X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=7e7be8e5a5b93d2823e73fb440c20e264f622466;hb=9077bb6ff1cc18470cdb173327773c9130ba5f70;hp=ba19abe3c21d58dc76f9404ff4de00fbcdf3e788;hpb=e44d10c8d84ca2c03a5fff4916470315038fcb50;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index ba19abe3..7e7be8e5 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/12/15 13:35:38 $ - Version: $Revision: 1.87 $ + Date: $Date: 2006/03/29 16:09:48 $ + Version: $Revision: 1.98 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,12 +26,17 @@ #include "gdcmSeqEntry.h" #include "gdcmSQItem.h" #include "gdcmDataEntry.h" +#include "gdcmDocEntry.h" #include "gdcmFile.h" #include "gdcmPixelReadConvert.h" #include "gdcmPixelWriteConvert.h" #include "gdcmDocEntryArchive.h" #include "gdcmDictSet.h" #include "gdcmOrientation.h" + +#if defined(__BORLANDC__) + #include // for memset +#endif #include @@ -69,7 +74,7 @@ fh->SetImageData( userPixels, userPixelsLength); fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB // (WriteMode is set) -fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation +fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation // Little Endian is the default // no other value is allowed (-->SetWriteType(ExplicitVR);) @@ -233,7 +238,7 @@ bool FileHelper::Load() * \return false if DataEntry not found */ bool FileHelper::SetEntryString(std::string const &content, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem) { return FileInternal->SetEntryString(content, group, elem); } @@ -249,7 +254,7 @@ bool FileHelper::SetEntryString(std::string const &content, * \return false if DataEntry not found */ bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, - uint16_t group, uint16_t elem) + uint16_t group, uint16_t elem) { return FileInternal->SetEntryBinArea(content, lgth, group, elem); } @@ -281,7 +286,7 @@ DataEntry *FileHelper::InsertEntryString(std::string const &content, * 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); } @@ -377,7 +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 () { @@ -386,7 +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 @@ -394,7 +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 @@ -403,12 +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) @@ -656,15 +661,44 @@ bool FileHelper::WriteAcr (std::string const &fileName) */ bool FileHelper::Write(std::string const &fileName) { + 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; + case ACR: case ACR_LIBIDO: // NOTHING is done here just for LibIDO. @@ -678,11 +712,13 @@ bool FileHelper::Write(std::string const &fileName) 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(); // -------------------------------------------------------------- @@ -762,6 +798,7 @@ bool FileHelper::CheckWriteIntegrity() size_t decSize = FileInternal->GetXSize() * FileInternal->GetYSize() * FileInternal->GetZSize() + * FileInternal->GetTSize() * FileInternal->GetSamplesPerPixel() * ( numberBitsAllocated / 8 ); size_t rgbSize = decSize; @@ -996,7 +1033,7 @@ 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() { @@ -1010,6 +1047,9 @@ void FileHelper::SetWriteFileTypeToJPEG() tss->Delete(); } +/** + * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian" + */ void FileHelper::SetWriteFileTypeToExplicitVR() { std::string ts = Util::DicomString( @@ -1017,7 +1057,6 @@ void FileHelper::SetWriteFileTypeToExplicitVR() DataEntry *tss = CopyDataEntry(0x0002,0x0010); tss->SetString(ts); - Archive->Push(tss); tss->Delete(); } @@ -1032,7 +1071,6 @@ void FileHelper::SetWriteFileTypeToImplicitVR() DataEntry *tss = CopyDataEntry(0x0002,0x0010); tss->SetString(ts); - Archive->Push(tss); tss->Delete(); } @@ -1183,22 +1221,86 @@ 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. + + +1) +'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image). + +1)3) +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) are set to + [Secondary Capture Image Storage] +'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" +Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image) + +2)4) +If 'SOP Class UID' exists in the native image ('true DICOM' image) + we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112) + --> 'Referenced SOP Class UID' (0x0008, 0x1150) + whose value is the original 'SOP Class UID' + --> 'Referenced SOP Instance UID' (0x0008, 0x1155) + whose value is the original 'SOP Class UID' + +3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images + or the Series, (or the Study ?) he used to created his image + (MIP, MPR, cartography image, ...) + These info should be stored (?) + 0008 1110 SQ 1 Referenced Study Sequence + 0008 1115 SQ 1 Referenced Series Sequence + 0008 1140 SQ 1 Referenced Image Sequence + +4) When user *knows* he didn't modified the pixels, we keep some informations unchanged : +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) +'Image Type' (0x0008,0x0008) +'Conversion Type' (0x0008,0x0064) + + +Bellow follows the full description (hope so !) of the consistency checks performed +by gdcm::FileHelper::CheckMandatoryElements() -->'Media Storage SOP Class UID' (0x0002,0x0002) --->'SOP Class UID' (0x0008,0x0016) are set to +-->'SOP Class UID' (0x0008,0x0016) are defaulted to [Secondary Capture Image Storage] - (Potentialy, the image was modified by user, and post-processed; - it's no longer a 'native' image) - Except if user told he wants to keep MediaStorageSOPClassUID, - when *he* knows he didn't modify the image (e.g. : he just anonymized the file) - --> 'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY" (The written image is no longer an 'ORIGINAL' one) - Except if user told he wants to keep MediaStorageSOPClassUID, - when *he* knows he didn't modify the image (e.g. : he just anonymized the file) - + Except if user knows he didn't modify the image (e.g. : he just anonymized the file) + + --> Conversion Type (0x0008,0x0064) + is defaulted to 'SYN' (Synthetic Image) + when *he* knows he created his own image ex nihilo + --> 'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing. (a fully user created image belongs to *no* modality) @@ -1228,16 +1330,17 @@ To be moved to User's guide / WIKI ? --> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency --> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0" --> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale) + --> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value ---> Instance Creation Date, Instance Creation Time, Study Date, Study Time - are force to current Date and Time - ---> Conversion Type (0x0008,0x0064) - is forced to 'SYN' (Synthetic Image) +--> Instance Creation Date, Instance Creation Time are forced to current Date and Time + +--> Study Date, Study Time are defaulted to current Date and Time + (they remain unchanged if they exist) --> Patient Orientation : (0x0020,0x0020), if not present, is deduced from - Image Orientation (Patient) : (0020|0037) + Image Orientation (Patient) : (0020|0037) or from + Image Orientation (RET) : (0020 0035) --> Study ID, Series Number, Instance Number, Patient Orientation (Type 2) are created, with empty value if there are missing. @@ -1247,14 +1350,15 @@ 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 ) { @@ -1275,7 +1379,7 @@ 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); @@ -1283,21 +1387,24 @@ void FileHelper::CheckMandatoryElements() Archive->Push(e_0002_0001); e_0002_0001->Delete(); - if ( KeepMediaStorageSOPClassUID) - // It up to the use to *know* whether he modified the pixels or not. - // he is allowed to keep the original 'Media Storage SOP Class UID' - CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); + if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE) + { + // we keep the original 'Media Storage SOP Class UID', we default it if missing + CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); + } else - // Potentialy this is a post-processed image + { + // It's *not* an image comming straight from a source. We force // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage] - CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); - + CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7"); + } + // '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 (?) + // seems to be Root UID + 4 digits (?) CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID()); // 'Implementation Version Name' @@ -1306,6 +1413,20 @@ void FileHelper::CheckMandatoryElements() CopyMandatoryEntry(0x0002,0x0013,version); } + // --------------------- For DataSet --------------------- + + 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"); + } + 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"); + } + // Push out 'LibIDO-special' entries, if any Archive->Push(0x0028,0x0015); Archive->Push(0x0028,0x0016); @@ -1367,22 +1488,26 @@ void FileHelper::CheckMandatoryElements() // '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 + 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); + 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) + + if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image + { + // 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 ) - { + + 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) ); @@ -1410,47 +1535,21 @@ void FileHelper::CheckMandatoryElements() Archive->Push(sis); sis->Delete(); - // 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"); - - } + // 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"); + } + } // 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) + if ( ContentType == USER_OWN_IMAGE) + { // Conversion Type. // Other possible values are : // See PS 3.3, Page 408 @@ -1463,12 +1562,19 @@ void FileHelper::CheckMandatoryElements() // SI = Scanned Image // DRW = Drawing // SYN = Synthetic Image - - CheckMandatoryEntry(0x0008,0x0064,"SYN"); - } - // ---- The user will never have to take any action on the following ---- + CheckMandatoryEntry(0x0008,0x0064,"SYN"); // 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()); @@ -1481,9 +1587,9 @@ void FileHelper::CheckMandatoryElements() CopyMandatoryEntry(0x0008,0x0013,time); // Study Date - CopyMandatoryEntry(0x0008,0x0020,date); + CheckMandatoryEntry(0x0008,0x0020,date); // Study Time - CopyMandatoryEntry(0x0008,0x0030,time); + CheckMandatoryEntry(0x0008,0x0030,time); // Accession Number //CopyMandatoryEntry(0x0008,0x0050,""); @@ -1529,11 +1635,14 @@ void FileHelper::CheckMandatoryElements() gdcm::Orientation *o = gdcm::Orientation::New(); std::string ori = o->GetOrientation ( FileInternal ); o->Delete(); - if (ori != "\\" ) + if (ori != "\\" && ori != GDCM_UNFOUND) CheckMandatoryEntry(0x0020,0x0020,ori); else CheckMandatoryEntry(0x0020,0x0020,""); - + + // Default Patient Position to HFS + CheckMandatoryEntry(0x0018,0x5100,"HFS"); + // Modality : if missing we set it to 'OTher' CheckMandatoryEntry(0x0008,0x0060,"OT"); @@ -1557,21 +1666,11 @@ void FileHelper::CheckMandatoryElements() // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory CheckMandatoryEntry(0x0008,0x0090,""); - - // Remove some inconstencies (probably some more will be added) - // if (0028 0008)Number of Frames exists - // Push out (0020 0052),Frame of Reference UID - // (only meaningfull within a Serie) - DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008); - if ( !e_0028_0008 ) - { - Archive->Push(0x0020, 0x0052); - } - + /* // Deal with element 0x0000 (group length) of each group. // First stage : get all the different Groups - /* + GroupHT grHT; DocEntry *d = FileInternal->GetFirstEntry(); while(d) @@ -1585,7 +1684,8 @@ void FileHelper::CheckMandatoryElements() CheckMandatoryEntry(it->first, 0x0000, "0"); } // Third stage : update all 'zero level' groups length -*/ +*/ + } void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value) @@ -1689,7 +1789,7 @@ void FileHelper::CallEndMethod() void FileHelper::Initialize() { UserFunction = 0; - KeepMediaStorageSOPClassUID = false; + ContentType = USER_OWN_IMAGE; WriteMode = WMODE_RAW; WriteType = ExplicitVR;