X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=cfb9a7c3257e3dab13348869ee806bfaec70c7ef;hb=db42e5541964319d882c965dc6d0284806ff0489;hp=94487717bc9c786e8fb7ecb7a064e70fb2ca7890;hpb=7fd1222c03038e650429f10a908d8dfac8b9c462;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 94487717..cfb9a7c3 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/11/03 08:46:03 $ - Version: $Revision: 1.78 $ + 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 @@ -114,6 +114,7 @@ fh1->Write(newFileName); namespace gdcm { +typedef std::map GroupHT; // Hash Table //------------------------------------------------------------------------- // Constructor / Destructor /** @@ -1148,8 +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 @@ -1158,7 +1159,7 @@ 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, @@ -1183,16 +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) @@ -1210,7 +1216,6 @@ 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) @@ -1223,7 +1228,7 @@ 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 1.0\1.0 +--> 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 @@ -1276,19 +1281,23 @@ void FileHelper::CheckMandatoryElements() false); e_0002_0001->SetLength(2); Archive->Push(e_0002_0001); - e_0002_0001->Delete(); + e_0002_0001->Delete(); - // FIXME : we should allow user to tell he *wants* to keep the original - // 'Media Storage 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' + 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"); - + 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' @@ -1348,18 +1357,24 @@ void FileHelper::CheckMandatoryElements() << " for consistency purpose"); } - // Imager Pixel Spacing : defaulted to 1.0\1.0 - // --> 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,"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 @@ -1396,9 +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, @@ -1406,12 +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()); @@ -1432,34 +1489,15 @@ void FileHelper::CheckMandatoryElements() //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 :-( - // FIXME : we should write it only when we are *sure* the image - // *does not* come from an imager (see also 0018,0x1164) - 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 @@ -1529,6 +1567,24 @@ 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) @@ -1576,6 +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); @@ -1602,7 +1660,8 @@ void FileHelper::RestoreWriteMandatory() void FileHelper::Initialize() { UserFunction = 0; - + KeepMediaStorageSOPClassUID = false; + WriteMode = WMODE_RAW; WriteType = ExplicitVR;