Implementation Version Name
+ //0002 0016 AE 1 Source Application Entity Title
+ //0002 0100 UI 1 Private Information Creator
+ //0002 0102 OB 1 Private Information
+
+
+ // Create them if not found
+ ValEntry *e0002_0000 = CopyValEntry(0x0002,0x0000);
+ e0002_0000->SetValue("0"); // for the moment
+ Archive->Push(e0002_0000);
+
+/* BinEntry *e0002_0001 = CopyBinEntry(0x0002,0x0001, "OB");
+ e0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),false);
+ e0002_0001->SetLength(2);*/
+
+/* ValEntry *e0002_0002 = CopyValEntry(0x0002,0x0002);
+ // [Secondary Capture Image Storage]
+ e0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ Archive->Push(e0002_0002);*/
+
+ // 'Media Stored SOP Instance UID'
+/* ValEntry *e0002_0003 = CopyValEntry(0x0002,0x0003);
+ e0002_0003->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e0002_0003); */
+
+/* ValEntry *e0002_0010 = CopyValEntry(0x0002,0x0010);
+ //[Explicit VR - Little Endian]
+ e0002_0010->SetValue("1.2.840.10008.1.2.1");
+ Archive->Push(e0002_0010);*/
+
+ // 'Implementation Class UID'
+/* ValEntry *e0002_0012 = CopyValEntry(0x0002,0x0012);
+ e0002_0012->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e0002_0012); */
+
+ // 'Implementation Version Name'
+ ValEntry *e0002_0013 = CopyValEntry(0x0002,0x0013);
+ e0002_0013->SetValue("GDCM 1.0");
+ Archive->Push(e0002_0013);
+
+ //'Source Application Entity Title' Not Mandatory
+ //ValEntry *e0002_0016 = CopyValEntry(0x0002,0x0016);
+ // e0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ // Archive->Push(e0002_0016);
+
+ // Push out 'LibIDO-special' entries, if any
+ Archive->Push(0x0028,0x0015);
+ Archive->Push(0x0028,0x0016);
+ Archive->Push(0x0028,0x0017);
+ Archive->Push(0x0028,0x00199);
+
+ // --- Check UID-related Entries ---
+
+ // If 'SOP Class UID' exists ('true DICOM' image)
+ ValEntry *e0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016);
+ if ( e0008_0016 != 0 )
+ {
+/* // Create 'Source Image Sequence' SeqEntry
+ SeqEntry *s = 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'
+ ValEntry *e0008_1150 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
+ e0008_1150->SetValue( e0008_0016->GetValue());
+ sqi->AddEntry(e0008_1150);
+
+ // create 'Referenced SOP Instance UID'
+ ValEntry *e0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
+ ValEntry *e0008_1155 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
+ e0008_1155->SetValue( e0008_0018->GetValue());
+ sqi->AddEntry(e0008_1155);
+
+ s->AddSQItem(sqi,1);
+ // temporarily replaces any previous 'Source Image Sequence'
+ Archive->Push(s);
+
+ // 'Image Type'
+ ValEntry *e0008_0008 = CopyValEntry(0x0008,0x0008);
+ e0008_0008->SetValue("DERIVED\\PRIMARY");
+ Archive->Push(e0008_0008);*/
+ }
+ else
+ {
+ // SOP Class UID
+/* e0008_0016 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0016) );
+ // [Secondary Capture Image Storage]
+ e0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ Archive->Push(e0008_0016); */
+ }
+
+ // new value for 'SOP Instance UID'
+ ValEntry *e0008_0018 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
+ e0008_0018->SetValue( Util::CreateUniqueUID() );
+ Archive->Push(e0008_0018);
+
+ // Instance Creation Date
+ ValEntry *e0008_0012 = CopyValEntry(0x0008,0x0012);
+ std::string date = Util::GetCurrentDate();
+ e0008_0012->SetValue(date.c_str());
+ Archive->Push(e0008_0012);
+
+ // Instance Creation Time
+ ValEntry *e0008_0013 = CopyValEntry(0x0008,0x0013);
+ std::string time = Util::GetCurrentTime();
+ e0008_0013->SetValue(time.c_str());
+ Archive->Push(e0008_0013);
+
+/* // new value for 'Serie Instance UID'
+ // TODO prevoir booleen pour figer la valeur d'un appel a l'autre
+ // calculer nouvelle valeur a chaque fois
+
+ ValEntry *e0020_000e = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
+ e0020_000e->SetValue( Util::CreateUniqueUID() );
+ Archive->Push(e0020_000e);
+
+ // new value for 'Study Instance UID'
+ // TODO prevoir flag pour figer la valeur d'un appel a l'autre
+ // calculer nouvelle valeur a chaque fois
+ // reutiliser la valeur image origine
+
+ ValEntry *e0020_000d = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
+ e0020_000d->SetValue( Util::CreateUniqueUID() );
+ Archive->Push(e0020_000d);
+*/
+
+// ----- Add Mandatory Entries if missing ---
+
+// Entries whose type is 1 are mandatory, with a mandatory value
+// Entries whose type is 1c are ?
+// Entries whose type is 2 are mandatory, with a optional value
+// Entries whose type is 2c are ?
+// Entries whose type is 3 are optional
+
+// ValEntry *e;
+
+ // Modality
+/* ValEntry *e0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
+ if ( !e0008_0060 )
+ {
+ e0008_0060 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) );
+ e0008_0060->SetValue("OT");
+ Archive->Push(e0008_0060);
+ }
+
+ // Manufacturer
+ ValEntry *e0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
+ if ( !e0008_0070 )
+ {
+ e0008_0070 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) );
+ e0008_0070->SetValue("GDCM Factory");
+ Archive->Push(e0008_0070);
+ }
+
+ // Institution Name
+ ValEntry *e0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
+ if ( !e0008_0080 )
+ {
+ e0008_0080 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) );
+ e0008_0080->SetValue("GDCM Hospital");
+ Archive->Push(e0008_0080);
+ }
+
+ // Patient's Name
+ ValEntry *e0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
+ if ( !e0010_0010 )
+ {
+ e0010_0010 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) );
+ e0010_0010->SetValue("GDCM_Patient");
+ Archive->Push(e0010_0010);
+ }
+
+ // Patient's ID
+ ValEntry *e_0010_0020 = FileInternal->GetValEntry(0x0010, 0x0020);
+ if ( !e )
+ {
+ e_0010_0020 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0020) );
+ e_0010_0020->SetValue("GDCM_Patient_ID");
+ Archive->Push(e_0010_0020);
+ }
+
+ // Patient's Birth Date
+ 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);
+ }
+
+ // Patient's Sex
+ 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);
+ }
+
+ // Referring Physician's Name
+ 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);
+ }*/
+}
+
//-----------------------------------------------------------------------------
-// Protected
+// Private
/**
* \brief Factorization for various forms of constructors.
*/
-void FileHelper::Initialise()
+void FileHelper::Initialize()
{
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
- Archive = new DocEntryArchive( HeaderInternal );
+ Archive = new DocEntryArchive( FileInternal );
- if ( HeaderInternal->IsReadable() )
+ if ( FileInternal->IsReadable() )
{
- PixelReadConverter->GrabInformationsFromHeader( HeaderInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal );
}
}
if ( ! raw )
{
// The Raw image migth not be loaded yet:
- std::ifstream *fp = HeaderInternal->OpenFile();
+ std::ifstream *fp = FileInternal->OpenFile();
PixelReadConverter->ReadAndDecompressPixelData( fp );
if(fp)
- HeaderInternal->CloseFile();
+ FileInternal->CloseFile();
raw = PixelReadConverter->GetRaw();
if ( ! raw )
{
- gdcmVerboseMacro( "Read/decompress of pixel data apparently went wrong.");
+ gdcmWarningMacro( "Read/decompress of pixel data apparently went wrong.");
return 0;
}
}
}
//-----------------------------------------------------------------------------
-// Private
+// Print
+void FileHelper::Print(std::ostream &os, std::string const &)
+{
+ FileInternal->SetPrintLevel(PrintLevel);
+ FileInternal->Print(os);
+
+ PixelReadConverter->SetPrintLevel(PrintLevel);
+ PixelReadConverter->Print(os);
+}
//-----------------------------------------------------------------------------
} // end namespace gdcm
-
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff