X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src%2FgdcmFileHelper.cxx;h=8bae1e02d661d26fd95595673ec49053944d8a5a;hb=7e9cd288c8f2138a56699721b33e572a6422d128;hp=49a6e9e315257d0ada7e5c8aae54c3aa4c5c9f6a;hpb=700d680181fa969f44a880211b0216884b518b61;p=gdcm.git diff --git a/src/gdcmFileHelper.cxx b/src/gdcmFileHelper.cxx index 49a6e9e3..8bae1e02 100644 --- a/src/gdcmFileHelper.cxx +++ b/src/gdcmFileHelper.cxx @@ -4,8 +4,8 @@ Module: $RCSfile: gdcmFileHelper.cxx,v $ Language: C++ - Date: $Date: 2005/11/07 09:50:52 $ - Version: $Revision: 1.79 $ + Date: $Date: 2006/01/19 11:46:45 $ + Version: $Revision: 1.88 $ 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 /** @@ -158,7 +159,7 @@ FileHelper::FileHelper(File *header) Initialize(); if ( FileInternal->IsReadable() ) { - PixelReadConverter->GrabInformationsFromFile( FileInternal ); + PixelReadConverter->GrabInformationsFromFile( FileInternal, this ); } } @@ -219,18 +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) @@ -240,14 +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) @@ -256,12 +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, @@ -271,14 +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, @@ -288,11 +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) @@ -1147,10 +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 + * 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 @@ -1159,6 +1158,7 @@ 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 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, @@ -1168,7 +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 ...) @@ -1182,6 +1183,73 @@ 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. +-2) user modified the pixels of an existing image. +-3) user created a new image, using existing images (eg MIP, MPR, cartography image) +-4) user anonymized an image without processing the pixels. + +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 allowed him to do that + + None of the 'shadow elements' are droped out. + + +1) +'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing. +'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image). +'Study Date', 'Study Time' are defaulted to current Date and Time. + +1)2)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, he may ask the writer to keep some +informations unchanged : +'Media Storage SOP Class UID' (0x0002,0x0002) +'SOP Class UID' (0x0008,0x0016) +'Image Type' (0x0008,0x0008) +'Conversion Type' (0x0008,0x0064) +He has to use gdcm::FileHelper::SetKeepMediaStorageSOPClassUID(true) +(probabely name has to be changed) + + +Bellow follows the full description (hope so !) of the consistency checks performed +by gdcm::FileHelper::CheckMandatoryElements() -->'Media Storage SOP Class UID' (0x0002,0x0002) @@ -1197,7 +1265,12 @@ To be moved to User's guide / WIKI ? (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) - + + --> Conversion Type (0x0008,0x0064) + is forced to 'SYN' (Synthetic 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) + --> 'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing. (a fully user created image belongs to *no* modality) @@ -1227,16 +1300,17 @@ 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. @@ -1357,19 +1431,19 @@ void FileHelper::CheckMandatoryElements() } std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030); - if ( pixelSpacing == GDCM_UNKNOWN ) + if ( pixelSpacing == GDCM_UNFOUND ) + { pixelSpacing = "1.0\\1.0"; - else // if missing, Pixel Spacing forced to "1.0\1.0" - CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0"); - + CopyMandatoryEntry(0x0028,0x0030,pixelSpacing); + } + // '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) - + // an imager (see also 0008,0x0064) CheckMandatoryEntry(0x0018,0x1164,pixelSpacing); - + // Samples Per Pixel (type 1) : default to grayscale CheckMandatoryEntry(0x0028,0x0002,"1"); @@ -1480,9 +1554,9 @@ 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,""); @@ -1525,8 +1599,9 @@ void FileHelper::CheckMandatoryElements() // Patient Orientation // Can be computed from (0020|0037) : Image Orientation (Patient) - gdcm::Orientation o; - std::string ori = o.GetOrientation ( FileInternal ); + gdcm::Orientation *o = gdcm::Orientation::New(); + std::string ori = o->GetOrientation ( FileInternal ); + o->Delete(); if (ori != "\\" ) CheckMandatoryEntry(0x0020,0x0020,ori); else @@ -1566,15 +1641,16 @@ 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=input->GetFirstEntry(); + DocEntry *d = FileInternal->GetFirstEntry(); while(d) { grHT[d->GetGroup()] = 0; - d=input->GetNextEntry(); + d=FileInternal->GetNextEntry(); } // Second stage : add the missing ones (if any) for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it) @@ -1582,7 +1658,7 @@ 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) @@ -1650,6 +1726,34 @@ void FileHelper::RestoreWriteMandatory() Archive->Restore(0x0020,0x000e); } + +/** + * \brief CallStartMethod + */ +void FileHelper::CallStartMethod() +{ + Progress = 0.0f; + Abort = false; + CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS); +} + +/** + * \brief CallProgressMethod + */ +void FileHelper::CallProgressMethod() +{ + CommandManager::ExecuteCommand(this,CMD_PROGRESS); +} + +/** + * \brief CallEndMethod + */ +void FileHelper::CallEndMethod() +{ + Progress = 1.0f; + CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS); +} + //----------------------------------------------------------------------------- // Private /**