1-1-1-1) Deal with the file header
1-1-1-2) Load the 'pixels' in memory
1-1-1-3) Get the value of a single Dicom DataElement
-1-1-1-4) Get the value of a Dicom Sequence
+1-1-1-4) Get the values within a Dicom Sequence
1-1-2) A File Set
1-2) using VTK
2-4) Retrictions for Python users
-3) Some 'Command line' utilities
+3) DICOMDIR
+===========
+3-1) How to read a DICIMDIR
+3-2) How to modifiy a DICOMDIR
+3-3) How to create a DICOMDIR
+
+4) Some 'Command line' utilities
================================
-3-) PrintFile
-3-) exSerieHelper
-3-) exXCoherentFileSet
+4-) PrintFile
+4-) exSerieHelper
+4-) exXCoherentFileSet
-3-) AnonymizeNoLoad
-3-) AnonymizeMultiPatient
-3-) AnonymizeDicomDir
+4-) AnonymizeNoLoad
+4-) AnonymizeMultiPatient
+4-) AnonymizeDicomDir
-3-) ReWrite
-3-) RawToDicom
-3-) exMoveImagesToSingleSerieUID
+4-) ReWrite
+4-) RawToDicom
+4-) exMoveImagesToSingleSerieUID
-3-) vtkgdcmViewer2
-3-) vtkgdcmSerieViewer2
+4-) vtkgdcmViewer2
+4-) vtkgdcmSerieViewer2
-3-) PrintDicomDir
-3-) MakeDicomDir
+4-) PrintDicomDir
+4-) MakeDicomDir
----------------------------------------------------------------------------
You will have to cast them, according to the knowledge you have about them.
LutRedData = (uint8_t*)f->GetEntryBinArea( 0x0028, 0x1201 );
-1-1-1-4) Get the value(s) of a Dicom Sequence
+1-1-1-4) Get the value(s) within a Dicom Sequence
Actually, a 'Dicom Sequence' is composed of a list a 'Sequence Items',
-each Sequence Item is a set of DataElement (that can be a Sequence Element, recursively).
+each Sequence Item is a set of DataElement (that can be Dicom Sequences, recursively).
You have to get the Sequence element, to get its number of Sequence items, to iterate on each one.
e.g.:
about the Patients, and so on)
A class gdcm::SerieHelper is designed to help solving this problem.
-Use it as follows.
+Use it as follows :
gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
while (int i=0; i < nbOfFiles; i++) {
If, for any reason of his own, user already get the file headers,
he may add the gdcm::File (instead of the file name) to the SerieHelper.
+ (Sorry, not available in Python)
gdcm::SerieHelper *sh = gdcm::SerieHelper::New();
while (int i=0; i < nbOfFiles; i++) {
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
+or various positions, at various times. (not only various positions, at a single
time, for a single orientation).
User may consider that dealing only with the 'Series Instance UID'
vtkGdcmReader *reader = vtkGdcmReader::New();
reader->SetFileName( yourDicomFilename );
- reader->SetLoadMode( yourLoadMode); // See C++ part
- reader->SetKeepOverlays( true/false); // See C++ part
+ reader->SetLoadMode( yourLoadMode ); // See C++ part
+ reader->SetKeepOverlays( true/false ); // See C++ part
reader->Update();
vtkImageData* ima = reader->GetOutput();
int* Size = ima->GetDimensions();
vtkGdcmReader *reader = vtkGdcmReader::New();
for(int i=1; i< yourNumberOfFiles; i++)
reader->AddFileName( yourTableOfFileNames[i] );
- reader->SetLoadMode( yourLoadMode); // See C++ part
- reader->SetKeepOverlays( true/false); // See C++ part
+ reader->SetLoadMode( yourLoadMode ); // See C++ part
+ reader->SetKeepOverlays( true/false ); // See C++ part
reader->Update();
vtkImageData* ima = reader->GetOutput();
int* Size = ima->GetDimensions();
---------------------------------
/// \todo : write it!
-3) Some 'Command line' utilities /// \todo: finish it!
-================================
-3-) PrintFile
-3-) exSerieHelper
-3-) exXCoherentFileSet
+3) DICOMDIR /// \todo: finish it!
+===========
+3-1) How to read a DICIMDIR
+3-2) How to modifiy a DICOMDIR
+3-3) How to create a DICOMDIR
-3-) AnonymizeNoLoad
-3-) AnonymizeMultiPatient
-3-) AnonymizeDicomDir
-3-) ReWrite
-3-) RawToDicom
-3-) exMoveImagesToSingleSerieUID
+4) Some 'Command line' utilities /// \todo: finish it!
+================================
-3-) vtkgdcmViewer2
-3-) vtkgdcmSerieViewer2
+4-) PrintFile
+4-) exSerieHelper
+4-) exXCoherentFileSet
+
+4-) AnonymizeNoLoad
+4-) AnonymizeMultiPatient
+4-) AnonymizeDicomDir
+4-) PatchHeader
+4-) ReWrite
+4-) RawToDicom
+4-) exMoveImagesToSingleSerieUID
+
+4-) vtkgdcmViewer2
+4-) vtkgdcmSerieViewer2
+
+4-) PrintDicomDir
+4-) MakeDicomDir
+
+
+ * PrintFile
+
+ Displays the header of any kind of ACR-NEMA/PAPYRUS/DICOM File
+ usage: PrintFile {filein=inputFileName|dirin=inputDirectoryName}[level=n]
+ [forceload=listOfElementsToForceLoad]
+ [4DLoc= ][dict= privateDirectory]
+ [ { [noshadowseq] | [noshadow][noseq] } ]
+ [debug] [warning]
+ level = 0,1,2 : depending on the amount of details user wants to see
+ 4DLoc: group-elem(in hexa, no space) of the DataEntry holdind 4thDim
+ listOfElementsToForceLoad : group-elem,g2-e2,... (in hexa, no space)
+ of Elements to load whatever their length
+ privateDirectory : source file full path name of Shadow Group elems
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ warning : user wants to be warned about any oddity in the File
+ showlut :user wants to display the Palette Color (as an int array)
+
+ [ { [noshadowseq] | [noshadow][noseq] } ] [debug] [usage]
+ level = 0,1,2 : depending on the amount of details user wants to see
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * Anonymize
+
+ Anonymizes a full gdcm-readable Dicom image
+ Warning : probably segfaults if pixels are not gdcm readable.
+ Use AnonymizeNoLoad instead.
+ usage: Anonymize filein=inputFileName fileout=anonymizedFileName [debug][usage]
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * AnonymizeNoLoad
+
+
+ Anonymizes a gdcm-readable Dicom image even if pixels aren't gdcm readable
+ Warning : the image is overwritten;
+ to preserve its integrity, use a copy.
+ usage: AnonymizeNoLoad {filein=inputFileName|dirin=inputDirectoryName}
+ [rubout=listOfPrivateElementsToRubOut]
+ [ { [noshadowseq] | [noshadow][noseq] } ] [debug]
+ inputFileName : Name of the (single) file user wants to anonymize
+ inputDirectoryName : user wants to anonymize *all* the files
+ within the (single Patient!) directory
+ listOfElementsToRubOut : group1-elem1,g2-e2,... (in hexa)
+ of extra Elements to rub out
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * ReWrite
+
+ Reads and rewrites a full gdcm-readable Dicom image
+ (usefull when the file header is not very straight).
+
+ usage: ReWrite filein=inputFileName fileout=outputFileName
+ [keepoverlays] [mode=write mode] [monochrome1]
+ [noshadow] [noseq][debug]
+ --> The following line to 'rubout' a burnt-in Patient name
+ [rubout=xBegin,xEnd,yBegin,yEnd [ruboutvalue=n (<255)] ]
+ --> The 2 following lines, to extract a sub image within some frames
+ [ROI=xBegin,xEnd,yBegin,yEnd]
+ [firstframe=beg] [lastframe=end]
+
+ mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels)
+ j (jpeg lossless), 2 (jpeg2000)
+ keepoverlays : user wants to keep ACR-NEMA-like overlays
+ monochrome1 = user wants MONOCHROME1 photom. interp. (0=white)
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ rgb : user wants to transform LUT (if any) to RGB pixels
+ warning : developper wants to run the program in 'warning mode'
+ debug : developper wants to run the program in 'debug mode' a full gdcm-readable Dicom image (compressed Pixels are expanded)
+ (usefull when the file is not very straight).
+ usage: ReWrite filein=inputFileName fileout=anonymizedFileName
+ [mode=write mode] [rgb]
+ [ { [noshadowseq] | [noshadow][noseq] } ] [debug] [usage]
+ write mode = a (ACR), x (Explicit VR Dicom), r (RAW : only pixels)
+ rgb : user wants to transform LUT (if any) into RGB
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * PrintDicomDir
+
+ Displays the tree-like structure of a DICOMDIR File
+ usage: PrintDicomDir filein=fileName [detail=n] [level=n] [debug] [usage]
+ detail = 1 : Patients, 2 : Studies, 3 : Series, 4 : Images
+ 5 : Full Content
+ level = 0,1,2 : depending on user (what he wants to see, when detail=5)
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * MakeDicomDir
+
+ Explores recursively the given directory, makes the relevant DICOMDIR
+ and writes it as 'NewDICOMDIR'
+ usage: MakeDicomDir dirname=rootDirectoryName
+ [ { [noshadowseq] | [noshadow][noseq] } ] [debug] [usage]
+ noshadowseq: user doesn't want to load Private Sequence
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * AnonymizeDicomDir
+
+ Anonymizes a gdcm-readable DICOMDIR even when some 'Objects'
+ are not yet taken into account
+ Warning : the DICOMDIR is overwritten;
+ to preserve its integrity, use a copy.
+ usage: AnonymizeDicomDir filein=dicomDirName [debug] [usage] [usage]
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
+
+ * PatchHeader
+
+ Allows aware user to patch a gdcm-parsable image header, without
+ loading image.
+ Warning : the image(s) is/are overwritten
+ to preserve image(s) integrity, use a copy.
+ WARNING : *NO CHECK* is performed on the new values.
+ Use only if you are sure the original values are wrong
+ *and* your values are right...
+ usage: PatchHeader {filein=inputFileName|dirin=inputDirectoryName}
+ [ { [size=] | [rows=][columns=] } ] [planes=]
+ [bitsallocated=] [bitsstored=]
+ [highbit=] [samplesperpixel=]
+ [pixelrepresentation=] [samplesperpixel=]
+ [ { [noshadowseq] | [noshadow][noseq] } ] [debug]
+
+ inputFileName : Name of the (single) file user wants to modify
+ inputDirectoryName : user wants to modify *all* the files
+ within the directory
+ newsize : new size, to overwrite old (wrong) one
+ or
+ rows : new Rows number, to overwrite old (wrong) one
+ columns : new Columns number, to overwrite old (wrong) one
+ planes : new Planes number, ...
+ bitsallocated : new Bits Allocated number, ...
+ bitsstored : new Bits Stored number, ...
+ highbit : new High Bit number, ...
+ samplesperpixel : new Samples Per Pixel, ...
+ pixelrepresentation : new Pixel Representation, ...
+
+ noshadowseq: user doesn't want to load Private Sequences
+ noshadow : user doesn't want to load Private groups (odd number)
+ noseq : user doesn't want to load Sequences
+ debug : user wants to run the program in 'debug mode'
+ usage : user wants to display usage
+
-3-) PrintDicomDir
-3-) MakeDicomDir
}}}
</pre>
projects / gdcm.git / commitdiff