Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/05/25 12:54:17 $
- Version: $Revision: 1.41 $
+ 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
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)
Document::WriteContent(fp, writetype);
* 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
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
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(),
PixelWriteConverter->GetUserDataSize() );
if ( ! FileInternal->GetValEntry(0x0008, 0x0010) )
FileInternal->InsertValEntry("", 0x0008, 0x0010);
SetWriteFileTypeToACR();
- SetWriteFileTypeToImplicitVR();
+ // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
}
CheckMandatoryElements();
/// \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);
}
*/
bool FileHelper::CheckWriteIntegrity()
{
- if(PixelWriteConverter->GetUserData())
+ if ( PixelWriteConverter->GetUserData() )
{
int numberBitsAllocated = FileInternal->GetBitsAllocated();
if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
* 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 "
*/
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);
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("");
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);
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
// Create them if not found
// Always modify the value
// Push the entries to the archive.
- ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000);
+ 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");
+ 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);
+ 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);
+ ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003);
e_0002_0003->SetValue(Util::CreateUniqueUID());
Archive->Push(e_0002_0003);
// 'Implementation Class UID'
- ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012);
+ ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012);
e_0002_0012->SetValue(Util::CreateUniqueUID());
Archive->Push(e_0002_0012);
// 'Implementation Version Name'
- ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013);
- e_0002_0013->SetValue("GDCM 1.0");
+ 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 *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);
*/
void FileHelper::Initialize()
{
+ UserFunction = 0;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
Archive = new DocEntryArchive( FileInternal );
-
- if ( FileInternal->IsReadable() )
- {
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
- }
}
/**
*/
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();
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