X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=c95a07cc5c8e01f03eeea8410cc42562a70174ec;hb=6537b093e30bffefce36d66f358c4015e773542a;hp=afb5ef92c92233956bc491fe99853369b4dc5cfb;hpb=7be24dfff4577d9d80ebfa864df09788f149f46d;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index afb5ef92..c95a07cc 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/12/14 10:02:13 $ - Version: $Revision: 1.86 $ + Date: $Date: 2006/07/06 12:38:06 $ + Version: $Revision: 1.108 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,12 +26,17 @@ #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmDataEntry.h" +#include "gdcmDocEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" #include "gdcmDocEntryArchive.h" #include "gdcmDictSet.h" #include "gdcmOrientation.h" + +#if defined(__BORLANDC__) + #include // for memset +#endif #include @@ -69,7 +74,7 @@ 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 +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation // Little Endian is the default // no other value is allowed (-->SetWriteType(ExplicitVR);) @@ -233,7 +238,7 @@ bool FileHelper::Load() * \return false if DataEntry not found */ bool FileHelper::SetEntryString(std::string const &content, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem) { return FileInternal->SetEntryString(content, group, elem); } @@ -249,7 +254,7 @@ bool FileHelper::SetEntryString(std::string const &content, * \return false if DataEntry not found */ bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem) { return FileInternal->SetEntryBinArea(content, lgth, group, elem); } @@ -264,9 +269,10 @@ bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, * failed). */ DataEntry *FileHelper::InsertEntryString(std::string const &content, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem, + VRKey const &vr ) { - return FileInternal->InsertEntryString(content, group, elem); + return FileInternal->InsertEntryString(content, group, elem, vr); } /** @@ -277,13 +283,15 @@ DataEntry *FileHelper::InsertEntryString(std::string const &content, * @param lgth new value length * @param group Group number of the Entry * @param elem Element number of the Entry + * @param vr Value Represenation of the DataElement to be inserted * \return pointer to the modified/created DataEntry (NULL when creation * failed). */ DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem, + VRKey const &vr ) { - return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); + return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr); } /** @@ -377,16 +385,16 @@ uint8_t *FileHelper::GetImageData() * - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane * @return Pointer to newly allocated pixel data. * (uint8_t is just for prototyping. feel free to cast) - * NULL if alloc fails + * NULL if alloc fails */ uint8_t *FileHelper::GetImageDataRaw () { return GetRaw(); } -#ifndef GDCM_LEGACY_REMOVE +//#ifndef GDCM_LEGACY_REMOVE /* - * \ brief Useless function, since PixelReadConverter forces us + * \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 @@ -394,7 +402,7 @@ uint8_t *FileHelper::GetImageDataRaw () * Transforms single Grey plane + 3 Palettes into a RGB Plane * Copies at most MaxSize bytes of pixel data to caller allocated * memory space. - * \ warning This function allows people that want to build a volume + * \warning This function allows people that want to build a volume * from an image stack *not to* have, first to get the image pixels, * and then move them to the volume area. * It's absolutely useless for any VTK user since vtk chooses @@ -403,14 +411,15 @@ uint8_t *FileHelper::GetImageDataRaw () * to load the image line by line, starting from the end. * VTK users have to call GetImageData * - * @ param destination Address (in caller's memory space) at which the + * @param destination Address (in caller's memory space) at which the * pixel data should be copied - * @ param maxSize Maximum number of bytes to be copied. When MaxSize + * @param maxSize Maximum number of bytes to be copied. When MaxSize * is not sufficient to hold the pixel data the copy is not * executed (i.e. no partial copy). - * @ return On success, the number of bytes actually copied. Zero on + * @return On success, the number of bytes actually copied. Zero on * failure e.g. MaxSize is lower than necessary. */ + /* size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) { if ( ! GetRaw() ) @@ -443,7 +452,8 @@ size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize) PixelReadConverter->GetRawSize() ); return PixelReadConverter->GetRawSize(); } -#endif +*/ +//#endif /** * \brief Points the internal pointer to the callers inData @@ -656,15 +666,50 @@ bool FileHelper::WriteAcr (std::string const &fileName) */ bool FileHelper::Write(std::string const &fileName) { + + CheckMandatoryElements(); //called once, here ! + + bool flag = false; + DocEntry *e; switch(WriteType) { case ImplicitVR: SetWriteFileTypeToImplicitVR(); break; + case Unknown: // should never happen; ExplicitVR is the default value case ExplicitVR: - SetWriteFileTypeToExplicitVR(); + + // User should ask gdcm to write an image in Explicit VR mode + // only when he is sure *all* the VR of *all* the DataElements is known. + // i.e : when there are *only* Public Groups + // or *all* the Shadow Groups are fully described in the relevant Shadow + // Dictionnary + // Let's just *dream* about it; *never* trust a user ! + // We turn to Implicit VR if at least the VR of one element is unknown. + + + e = FileInternal->GetFirstEntry(); + while (e != 0) + { + if (e->GetVR() == " ") + { + SetWriteTypeToDcmImplVR(); + SetWriteFileTypeToImplicitVR(); + flag = true; + break; + } + e = FileInternal->GetNextEntry(); + } + + if (!flag) + { + SetWriteFileTypeToExplicitVR(); + } break; + + SetWriteFileTypeToExplicitVR(); // to see JPRx + break; case ACR: case ACR_LIBIDO: // NOTHING is done here just for LibIDO. @@ -674,16 +719,21 @@ bool FileHelper::Write(std::string const &fileName) // (shame on him !) // We add Recognition Code (RET) if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) ) - FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010); + FileInternal->InsertEntryString("ACR-NEMA V1.0 ", + 0x0008, 0x0010, "LO"); SetWriteFileTypeToACR(); // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; + + /// \todo FIXME : JPEG may be either ExplicitVR or ImplicitVR case JPEG: SetWriteFileTypeToJPEG(); - std::cerr << "Writting as JPEG" << std::endl; + break; + + case JPEG2000: + SetWriteFileTypeToJPEG2000(); break; } - CheckMandatoryElements(); // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -715,15 +765,16 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length - if (WriteType == JPEG ) check = true; + if (WriteType == JPEG || WriteType == JPEG2000) check = true; if (check) { check = FileInternal->Write(fileName,WriteType); } - RestoreWrite(); - RestoreWriteFileType(); - RestoreWriteMandatory(); + RestoreWrite(); + // RestoreWriteFileType(); + // RestoreWriteMandatory(); + // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -762,6 +813,7 @@ bool FileHelper::CheckWriteIntegrity() size_t decSize = FileInternal->GetXSize() * FileInternal->GetYSize() * FileInternal->GetZSize() + * FileInternal->GetTSize() * FileInternal->GetSamplesPerPixel() * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; @@ -808,7 +860,7 @@ void FileHelper::SetWriteToRaw() } else { - DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS"); if (FileInternal->HasLUT() ) { photInt->SetString("PALETTE COLOR "); @@ -826,6 +878,11 @@ void FileHelper::SetWriteToRaw() vr = "OW"; if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files vr = "OB"; + // For non RAW data. Mainly JPEG + if( WriteType == JPEG || WriteType == JPEG2000) + { + vr = "OW"; + } DataEntry *pixel = CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr); pixel->SetFlag(DataEntry::FLAG_PIXELDATA); @@ -853,13 +910,13 @@ void FileHelper::SetWriteToRGB() { PixelReadConverter->BuildRGBImage(); - DataEntry *spp = CopyDataEntry(0x0028,0x0002); + DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US"); spp->SetString("3 "); - DataEntry *planConfig = CopyDataEntry(0x0028,0x0006); + DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US"); planConfig->SetString("0 "); - DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS"); photInt->SetString("RGB "); if ( PixelReadConverter->GetRGB() ) @@ -910,13 +967,13 @@ void FileHelper::SetWriteToRGB() // samples per pixels = 1 (in the read file) if ( FileInternal->GetBitsAllocated()==24 ) { - DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100); + DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US"); bitsAlloc->SetString("8 "); - DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101); + DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US"); bitsStored->SetString("8 "); - DataEntry *highBit = CopyDataEntry(0x0028,0x0102); + DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US"); highBit->SetString("7 "); Archive->Push(bitsAlloc); @@ -939,8 +996,10 @@ void FileHelper::SetWriteToRGB() */ void FileHelper::RestoreWrite() { + Archive->Restore(0x0028,0x0002); Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); @@ -960,7 +1019,6 @@ void FileHelper::RestoreWrite() // 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); @@ -972,6 +1030,7 @@ void FileHelper::RestoreWrite() Archive->Restore(0x0002,0x0016); Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); + } /** @@ -995,29 +1054,46 @@ void FileHelper::SetWriteFileTypeToACR() Archive->Push(0x0002,0x0102); } + /** + * \brief Sets in the File the TransferSyntax to 'JPEG2000' + */ +void FileHelper::SetWriteFileTypeToJPEG2000() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); + tss->SetString(ts); + + Archive->Push(tss); + tss->Delete(); +} + /** - * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" + * \brief Sets in the File the TransferSyntax to 'JPEG' */ void FileHelper::SetWriteFileTypeToJPEG() { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) ); - DataEntry *tss = CopyDataEntry(0x0002,0x0010); + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); tss->SetString(ts); Archive->Push(tss); tss->Delete(); } +/** + * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" + */ void FileHelper::SetWriteFileTypeToExplicitVR() { std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) ); - DataEntry *tss = CopyDataEntry(0x0002,0x0010); + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); tss->SetString(ts); - Archive->Push(tss); tss->Delete(); } @@ -1030,9 +1106,8 @@ void FileHelper::SetWriteFileTypeToImplicitVR() std::string ts = Util::DicomString( Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) ); - DataEntry *tss = CopyDataEntry(0x0002,0x0010); + DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI"); tss->SetString(ts); - Archive->Push(tss); tss->Delete(); } @@ -1057,9 +1132,12 @@ void FileHelper::SetWriteToLibido() { std::string rows, columns; - DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry()); - DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry()); - + //DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry()); + //DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry()); + + DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US"); + DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US"); + newRow->Copy(oldCol); newCol->Copy(oldRow); @@ -1073,7 +1151,7 @@ void FileHelper::SetWriteToLibido() newCol->Delete(); } - DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO"); libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); libidoCode->Delete(); @@ -1089,7 +1167,7 @@ void FileHelper::SetWriteToNoLibido() { if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" ) { - DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); + DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO"); libidoCode->SetString(""); Archive->Push(libidoCode); libidoCode->Delete(); @@ -1118,11 +1196,10 @@ void FileHelper::RestoreWriteOfLibido() * @param group Group number of the Entry * @param elem Element number of the Entry * @param vr Value Representation of the Entry - * FIXME : what is it used for? * \return pointer to the new Bin Entry (NULL when creation failed). */ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, - const TagName &vr) + const VRKey &vr) { DocEntry *oldE = FileInternal->GetDocEntry(group, elem); DataEntry *newE; @@ -1133,7 +1210,8 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, if ( oldE ) { - newE = DataEntry::New(oldE->GetDictEntry()); + //newE = DataEntry::New(oldE->GetDictEntry()); + newE = DataEntry::New(group, elem, vr); newE->Copy(oldE); } else @@ -1183,22 +1261,87 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, /* ------------------------------------------------------------------------------------- To be moved to User's guide / WIKI ? +We have to deal with 4 *very* different cases : +-1) user created ex nihilo his own image and wants to write it as a Dicom image. + USER_OWN_IMAGE +-2) user modified the pixels of an existing image. + FILTERED_IMAGE +-3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image) + CREATED_IMAGE +-4) user modified/added some tags *without processing* the pixels (anonymization.. + UNMODIFIED_PIXELS_IMAGE +-Probabely some more to be added + +gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases. + +1)2)3)4) +0008 0012 Instance Creation Date +0008 0013 Instance Creation Time +0008 0018 SOP Instance UID +are *always* created with the current values; user has *no* possible intervention on +them. + +'Serie Instance UID'(0x0020,0x000e) +'Study Instance UID'(0x0020,0x000d) are kept as is if already exist, + created if it doesn't. + The user is allowed to create his own Series/Studies, + keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images + Warning : + The user shouldn't add any image to a 'Manufacturer Serie' + but there is no way no to allow him to do that + + None of the 'shadow elements' are droped out. + + +1) +'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image). + +1)3) +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) are set to + [Secondary Capture Image Storage] +'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" +Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image) + +2)4) +If 'SOP Class UID' exists in the native image ('true DICOM' image) + we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112) + --> 'Referenced SOP Class UID' (0x0008, 0x1150) + whose value is the original 'SOP Class UID' + --> 'Referenced SOP Instance UID' (0x0008, 0x1155) + whose value is the original 'SOP Class UID' + +3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images + or the Series, (or the Study ?) he used to created his image + (MIP, MPR, cartography image, ...) + These info should be stored (?) + 0008 1110 SQ 1 Referenced Study Sequence + 0008 1115 SQ 1 Referenced Series Sequence + 0008 1140 SQ 1 Referenced Image Sequence + +4) When user *knows* he didn't modified the pixels, we keep some informations unchanged : +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) +'Image Type' (0x0008,0x0008) +'Conversion Type' (0x0008,0x0064) + + +Bellow follows the full description (hope so !) of the consistency checks performed +by gdcm::FileHelper::CheckMandatoryElements() -->'Media Storage SOP Class UID' (0x0002,0x0002) --->'SOP Class UID' (0x0008,0x0016) are set to +-->'SOP Class UID' (0x0008,0x0016) are defaulted to [Secondary Capture Image Storage] - (Potentialy, the image was modified by user, and post-processed; - it's no longer a 'native' image) - Except if user told he wants to keep MediaStorageSOPClassUID, - when *he* knows he didn't modify the image (e.g. : he just anonymized the file) - --> 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" (The written image is no longer an 'ORIGINAL' one) - Except if user told he wants to keep MediaStorageSOPClassUID, - when *he* knows he didn't modify the image (e.g. : he just anonymized the file) - + Except if user knows he didn't modify the image (e.g. : he just anonymized the file) + + --> Conversion Type (0x0008,0x0064) + is defaulted to 'SYN' (Synthetic Image) + when *he* knows he created his own image ex nihilo + --> 'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing. (a fully user created image belongs to *no* modality) @@ -1228,16 +1371,17 @@ To be moved to User's guide / WIKI ? --> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency --> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0" --> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale) + --> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value ---> Instance Creation Date, Instance Creation Time, Study Date, Study Time - are force to current Date and Time - ---> Conversion Type (0x0008,0x0064) - is forced to 'SYN' (Synthetic Image) +--> Instance Creation Date, Instance Creation Time are forced to current Date and Time + +--> Study Date, Study Time are defaulted to current Date and Time + (they remain unchanged if they exist) --> Patient Orientation : (0x0020,0x0020), if not present, is deduced from - Image Orientation (Patient) : (0020|0037) + Image Orientation (Patient) : (0020|0037) or from + Image Orientation (RET) : (0020 0035) --> Study ID, Series Number, Instance Number, Patient Orientation (Type 2) are created, with empty value if there are missing. @@ -1247,14 +1391,15 @@ To be moved to User's guide / WIKI ? --> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2) --> Referring Physician's Name (Type 2) - are created, with empty value if there are missing. + are created, with empty value if there are missing. -------------------------------------------------------------------------------------*/ - + void FileHelper::CheckMandatoryElements() { std::string sop = Util::CreateUniqueUID(); - + + // --------------------- For Meta Elements --------------------- // just to remember : 'official' 0002 group if ( WriteType != ACR && WriteType != ACR_LIBIDO ) { @@ -1270,12 +1415,17 @@ void FileHelper::CheckMandatoryElements() //0002 0016 AE 1 Source Application Entity Title //0002 0100 UI 1 Private Information Creator //0002 0102 OB 1 Private Information + + // Push out 'ACR-NEMA-special' entries, if any + Archive->Push(0x0008,0x0001); // Length to End + Archive->Push(0x0008,0x0010); // Recognition Code + Archive->Push(0x0028,0x0005); // Image Dimension // Create them if not found // Always modify the value // Push the entries to the archive. - CopyMandatoryEntry(0x0002,0x0000,"0"); - + CopyMandatoryEntry(0x0002,0x0000,"0","UL"); + DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB"); e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(), false); @@ -1283,40 +1433,119 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0002_0001); e_0002_0001->Delete(); - if ( KeepMediaStorageSOPClassUID) - // It up to the use to *know* whether he modified the pixels or not. - // he is allowed to keep the original 'Media Storage SOP Class UID' - CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); + if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE) + { + // we keep the original 'Media Storage SOP Class UID', we default it if missing + CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI"); + } else - // Potentialy this is a post-processed image + { + // It's *not* an image comming straight from a source. We force // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] - CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI"); + } + // 'Media Storage SOP Instance UID' - CopyMandatoryEntry(0x0002,0x0003,sop); + CopyMandatoryEntry(0x0002,0x0003,sop,"UI"); // 'Implementation Class UID' // FIXME : in all examples we have, 0x0002,0x0012 is not so long : - // semms to be Root UID + 4 digits (?) - CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); + // seems to be Root UID + 4 digits (?) + CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI"); // 'Implementation Version Name' std::string version = "GDCM "; version += Util::GetVersion(); - CopyMandatoryEntry(0x0002,0x0013,version); + CopyMandatoryEntry(0x0002,0x0013,version,"SH"); } + // --------------------- For DataSet --------------------- + + if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image + { + + gdcmDebugMacro( "USER_OWN_IMAGE (1)"); + // If 'SOP Class UID' exists ('true DICOM' image) + // we create the 'Source Image Sequence' SeqEntry + // to hold informations about the Source Image + + DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); + if ( e_0008_0016 ) + { + // Create 'Source Image Sequence' SeqEntry +// SeqEntry *sis = SeqEntry::New ( +// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); + SeqEntry *sis = SeqEntry::New (0x0008, 0x2112); + SQItem *sqi = SQItem::New(1); + // (we assume 'SOP Instance UID' exists too) + // create 'Referenced SOP Class UID' +// DataEntry *e_0008_1150 = DataEntry::New( +// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); + DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI"); + e_0008_1150->SetString( e_0008_0016->GetString()); + sqi->AddEntry(e_0008_1150); + e_0008_1150->Delete(); + + // create 'Referenced SOP Instance UID' + DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); +// DataEntry *e_0008_1155 = DataEntry::New( +// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); + DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI"); + e_0008_1155->SetString( e_0008_0018->GetString()); + sqi->AddEntry(e_0008_1155); + e_0008_1155->Delete(); + + sis->AddSQItem(sqi,1); + sqi->Delete(); + + // temporarily replaces any previous 'Source Image Sequence' + Archive->Push(sis); + sis->Delete(); + + // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'? + if ( ContentType == FILTERED_IMAGE) + // the user *knows* he just modified the pixels + // the image is no longer an 'Original' one + CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS"); + } + } + + if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE) + { + // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !) + CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI"); + } + else + { + // It's *not* an image comming straight from a source. We force + // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] + CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI"); + } + + Archive->Push(0x0028,0x005); // [Image Dimensions (RET) // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); Archive->Push(0x0028,0x0016); Archive->Push(0x0028,0x0017); - Archive->Push(0x0028,0x00199); + Archive->Push(0x0028,0x0198); // very old versions + Archive->Push(0x0028,0x0199); + + // Replace deprecated 0028 0012 US Planes + // by new 0028 0008 IS Number of Frames + + ///\todo : find if there is a rule! + DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012); + if ( e_0028_0012 ) + { + CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS"); + Archive->Push(0x0028,0x0012); + } // Deal with the pb of (Bits Stored = 12) // - we're gonna write the image as Bits Stored = 16 if ( FileInternal->GetEntryString(0x0028,0x0100) == "12") { - CopyMandatoryEntry(0x0028,0x0100,"16"); + CopyMandatoryEntry(0x0028,0x0100,"16","US"); } // Check if user wasn't drunk ;-) @@ -1326,7 +1555,7 @@ void FileHelper::CheckMandatoryElements() int nbBitsAllocated = FileInternal->GetBitsAllocated(); if ( nbBitsAllocated == 0 || nbBitsAllocated > 32) { - CopyMandatoryEntry(0x0028,0x0100,"16"); + CopyMandatoryEntry(0x0028,0x0100,"16","US"); gdcmWarningMacro("(0028,0100) changed from " << nbBitsAllocated << " to 16 for consistency purpose"); nbBitsAllocated = 16; @@ -1337,7 +1566,7 @@ void FileHelper::CheckMandatoryElements() { s.str(""); s << nbBitsAllocated; - CopyMandatoryEntry(0x0028,0x0101,s.str()); + CopyMandatoryEntry(0x0028,0x0101,s.str(),"US"); gdcmWarningMacro("(0028,0101) changed from " << nbBitsStored << " to " << nbBitsAllocated << " for consistency purpose" ); @@ -1351,106 +1580,89 @@ void FileHelper::CheckMandatoryElements() { s.str(""); s << nbBitsStored - 1; - CopyMandatoryEntry(0x0028,0x0102,s.str()); + CopyMandatoryEntry(0x0028,0x0102,s.str(),"US"); gdcmWarningMacro("(0028,0102) changed from " << highBitPosition << " to " << nbBitsAllocated-1 << " for consistency purpose"); } std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); - if ( pixelSpacing == GDCM_UNKNOWN ) + if ( pixelSpacing == GDCM_UNFOUND ) { pixelSpacing = "1.0\\1.0"; // if missing, Pixel Spacing forced to "1.0\1.0" - CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS"); } + // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing' // --> This one is the *legal* one ! - // FIXME : we should write it only when we are *sure* the image comes from - // an imager (see also 0008,0x0064) - - CheckMandatoryEntry(0x0018,0x1164,pixelSpacing); + if ( ContentType != USER_OWN_IMAGE) + // we write it only when we are *sure* the image comes from + // an imager (see also 0008,0x0064) + CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS"); - // Samples Per Pixel (type 1) : default to grayscale - CheckMandatoryEntry(0x0028,0x0002,"1"); - - // --- Check UID-related Entries --- - // If 'SOP Class UID' exists ('true DICOM' image) - // we create the 'Source Image Sequence' SeqEntry - // to hold informations about the Source Image - DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016); - if ( e_0008_0016 ) - { - // Create 'Source Image Sequence' SeqEntry - SeqEntry *sis = SeqEntry::New ( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); - SQItem *sqi = SQItem::New(1); - // (we assume 'SOP Instance UID' exists too) - // create 'Referenced SOP Class UID' - DataEntry *e_0008_1150 = DataEntry::New( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) ); - e_0008_1150->SetString( e_0008_0016->GetString()); - sqi->AddEntry(e_0008_1150); - e_0008_1150->Delete(); - - // create 'Referenced SOP Instance UID' - DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018); - DataEntry *e_0008_1155 = DataEntry::New( - Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) ); - e_0008_1155->SetString( e_0008_0018->GetString()); - sqi->AddEntry(e_0008_1155); - e_0008_1155->Delete(); - - sis->AddSQItem(sqi,1); - sqi->Delete(); - - // temporarily replaces any previous 'Source Image Sequence' - Archive->Push(sis); - sis->Delete(); +/* +///Exact meaning of RETired fields + +// See page 73 of ACR-NEMA_300-1988.pdf ! + +// 0020,0020 : Patient Orientation : +Patient direction of the first row and +column of the images. The first entry id the direction of the raws, given by the +direction of the last pixel in the first row from the first pixel in tha row. +the second entry is the direction of the columns, given by the direction of the +last pixel in the first column from the first pixel in that column. +L : Left, F : Feet, A : Anterior, P : Posterior. +Up to 3 letters can be used in combination to indicate oblique planes. + +//0020,0030 Image Position (RET) +x,y,z coordinates im mm of the first pixel in the image + +// 0020,0035 Image Orientation (RET) +Direction cosines of the R axis of the image system with respect to the +equipment coordinate axes x,y,z, followed by direction cosines of the C axis of +the image system with respect to the same axes + +//0020,0050 Location +An image location reference, standard for the modality (such as CT bed +position), used to indicate position. Calculation of position for other purposes +is only from (0020,0030) and (0020,0035) +*/ - // FIXME : is 'Image Type' *really* depending on the presence of'SOP Class UID'? - if ( KeepMediaStorageSOPClassUID) - // It up to the use to *know* whether he modified the pixels or not. - // he is allowed to keep the original 'Media Storage SOP Class UID' - // and 'Image Type' as well - CheckMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); - else - // Potentialy this is a post-processed image - // (The written image is no longer an 'ORIGINAL' one) - CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); +/* +// if imagePositionPatient not found, default it with imagePositionRet, if any +// if imageOrientationPatient not found, default it with imageOrientationRet, if any - } + std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030); + std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035); + std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032); + std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037); + + if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND + && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND) + { + CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS"); + Archive->Push(0x0020,0x0030); + CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS"); + Archive->Push(0x0020,0x0035); + } +*/ + + // Samples Per Pixel (type 1) : default to grayscale + CheckMandatoryEntry(0x0028,0x0002,"1","US"); + // --- Check UID-related Entries --- + // At the end, not to overwrite the original ones, // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID' // 'SOP Instance UID' - CopyMandatoryEntry(0x0008,0x0018,sop); - - // the gdcm written image is a [Secondary Capture Image Storage] - // except if user told us he dind't modify the pixels, and, therefore - // he want to keep the 'Media Storage SOP Class UID' - - // 'Media Storage SOP Class UID' : [Secondary Capture Image Storage] - if ( KeepMediaStorageSOPClassUID) - { - // It up to the use to *know* whether he modified the pixels or not. - // he is allowed to keep the original 'Media Storage SOP Class UID' - CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); - } - else - { - // Potentialy this is a post-processed image - // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] - CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); - - // FIXME : Must we Force Value, or Default value ? - // Is it Type 1 for any Modality ? - // --> Answer seems to be NO :-( - // FIXME : we should write it only when we are *sure* the image - // *does not* come from an imager (see also 0018,0x1164) + CopyMandatoryEntry(0x0008,0x0018,sop,"UI"); + if ( ContentType == USER_OWN_IMAGE) + { + gdcmDebugMacro( "USER_OWN_IMAGE (2)"); // Conversion Type. // Other possible values are : // See PS 3.3, Page 408 @@ -1463,31 +1675,38 @@ void FileHelper::CheckMandatoryElements() // SI = Scanned Image // DRW = Drawing // SYN = Synthetic Image - - CheckMandatoryEntry(0x0008,0x0064,"SYN"); - } - // ---- The user will never have to take any action on the following ---- + CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not? + } +/* + if ( ContentType == CREATED_IMAGE) + { + /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image + } +*/ + + // ---- The user will never have to take any action on the following ---- + // new value for 'SOP Instance UID' //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); // Instance Creation Date const std::string &date = Util::GetCurrentDate(); - CopyMandatoryEntry(0x0008,0x0012,date); + CopyMandatoryEntry(0x0008,0x0012,date,"DA"); // Instance Creation Time const std::string &time = Util::GetCurrentTime(); - CopyMandatoryEntry(0x0008,0x0013,time); + CopyMandatoryEntry(0x0008,0x0013,time,"TM"); // Study Date - CopyMandatoryEntry(0x0008,0x0020,date); + CheckMandatoryEntry(0x0008,0x0020,date,"DA"); // Study Time - CopyMandatoryEntry(0x0008,0x0030,time); + CheckMandatoryEntry(0x0008,0x0030,time,"TM"); // Accession Number //CopyMandatoryEntry(0x0008,0x0050,""); - CheckMandatoryEntry(0x0008,0x0050,""); + CheckMandatoryEntry(0x0008,0x0050,"","SH"); // ----- Add Mandatory Entries if missing --- @@ -1505,7 +1724,7 @@ void FileHelper::CheckMandatoryElements() // 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 - CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); + CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI"); // 'Serie Instance UID' // Keep the value if exists @@ -1513,65 +1732,58 @@ void FileHelper::CheckMandatoryElements() // keeping the same 'Serie Instance UID' for various images // The user shouldn't add any image to a 'Manufacturer Serie' // but there is no way no to prevent him for doing that - CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI"); // Study ID - CheckMandatoryEntry(0x0020,0x0010,""); + CheckMandatoryEntry(0x0020,0x0010,"","SH"); // Series Number - CheckMandatoryEntry(0x0020,0x0011,""); + CheckMandatoryEntry(0x0020,0x0011,"","IS"); // Instance Number - CheckMandatoryEntry(0x0020,0x0013,""); + CheckMandatoryEntry(0x0020,0x0013,"","IS"); // Patient Orientation // Can be computed from (0020|0037) : Image Orientation (Patient) gdcm::Orientation *o = gdcm::Orientation::New(); std::string ori = o->GetOrientation ( FileInternal ); o->Delete(); - if (ori != "\\" ) - CheckMandatoryEntry(0x0020,0x0020,ori); + if (ori != "\\" && ori != GDCM_UNFOUND) + CheckMandatoryEntry(0x0020,0x0020,ori,"CS"); else - CheckMandatoryEntry(0x0020,0x0020,""); - + CheckMandatoryEntry(0x0020,0x0020,"","CS"); + + // Default Patient Position to HFS + CheckMandatoryEntry(0x0018,0x5100,"HFS","CS"); + // Modality : if missing we set it to 'OTher' - CheckMandatoryEntry(0x0008,0x0060,"OT"); + CheckMandatoryEntry(0x0008,0x0060,"OT","CS"); // Manufacturer : if missing we set it to 'GDCM Factory' - CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory"); + CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO"); // Institution Name : if missing we set it to 'GDCM Hospital' - CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital"); + CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO"); // Patient's Name : if missing, we set it to 'GDCM^Patient' - CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); + CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN"); - // Patient ID - CheckMandatoryEntry(0x0010,0x0020,""); + // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry. + CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO"); // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory - CheckMandatoryEntry(0x0010,0x0030,""); + CheckMandatoryEntry(0x0010,0x0030,"","DA"); // Patient's Sex :'type 2' entry -> must exist, value not mandatory - CheckMandatoryEntry(0x0010,0x0040,""); + CheckMandatoryEntry(0x0010,0x0040,"","CS"); // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory - CheckMandatoryEntry(0x0008,0x0090,""); - - // Remove some inconstencies (probably some more will be added) + CheckMandatoryEntry(0x0008,0x0090,"","PN"); - // if (0028 0008)Number of Frames exists - // Push out (0020 0052),Frame of Reference UID - // (only meaningfull within a Serie) - DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); - if ( !e_0028_0008 ) - { - Archive->Push(0x0020, 0x0052); - } - + /* // Deal with element 0x0000 (group length) of each group. // First stage : get all the different Groups - /* + GroupHT grHT; DocEntry *d = FileInternal->GetFirstEntry(); while(d) @@ -1585,32 +1797,36 @@ void FileHelper::CheckMandatoryElements() CheckMandatoryEntry(it->first, 0x0000, "0"); } // Third stage : update all 'zero level' groups length -*/ +*/ + } -void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr ) { DataEntry *entry = FileInternal->GetDataEntry(group,elem); if ( !entry ) { - entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry = DataEntry::New(group,elem,vr); entry->SetString(value); Archive->Push(entry); entry->Delete(); - } + } } -void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +/// \todo : what is it used for ? (FileHelper::SetMandatoryEntry) +void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr) { - DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + DataEntry *entry = DataEntry::New(group,elem,vr); entry->SetString(value); Archive->Push(entry); entry->Delete(); } -void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value) +void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr) { - DataEntry *entry = CopyDataEntry(group,elem); + DataEntry *entry = CopyDataEntry(group,elem,vr); entry->SetString(value); Archive->Push(entry); entry->Delete(); @@ -1689,7 +1905,7 @@ void FileHelper::CallEndMethod() void FileHelper::Initialize() { UserFunction = 0; - KeepMediaStorageSOPClassUID = false; + ContentType = USER_OWN_IMAGE; WriteMode = WMODE_RAW; WriteType = ExplicitVR; @@ -1748,3 +1964,155 @@ void FileHelper::Print(std::ostream &os, std::string const &) //----------------------------------------------------------------------------- } // end namespace gdcm + + +/* Probabely something to be added to use Rescale Slope/Intercept +Have a look ,at ITK code ! + +// Internal function to rescale pixel according to Rescale Slope/Intercept +template +void RescaleFunction(TBuffer* buffer, TSource *source, + double slope, double intercept, size_t size) +{ + size /= sizeof(TSource); + + if (slope != 1.0 && intercept != 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else if (slope == 1.0 && intercept != 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else if (slope != 1.0 && intercept == 0.0) + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + else + { + // Duff's device. Instead of this code: + // + // for(unsigned int i=0; i 0); + } + } + + +} + + +template +void RescaleFunction(ImageIOBase::IOComponentType bufferType, + void* buffer, TSource *source, + double slope, double intercept, size_t size) +{ + switch (bufferType) + { + case ImageIOBase::UCHAR: + RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::CHAR: + RescaleFunction( (char *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::USHORT: + RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size); + break; + case ImageIOBase::SHORT: + RescaleFunction( (short *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::UINT: + RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::INT: + RescaleFunction( (int *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::FLOAT: + RescaleFunction( (float *)buffer, source, slope, intercept, size); + break; + case ImageIOBase::DOUBLE: + RescaleFunction( (double *)buffer, source, slope, intercept, size); + break; + default: + ::itk::OStringStream message; + message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType; + ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION); + throw e; + } +} +*/