Program: gdcm
Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/02/23 09:54:59 $
- Version: $Revision: 1.20 $
+
+ Date: $Date: 2005/09/07 08:55:23 $
+ Version: $Revision: 1.58 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <fstream>
+/*
+// ----------------------------- WARNING -------------------------
+
+These lines will be moved to the document-to-be 'User's Guide'
+
+// To read an image, user needs a gdcm::File
+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 = f->GetEntryValue(groupNb,ElementNb);
+
+// to get the pixels, user needs a gdcm::FileHelper
+gdcm::FileHelper *fh = new gdcm::FileHelper(f);
+// user may ask not to convert Palette to RGB
+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
+
+fh->SetImageData( userPixels, userPixelsLength);
+fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
+ // (WriteMode is set)
+
+fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
+ // Little Endian is the default
+ // no other value is allowed
+ (-->SetWriteType(ExplicitVR);)
+ -->WriteType = ExplicitVR;
+fh->Write(newFileName); // overwrites the file, if any
+
+// or :
+fh->WriteDcmExplVR(newFileName);
+
+
+// ----------------------------- WARNING -------------------------
+
+These lines will be moved to the document-to-be 'Developer's Guide'
+
+WriteMode : WMODE_RAW / WMODE_RGB
+WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
+
+fh1->Write(newFileName);
+ SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR();
+ (modifies TransferSyntax)
+ SetWriteToRaw(); / SetWriteToRGB();
+ (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 )
+ CheckWriteIntegrity();
+ (checks user given pixels length)
+ FileInternal->Write(fileName,WriteType)
+ fp = opens file(fileName);
+ ComputeGroup0002Length( );
+ BitsAllocated 12->16
+ RemoveEntryNoDestroy(palettes, etc)
+ Document::WriteContent(fp, writetype);
+ RestoreWrite();
+ (moves back to the File all the archived elements)
+ RestoreWriteFileType();
+ (pushes back group 0002, with TransferSyntax)
+*/
+
+
+
+
namespace gdcm
{
//-------------------------------------------------------------------------
* 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;
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
FileInternal = header;
SelfHeader = false;
Initialize();
+ if ( FileInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ }
}
+#ifndef GDCM_LEGACY_REMOVE
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
+ * \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.
* 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( filename );
+ FileInternal = new File( );
+ FileInternal->SetFileName( filename );
+ FileInternal->Load();
SelfHeader = true;
Initialize();
+ if ( FileInternal->IsReadable() )
+ {
+ PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ }
}
+#endif
/**
* \brief canonical destructor
*/
FileHelper::~FileHelper()
{
- if( PixelReadConverter )
+ if ( PixelReadConverter )
{
delete PixelReadConverter;
}
- if( PixelWriteConverter )
+ if ( PixelWriteConverter )
{
delete PixelWriteConverter;
}
- if( Archive )
+ if ( Archive )
{
delete Archive;
}
- if( SelfHeader )
+ if ( SelfHeader )
{
delete FileInternal;
}
//-----------------------------------------------------------------------------
// Public
+
+/**
+ * \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 );
+ return true;
+}
+
/**
* \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
ValEntry *FileHelper::InsertValEntry(std::string const &content,
uint16_t group, uint16_t elem)
{
- return FileInternal->InsertValEntry(content,group,elem);
+ return FileInternal->InsertValEntry(content, group, elem);
}
/**
{
return PixelWriteConverter->GetUserDataSize();
}
-
return PixelReadConverter->GetRGBSize();
}
{
return PixelWriteConverter->GetUserDataSize();
}
-
return PixelReadConverter->GetRawSize();
}
return GetRaw();
}
+#ifndef GDCM_LEGACY_REMOVE
/**
- * \brief
- * Read the pixels from disk (uncompress if necessary),
+ * \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
return 0;
}
memcpy( destination,
- (void*)PixelReadConverter->GetRaw(),
+ (void *)PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize() );
return PixelReadConverter->GetRawSize();
}
+#endif
/**
- * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
+ * \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
* \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 )
}
/**
- * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
+ * \brief Set the image data defined by the user
* \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)
*/
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".
*/
bool FileHelper::WriteRawData(std::string const &fileName)
{
- std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
if (!fp1)
{
gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str());
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:
+ // 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 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);
SetWriteFileTypeToACR();
+ // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
- default:
- SetWriteFileTypeToExplicitVR();
- CheckMandatoryElements();
}
+ CheckMandatoryElements();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
// just before writting ...
/// \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 (check)
{
check = FileInternal->Write(fileName,WriteType);
}
RestoreWrite();
RestoreWriteFileType();
+ RestoreWriteMandatory();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
*/
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())
+ if (FileInternal->HasLUT() )
{
photInt->SetValue("PALETTE COLOR ");
}
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);
*/
void FileHelper::SetWriteToRGB()
{
- if(FileInternal->GetNumberOfScalarComponents()==3)
+ if ( FileInternal->GetNumberOfScalarComponents()==3 )
{
PixelReadConverter->BuildRGBImage();
ValEntry *photInt = CopyValEntry(0x0028,0x0004);
photInt->SetValue("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);
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 ");
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);
Archive->Push(0x0002,0x0001);
Archive->Push(0x0002,0x0002);
Archive->Push(0x0002,0x0003);
- Archive->Push(0x0002,0x0010);// Only TransferSyntax was pushed out !
+ Archive->Push(0x0002,0x0010);
Archive->Push(0x0002,0x0012);
Archive->Push(0x0002,0x0013);
Archive->Push(0x0002,0x0016);
*/
void FileHelper::RestoreWriteFileType()
{
- // 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);
}
/**
ValEntry *oldCol = dynamic_cast<ValEntry *>
(FileInternal->GetDocEntry(0x0028, 0x0011));
- if( oldRow && oldCol )
+ if ( oldRow && oldCol )
{
std::string rows, columns;
{
ValEntry *recCode = dynamic_cast<ValEntry *>
(FileInternal->GetDocEntry(0x0008,0x0010));
- if( recCode )
+ if ( recCode )
{
- if( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
+ if ( recCode->GetValue() == "ACRNEMA_LIBIDO_1.1" )
{
ValEntry *libidoCode = CopyValEntry(0x0008,0x0010);
libidoCode->SetValue("");
Archive->Restore(0x0028,0x0010);
Archive->Restore(0x0028,0x0011);
Archive->Restore(0x0008,0x0010);
+
+ // Restore 'LibIDO-special' entries, if any
+ Archive->Restore(0x0028,0x0015);
+ Archive->Restore(0x0028,0x0016);
+ Archive->Restore(0x0028,0x0017);
+ Archive->Restore(0x0028,0x00199);
}
/**
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
ValEntry *newE;
- if( oldE )
+ if ( oldE )
{
newE = new ValEntry(oldE->GetDictEntry());
newE->Copy(oldE);
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
BinEntry *newE;
- if( oldE )
- if( oldE->GetVR()!=vr )
+ if ( oldE )
+ if ( oldE->GetVR()!=vr )
oldE = NULL;
- if( oldE )
+ if ( oldE )
{
newE = new BinEntry(oldE->GetDictEntry());
newE->Copy(oldE);
}
/**
- * \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)
+ * \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 ...)
+ *
+ * Just before writting :
+ * - we check the Entries
+ * - we create the mandatory entries if they are missing
+ * - we modify the values if necessary
+ * - 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.
+ *
+ * \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 ...)
+ * - read the whole PS 3.3 Part of DICOM (890 pages)
+ * and write a *full* checker (probably one method per Modality ...)
+ * Any contribution is welcome.
+ * - write a user callable full checker, to allow post reading
+ * and/or pre writting image consistency check.
*/
+
void FileHelper::CheckMandatoryElements()
{
// 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
//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);
+ // 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 *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);*/
+ BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB");
+ e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
+ false);
+ e_0002_0001->SetLength(2);
+ Archive->Push(e_0002_0001);
+
+ // 'Media Stored SOP Class UID'
+ 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 *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);*/
-
+ ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003);
+ e_0002_0003->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e_0002_0003);
+
// 'Implementation Class UID'
-/* ValEntry *e0002_0012 = CopyValEntry(0x0002,0x0012);
- e0002_0012->SetValue(Util::CreateUniqueUID());
- Archive->Push(e0002_0012); */
+ ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012);
+ e_0002_0012->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e_0002_0012);
// 'Implementation Version Name'
- ValEntry *e0002_0013 = CopyValEntry(0x0002,0x0013);
- e0002_0013->SetValue("GDCM 1.0");
- Archive->Push(e0002_0013);
+ ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013);
+ std::string version = "GDCM ";
+ version += Util::GetVersion();
+ e_0002_0013->SetValue(version);
+ Archive->Push(e_0002_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);
+ //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);
+ }
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
Archive->Push(0x0028,0x0017);
Archive->Push(0x0028,0x00199);
- // --- Check UID-related Entries ---
+ // Deal with the pb of (Bits Stored = 12)
+ // - we're gonna write the image as Bits Stored = 16
+ if ( FileInternal->GetEntryValue(0x0028,0x0100) == "12")
+ {
+ ValEntry *e_0028_0100 = CopyValEntry(0x0028,0x0100);
+ e_0028_0100->SetValue("16");
+ Archive->Push(e_0028_0100);
+ }
+
+ // Check if user wasn't drunk ;-)
+
+ std::ostringstream s;
+ // check 'Bits Allocated' vs decent values
+ int nbBitsAllocated = FileInternal->GetBitsAllocated();
+ if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
+ {
+ ValEntry *e_0028_0100 = CopyValEntry(0x0028,0x0100);
+ e_0028_0100->SetValue("16");
+ Archive->Push(e_0028_0100);
+ 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 << nbBitsAllocated;
+ ValEntry *e_0028_0101 = CopyValEntry(0x0028,0x0101);
+ e_0028_0101->SetValue( s.str() );
+ Archive->Push(e_0028_0101);
+ 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 )
+ {
+ ValEntry *e_0028_0102 = CopyValEntry(0x0028,0x0102);
+
+ s << nbBitsStored - 1;
+ e_0028_0102->SetValue( s.str() );
+ Archive->Push(e_0028_0102);
+ gdcmWarningMacro("(0028,0102) changed from "
+ << highBitPosition << " to " << nbBitsAllocated-1
+ << " for consistency purpose");
+ }
+ // --- Check UID-related Entries ---
// If 'SOP Class UID' exists ('true DICOM' image)
- ValEntry *e0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016);
- if ( e0008_0016 != 0 )
+ // 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 )
{
-/* // Create 'Source Image Sequence' SeqEntry
- SeqEntry *s = new SeqEntry (
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
+ // 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'
- ValEntry *e0008_1150 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
- e0008_1150->SetValue( e0008_0016->GetValue());
- sqi->AddEntry(e0008_1150);
+ ValEntry *e_0008_1150 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
+ e_0008_1150->SetValue( e_0008_0016->GetValue());
+ sqi->AddEntry(e_0008_1150);
// create 'Referenced SOP Instance UID'
- ValEntry *e0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
- ValEntry *e0008_1155 = new ValEntry(
+ ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
+ ValEntry *e_0008_1155 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
- e0008_1155->SetValue( e0008_0018->GetValue());
- sqi->AddEntry(e0008_1155);
+ e_0008_1155->SetValue( e_0008_0018->GetValue());
+ sqi->AddEntry(e_0008_1155);
- s->AddSQItem(sqi,1);
+ sis->AddSQItem(sqi,1);
// temporarily replaces any previous 'Source Image Sequence'
- Archive->Push(s);
+ Archive->Push(sis);
- // 'Image Type'
- ValEntry *e0008_0008 = CopyValEntry(0x0008,0x0008);
- e0008_0008->SetValue("DERIVED\\PRIMARY");
- Archive->Push(e0008_0008);*/
+ // '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
{
- // SOP Class UID
-/* e0008_0016 = new ValEntry(
+ // 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]
- e0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
- Archive->Push(e0008_0016); */
+ e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ Archive->Push(e_0008_0016);
}
+// ---- The user will never have to take any action on the following ----.
+
// 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);
+ ValEntry *e_0008_0018 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
+ e_0008_0018->SetValue( Util::CreateUniqueUID() );
+ Archive->Push(e_0008_0018);
// Instance Creation Date
- ValEntry *e0008_0012 = CopyValEntry(0x0008,0x0012);
+ ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012);
std::string date = Util::GetCurrentDate();
- e0008_0012->SetValue(date.c_str());
- Archive->Push(e0008_0012);
+ e_0008_0012->SetValue(date.c_str());
+ Archive->Push(e_0008_0012);
// Instance Creation Time
- ValEntry *e0008_0013 = CopyValEntry(0x0008,0x0013);
+ ValEntry *e_0008_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);
-*/
+ e_0008_0013->SetValue(time.c_str());
+ Archive->Push(e_0008_0013);
// ----- 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 1c are mandatory-inside-a-Sequence
// Entries whose type is 2 are mandatory, with a optional value
-// Entries whose type is 2c are ?
+// Entries whose type is 2c are mandatory-inside-a-Sequence
// Entries whose type is 3 are optional
-// ValEntry *e;
+ // '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);
+ }
+
+ // '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);
+ }
- // Modality
-/* ValEntry *e0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
- if ( !e0008_0060 )
+ // Modality : if missing we set it to 'OTher'
+ ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
+ if ( !e_0008_0060 )
{
- e0008_0060 = new ValEntry(
+ e_0008_0060 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) );
- e0008_0060->SetValue("OT");
- Archive->Push(e0008_0060);
+ e_0008_0060->SetValue("OT");
+ Archive->Push(e_0008_0060);
}
- // Manufacturer
- ValEntry *e0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
- if ( !e0008_0070 )
+ // Manufacturer : if missing we set it to 'GDCM Factory'
+ ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
+ if ( !e_0008_0070 )
{
- e0008_0070 = new ValEntry(
+ e_0008_0070 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) );
- e0008_0070->SetValue("GDCM Factory");
- Archive->Push(e0008_0070);
- }
+ e_0008_0070->SetValue("GDCM Factory");
+ Archive->Push(e_0008_0070);
+ }
- // Institution Name
- ValEntry *e0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
- if ( !e0008_0080 )
+ // Institution Name : if missing we set it to 'GDCM Hospital'
+ ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
+ if ( !e_0008_0080 )
{
- e0008_0080 = new ValEntry(
+ e_0008_0080 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) );
- e0008_0080->SetValue("GDCM Hospital");
- Archive->Push(e0008_0080);
- }
+ e_0008_0080->SetValue("GDCM Hospital");
+ Archive->Push(e_0008_0080);
+ }
- // Patient's Name
- ValEntry *e0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
- if ( !e0010_0010 )
+ // Patient's Name : if missing, we set it to 'GDCM^Patient'
+ ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
+ if ( !e_0010_0010 )
{
- e0010_0010 = new ValEntry(
+ e_0010_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);
- }
+ e_0010_0010->SetValue("GDCM^Patient");
+ Archive->Push(e_0010_0010);
+ }
- // Patient's Birth Date
+ // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030);
if ( !e_0010_0030 )
{
Archive->Push(e_0010_0030);
}
- // Patient's Sex
+ // Patient's Sex :'type 2' entry -> must exist, value not mandatory
ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040);
if ( !e_0010_0040 )
{
Archive->Push(e_0010_0040);
}
- // Referring Physician's Name
+ // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090);
if ( !e_0008_0090 )
{
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) );
e_0008_0090->SetValue("");
Archive->Push(e_0008_0090);
- }*/
+ }
+
+ // 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);
+ if ( !e_0028_0008 )
+ {
+ Archive->Push(0x0020, 0X0052);
+ }
}
+/**
+ * \brief Restore in the File the initial group 0002
+ */
+void FileHelper::RestoreWriteMandatory()
+{
+ // 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);
+
+ 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);
+
+}
+
//-----------------------------------------------------------------------------
// Private
/**
*/
void FileHelper::Initialize()
{
+ UserFunction = 0;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
- PixelReadConverter = new PixelReadConvert;
+ 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 ValEntry, BinEntry, 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