X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=12bfe7cf5767b985b32f67fefb479b996c5527cf;hb=17ebda2271dd65565f512e835546b22c22ebbbb0;hp=94487717bc9c786e8fb7ecb7a064e70fb2ca7890;hpb=7fd1222c03038e650429f10a908d8dfac8b9c462;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 94487717..12bfe7cf 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/11/03 08:46:03 $ - Version: $Revision: 1.78 $ + Date: $Date: 2006/04/11 16:03:26 $ + Version: $Revision: 1.99 $ 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);) @@ -114,6 +119,7 @@ fh1->Write(newFileName); namespace gdcm { +typedef std::map GroupHT; // Hash Table //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -158,7 +164,7 @@ FileHelper::FileHelper(File *header) Initialize(); if ( FileInternal->IsReadable() ) { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); + PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); } } @@ -219,49 +225,47 @@ bool FileHelper::Load() if ( !FileInternal->Load() ) return false; - PixelReadConverter->GrabInformationsFromFile( FileInternal ); + PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); return true; } /** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. + * \brief Accesses an existing DataEntry through it's (group, element) + * and modifies it's content with the given value. * @param content new value (string) to substitute with * @param group group number of the Dicom Element to modify * @param elem element number of the Dicom Element to modify - * \return false if DocEntry not found + * \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); } /** - * \brief Accesses an existing DocEntry (i.e. a Dicom Element) - * through it's (group, element) and modifies it's content with - * the given value. + * \brief Accesses an existing DataEntry through it's (group, element) + * and modifies it's content with the given value. * @param content new value (void* -> uint8_t*) to substitute with * @param lgth new value length * @param group group number of the Dicom Element to modify * @param elem element number of the Dicom Element to modify - * \return false if DocEntry not found + * \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); } /** - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Creates it with the given value when unexistant. - * @param content (string)value to be set + * \brief Modifies the value of a given DataEntry when it exists. + * Creates it with the given value when unexistant. + * @param content (string) value to be set * @param group Group number of the Entry * @param elem Element number of the Entry - * \return pointer to the modified/created Dicom entry (NULL when creation + * \return pointer to the modified/created DataEntry (NULL when creation * failed). */ DataEntry *FileHelper::InsertEntryString(std::string const &content, @@ -271,28 +275,28 @@ DataEntry *FileHelper::InsertEntryString(std::string const &content, } /** - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Creates it with the given value when unexistant. + * \brief Modifies the value of a given DataEntry when it exists. + * Creates it with the given value when unexistant. * A copy of the binArea is made to be kept in the Document. * @param binArea (binary)value to be set * @param lgth new value length * @param group Group number of the Entry * @param elem Element number of the Entry - * \return pointer to the modified/created Dicom entry (NULL when creation + * \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) { return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem); } /** - * \brief Modifies the value of a given DocEntry (Dicom entry) - * when it exists. Creates it, empty (?!) when unexistant. + * \brief Adds an empty SeqEntry + * (remove any existing entry with same group,elem) * @param group Group number of the Entry * @param elem Element number of the Entry - * \return pointer to the modified/created Dicom entry (NULL when creation + * \return pointer to the created SeqEntry (NULL when creation * failed). */ SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem) @@ -378,7 +382,7 @@ 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 () { @@ -387,7 +391,7 @@ uint8_t *FileHelper::GetImageDataRaw () #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 @@ -395,7 +399,7 @@ 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 @@ -404,12 +408,12 @@ 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) @@ -657,15 +661,50 @@ 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. @@ -675,17 +714,18 @@ 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; } - CheckMandatoryElements(); - + // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images // @@ -722,9 +762,10 @@ bool FileHelper::Write(std::string const &fileName) check = FileInternal->Write(fileName,WriteType); } - RestoreWrite(); - RestoreWriteFileType(); - RestoreWriteMandatory(); + RestoreWrite(); + // RestoreWriteFileType(); + // RestoreWriteMandatory(); + // -------------------------------------------------------------- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images @@ -763,6 +804,7 @@ bool FileHelper::CheckWriteIntegrity() size_t decSize = FileInternal->GetXSize() * FileInternal->GetYSize() * FileInternal->GetZSize() + * FileInternal->GetTSize() * FileInternal->GetSamplesPerPixel() * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; @@ -809,7 +851,7 @@ void FileHelper::SetWriteToRaw() } else { - DataEntry *photInt = CopyDataEntry(0x0028,0x0004); + DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS"); if (FileInternal->HasLUT() ) { photInt->SetString("PALETTE COLOR "); @@ -854,13 +896,13 @@ 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() ) @@ -911,13 +953,13 @@ 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); @@ -940,8 +982,10 @@ void FileHelper::SetWriteToRGB() */ void FileHelper::RestoreWrite() { + Archive->Restore(0x0028,0x0002); Archive->Restore(0x0028,0x0004); + Archive->Restore(0x0028,0x0006); Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel()); @@ -961,7 +1005,6 @@ 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); @@ -973,6 +1016,7 @@ void FileHelper::RestoreWrite() Archive->Restore(0x0002,0x0016); Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); + } /** @@ -997,28 +1041,30 @@ void FileHelper::SetWriteFileTypeToACR() } /** - * \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(); } @@ -1031,9 +1077,8 @@ 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(); } @@ -1058,9 +1103,12 @@ 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); @@ -1074,7 +1122,7 @@ 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(); @@ -1090,7 +1138,7 @@ 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(); @@ -1119,11 +1167,10 @@ 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; @@ -1134,7 +1181,8 @@ 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 @@ -1147,10 +1195,10 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, /** * \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 ...) - * + * 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 @@ -1158,7 +1206,8 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, * - 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. + * see the entries just as they were before he decided to write. + * * \note * - Entries whose type is 1 are mandatory, with a mandatory value * - Entries whose type is 1c are mandatory-inside-a-Sequence, @@ -1168,7 +1217,8 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, * with an optional value * - Entries whose type is 3 are optional * - * \todo : - warn the user if we had to add some entries : + * \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 ...) @@ -1182,17 +1232,86 @@ 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 existing images (eg MIP, MPR, cartography image) + CREATED_IMAGE +-4) user modified/added some tags *without processing* the pixels (anonymization.. + UNMODIFIED_PIXELS_IMAGE + +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. + --->'Media Storage SOP Class UID' (0x0002,0x0002) --->'SOP Class UID' (0x0008,0x0016) are set to +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] - (Potentialy, the image was modified by user, and post-processed; - it's no longer a 'native' image) +'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 defaulted to + [Secondary Capture Image Storage] --> 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" (The written image is no longer an 'ORIGINAL' one) - + 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) @@ -1210,7 +1329,6 @@ To be moved to User's guide / WIKI ? Warning : The user shouldn't add any image to a 'Manufacturer Serie' but there is no way no to allowed him to do that - --> If 'SOP Class UID' exists in the native image ('true DICOM' image) we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112) @@ -1223,16 +1341,17 @@ 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 1.0\1.0 ---> 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) +--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value + +--> 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. @@ -1242,14 +1361,15 @@ 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 ) { @@ -1269,33 +1389,103 @@ void FileHelper::CheckMandatoryElements() // 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); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); - e_0002_0001->Delete(); + e_0002_0001->Delete(); - // FIXME : we should allow user to tell he *wants* to keep the original - // 'Media Storage SOP Class UID' - // Potentialy this is a post-processed image + 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 + { + // 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' - CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); + // FIXME : in all examples we have, 0x0002,0x0012 is not so long : + // 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"); + } // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); @@ -1307,7 +1497,7 @@ void FileHelper::CheckMandatoryElements() // - 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 ;-) @@ -1317,7 +1507,7 @@ 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; @@ -1328,7 +1518,7 @@ 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" ); @@ -1342,124 +1532,94 @@ 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"); } - // Imager Pixel Spacing : defaulted to 1.0\1.0 - // --> 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,"1.0\\1.0"); - // Pixel Spacing : defaulted to 1.0\1.0 - CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); - - // 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 ) + std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); + if ( pixelSpacing == GDCM_UNFOUND ) { - // 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(); - - // FIXME : is 'Image Type' *really* depending on the presence of'SOP Class UID'? - - // 'Image Type' (The written image is no longer an 'ORIGINAL' one) - CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY"); + pixelSpacing = "1.0\\1.0"; + // if missing, Pixel Spacing forced to "1.0\1.0" + CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS"); } + + // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing' + // --> This one is the *legal* one ! + 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","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); + 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 - // whether a 'SOP Class UID' already exists or not in the original image - // the gdcm written image *is* a [Secondary Capture Image Storage] ! - // 'SOP Class UID' : [Secondary Capture Image Storage] - CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); - -// ---- The user will never have to take any action on the following ----. + // DV = Digitized Video + // DI = Digital Interface + // DF = Digitized Film + // WSD = Workstation + // SD = Scanned Document + // SI = Scanned Image + // DRW = Drawing + // SYN = Synthetic Image + + 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,""); - - // Conversion Type. - // Other possible values are : - // See PS 3.3, Page 408 + CheckMandatoryEntry(0x0008,0x0050,"","SH"); - // DV = Digitized Video - // DI = Digital Interface - // DF = Digitized Film - // WSD = Workstation - // SD = Scanned Document - // SI = Scanned Image - // DRW = Drawing - // SYN = Synthetic Image - - // 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(0x0008,0x0064,"SYN"); - -// ----- Add Mandatory Entries if missing --- - // Entries whose type is 1 are mandatory, with a mandatory value - // Entries whose type is 1c are mandatory-inside-a-Sequence, - // with a mandatory value - // Entries whose type is 2 are mandatory, with an optional value - // Entries whose type is 2c are mandatory-inside-a-Sequence, - // with an optional value - // Entries whose type is 3 are optional + + // ----- Add Mandatory Entries if missing --- + // Entries whose type is 1 are mandatory, with a mandatory value + // Entries whose type is 1c are mandatory-inside-a-Sequence, + // with a mandatory value + // Entries whose type is 2 are mandatory, with an optional value + // Entries whose type is 2c are mandatory-inside-a-Sequence, + // with an optional value + // Entries whose type is 3 are optional // 'Study Instance UID' // Keep the value if exists @@ -1467,7 +1627,7 @@ 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 @@ -1475,85 +1635,101 @@ 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; - std::string ori = o.GetOrientation ( FileInternal ); - if (ori != "\\" ) - CheckMandatoryEntry(0x0020,0x0020,ori); + gdcm::Orientation *o = gdcm::Orientation::New(); + std::string ori = o->GetOrientation ( FileInternal ); + o->Delete(); + 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,""); + CheckMandatoryEntry(0x0010,0x0020,"","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,""); + CheckMandatoryEntry(0x0008,0x0090,"","PN"); + + /* + // Deal with element 0x0000 (group length) of each group. + // First stage : get all the different Groups - // Remove some inconstencies (probably some more will be added) + GroupHT grHT; + DocEntry *d = FileInternal->GetFirstEntry(); + while(d) + { + grHT[d->GetGroup()] = 0; + d=FileInternal->GetNextEntry(); + } + // Second stage : add the missing ones (if any) + for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it) + { + CheckMandatoryEntry(it->first, 0x0000, "0"); + } + // Third stage : update all 'zero level' groups length +*/ - // 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); - } } -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(); @@ -1576,6 +1752,8 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0002,0x0100); Archive->Restore(0x0002,0x0102); + // FIXME : Check if none is missing ! + Archive->Restore(0x0008,0x0012); Archive->Restore(0x0008,0x0013); Archive->Restore(0x0008,0x0016); @@ -1594,6 +1772,34 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000e); } + +/** + * \brief CallStartMethod + */ +void FileHelper::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); +} + +/** + * \brief CallProgressMethod + */ +void FileHelper::CallProgressMethod() +{ + CommandManager::ExecuteCommand(this,CMD_PROGRESS); +} + +/** + * \brief CallEndMethod + */ +void FileHelper::CallEndMethod() +{ + Progress = 1.0f; + CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); +} + //----------------------------------------------------------------------------- // Private /** @@ -1602,7 +1808,8 @@ void FileHelper::RestoreWriteMandatory() void FileHelper::Initialize() { UserFunction = 0; - + ContentType = USER_OWN_IMAGE; + WriteMode = WMODE_RAW; WriteType = ExplicitVR;