X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=src%2FgdcmFileHelper.cxx;h=c44839ede63fad2fd032506a68d3eb7c7f13e641;hb=33b1eec26f02131242fbfdef52184b24763cf4e6;hp=40dd9d0b647efe8d463d4edbe2a1eb0f98585102;hpb=3b2424c25301a49dc03fc708c093ca76b2cd6fc8;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 40dd9d0b..c44839ed 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/10/27 17:25:04 $ - Version: $Revision: 1.77 $ + Date: $Date: 2005/11/29 17:21:35 $ + Version: $Revision: 1.84 $ 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 @@ -113,6 +114,7 @@ fh1->Write(newFileName); namespace gdcm { +typedef std::map GroupHT; // Hash Table //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -157,7 +159,7 @@ FileHelper::FileHelper(File *header) Initialize(); if ( FileInternal->IsReadable() ) { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); + PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); } } @@ -218,18 +220,17 @@ 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) @@ -239,14 +240,13 @@ bool FileHelper::SetEntryString(std::string const &content, /** - * \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) @@ -255,12 +255,12 @@ bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth, } /** - * \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, @@ -270,14 +270,14 @@ 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, @@ -287,11 +287,11 @@ DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth, } /** - * \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) @@ -1146,10 +1146,10 @@ 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 @@ -1157,7 +1157,8 @@ 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, @@ -1167,7 +1168,8 @@ 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 ...) @@ -1182,16 +1184,21 @@ DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, 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) @@ -1209,26 +1216,29 @@ 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) --> 'Referenced SOP Class UID' (0x0008, 0x1150) whose value is the original 'SOP Class UID' - ---> 'Referenced SOP Instance UID' (0x0008, 0x1155) + --> '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. @@ -1265,22 +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(); + e_0002_0001->Delete(); - // 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"); - + 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' @@ -1340,17 +1357,24 @@ void FileHelper::CheckMandatoryElements() << " for consistency purpose"); } - // Imager Pixel Spacing : defaulted to 1.0\1.0 - // --> This one is the *legal* one ! - CheckMandatoryEntry(0x0018,0x1164,"1.0\\1.0"); - // Pixel Spacing : defaulted to 1.0\1.0 - CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); + 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 --- + // --- Check UID-related Entries --- // If 'SOP Class UID' exists ('true DICOM' image) // we create the 'Source Image Sequence' SeqEntry @@ -1387,9 +1411,16 @@ void FileHelper::CheckMandatoryElements() 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) + 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"); + } // At the end, not to overwrite the original ones, @@ -1397,12 +1428,47 @@ void FileHelper::CheckMandatoryElements() // '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 ----. + // 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()); @@ -1420,41 +1486,25 @@ void FileHelper::CheckMandatoryElements() CopyMandatoryEntry(0x0008,0x0030,time); // Accession Number - CopyMandatoryEntry(0x0008,0x0050,""); + //CopyMandatoryEntry(0x0008,0x0050,""); + CheckMandatoryEntry(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 - // 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 // 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' @@ -1462,7 +1512,7 @@ void FileHelper::CheckMandatoryElements() // 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 + // but there is no way no to prevent him for doing that CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID()); // Study ID @@ -1473,9 +1523,16 @@ void FileHelper::CheckMandatoryElements() // Instance Number CheckMandatoryEntry(0x0020,0x0013,""); - - // Patient Orientation FIXME 1\0\0\0\1\0 or empty ? - CheckMandatoryEntry(0x0020,0x0020,""); + + // Patient Orientation + // Can be computed from (0020|0037) : Image Orientation (Patient) + gdcm::Orientation *o = gdcm::Orientation::New(); + std::string ori = o->GetOrientation ( FileInternal ); + o->Delete(); + if (ori != "\\" ) + CheckMandatoryEntry(0x0020,0x0020,ori); + else + CheckMandatoryEntry(0x0020,0x0020,""); // Modality : if missing we set it to 'OTher' CheckMandatoryEntry(0x0008,0x0060,"OT"); @@ -1511,6 +1568,24 @@ void FileHelper::CheckMandatoryElements() { 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) @@ -1558,6 +1633,8 @@ 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); @@ -1584,7 +1661,8 @@ void FileHelper::RestoreWriteMandatory() void FileHelper::Initialize() { UserFunction = 0; - + KeepMediaStorageSOPClassUID = false; + WriteMode = WMODE_RAW; WriteType = ExplicitVR;