X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=Doc%2FWebsite%2FNews.html;h=f17bb7b97616d8656f50eaae426ad6c6389af056;hb=779c8f5232ad160d353b90d3fa47d0503e17965d;hp=80a89551c8a57188d9a8349749d2471d19b0d048;hpb=5544a1627fc9bb02b2d4c20b4ffa3ba8fa81c0ae;p=gdcm.git diff --git a/Doc/Website/News.html b/Doc/Website/News.html index 80a89551..f17bb7b9 100644 --- a/Doc/Website/News.html +++ b/Doc/Website/News.html @@ -7,63 +7,538 @@ - + +

Gdcm News

+ + +

+ + Missing features +

+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. +

Decoders +
- gdcm doesn't read yet JPEG-LS encoded files. +
  +
- gdcm doesn't read yet all JPEG2000 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 + Shadow groups (if any) +
- Allow user to tell the Writer which compression mode he wants
  + (Right now, no one is available) +
- 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 (belonging to the file header Dicom + entries)to the default entry list, before + making a DICOMDIR from a root directory +
- 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 +
- 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 + carved in the Pixels :-( +
+

- Current Version + Current Version (CVS)

Final check of the jpeg sub-library: all 'classical' jpeg - compressed Dicom files can be read
- All the previously gdcm-breaker images are now readable
- gdcm doesn't read yet JPEG-LS and JPEG2000 encoded files. -
Use of namespace : all the methods formerly called - className::gdcmXxx() are now called className::Xxx() -
Removal of accessors GetXxxByname, SetXxxByname - and GetXxxByNumber, SetXxxByNumber - replaced by GetXxx, SetXxx -
a gdcm::Document is now specialized in gdcm::DicomDir and gdcm::File -
A huge number of memory leaks removed -
Improvement of write process -

-
-

-For people who get this new release :
-
-We consider now that :
-- any dicom related file is a gdcm::Document.
-- a gdcm::Document can be :
-      - a gdcm::File,     if it contains pixel data,
-      - a gdcm::DicomDir, if it contains only informations 
-                          on the files in a given directory
-
-- in a gdcm::Document, there are gdcm::DocEntry, that can be :
-     - gdcm::ContentEntry (any entry that has an actual value,
-                           *not* an embedded set of other gdcm::DocEntry)
-                           a gdcm::ContentEntry can be :
-          - gdcm::ValEntry (whose value is std::string representable 
-                            e.g. character values, or integers),
-          - gdcm::BinEntry (whose value is not std::string representable 
-                            e.g. color palettes, overlays, icons , ...)
-     - gdcm::Sequence (no proper 'value', but a set of gdcm::SQItems, 
-                       composed of a set of gdc::DocEntry, recursively)
+    Missing Features
+   
State of the art
+       
+      
+         gdcm UML Class Diagram current version.
+      
 User Documentation
+      
 Developper
+         Documentation 
+   
 New Features
+   
+       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 ...
+      
 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 !-
+      

+      

+   
+
+   
 API breaking modifications (since previous version)
+   
+       Stupid difference between gdcm::ValEntry 
+           and gdcm::BinEntry removed. 

+           Only gdcm::DataEntry exist, now. 
  
+      

+      

+    
+      
+   
 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.
+      

+      

+   
  
-- in a gdcm::DicomDir, we only deal, hierarchically, with :
-     - gdcmPatient
-     - gdcmStudy
-     - gdcmSerie
-     - gdcmImage
-

-You can see gdcm UML Class Diagram +

+ + + + + +

+ + Version 1.1 (September 14 2005) +

State of the art +

+ gdcm 1.1 UML Class Diagram version. +
User Documentation +
Developper + Documentation +
New Features +
- 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 + does not request any longer from the user to build up + '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 +
+ +

+ +

+ + Version 1.0 (Feb 14 2005) +

State of the art +
- + gdcm 1.0 UML Class Diagram version. +
- User Documentation" +
- Developper + Documentation" +
- Final check of the jpeg sub-library: all 'classical' jpeg + compressed Dicom files can be read
  +
- All the previously gdcm-breaker images are now readable
  +
- A huge number of memory leaks removed +
- Improvement of write process +
+ + +
A.P.I. breaking modifications (since previous version : 0.6) +
- Use of namespace : all the methods formerly named + className::gdcmXxx() are now named className::Xxx() +
  End user will have to call them as gdcm::className::Xxx() +
- a gdcm::Document is now specialized in : +
  - gdcm::DicomDir +
  - gdcm::File +
  +
- a gdcm::DicomElementSet is composed of a set of + gdcm::DicomDocEntry +
- a gdcm::DicomDocEntry can be : +
  - a gdcm::ContentEntry, specialized in : +
    - gdcm::ValEntry +
    - gdcm::BinEntry (no longer a specialization of + gdcm::ValEntry) +
    +
  - a gdcm::SeqEntry +
  +
- Removal of useless accessors GetXxxByname, SetXxxByname +
- Renaming of accessors GetXxxByNumber, SetXxxByNumber + as follow : +
  - GetEntryByNumber + + --> GetEntryValue +
  - GetEntryLengthByNumber --> GetEntryLength +
  - GetEntryOffsetByNumber --> GetEntryOffset +
  - GetEntryVRByNumber + --> GetEntryVR +
  - +
  - GetDocEntryByNumber + --> GetDocEntry +
  - GetValEntryByNumber + --> GetValEntry +
  - GetBinEntryByNumber + --> GetBinEntry +
  - GetSeqEntryByNumber + --> GetSeqEntry +
  +
+

@@ -72,28 +547,40 @@ You can see gdcm UML Class Diagram

ITK

User Documentation" +
Developper Documentation"
The new gdcmDocument class is a parent class of gdcmHeader class and gdcmDicomDir class.
Massive modifications in the Class Diagram :
- Entries (gdcmEntry) are now separated into - ValEntry and SeqEntry (whose VR = - SQ) -
- a gdcmDocument is_a gdcmElementSet, - composed of a set of gdcmValEntry - and gdcmSeqEntry -
- a gdcmSeqEntry is considered as a set - of gdcmSQItem -
- Dicom Sequences (VR = SQ) are now dealt as tree-like - structures within gdcmSQItem class.
  - they are considered as a set of gdcmSQItems -
- a gdcmSQItem is_a gdcmElementSet -
-
Improvement of the jpeg sub-library: jpeg - compressed Dicom files (lossless and lossy) - might be read (check-it out) +
any dicom related file is a gdcmDocument +
a gdcmDocument can be : +
- a gdcmHeader, if it contains pixel data +
- a gdcmDicomDir, if it contains only informations + on the files in a given directory +
+ +
a gdcmDocument is_a gdcmElementSet, + composed of a set of gdcmEntry separated into : +
- gdcmValEntry
  + a specialization of gdcmValEntry, for 'non + std::string representable' values is + gdcmBinEntry +
- gdcmSeqEntry (VR = SQ, i.e Dicom Sequences)
  + they are dealt as tree-like structures :
  + - a gdcmSeqEntry is considered as a set + of gdcmSQItem,
  + - a gdcmSQItem is_a gdcmElementSet, composed + of gdcmDocEntries, recursively
  +
+

Improvement of the jpeg sub-library: jpeg + compressed Dicom files (lossless and lossy) + might be read (check-it out) @@ -103,6 +590,11 @@ You can see gdcm UML Class Diagram Version 0.4 (February 6 2004)

gdcm 0.4 UML Class Diagram. +
User Documentation" +
Developper Documentation +
Introduction of a jpeg sub-library: some very simple jpeg-lossy compressed Dicom files might be working (check-it out).
And also, fewer memory leaks, cleaned-up stl usage (should work @@ -110,6 +602,10 @@ You can see gdcm UML Class Diagram supporting both Swig and vtk wrapping.
Introduction of a RLE (Run-Time Encoding) library
Color images (RGB or Palette Color) are dealt with +
Confusing names gdcmPatient, gdcmStudy, + gdcmSerie, gdcmPatient changed to + gdcmDicomDirPatient, gdcmDicomDirStudy, + gdcmDicomDirSerie, gdcmDicomDirPatient