X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=0d5cd3312282e3eac92df06859f1b282e92515a6;hb=8932b26860546fddfa6d5805c075aab116b93bd4;hp=1b454c60de9f0534104818aa9eadddb932910319;hpb=1d9ac5cec02b9daa18b16835882b531731b125ad;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 1b454c60..0d5cd331 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 12:58:28 $ - Version: $Revision: 1.62 $ + Date: $Date: 2005/10/25 12:42:01 $ + Version: $Revision: 1.73 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -100,7 +100,7 @@ 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) @@ -161,20 +161,20 @@ FileHelper::FileHelper(File *header) } #ifndef GDCM_LEGACY_REMOVE -/** - * \brief DEPRECATED : use SetFilename() + SetLoadMode() + Load() methods +/* + * 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 + * 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 + * param filename file to be opened for parsing + * deprecated use SetFilename() + Load() methods */ FileHelper::FileHelper(std::string const &filename ) { @@ -222,8 +222,7 @@ 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 +350,7 @@ 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 +366,15 @@ 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 +402,14 @@ 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 +418,8 @@ 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 +427,7 @@ 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 +436,12 @@ 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) @@ -708,6 +711,10 @@ bool FileHelper::Write(std::string const &fileName) SetWriteFileTypeToACR(); // SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR ! break; + case JPEG: + SetWriteFileTypeToJPEG(); + std::cerr << "Writting as JPEG" << std::endl; + break; } CheckMandatoryElements(); @@ -741,6 +748,7 @@ bool FileHelper::Write(std::string const &fileName) } bool check = CheckWriteIntegrity(); // verifies length + if (WriteType == JPEG ) check = true; if (check) { check = FileInternal->Write(fileName,WriteType); @@ -859,6 +867,9 @@ void FileHelper::SetWriteToRaw() Archive->Push(photInt); Archive->Push(pixel); + + photInt->Delete(); + pixel->Delete(); } } @@ -911,6 +922,11 @@ 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); @@ -939,6 +955,10 @@ void FileHelper::SetWriteToRGB() Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); + + bitsAlloc->Delete(); + bitsStored->Delete(); + highBit->Delete(); } } else @@ -1011,6 +1031,18 @@ 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( @@ -1020,6 +1052,7 @@ void FileHelper::SetWriteFileTypeToExplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } /** @@ -1034,6 +1067,7 @@ void FileHelper::SetWriteFileTypeToImplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } @@ -1056,8 +1090,8 @@ 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); @@ -1067,11 +1101,15 @@ 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(); } /** @@ -1087,6 +1125,7 @@ void FileHelper::SetWriteToNoLibido() DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString(""); Archive->Push(libidoCode); + libidoCode->Delete(); } } } @@ -1127,7 +1166,7 @@ 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 @@ -1152,6 +1191,14 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, * 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. + * \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 @@ -1163,9 +1210,74 @@ 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) + +--> 'Image Type' (0x0008,0x0008) + is forced to "DERIVED\PRIMARY" + (The written image is no longer an 'ORIGINAL' one) + +--> '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) + +--> 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' + +--> 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 ) { @@ -1192,14 +1304,15 @@ void FileHelper::CheckMandatoryElements() 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"); + // Potentialy post-processed image --> [Secondary Capture Image Storage] + // 'Media Storage SOP Class UID' + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - // 'Media Stored SOP Instance UID' - CopyMandatoryEntry(0x0002,0x0003,Util::CreateUniqueUID()); - + // 'Media Storage SOP Instance UID' + CopyMandatoryEntry(0x0002,0x0003,sop); + // 'Implementation Class UID' CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); @@ -1259,6 +1372,14 @@ void FileHelper::CheckMandatoryElements() << highBitPosition << " to " << nbBitsAllocated-1 << " for consistency purpose"); } + + // 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) @@ -1269,19 +1390,19 @@ 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); // (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); // 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); @@ -1289,36 +1410,64 @@ void FileHelper::CheckMandatoryElements() sis->AddSQItem(sqi,1); // 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"); - } - 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"); } + // 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); + + // 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 ----. // 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); + + // Study Date + CopyMandatoryEntry(0x0008,0x0020,date); + // Study Time + CopyMandatoryEntry(0x0008,0x0030,time); + + // Accession Number + CopyMandatoryEntry(0x0008,0x0050,""); + + // Conversion Type ... FIXME (type 1) + // See PS 3.3, Page 408 + 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 -// 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 + // 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 + CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); // 'Serie Instance UID' // Keep the value if exists @@ -1328,14 +1477,18 @@ void FileHelper::CheckMandatoryElements() // but there is no way no to allowed him to do that CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); - // '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 - CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID()); + // Study ID + CheckMandatoryEntry(0x0020,0x0010,""); + + // Series Number + CheckMandatoryEntry(0x0020,0x0011,""); + // Instance Number + CheckMandatoryEntry(0x0020,0x0013,""); + + // Patient Orientation FIXME 1\0\0\0\1\0 or empty ? + CheckMandatoryEntry(0x0020,0x0020,""); + // Modality : if missing we set it to 'OTher' CheckMandatoryEntry(0x0008,0x0060,"OT"); @@ -1348,6 +1501,9 @@ 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,""); @@ -1356,9 +1512,6 @@ 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) @@ -1368,7 +1521,7 @@ void FileHelper::CheckMandatoryElements() DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { - Archive->Push(0x0020, 0X0052); + Archive->Push(0x0020, 0x0052); } } @@ -1377,17 +1530,19 @@ 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) @@ -1395,6 +1550,7 @@ 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(); } /** @@ -1430,7 +1586,6 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000d); Archive->Restore(0x0020,0x000e); - } //-----------------------------------------------------------------------------