X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Doc%2FWebsite%2FNews.html;h=4958c06bb6402f1dc0c55323472da0478acaeadf;hb=0ee1d8c4c2c59be9b1ff698b219835a76ac86f2a;hp=5c61e98a3f0c7569864a612924e56e6adec2eddb;hpb=5d500da6efca5f90d38223dbb65f7f521a276a1a;p=gdcm.git diff --git a/Doc/Website/News.html b/Doc/Website/News.html index 5c61e98a..4958c06b 100644 --- a/Doc/Website/News.html +++ b/Doc/Website/News.html @@ -8,10 +8,10 @@ - +

Gdcm News

- +

@@ -21,89 +21,605 @@ We know the following are missing; don't loose time looking for them ...
We know they could be helpfull. We shall add them some day.
Any contribution is welcome. -

gdcm doesn't read yet JPEG-LS and JPEG2000 encoded files. -
Allow user to tell gdcm::Document constructor he doesn't - want to deal with SeqEntry Allow user to tell gdcm::Document constructor he doesn't - want to deal with Shadow groups -
Allow user to tell gdcm::Document constructor he just wants - to load a given list of DocEntries (to save CPU time and RAM - space) -
Allow user to tell the Writer he doesn't want to write down +
Decoders +
- gdcm doesn't read yet JPEG-LS encoded files. +
  +
- gdcm doesn't read yet MPEG2 encoded files. + +
+
Reader +
- Allow user to tell gdcm::Document constructor he just wants + to load a given list of DocEntries + (to save CPU time and RAM space) +
- Allow 'frame by frame' reading (should be helpfull for huge + multiframe images) +
- Allow subvolume selection / frames selection before reading. +
- Expose Read/Decompression mechanisms to allow user getting + information from DICOMDIR
  -or from his own Data Base- + and reading his images without parsing + the header, one more time. +
+
Writer +
- Allow user to tell the Writer he doesn't want to write down SeqEntry (if any) -
- Allow user to tell the Writer he doesn't want to write down +
- Allow user to tell the Writer he doesn't want to write down Shadow groups (if any) -
- Icon Image management (Read and Write) -
- DICOMDIR full management (not limited to +
- Allow user to tell the Writer he wants to split a + Multiframe image into a serie of + Single frame images. +
- Allow user to tell the Writer he wants to agregate a + Serie of Single frame images into a + Multiframe image. +
+
Reader / Writer +
- Full Icon Image management (Read and Write) +
- Full Overlays management (Read and Write)
  + both for 'ACR-NEMA style' (using groups 0x6000 + and next) and 'DICOM V3 style' (using Sequences) +
+
DICOMDIR +
- DICOMDIR full management (not limited to PATIENT/STUDY/SERIE/IMAGE) -
- Allow user to add an Entry to the default entry list, before +
- Allow user to add an entry (belonging to the file header Dicom + entries)to the default entry list, before making a DICOMDIR from a root directory -
- DICOMDIR anonymiser (Load and Noload mode) -
- 16-bits-LUT full Management -
- User friendly management of Rescale Slope and - Rescale Intercept -
- Allow parsing the Shadow groups against a user supplied - private Dicom Dictionary (pfff!...) -
- An accurate SerieHelper -
+
Allow user to add an entry of his owns (for instance an Icon + to each image, or to each Serie). +

SerieHelper +

An accurate SerieHelper
+ Right now SerieHelper only works on 'bona fide Series', and + breaks on wrongly forged Series.
+ We are still looking for any heuristics... +
A SerieHelper that would use the DICOMDIR (if any) + instead of parsing all the files within the Root Directory +

Other +

16-bits-LUT full Management +
User friendly management of Rescale Slope and + Rescale Intercept.
+ (Well... Maybe it's up to the application to deal with it, not to + gdcm ?) +
Allow manual adjunction / automatic recognition (pfff!...) + of the private Dicom Dictionary + to be used to parse Shadow groups against. +
User friendly way of anonymizing image when Patient's name is + burnt-in within the Pixels :-( +

- Current Version + Current Version (CVS)

Missing Features
State of the art
- - gdcm UML Class Diagram current version. + gdcm UML Class Diagram current version. +
- User Documentation +
- Developper + Documentation +
- New Features + +
  - To be able to use gdcm1.3.x and ITK, developer is now allowed to + choose his own namespace for gdcm at CMake time : see GDCM_NAME_SPACE + option. +
  - JPEG and JPEG2000 compression writting are now available. + see Examples/WriteDicomAsJPEG.cxx and Examples/WriteDicomAsJPEG2000.cxx +
  - To try to make gdcm images PACS usable, user is now allowed to + gdcm what kind of image he wants to write, using :
    + void FileHelper::SetContentType (ImageContentType c);
    + Four different types are identify (probabely more will be added) : +
    - + 1) user created ex nihilo his own image and wants to write it as a Dicom image.
      + c : USER_OWN_IMAGE +
    - + 2) user modified the pixels of an existing image, using mathematical operations.
      + c : FILTERED_IMAGE +
    - + 3) user created a new image, using existing images (eg MIP, MPR, cartography image)
      + c : CREATED_IMAGE +
    - + 4) user modified/added some tags *without processing* the pixels (anonymization, etc)
      + c : UNMODIFIED_PIXELS_IMAGE +
    +
  - Stupid difference between gdcm::ValEntry + and gdcm::BinEntry removed.
    + Only gdcm::DataEntry exist, now. + Should have been considered as a 'Bug Fix'.
    + Actually, it's an API breaking modification ... +
    - + std::string const &DataEntry::GetString() const
      + returns as a string (when possible) the value of the DataEntry +
    - + void DataEntry::SetString(std::string const &value)
      + Sets the 'value' of a DataEntry, passed as a std::string +
    - + void DataEntry::SetBinArea( uint8_t *area, bool self )
      + Sets the value (non string) of the current Dicom DataEntry +
    - + void DataEntry::CopyBinArea( uint8_t *area, uint32_t length )
      + Inserts the value (non string) into the current DataEntry +
    - + void DataEntry::SetValue(const uint32_t &id, const double + &val)
      + Inserts the elementary (non string) value into the current + (multivaluated) DataEntry, at the id> position. +
    - + double DataEntry::GetValue(const uint32_t &id) const
      + returns, as a double one of the values (when entry is + multivaluated), identified by its index id. +
    +
  - + DocEntrySet::GetEntryValue() replaced by + DocEntrySet::GetEntryString()
    +
  - SerieHelper :
    + Add some methods, to split a 'SingleSerieUID' Fileset into + 'Extra Coherent' FileSets.
    + They return a std::map of 'Filesets' (actually : std::vector + of gdcm::File*)
    + The key is the 'Orientation', the 'Position' + or the value of a user choosen 'Tag'
    + - XCoherentFileSetmap SplitOnOrientation(FileList *fileSet); +
    + - XCoherentFileSetmap SplitOnPosition(FileList *fileSet); +
    + - XCoherentFileSetmap SplitOnTagValue(FileList *fileSet, + uint16_t group, uint16_t element); +
    + These methods must be called by user, depending on what he wants + to do, at application time.- *he* only knows what his Series + contain !- +
  - To avoid memory leaks and seg faults the user intended classes + use now a Reference Counter.
    +
    - new() and delete() are replaced by + New() and Delete() +
    - Register() and Unregister() methods are + available. +
    - --> Well ... People from ITK don't seem to agree too much with + that feature.
      + They demand to be allowed to allocate gdcm objects in the stack as + well, not only in the heap. +
    +
  - +
  + +
- API breaking modifications (since previous version) +
  - Stupid difference between gdcm::ValEntry + and gdcm::BinEntry removed.
    + Only gdcm::DataEntry exist, now.
    +
```
+   ValEntry(DictEntry *e);
+   BinEntry(DictEntry *e);
+-->DataEntry *New(uint16_t group,uint16_t elem, VRKey const &vr);
+
+   std::string const &ValEntry::GetValue() const;
+   std::string const &BinEntry::GetValue() const;
+-->std::string const &DataEntry::GetString() const;
+
+   uint8_t *BinEntry::GetBinArea();
+-->uint8_t *DataEntry::GetBinArea();
+
+   void ValEntry::SetValue(std::string const &value);
+   void BinEntry::SetValue(std::string const &value);   
+-->void DataEntry::SetString(std::string const &value);
+
+   void BinEntry::SetBinArea( uint8_t *area, bool self = true );
+-->void DataEntry::SetBinArea( uint8_t *area, bool self = true );
+
+   void ValEntry::CopyValEntry(uint16_t gr, uint16_t el);
+-->void DataEntry::CopyDataEntry(uint16_t gr, uint16_t el, VRKey const &vr);
+
```
    + +
```
+Example :
+
+old way :
+        DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050);
+        if( !p3 ) return false;
+        ContentEntry *entry2 = dynamic_cast(p3);
+        std::string thickness = entry2->GetValue();
+
+new way :
+        DocEntry *p3 = item2->GetDocEntry(0x0018,0x0050);
+        if( !p3 ) return false;
+        DataEntry *entry2 = dynamic_cast(p3);
+        std::string thickness = entry2->GetString();
+
+
```
    + +
  - Avoid tons of CPU time consuming accesses to DICOM Dictionnary +
```
+   DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem);
+-->DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem, 
+                                        const VRKey &vr = GDCM_VRUNKNOWN);
 
+   void FileHelper::CheckMandatoryEntry(uint16_t group, uint16_t elem, std::string value);
+-->void FileHelper::CheckMandatoryEntry(uint16_t group, uint16_t elem, std::string value,
+                                        const VRKey &vr = GDCM_VRUNKNOWN);
+      
+   void FileHelper::SetMandatoryEntry(uint16_t group, uint16_t elem, std::string value);       
+-->void FileHelper::SetMandatoryEntry(uint16_t group, uint16_t elem, std::string value,
+                                      const VRKey &vr = GDCM_VRUNKNOWN);
+
+   void FileHelper::CopyMandatoryEntry(uint16_t group, uint16_t elem, std::string value);      
+-->void FileHelper::CopyMandatoryEntry(uint16_t group, uint16_t elem, std::string value,
+                                       const VRKey &vr = GDCM_VRUNKNOWN);
+
```
    +
  - New features : +
```
+For multivaluated numeric DataEntries
+-->void DataEntry::SetValue(const uint32_t &id,const double &val);
+-->double DataEntry::GetValue(const uint32_t &id) const;
+-->uint32_t DataEntry::GetValueCount() const;
+
+For converting 'Decimal String'
+-->bool GetDSValue(std::vector <double> &valueVector);  
+
```
    + +
  - Avoid too many source file modifications from gdcm1.2 to gdcm1.3 +
```
+use :
+
+#define ValEntry                      DataEntry
+#define BinEntry                      DataEntry
+
+#define GetEntryValue(g,e)            GetEntryString(g,e)
+#define GetEntryForcedAsciiValue(g,e) GetEntryString(g,e)
+
+#define GetValEntry(g,e)              GetDataEntry(g,e)
+#define GetBinEntry(g,e)              GetDataEntry(g,e)
+#define GetValue()                    GetString()
+
+#define InsertValEntry(v,g,e,vr)      InsertEntryString(v,g,e,vr) // warning mind the VR!
+#define InsertBinEntry(b,l,g,e,vr)    InsertEntryBinArea(b,l,g,e,vr)
+
+#define SetValEntry(c,g,e)            SetEntryString(c,g,e)  | !!
+#define SetValEntry(c,en)             SetEntryString(c,en)   | !!
+
+#define SetBinEntry(c,l,en)           SetEntryBinArea(c,l,en)   | !!
+#define SetBinEntry(c,l,g,e)          SetEntryBinArea(c,l,g,e)  | !!
+
+#define NewValEntry(g,e,vr)           NewDataEntry(g,e,vr)
+#define NewBinEntry(g,e,vr)           NewDataEntry(g,e,vr)       
+
+
```
    +
  + +
- Bug fixes +
  - Implicit VR - Big Endian (G.E Private) Transfert Syntax 16 Bits + images are now read correctly. +
  - File::GetZOrigin() returns accurate result in any case. +
  - +
  - +
  + +
- Known Bugs +
  - Use of Implicit Value Representation writting mode may + causes troubles, when there are some SQ belonging to a + Shadow Group.
    + Better you use Explicit Value Representation writting mode ... +
  - Troubles on 'Big endian' processors (i.e. Apple/Motorola, SunSparc + ...) when writting 16 Bits images. +
  - Troubles on 64-bits processors. +
  + +
  
  +
+ + + + + + +
+
+ + Version 1.1 (September 14 2005) +
+
State of the art +
- + gdcm 1.1 UML Class Diagram version. +
- User Documentation +
- Developper + Documentation
- New Features
  - Both vtkgdcmViewer and vtkgdcmViewer2 - are available to allow easy displaying of single/multiframe - GreyLevel/RGB/PaletteColor images +
  - Add the methods + gdcm::Dict:AddDict(std::string fullPathPrivateDictionaryFileName) +
    and
    + gdcm::Dict::RemoveDict(std::string fullPathPrivateDictionaryFileName) +
    + to allow user to choose the 'Private Dictionary' he wants to work with. +
    + One can dream about a better API;
    + This one allow right now anybody to see very easyly if the use + of a given private dicom dictionary is of any help or not. +
    
    +
  - + PrintFile has now a new command line argument manager option :
    + dict=fullPathNamePrivateDictionaryFile
    + to allow user to see with no extra coding what differences + makes the use or not of a private Dicom Dictionary.
    + e.g. : use it as follow
    + PrintFile filein=myGEdicomFile.dcm + dict=/user/userName/gdcm/Dicts/GEMS-Advance.dic +
    
    +
  - + (Not a great one ...) + Stupid method names :
    DicomDir::WriteDicomDir() + and DicomDir::AnonymizeDicomDir()
    replaced by :
    + DicomDir::Write() + and DicomDir::Anonymize() +
    
    +
  - + void Document::AddForceLoadElement(uint16_t group, uint16_t elem); +
    + allows user to tell gdcm::Document Loader he wants + to force the loading of a given set of DocEntries, + even if their length exceeds the current + MAX_SIZE_LOAD_ELEMENT_VALUE. +
    
    +
  - + Many users expect from vtkGdcmReader it 'orders' the images + (that's the job of gdcm::SerieHelper ...)
    + When user knows the files with same Serie UID + have same sizes, same 'pixel' type, same color convention, ... + the right way to proceed is as follow : +
```
+        gdcm::SerieHelper *sh= new gdcm::SerieHelper();
+   //      if user wants *not* to load some parts of the file headers
+        sh->SetLoadMode(loadMode);
+
+   //      if user wants *not* to load some files
+        sh->AddRestriction(group, element, value, operator);
+        sh->AddRestriction( ...
+        sh->SetDirectory(directoryWithImages);
+
+   //      if user *knows* how to order his files
+        sh->SetUserLessThanFunction(userSuppliedComparisonFunction);
+   //      or/and
+   //      if user wants to sort reverse order
+        sh->SetSortOrderToReverse();
+   
+   //      here, we suppose only the first 'Single SerieUID' Fileset is of interest
+   //      Just iterate using sh->NextSingleSerieUIDFileSet()
+   //      if you want to get all of them
+        gdcm::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
+
+   //      if user is doesn't trust too much the files with same Serie UID
+        if ( !sh->IsCoherent(l) )
+           return; // not same sizes, or not same 'pixel type' -> stop
+
+        sh->OrderFileList(l);        // sort the list
+
+        vtkGdcmReader *reader = vtkGdcmReader::New();
+   //      if user wants to modify pixel order (Mirror, TopDown, ...)
+   //      he has to supply the function that does the job
+   //      (a *very* simple example is given in vtkgdcmSerieViewer.cxx)
+        reader->SetUserFunction (userSuppliedFunction);
 
+   //      to pass a 'Single SerieUID' Fileset as produced by gdcm::SerieHelper
+        reader->SetCoherentFileList(l);
+        reader->Update();
+   
```
    + You can see a full example in vtk/vtkgdcmSerieViewer.cxx
    + e.g.
    + + vtkgdcmSerieViewer dirname=Dentist mirror
    + vtkgdcmSerieViewer dirname=Dentist reverse
    + vtkgdcmSerieViewer dirname=Dentist reverse topdown
    + +
    + +
  - vtkGdcmReader::SetUserFunction (userSuppliedFunction)
    + with :
    + void userSuppliedFunction(uint8_t *imageData, File *f);
    + allows user to reorganize the pixels of each image just after reading + it (to mirror, or topdown the image, for instance)
    + Note : uint8_t * doesn't mean it works only on 8 Bits images. +
    It's for prototyping. Feel free to cast it. +
    
    +
  - + SerieHelper::SetUserLessThanFunction(userSuppliedComparisonFunction) +
    with :
    + bool userSuppliedComparisonFunction(File *, File *);
    + allows user -when he knows more about his files than gdcm does- + to give his own comparison function. +
  - SerieHelper::SetSortOrderToReverse allows user to ask + to sort the Files reverse order. +
  - SerieHelper::AddRestriction has now a new constructor
    + AddRestriction(group, element, value, operator);
    + allows user to exclude some files from the sorting, according to + any comparison operator
    + (GDCM_EQUAL, GDCM_DIFFERENT, + GDCM_GREATER, GDCM_GREATEROREQUAL, + GDCM_LESS, GDCM_LESSOREQUAL), not only on the + equality. +
    
    +
  - AnonymizeNoLoad used with dirin=inputDirectoryName + anonymizes all the files within the given Directory. +
    + User may also choose extra elements he wants to rub out:
    + rubout=listOfElementsToRubOut
    + with listOfElementsToRubOut : group1-elem1,group2-elem2, + ... (in hexa, no space within the list ) +
    
    +
  - gdcm::SerieHelper() has a new method + void AddGdcmFile(File *header), that allows aware user to + create a 'FileList' (actually a + std::vector< File* > ).
    + The FileList created this way will be the + 'first one' in the gdcm::FileHelper() (retrieve it with + FileList *GetFirstCoherentFileList() ).
    + It may be sorted using OrderFileList.
    + No 'coherence check' will be performed on this FileList + before sorting.
    + It may be passed to a vtkGdcmReader + (to avoid parsing twice the files) +
    
    +
  - vtkGdcmReader can now get the result of + gdcm::SerieHelper (to avoid parsing twice the files)
    + Proceed as follow :
    +
```
+           gdcmSerieHelper *sh = new gdcmSerieHelper();
+           sh->SetDirectory(myImageDirectory, true);
+           gdcmFileList *l = s->GetFirstCoherentFileList();
+           s->OrderFileList(l);
+
+           vtkGdcmReader *gr = new vtkGdcmReader();
+           gr->SetCoherentFileList(l);
+           gr->Update();  
+           
```
    + This works with a directory that contains only one 'Serie' + (same Serie UID for all the images).
    + If it contains more than one Serie, you'll have to loop + on the Series, using GetNextCoherentFileList();
    + It will be up to the user to delete the gdcm::File. +
    
    + See vtkgdcmSerieViewer for an example. +
    
    +
  - Both vtkgdcmViewer and vtkgdcmViewer2 + are available to allow easy displaying of single/multiframe + GreyLevel/RGB/PaletteColor images
    
    +
  - DICOMDIR anonymiser (Load and Noload mode) +
    
    +
  - Because the gdcm::DicomDir::Load() method may be used + either for loading an already made DICOMDIR file or for + parsing all the dicom files with a given root directory we + syntaxically separated the operations:
    + For loading an already made DICOMDIR file, use :
    +
```
+           gdcm::DicomDir *d = new gdcm::DicomDir();
+           d->SetFileName(fileName);
+           d->Load( );  
+           
```
    + + For parsing all the dicom files within a given root directory, use :
    +
```
+           gdcm::DicomDir *d = new gdcm::DicomDir();
+           d->SetDirectoryName(dirName);
+           d->Load( )  
+           
```
    + + Don't use any longer old deprecated style:
    + + gdcm::DicomDir *d = new gdcm::DicomDir(); + d->SetParseDir(true); //or d->SetParseDir(false); + d->Load( fileName ); + +
    +
  - User is now allowed to tell gdcm::Document constructor + he doesn't want to deal with SeqEntry + (every time it's possible, i.e for 'true length' Sequences)
    + and/or he doesn't want to deal with Shadow groups + (every time it's possible i.e. when element 0x0000 + exists for this Group)
    + or he doesn't want to deal with SeqEntry that belong to a + Shadow group (every time it's possible + -'true length' Sequence-)
    + use :
    +
```
+           gdcm::File *f = new gdcm::File();
+                  f->SetLoadMode(NO_SEQ);            | depending on what
+                  f->SetLoadMode(NO_SHADOW);         | you want *not* 
+                  f->SetLoadMode(NO_SEQ | NO_SHADOW);| to load from the
+                  f->SetLoadMode(NO_SHADOWSEQ);      | target file
+            f->SetFileName(fileName);
+            f->Load( );
+            
```
    + Don't use any longer old deprecated style:
    + + gdcm::File *f = new gdcm::File(fileName);
    +
    +
  - User is now allowed to tell gdcm::DicomDir constructor + he doesn't want to deal with SeqEntry + (every time it's possible, i.e for 'true length' Sequences)
    + and/or he doesn't want to deal with Shadow groups + (every time it's possible i.e. when element 0x0000 + exists for this Group)
    + or he doesn't want to deal with SeqEntry that belong to a + Shadow group (every time it's possible + -'true length' Sequence-)
    + when he parses all the Dicom files within a given directory.
    + use :
    +
```
+             gdcm::DicomDir *f = new gdcm::DicomDir();
+                  f->SetLoadMode(NO_SEQ);            | depending on what
+                  f->SetLoadMode(NO_SHADOW);         | you want *not* 
+                  f->SetLoadMode(NO_SEQ | NO_SHADOW);| to load from the files
+                  f->SetLoadMode(NO_SHADOWSEQ);      | within the root directory 
+             f->SetDirectoryName(rootDirectoryName);
+             f->Load( );
+            
```
    + Don't use any longer old deprecated style:
    + + gdcm::DicomDir *dcmdir = new gdcm::DicomDir(dirName, true);
    +
- Bug fixes
  - No more trouble when the 'endianess' switches within Sequences. +
  - No more trouble with 'no length Sequences' belonging to a + Shadow Group when they are 'Implicit VR'.
  - The difference between MONOCHROME1 (low values = bright, high values = dark) and MONOCHROME2 (low values = dark, high values = bright) is now taken into account.
    It's no longer up to the user to change the pixels value -
  - Writing a 'True Dicom' image after reading an ACR-NEMA image +
  - Writing a 'True Dicom' image after reading an ACR-NEMA image does not request any longer from the user to build up - 'manually' the Meta Elements group (0002) -
  - Old '24 Bits' ACR-NEMA are now correctly re-written in DICOM mode. - + 'manually' the Meta Elements group (0x0002) +
  - Old '24 Bits' ACR-NEMA are now correctly re-written + in DICOM V3 mode. +
  - Element 0x0000 of Shadow groups is always forced to be a + ValEntry and its VR is forced to UL +
- A.P.I. breaking modifications (since previous version : 1.0)
  - NEVER more API breaking modifications !!! - +
  -
- Known bugs
  - -
  -
- Sample Data -
  +
@@ -154,24 +670,24 @@ Any contribution is welcome.

Removal of useless accessors GetXxxByname, SetXxxByname

Renaming of accessors GetXxxByNumber, SetXxxByNumber -as follow : + as follow :

GetEntryByNumber - --> GetEntryValue -
GetEntryLengthByNumber --> GetEntryLength -
GetEntryOffsetByNumber --> GetEntryOffset + --> GetEntryValue +
GetEntryLengthByNumber --> GetEntryLength +
GetEntryOffsetByNumber --> GetEntryOffset
GetEntryVRByNumber - --> GetEntryVR + --> GetEntryVR
GetDocEntryByNumber - --> GetDocEntry + --> GetDocEntry
GetValEntryByNumber - --> GetValEntry + --> GetValEntry
GetBinEntryByNumber - --> GetBinEntry + --> GetBinEntry
GetSeqEntryByNumber - --> GetSeqEntry + --> GetSeqEntry

Gdcm News

- Current Version + Current Version (CVS)

+ + Version 1.1 (September 14 2005) +