X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=e2326b53faf0abf8d6af3649d64fcfa207fd5c36;hb=b08873f37c7696af28217a92f2ee41bf76e98a63;hp=e014d45510db3ae4c4e3cd94faddb77789499838;hpb=1db7fb8e0037a6797c113bd13c33461c7aa9cc78;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index e014d455..e2326b53 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/10/23 15:24:47 $ - Version: $Revision: 1.69 $ + Date: $Date: 2005/10/26 08:28:58 $ + Version: $Revision: 1.76 $ 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) @@ -130,8 +130,7 @@ namespace gdcm */ FileHelper::FileHelper( ) { - FileInternal = new File( ); - SelfHeader = true; + FileInternal = File::New( ); Initialize(); } @@ -151,44 +150,16 @@ 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 +181,7 @@ FileHelper::~FileHelper() delete Archive; } - if ( SelfHeader ) - { - delete FileInternal; - } - FileInternal = 0; + FileInternal->Unregister(); } //----------------------------------------------------------------------------- @@ -374,6 +341,7 @@ size_t FileHelper::GetImageDataRawSize() * - 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() @@ -408,6 +376,7 @@ uint8_t *FileHelper::GetImageData() * - 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 () @@ -865,6 +834,9 @@ void FileHelper::SetWriteToRaw() Archive->Push(photInt); Archive->Push(pixel); + + photInt->Delete(); + pixel->Delete(); } } @@ -917,6 +889,11 @@ 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); @@ -945,6 +922,10 @@ void FileHelper::SetWriteToRGB() Archive->Push(bitsAlloc); Archive->Push(bitsStored); Archive->Push(highBit); + + bitsAlloc->Delete(); + bitsStored->Delete(); + highBit->Delete(); } } else @@ -1026,6 +1007,7 @@ void FileHelper::SetWriteFileTypeToJPEG() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } void FileHelper::SetWriteFileTypeToExplicitVR() @@ -1037,6 +1019,7 @@ void FileHelper::SetWriteFileTypeToExplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } /** @@ -1051,6 +1034,7 @@ void FileHelper::SetWriteFileTypeToImplicitVR() tss->SetString(ts); Archive->Push(tss); + tss->Delete(); } @@ -1073,8 +1057,8 @@ 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); @@ -1084,11 +1068,15 @@ 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(); } /** @@ -1104,6 +1092,7 @@ void FileHelper::SetWriteToNoLibido() DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010); libidoCode->SetString(""); Archive->Push(libidoCode); + libidoCode->Delete(); } } } @@ -1144,7 +1133,7 @@ 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 @@ -1169,6 +1158,14 @@ 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 @@ -1180,6 +1177,69 @@ 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' (Synthetic Image) + +--> 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() { @@ -1211,6 +1271,7 @@ void FileHelper::CheckMandatoryElements() false); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); + e_0002_0001->Delete(); // Potentialy post-processed image --> [Secondary Capture Image Storage] // 'Media Storage SOP Class UID' @@ -1278,6 +1339,14 @@ 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) @@ -1288,27 +1357,34 @@ 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(); + // 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"); } @@ -1328,10 +1404,38 @@ void FileHelper::CheckMandatoryElements() //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. + // 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 + + // FIXME : Must we Force Value, or Default value ? + // Is it Type 1 for any Modality ? + // --> Answer seems to be NO :-( + CopyMandatoryEntry(0x0008,0x0064,"SYN"); // ----- Add Mandatory Entries if missing --- // Entries whose type is 1 are mandatory, with a mandatory value @@ -1357,6 +1461,18 @@ void FileHelper::CheckMandatoryElements() // 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()); + + // 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"); @@ -1370,6 +1486,9 @@ 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,""); @@ -1378,9 +1497,6 @@ 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) @@ -1390,7 +1506,7 @@ void FileHelper::CheckMandatoryElements() DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); if ( !e_0028_0008 ) { - Archive->Push(0x0020, 0X0052); + Archive->Push(0x0020, 0x0052); } } @@ -1399,17 +1515,19 @@ 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) @@ -1417,6 +1535,7 @@ 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(); } /** @@ -1452,7 +1571,6 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000d); Archive->Restore(0x0020,0x000e); - } //-----------------------------------------------------------------------------