--- /dev/null
+<pre>
+{{{
+This is a vi-able/notepad-able document to (try to) explain in a few words
+how to use efficently gdcm.
+-->Feel free to send/add your comments/suggestions/modifications.
+-->Don't try to 'beautify' this page.
+(I plane to rewrite it, and add it to the gdcm site as soon as
+there is enough 'content' within it)
+
+HTH
+Jean-Pierre Roux
+
+------------------------------------------------------------------------
+0) Intro
+1) How to Read a DICOM file
+1-1) using raw C++
+1-1-1) A single file
+1-1-2) A File Set
+1-2) using VTK
+1-2-1) A single file
+1-2-2) A File Set
+1-3) using ITK
+1-3-1) A single file
+1-3-2) A File Set
+1-4) Retrictions for Python users
+
+2) How to write DICOM file
+2-1) using raw C++
+2-1-1) A single file
+2-1-2) A File Set
+2-2) using VTK
+2-3) using ITK
+
+----------------------------------------------------------------------------
+
+0) Intro
+--------
+
+If you are not familiar with DICOM files , use :
+
+PrintFile filein=yourDicomFile.dcm
+
+and have a look at the output.
+You'll see a lot of self explanatory (?) lines, e.g.
+
+D 0008|0021 [DA] [Series Date] [20020524]
+D 0008|0060 [CS] [Modality] [US]
+D 0018|602c [FD] [Physical Delta X][0]
+D 0020|0013 [IS] [Instance Number] [5 ]
+D 0028|0010 [US] [Rows] [480]
+D 0011|0010 [ ] [gdcm::Unknown] [DLX_PATNT_01]
+
+0008|0021 : 'Group Number'|'Element Number' -> The Element identifier
+Have a look at gdcm/Dicts/dicomV3.dic for the whole list of Elements
+
+DA : The 'Value Representation' : DA for Date, US for Unsigned Short, ...
+Have a look at gdcm/Dicts/dicomVR.dic for the set of possible values
+
+[Series Date] : The 'official' English name of the Element
+(When *you* have to deal with a given Element, its meaning should be clear for
+*you*)
+
+[20020524] : the value, printed in a human readable way.
+
+If something like :
+D 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ ===> [gdcm::Binary data loaded;length = 113784]
+is displayed, it means that it's a 'long' binary area, gdcm (I) decided not to
+show.
+
+D 0011|0010 [ ] [gdcm::Unknown] [DLX_PATNT_01]
+is a 'Private (or Shadow) Element', depending on the manufacturer.
+It's *not* known within the 'official' Dicom Dictionnary.
+Except if someone told you, you cannot guess the meaning of such an element.
+Probabely, you'll never have to deal with Shadow Elements (hope so!).
+
+You can find also something like :
+
+S 0018|6011 [SQ] [Sequence of Ultrasound Regions]
+ | --- SQItem number 0
+ | D fffe|e000 [UL] [Item]
+ | D 0018|6018 [UL] [Region Location Min X0] [32]
+ | D 0018|601a [UL] [Region Location Min Y0] [24]
+ | D 0018|601c [UL] [Region Location Max X1] [335]
+ | D 0018|601e [UL] [Region Location Max Y1] [415]
+ | D 0018|602c [FD] [Physical Delta X] [0.0382653]
+ | D 0018|602e [FD] [Physical Delta Y] [0.0382653]
+ | --- SQItem number 1
+ | D fffe|e000 [UL] [Item]
+ | D 0018|6018 [UL] [Region Location Min X0] [336]
+ | D 0018|601a [UL] [Region Location Min Y0] [24]
+ | D 0018|601c [UL] [Region Location Max X1] [639]
+ | D 0018|601e [UL] [Region Location Max Y1] [415]
+ | D 0018|602c [FD] [Physical Delta X] [0.0382653]
+ | D 0018|602e [FD] [Physical Delta Y] [0.0382653]
+ | --- SQItem number 2
+ | D fffe|e000 [UL] [Item]
+ | D 0018|6018 [UL] [Region Location Min X0] [32]
+ | D 0018|601a [UL] [Region Location Min Y0] [40]
+ | D 0018|601c [UL] [Region Location Max X1] [63]
+ | D 0018|601e [UL] [Region Location Max Y1] [103]
+ | D 0018|6024 [US] [Physical Units X Direction] [0]
+ | D 0018|6026 [US] [Physical Units Y Direction] [0]
+ | D 0018|602c [FD] [Physical Delta X] [0]
+ | D 0018|602e [FD] [Physical Delta Y] [0]
+
+0018|6011 is a 'Sequence' (SQ), composed of various Sequence Items(SQItem)
+Each SQItem is a set of Elements (an Element may be a DataElement (D) or a
+Sequence (S), recursively.
+Probabely, you'll never have to deal with Sequences (hope so!).
+
+1) How to Read a DICOM File
+===========================
+
+1-1) using raw C++
+------------------
+
+1-1-1) A single file
+--------------------
+
+The first step is to load the file header :
+
+ 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( );
+
+Except if someone told you -he knows the file headers are bugged-,
+do *not* use SetLoadMode().
+
+Check if the file is gdcm-readable.
+
+ if ( !f->IsReadable() )
+ std::cout << "major troubles on [" << f->GetFileName() <<"]"
+ << std::endl;
+
+Decide if this is a 'File Of Interest' for you.
+Check some fields, e.g
+
+ std::string StudyDate = f->GetEntryString(0x0008,0x0020);
+ std::string PatientName = f->GetEntryString(0x0010,0x0010);
+ std::string PatientID = f->GetEntryString(0x0010,0x0020);
+ std::string PatientSex = f->GetEntryString(0x0010,0x0040);
+ std::string Modality = f->GetEntryString(0x0008,0x0060);
+
+(or whatever you feel like ...)
+
+Next step is to load the pixels in memory.
+Uncompression (JPEG lossless, JPEG lossy, JPEG 2000, RLE, ...)
+is automatically performed if necessary.
+
+ gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
+ void *imageData = fh->GetImageDataRaw();
+ uint32_t dataSize = fh->GetImageDataRawSize();
+
+Generally, you work on 'Grey level' images (as opposed to RGB images).
+Depending on the Pixel size (8/16/32 bits) and the Pixel Type (signed/unsigned),
+you cast the imageData
+
+ std::string pixelType = f->GetPixelType();
+
+Possible values are :
+
+- "8U" unsigned 8 bit,
+- "8S" signed 8 bit,
+- "16U" unsigned 16 bit,
+- "16S" signed 16 bit,
+- "32U" unsigned 32 bit,
+- "32S" signed 32 bit,
+
+
+ int dimX = f->GetXcurrentFileName[i]Size();
+ int dimY = f->GetYSize();
+ int dimZ = f->GetZSize();
+ int dimT = f->GetTSize();
+
+Now, you can enjoy your image !
+
+Sometimes, you deal with 'colour' images :-(
+They may be stored, on disc, as RGB pixels, RGB planes, YBR pixels, YBR planes
+Grey level images + LUT.
+
+You'll get an 'RGB Pixels' image in memory if you use:
+
+ gdcm::FileHelper *fh = gdcm::FileHelper::New(f);
+ void *imageData = fh->GetImageData();
+ uint32_t dataSize = fh->GetImageDataSize();
+
+
+1-1-2) A File Set
+-----------------
+
+If you are 150 % sure of the files you're dealing with, just read the files you
+feel like, and concatenate the pixels.
+
+Sometimes you are not sure at all (say : you were given a CDROM with an amount
+of images, laying in a Directories tree-like structure, you don't know anything
+about the Patients, and so on)
+
+A class gdcm::SerieHelper is designed to help solving this problem.
+Use it as follows.
+
+ gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
+ while (int i=0; i<nbOfFiles; i++) {
+ sh->AddFileName(currentFileName[i]);
+ }
+
+You can also pass a 'root directory', and ask or not for recursive parsing.
+ gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
+ sh->SetDirectory(yourRootDirectoryName, true); // true : recursive parsing
+
+Files are 'splitted' into as many 'Single Serie UID File Set'
+ as Series Instance UID ( 0020|000e );
+
+If you want to 'order' the files within each 'Single Serie UID File Set'
+(to build a volume, for instance), use :
+
+ gdcm::FileList *l = sh->GetFirstSingleSerieUIDFileSet();
+ while (l)
+ {
+ sh->OrderFileList(l); // sort the list
+ l = sh->GetNextSingleSerieUIDFileSet();
+ }
+
+ The sorting will be performed on the ImagePositionPatient;
+ if not found, on ImageNumber;
+ if not found, on the File Name.
+
+ Aware user is allowed to pass his own comparison function
+ (if he knows, for instance, the files must be sorted on 'Trigger Time')
+ He will use the method
+ void SerieHelper::SetUserLessThanFunction( bool(*) userFunc((File *,File *) );
+ He may ask for a reverse sorting :
+ sh->SetSortOrderToReverse();
+ or back to Direct Order
+ sh->SetSortOrderToDirect();
+
+ If, for any reason of is own, user already get the file headers,
+ he may add the gdcm::File (instead of the file name) to the SerieHelper.
+
+ gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
+ while (int i=0; i<nbOfFiles; i++) {
+ sh->AddFile(currentFile[i]);
+ }
+ * \warning : this method should be used by aware users only!
+ * User is supposed to know the files he want to deal with
+ * and consider them they belong to the same Set
+ * (even if their Serie UID is different)
+ * user will probabely OrderFileList() this list (actually, ordering
+ * user choosen gdm::File is the sole interest of this method)
+ * Moreover, using vtkGdcmReader::SetCoherentFileList() will avoid
+ * vtkGdcmReader parsing twice the same files.
+ * *no* coherence check is performed, but those specified
+ * by SerieHelper::AddRestriction()
+
+ User may want to exclude some files.
+ He will use
+ void SerieHelper::AddRestriction(uint16_t group, uint16_t elem,
+ std::string const &value, int op);
+op belongs to :
+
+/// \brief comparaison operators
+ GDCM_EQUAL ,
+ GDCM_DIFFERENT,
+ GDCM_GREATER,
+ GDCM_GREATEROREQUAL,
+ GDCM_LESS,
+ GDCM_LESSOREQUAL
+e.g.
+ gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
+ sh->AddRestriction(0x0010,0x0040,"F",GDCM_EQUAL); // Patient's Sex
+ sh->AddRestriction(0x0008,0x0060,"MR",GDCM_DIFFERENT); // Modality
+ while (int i=0; i<nbOfFiles; i++) {
+ ...
+User wants to deal only with Female patient, any Modality but MR (why not?)
+
+Sometimes the previous stuff is *not enough* !
+
+Within a SingleSerieUIDFileSet, you can have have various orientations,
+or various positions, at various times. (not only various position , at a single
+time, for a single orientation).
+
+User may consider that dealing only with the 'Series Instance UID'
+is not enough and wishes to 'refine' the image selection :
+
+Suppose he has a Single Serie UID File Set (gdcm::FileList).
+He may ask to split it into several 'X Coherent File Sets' (X stands for
+'Extra').
+
+gdcm::SerieHelper *s;
+gdcm::XCoherentFileSetmap xcm;
+gdcm::FileList *l = s->GetFirstSingleSerieUIDFileSet(); // or what you want
+
+
+ The following methods must be called by user, depending on
+ what *he* wants to do, at application time.
+ - *he* only knows what his Series contain ! -
+ They return a std::map of Filesets (actually : std::vector of gdcm::File*).
+
+He may ask for 'splitting' on the Orientation:
+ xcm = s->SplitOnOrientation(l);
+
+He may ask for 'splitting' on the Position:
+ xcm = s->SplitOnPosition(l);
+
+He may ask for 'splitting' on the any DataElement you feel like :
+ xcm = s->SplitOnTagValue(l, groupelem[0],groupelem[1]);
+
+
+He can now work on each 'X Coherent File Set' within the std::map
+
+for (gdcm::XCoherentFileSetmap::iterator i = xcm.begin();
+ i != xcm.end();
+ ++i)
+{
+
+ // ask for 'ordering' according to the 'Image Position Patient'
+ s->OrderFileList((*i).second); // sort the XCoherent Fileset
+}
+
+(have a look at gdcm/Examples/exXCoherentFileSet.cxx for an exmaple)
+
+1-2) using VTK
+--------------
+a vtkGdcmReader() method ( derived from vtkReader() ) is available.
+
+
+
+1-2-1) A single file
+--------------------
+
+ vtkGdcmReader *reader = vtkGdcmReader::New();
+ reader->SetFileName( yourDicomFilename );
+ reader->SetLoadMode( yourLoadMode); // See C++ part
+ reader->Update();
+ vtkImageData* ima = reader->GetOutput();
+ int* Size = ima->GetDimensions();
+ // -> Enjoy it.
+
+1-2-2) A File Set
+-----------------
+
+If you are 150 % sure of the files you're dealing with, just 'add' the files you
+feel like:
+
+ vtkGdcmReader *reader = vtkGdcmReader::New();
+ for(int i=1; i< yourNumberOfFiles; i++)
+ reader->AddFileName( yourTableOfFileNames[i] );
+ reader->SetLoadMode( yourLoadMode); // See C++ part
+ reader->Update();
+ vtkImageData* ima = reader->GetOutput();
+ int* Size = ima->GetDimensions();
+ // -> Enjoy it.
+
+ Warning : The first file is assumed to be the reference file.
+ All the inconsistent files (different sizes, pixel types, etc) are discarted
+ and replaced by a black image !
+
+ User is allowed to pass a Pointer to a function of his own
+ to allow modification of pixel order (i.e. : Mirror, TopDown, )
+ to gdcm::FileHeleper, using SetUserFunction(userSuppliedFunction)
+
+ described as : void userSuppliedFunction(uint8_t *im, gdcm::File *f);
+
+ NB : the "uint8_t *" type of first param is just for prototyping.
+ User will Cast it according what he found with f->GetPixelType()
+ See vtkgdcmSerieViewer for an example
+
+
+Many users expect from vtkGdcmReader it 'orders' the images
+(Actually, 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(yourLoadMode);
+
+ // 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();
+
+
+//-----------------
+(*)
+User may also pass an 'X Coherent Fileset', created by one of the following
+methods : (see 1-1-2 for more details)
+
+ xcm = sh->SplitOnOrientation(l);
+ xcm = sh->SplitOnPosition(l);
+ xcm = sh->SplitOnTagValue(l, groupelem[0],groupelem[1]);
+//----------------
+
+You can see a full example in vtk/vtkgdcmSerieViewer.cxx
+e.g.
+vtkgdcmSerieViewer dirname=Dentist mirror
+vtkgdcmSerieViewer dirname=Dentist reverse
+vtkgdcmSerieViewer dirname=Dentist reverse upsidedown
+
+
+1-4) Retrictions for Python users
+---------------------------------
+
+None of the methods receiving a function pointer, or a gdcm::File as a parameter
+is wrapable by swig.
+:-(
+
+
+2) How to write DICOM file
+==========================
+
+ // gdcm cannot guess how user built his image
+ // (and therefore cannot be clever about some Dicom fields)
+ // It's up to the user to tell gdcm what he did.
+ // -1) user created ex nihilo his own image and wants to write it
+ // as a Dicom image.
+ // USER_OWN_IMAGE
+ // -2) user modified the pixels of an existing image.
+ // FILTERED_IMAGE
+ // -3) user created a new image, using existing a set of images
+ // (eg MIP, MPR, cartography image)
+ // CREATED_IMAGE
+ // -4) user modified/added some tags *without processing* the pixels
+ // (anonymization..
+ // UNMODIFIED_PIXELS_IMAGE
+ // -Probabely some more to be added
+ //(see gdcmFileHelper.h for more explanations)
+
+ // User is allowed to use the following methods:
+
+ void SetContentTypeToUserOwnImage()
+ {SetContentType(VTK_GDCM_WRITE_TYPE_USER_OWN_IMAGE);}
+ void SetContentTypeToFilteredImage()
+ {SetContentType(VTK_GDCM_WRITE_TYPE_FILTERED_IMAGE);}
+ void SetContentTypeToUserCreatedImage()
+ {SetContentType(VTK_GDCM_WRITE_TYPE_CREATED_IMAGE);}
+ void SetContentTypeToUnmodifiedPixelsImage()
+ {SetContentType(VTK_GDCM_WRITE_TYPE_UNMODIFIED_PIXELS_IMAGE);}
+
+2-1) using raw C++
+------------------
+In C++, if you have already the pixels in main memory,
+you just have to process as follow :
+
+--> Create an empty gdcm::File
+ gdcm::File *file = gdcm::File::New();
+
+ std::ostringstream str;
+
+// --> Set the mandatory fields
+// Set the image size
+ str.str("");
+ str << sizeX;
+ file->InsertEntryString(str.c_str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << sizeY;
+ file->InsertEntryString(str.c_str(),0x0028,0x0011,"US"); // Columns
+ str.str("");
+ str << sizeZ;
+ file->InsertEntryString(str.c_str(),0x0028,0x0008, "IS"); // Nbr of Frames
+ // Set the pixel type
+ str.str("");
+ str << componentSize; //8, 16, 32
+ file->InsertEntryString(str.c_str(),0x0028,0x0100,"US"); // Bits Allocated
+ str.str("");
+ str << componentUse; // may be 12 or 16 if componentSize =16
+ file->InsertEntryString(str.c_str(),0x0028,0x0101,"US"); // Bits Stored
+ str.str("");
+ str << componentSize - 1 ;
+ file->InsertEntryString(str.c_str(),0x0028,0x0102,"US"); // High Bit
+ // Set the pixel representation // 0/1
+ str.str("");
+ str << img.sign;
+ file->InsertEntryString(str.c_str(),0x0028,0x0103, "US"); // Pixel Representation
+ // Set the samples per pixel // 1:Grey level, 3:RGB
+ str.str("");
+ str << components;
+ file->InsertEntryString(str.c_str(),0x0028,0x0002, "US"); // Samples per Pixel
+
+//--> Set Optional fields
+//(patient name, patient ID, modality, or what you want
+//Have look at gdcm/Dict/dicomV3.dic to see what are the various DICOM fields)
+
+//--> Create a gdcm::FileHelper
+
+ gdcm::FileHelper *fileH = gdcm::FileHelper::New(file);
+ fileH->SetImageData((unsigned char *)imageData,size);
+
+//casting as 'unsigned char *' is just to avoid warnings.
+// It doesn't change the values.
+
+ fileH->SetWriteModeToRaw();
+ fileH->SetWriteTypeToDcmExplVR();
+ fileH->Write(fileName.str());
+
+//This works for a single image (singleframe or multiframe)
+
+// If you deal with a Serie of images, it up to you to tell gdcm, for each image,
+// what are the values of
+// 0020 0032 DS 3 Image Position (Patient)
+// 0020 0037 DS 6 Image Orientation (Patient)
+
+2-1-1) A single file
+--------------------
+/// \todo : write it!
+
+2-1-2) A File Set
+-----------------
+/// \todo : write it!
+
+
+
+2-2) using VTK
+--------------
+
+2-2-1) A single file
+--------------------
+
+// User of the CVS version of VTK 5 may set some 'Medical Image Properties'
+// Only the predefined DataElements are available :
+// PatientName, PatientID, PatientAge, PatientSex, PatientBirthDate, StudyID
+// It's reasonablt enough for any 'decent use'
+vtkMedicalImageProperties
+
+ // Aware user is allowed to pass his own gdcm::File *,
+ // so he may set *any Dicom field* he wants.
+ // (including his own Shadow Eleents, or any gdcm::SeqEntry)
+ // gdcm::FileHelper::CheckMandatoryElements() will check inconsistencies,
+ // as far as it knows how.
+ // Sorry, not yet available under Python.
+vtkSetMacro(GdcmFile, gdcm::File *);
+
+
+2-2-2) A File Set
+-----------------
+/// \todo : write it!
+
+
+2-3) using ITK
+--------------
+/// \todo : write it!
+
+}}}
+</pre>
projects / gdcm.git / commitdiff