Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/03/03 11:55:00 $
- Version: $Revision: 1.24 $
+ Date: $Date: 2005/05/27 10:51:00 $
+ Version: $Revision: 1.42 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
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 0;
}
memcpy( destination,
- (void*)PixelReadConverter->GetRaw(),
+ (void *)PixelReadConverter->GetRaw(),
PixelReadConverter->GetRawSize() );
return PixelReadConverter->GetRawSize();
}
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 )
{
SetWriteToLibido();
RestoreWrite();
RestoreWriteFileType();
+ RestoreWriteMandatory();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
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() )
rgbSize = decSize * 3;
}
break;
}
- }
-
+ }
return true;
}
*/
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);
- Archive->Restore(0x0002,0x0012);
- Archive->Restore(0x0002,0x0013);
- Archive->Restore(0x0002,0x0016);
- Archive->Restore(0x0002,0x0100);
- Archive->Restore(0x0002,0x0102);
}
/**
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);
BinEntry *newE;
- if( oldE )
+ if( oldE )
if( oldE->GetVR()!=vr )
oldE = NULL;
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);
- ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002);
+ // '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 *e_0002_0003 = CopyValEntry(0x0002,0x0003);
+ ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003);
e_0002_0003->SetValue(Util::CreateUniqueUID());
Archive->Push(e_0002_0003);
- ValEntry *e_0002_0010 = CopyValEntry(0x0002,0x0010);
- //[Explicit VR - Little Endian]
- e_0002_0010->SetValue("1.2.840.10008.1.2.1");
- Archive->Push(e_0002_0010);
-
// '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);
+ ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013);
e_0002_0013->SetValue("GDCM 1.0");
Archive->Push(e_0002_0013);
//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)
// we create the 'Source Image Sequence' SeqEntry
if ( e_0008_0016 != 0 )
{
// Create 'Source Image Sequence' SeqEntry
- SeqEntry *s = new SeqEntry (
+ SeqEntry *sis = new SeqEntry (
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
SQItem *sqi = new SQItem(1);
// (we assume 'SOP Instance UID' exists too)
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' (The written image is no longer an 'ORIGINAL' one)
ValEntry *e_0008_0008 = CopyValEntry(0x0008,0x0008);
// the source image was NOT a true Dicom one.
// We consider the image is a 'Secondary Capture' one
// SOP Class UID
- ValEntry *e_0008_0016 = new ValEntry(
+ 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_0010_0010);
}
- // Patient's ID : if missing, we set it to 'GDCM_Patient_ID'
- ValEntry *e_0010_0020 = FileInternal->GetValEntry(0x0010, 0x0020);
- if ( !e_0010_0020 )
- {
- 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 :'type 2' entry -> must exist, value not mandatory
+ // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030);
if ( !e_0010_0030 )
{
}
}
+/**
+ * \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
/**
}
/**
- * \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()
{
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);
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff