X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=cfb9a7c3257e3dab13348869ee806bfaec70c7ef;hb=e362e154b84f087750d1ed1f6671a34b3bf5ff7a;hp=c4435ba4b2759d590b88da7f117446f2d58b9fad;hpb=3ccb0db5e229de47c8a1fdc09deb3561315ec282;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index c4435ba4..cfb9a7c3 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/10/18 18:39:49 $ - Version: $Revision: 1.63 $ + Date: $Date: 2005/11/07 14:10:39 $ + Version: $Revision: 1.81 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -31,6 +31,7 @@ #include "gdcmPixelWriteConvert.h" #include "gdcmDocEntryArchive.h" #include "gdcmDictSet.h" +#include "gdcmOrientation.h" #include @@ -100,7 +101,7 @@ fh1->Write(newFileName); fp = opens file(fileName); ComputeGroup0002Length( ); BitsAllocated 12->16 - RemoveEntryNoDestroy(palettes, etc) + RemoveEntry(palettes, etc) Document::WriteContent(fp, writetype); RestoreWrite(); (moves back to the File all the archived elements) @@ -113,6 +114,7 @@ fh1->Write(newFileName); namespace gdcm { +typedef std::map GroupHT; // Hash Table //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -130,8 +132,7 @@ namespace gdcm */ FileHelper::FileHelper( ) { - FileInternal = new File( ); - SelfHeader = true; + FileInternal = File::New( ); Initialize(); } @@ -151,44 +152,16 @@ FileHelper::FileHelper( ) */ FileHelper::FileHelper(File *header) { - FileInternal = header; - SelfHeader = false; - Initialize(); - if ( FileInternal->IsReadable() ) - { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); - } -} + gdcmAssertMacro(header); -#ifndef GDCM_LEGACY_REMOVE -/** - * \brief DEPRECATED : use SetFilename() + SetLoadMode() + Load() methods - * Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3 - * file (gdcm::File only deals with the ... header) - * Opens (in read only and when possible) an existing file and checks - * for DICOM compliance. Returns NULL on failure. - * It will be up to the user to load the pixels into memory - * \note the in-memory representation of all available tags found in - * the DICOM header is post-poned to first header information access. - * This avoid a double parsing of public part of the header when - * one sets an a posteriori shadow dictionary (efficiency can be - * seen as a side effect). - * @param filename file to be opened for parsing - * @deprecated use SetFilename() + Load() methods - */ -FileHelper::FileHelper(std::string const &filename ) -{ - FileInternal = new File( ); - FileInternal->SetFileName( filename ); - FileInternal->Load(); - SelfHeader = true; + FileInternal = header; + FileInternal->Register(); Initialize(); if ( FileInternal->IsReadable() ) { PixelReadConverter->GrabInformationsFromFile( FileInternal ); } } -#endif /** * \brief canonical destructor @@ -210,11 +183,7 @@ FileHelper::~FileHelper() delete Archive; } - if ( SelfHeader ) - { - delete FileInternal; - } - FileInternal = 0; + FileInternal->Unregister(); } //----------------------------------------------------------------------------- @@ -222,8 +191,7 @@ FileHelper::~FileHelper() /** * \brief Sets the LoadMode of the internal gdcm::File as a boolean string. - * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ - *... (nothing more, right now) + * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now) * WARNING : before using NO_SHADOW, be sure *all* your files * contain accurate values in the 0x0000 element (if any) * of *each* Shadow Group. The parser will fail if the size is wrong ! @@ -351,7 +319,7 @@ size_t FileHelper::GetImageDataSize() } /** - * \brief Get the size of the image data + * \brief Get the size of the image data. * If the image could be converted to RGB using a LUT, * this transformation is not taken into account by GetImageDataRawSize * (use GetImageDataSize if you wish) @@ -367,13 +335,15 @@ size_t FileHelper::GetImageDataRawSize() } /** - * \brief - Allocates necessary memory, + * \brief brings pixels into memory : + * - Allocates necessary memory, * - Reads the pixels from disk (uncompress if necessary), * - Transforms YBR pixels, if any, into RGB pixels, * - Transforms 3 planes R, G, B, if any, into a single RGB Plane * - Transforms single Grey plane + 3 Palettes into a RGB Plane * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. * @return Pointer to newly allocated pixel data. + * (uint8_t is just for prototyping. feel free to cast) * NULL if alloc fails */ uint8_t *FileHelper::GetImageData() @@ -401,12 +371,14 @@ uint8_t *FileHelper::GetImageData() } /** - * \brief Allocates necessary memory, - * Transforms YBR pixels (if any) into RGB pixels - * Transforms 3 planes R, G, B (if any) into a single RGB Plane - * Copies the pixel data (image[s]/volume[s]) to newly allocated zone. - * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane + * \brief brings pixels into memory : + * - Allocates necessary memory, + * - Transforms YBR pixels (if any) into RGB pixels + * - Transforms 3 planes R, G, B (if any) into a single RGB Plane + * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone. + * - 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 */ uint8_t *FileHelper::GetImageDataRaw () @@ -415,8 +387,8 @@ 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 @@ -424,7 +396,7 @@ 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 @@ -433,12 +405,12 @@ 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) @@ -709,6 +681,7 @@ bool FileHelper::Write(std::string const &fileName) // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; case JPEG: + SetWriteFileTypeToJPEG(); std::cerr << "Writting as JPEG" << std::endl; break; } @@ -863,6 +836,9 @@ void FileHelper::SetWriteToRaw() Archive->Push(photInt); Archive->Push(pixel); + + photInt->Delete(); + pixel->Delete(); } } @@ -915,6 +891,11 @@ void FileHelper::SetWriteToRGB() Archive->Push(photInt); Archive->Push(pixel); + spp->Delete(); + planConfig->Delete(); + photInt->Delete(); + pixel->Delete(); + // Remove any LUT Archive->Push(0x0028,0x1101); Archive->Push(0x0028,0x1102); @@ -943,6 +924,10 @@ void FileHelper::SetWriteToRGB() Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); + + bitsAlloc->Delete(); + bitsStored->Delete(); + highBit->Delete(); } } else @@ -1015,6 +1000,18 @@ void FileHelper::SetWriteFileTypeToACR() /** * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" */ +void FileHelper::SetWriteFileTypeToJPEG() +{ + std::string ts = Util::DicomString( + Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) ); + + DataEntry *tss = CopyDataEntry(0x0002,0x0010); + tss->SetString(ts); + + Archive->Push(tss); + tss->Delete(); +} + void FileHelper::SetWriteFileTypeToExplicitVR() { std::string ts = Util::DicomString( @@ -1024,6 +1021,7 @@ void FileHelper::SetWriteFileTypeToExplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } /** @@ -1038,6 +1036,7 @@ void FileHelper::SetWriteFileTypeToImplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } @@ -1060,8 +1059,8 @@ void FileHelper::SetWriteToLibido() { std::string rows, columns; - DataEntry *newRow=new DataEntry(oldRow->GetDictEntry()); - DataEntry *newCol=new DataEntry(oldCol->GetDictEntry()); + DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry()); + DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry()); newRow->Copy(oldCol); newCol->Copy(oldRow); @@ -1071,11 +1070,15 @@ void FileHelper::SetWriteToLibido() Archive->Push(newRow); Archive->Push(newCol); + + newRow->Delete(); + newCol->Delete(); } DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString("ACRNEMA_LIBIDO_1.1"); Archive->Push(libidoCode); + libidoCode->Delete(); } /** @@ -1091,6 +1094,7 @@ void FileHelper::SetWriteToNoLibido() DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString(""); Archive->Push(libidoCode); + libidoCode->Delete(); } } } @@ -1131,7 +1135,7 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, if ( oldE ) { - newE = new DataEntry(oldE->GetDictEntry()); + newE = DataEntry::New(oldE->GetDictEntry()); newE->Copy(oldE); } else @@ -1145,8 +1149,8 @@ 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 ...) + * 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 @@ -1155,7 +1159,15 @@ 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, + * 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 * * \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 @@ -1167,9 +1179,82 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, * - write a user callable full checker, to allow post reading * and/or pre writting image consistency check. */ + +/* ------------------------------------------------------------------------------------- +To be moved to User's guide / WIKI ? + + + +-->'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) + 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) + +--> 'Modality' (0x0008,0x0060) + is defaulted to "OT" (other) if missing. + (a fully user created image belongs to *no* modality) + +--> 'Media Storage SOP Instance UID' (0x0002,0x0003) +--> 'Implementation Class UID' (0x0002,0x0012) + are automatically generated; no user intervention possible + +--> '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 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) + + --> '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' + +--> 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) + +--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from + Image Orientation (Patient) : (0020|0037) + +--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2) + are created, with empty value if there are missing. + +--> Manufacturer, Institution Name, Patient's Name, (Type 2) + are defaulted with a 'gdcm' value. + +--> 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. + + -------------------------------------------------------------------------------------*/ void FileHelper::CheckMandatoryElements() { + std::string sop = Util::CreateUniqueUID(); + // just to remember : 'official' 0002 group if ( WriteType != ACR && WriteType != ACR_LIBIDO ) { @@ -1190,21 +1275,29 @@ void FileHelper::CheckMandatoryElements() // Always modify the value // Push the entries to the archive. CopyMandatoryEntry(0x0002,0x0000,"0"); - + 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(); - // 'Media Stored SOP Class UID' - // [Secondary Capture Image Storage] - CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - - // 'Media Stored SOP Instance UID' - CopyMandatoryEntry(0x0002,0x0003,Util::CreateUniqueUID()); - + 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"); + else + // Potentialy this is a post-processed image + // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); + + // 'Media Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop); + // '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()); // 'Implementation Version Name' @@ -1263,7 +1356,25 @@ void FileHelper::CheckMandatoryElements() << highBitPosition << " to " << nbBitsAllocated-1 << " for consistency purpose"); } - // --- Check UID-related Entries --- + + std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); + if ( pixelSpacing == GDCM_UNKNOWN ) + pixelSpacing = "1.0\\1.0"; + else + // if missing, Pixel Spacing forced to "1.0\1.0" + CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + + // '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); + + // 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 @@ -1273,73 +1384,155 @@ void FileHelper::CheckMandatoryElements() if ( e_0008_0016 ) { // Create 'Source Image Sequence' SeqEntry - SeqEntry *sis = new SeqEntry ( + SeqEntry *sis = SeqEntry::New ( Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) ); - SQItem *sqi = new SQItem(1); + SQItem *sqi = SQItem::New(1); // (we assume 'SOP Instance UID' exists too) // create 'Referenced SOP Class UID' - DataEntry *e_0008_1150 = new DataEntry( + 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 = new DataEntry( + 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(); - sis->AddSQItem(sqi,1); // temporarily replaces any previous 'Source Image Sequence' Archive->Push(sis); + sis->Delete(); - // 'Image Type' (The written image is no longer an 'ORIGINAL' one) + // 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"); - } - else - { - // There was no 'SOP Class UID'. - // the source image was NOT a true Dicom one. - // We consider the image is a 'Secondary Capture' one - // SOP Class UID - // [Secondary Capture Image Storage] - SetMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7"); + } -// ---- The user will never have to take any action on the following ----. + // 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) + + // Conversion Type. + // Other possible values are : + // See PS 3.3, Page 408 + + // 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"); + } + + // ---- The user will never have to take any action on the following ---- + // new value for 'SOP Instance UID' - SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); + //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID()); // Instance Creation Date - CopyMandatoryEntry(0x0008,0x0012,Util::GetCurrentDate().c_str()); + const std::string &date = Util::GetCurrentDate(); + CopyMandatoryEntry(0x0008,0x0012,date); // Instance Creation Time - CopyMandatoryEntry(0x0008,0x0013,Util::GetCurrentTime().c_str()); + const std::string &time = Util::GetCurrentTime(); + CopyMandatoryEntry(0x0008,0x0013,time); -// ----- 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 -// Entries whose type is 2 are mandatory, with a optional value -// Entries whose type is 2c are mandatory-inside-a-Sequence -// Entries whose type is 3 are optional + // Study Date + CopyMandatoryEntry(0x0008,0x0020,date); + // Study Time + CopyMandatoryEntry(0x0008,0x0030,time); - // 'Serie Instance UID' - // Keep the value if exists - // The user is allowed to create his own Series, - // keeping the same 'Serie Instance UID' for various images - // The user shouldn't add any image to a 'Manufacturer Serie' - // but there is no way no to allowed him to do that - CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); + // Accession Number + //CopyMandatoryEntry(0x0008,0x0050,""); + CheckMandatoryEntry(0x0008,0x0050,""); + + + // ----- 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 // The user is allowed to create his own Study, // keeping the same 'Study Instance UID' for various images // The user may add images to a 'Manufacturer Study', - // adding new series to an already existing Study + // adding new Series to an already existing Study CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); + // 'Serie Instance UID' + // Keep the value if exists + // The user is allowed to create his own Series, + // keeping the same 'Serie Instance UID' for various images + // The user shouldn't add any image to a 'Manufacturer Serie' + // but there is no way no to prevent him for doing that + CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); + + // Study ID + CheckMandatoryEntry(0x0020,0x0010,""); + + // Series Number + CheckMandatoryEntry(0x0020,0x0011,""); + + // Instance Number + CheckMandatoryEntry(0x0020,0x0013,""); + + // 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); + else + CheckMandatoryEntry(0x0020,0x0020,""); + // Modality : if missing we set it to 'OTher' CheckMandatoryEntry(0x0008,0x0060,"OT"); @@ -1352,6 +1545,9 @@ void FileHelper::CheckMandatoryElements() // Patient's Name : if missing, we set it to 'GDCM^Patient' CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient"); + // Patient ID + CheckMandatoryEntry(0x0010,0x0020,""); + // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0010,0x0030,""); @@ -1360,9 +1556,6 @@ void FileHelper::CheckMandatoryElements() // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0008,0x0090,""); - - // Pixel Spacing : defaulted to 1.0\1.0 - CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); // Remove some inconstencies (probably some more will be added) @@ -1372,8 +1565,26 @@ void FileHelper::CheckMandatoryElements() DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { - Archive->Push(0x0020, 0X0052); + 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) + { + 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 +*/ } void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value) @@ -1381,17 +1592,19 @@ void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string va DataEntry *entry = FileInternal->GetDataEntry(group,elem); if ( !entry ) { - entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); entry->SetString(value); Archive->Push(entry); + entry->Delete(); } } void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value) { - DataEntry *entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); + DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem)); entry->SetString(value); Archive->Push(entry); + entry->Delete(); } void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value) @@ -1399,6 +1612,7 @@ void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string val DataEntry *entry = CopyDataEntry(group,elem); entry->SetString(value); Archive->Push(entry); + entry->Delete(); } /** @@ -1418,6 +1632,8 @@ 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); @@ -1434,7 +1650,6 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000d); Archive->Restore(0x0020,0x000e); - } //----------------------------------------------------------------------------- @@ -1445,7 +1660,8 @@ void FileHelper::RestoreWriteMandatory() void FileHelper::Initialize() { UserFunction = 0; - + KeepMediaStorageSOPClassUID = false; + WriteMode = WMODE_RAW; WriteType = ExplicitVR;