MetaIO - National Alliance for Medical Image Computing
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1. Add 10 points to the list of tubePoints TubePnt pnt for unsigned int 1 0 1 lt 10 1 pnt new TubePnt 3 pnt gt m_X 0 1 position pnt gt m_X 1 1 pnt gt m_X 2 1 pnt gt m_R i radius tubel gt GetPoints push_back pnt MetaScene A metaScene is a metaObject that contains a flat list of metaObjects Member functions Add an object to the scene 18 void AddObject MetaObject object Return the number of objects in the scene int NObjects void const Get a list of objects present in the scene ObjectListT ype GetObjectList void return amp m_ObjectList Example Define a 3D Scene MetaScene scene 3 MetaEllipse el new MetaEllipse 3 el gt ID 0 el gt Radius 3 MetaGroup g0 MetaGroup gl new MetaGroup 3 gl gt ID 2 s gt AddObject gl s gt AddObject el s gt Write scene scn scene Clear s gt Read scene scn Annex Output File Example Here is the example of a metafile with a scene that contains metaObjects ObjectType Scen NDims 3 NObjects 3 ObjectType Group NDims 3 ID 2 EndGroup ObjectType Ellipse NDims 3 ID 0 ParentID Radius 1 2 3 ObjectType Lin NDims 3 ID 0 BinaryData False BinaryDataByteOrderMSB Fals ElementType MET FLOAT PointDim x y z vix vly viz NPoints 3 Points 12 3000 123000 19 1 2 3 00 00 ObjectType Landmark NDims2. be 1 4 To specify a particular byte ordering use ElementByteOrderMSB Tru or ElementByteOrderMSB Fals MSB aka big endian ordering is common to SPARC and Motorola processors e g Macintoshes LSB aka little endian ordering is common to Intel processors e g PC compatibles Putting it all together to convert a file containing the image data in a continuous block at the end of the file specify the header ObjectType Imag NDims 3 DimSize 256 256 64 ElementType MET USHORT HeaderSize 1 ElementSize 1 1 3 ElementSpacing 1 1 1 ElementByteOrderMSB Fals ElementDataFile image raw Reading DICOM and Other One Slice Per File Data Formats If the data is split to be one slice per file as is done with DICOM data only the ElementDataFile tag s option needs to change Since the MetaLibrary cannot automatically parse DICOM headers those headers must be skipped and the user must specify the image dimensions and other essential image information For DICOM files the MetaLibrary must automatically calculate the header size of each file luckily for almost every type of DICOM object in common use the image data is stored at the end To specify which files comprise the volume they can be specified as an ordered list in the MetaHeader using the ElementDataFile LIST option The filenames should be listed at the end of the MetaHeader after the ElementDataFile option and the filena
3. blob GetPoints MetaBlob PointListType const_iterator it plist begin 12 while it plist end for unsigned int d 0 d lt 3 d std cout lt lt it gt m_X d lt lt std cout lt lt std endl itt MetaEllipse MetaEllipse is an N Dimensional object to define ellipsoids like circles spheres or even hyper ellipsoids The only field you need to provide is the Radius There are several ways to input the radius a As an array of floats void Radius const float radius b As a single value which means that we are defining an hyper sphere void Radius float radius c A convenient way to define a 2D ellipse void Radius float rl float r2 d A convenient way to define a 3D ellipse void Radius float rl float r2 float r3 Example Create a sphere MetaEllipse myEllipse 3 myEllipse gt Radius 3 radius of 3 MetaGroup MetaGroup does not have added functionalities compared to metaObject It allows to group object in a metafile Metalmage Constructors Simple constructor by specifying the filename Metalmage const char headerName Constructor by shared memory Metalmage Metalmage im Other constructors Metalmage int nDims const int dimSize const float _elementSpacing MET ValueEnumType _elementType 13 int_elementNumberOfChannels 1 void elementData NULL Metalmage int x int _y float elementSpacingX float elementSpacingY MET ValueE
4. const float CenterOfRotation void const float CenterOfRotation int _ i const void CenterOfRotation const float position void CenterOfRotation int 1 float value Anatomical Orientation const char AnatomicalOrientationAcronym void const const MET OrientationEnumType AnatomicalOrientation void const MET OrientationEnumType AnatomicalOrientation int _dim const void AnatomicalOrientation const char _ao void AnatomicalOrientation const MET OrientationEnumType _ao void AnatomicalOrientation int dim MET OrientationEnumType _ao void AnatomicalOrientation int _dim char ao Element Spacing Physical Spacing in same units as position const float ElementSpacing void const float ElementSpacing int _1 const void ElementSpacing const float elementSpacing void ElementSpacing int 1 float value For simplicity some dynamic functions have been recently added They allow the user to add fields dynamically The function AddUserField is defined by template lt class T gt bool AddUserField const char fieldName MET_ValueEnumType _type int length T _v bool required true int dependsOn 1 The user may also want to clear the fields created by using ClearUserFields void GetUserField const char name Note When using GetUserField function the user is responsible for the deletion of the pointer created See the following example for details Example We create a simple 3D metaObject with some p
5. image raw matches the byte ordering native to the machine the application is running on e g PC s use LSB ordering and Suns Macs use MSB ordering If these assumptions are false the data will not be loaded correctly by the application To fix these problems 1 To skip the header bytes in the image data file use HeaderSize X where X is the number of bytes to skip at the beginning of the file before reading image data If you know there are no trailing bytes extra bytes at the end of the file you can specify HeaderSize 1 and Metalmage will automatically calculate the number of extract bytes in the data file assume they those bytes are at the head of the data file and automatically skip them before beginning to read the image data 2 To specify the spacing of the voxels use ElementSpacing X Y Z where X is the distance between of the centers of the voxels along the x dimension Y is the spacing in the y dimension and Z is the spacing in the z dimension Therefore to specify a 1x1x3mm voxel spacing use ElementSpacing 1 1 3 NOTE If ElementSpacing is not specified it is assumed to be equal to ElementSize If neither is specified both are assumed to be 1 3 To specify a voxel size use ElementSize X Y Z where X Y Z represent the size in the x y and z dimensions respectively NOTE If ElementSize is not specified it is assumed to be equal to ElementSpacing If neither is specified both are assumed to
6. not need to free the allocated memory Example MetaSurface surface 3 SurfacePnt pnt for unsigned int 1 0 1 lt 10 1 pnt new SurfacePnt 3 Position pnt gt m_X 0 float 0 2 pnt gt m_X 1 1 pnt gt m_X 2 1 17 Normal pnt gt m_V 0 float 0 8 pnt gt m_V 1 1 pnt gt m_V 2 1 surface gt GetPoints push_back pnt MetaTube A metaTube is a tubular structure defined by a list of connected points like a metaLine but more fields have been added for a complete representation especially the one of blood vessels To specify a point that belongs to the tube the user can define the position the radius at that point the normal s the tangent the color the Identification number the medialness the branchness the ridgeness and three alpha values that represents the ratio of the eigen values at that points Note that metaTube supports only 2D and 3D tubes Also for a metaTube the ID of the root can be specified by the command Root int rootID and the ID of the parent point can also be assessed using ParentPoint int parentpoint To access the internal list of points user should use the GetPoints function which returns the internal list by reference Note that the list is a list of pointers to point and is deleted automatically by the object itself so the user does not need to free the allocated memory Example Create a 3D tube MetaTube tubel new MetaTube 3 tube1 gt ID 0
7. 3 ID 0 BinaryData True BinaryDataByteOrderMSB Fals ElementType MET FLOAT PointDim x y z red green blue alpha NPoints 2 Points T2603 16 0 0000 DO de 23s 1 0 0 20 0 0 2 20 12 3 22 0 05 0 08 05 2 0 Annex Spatial Objects MetalO has also been chosen to support Spatial Objects IO To obtain a complete documentation of Spatial Objects and how to read write them out please see the Insight user s manual available at www itk org Reference Tags of Metalmage MetaObject Tags The tags of MetaObject are Comment MET_STRING User defined arbitrary ObjectType MET STRING Defined by derived objects e g Tube Image ObjectSubType MET STRING Defined by derived objects currently not used TransformType MET STRING Defined by derived objects e g Rigid NDims MET INT Defined at object instantiation Name MET_STRING User defined ID MET_INT User defined else 1 ParentID MET_INT User defined else 1 BinaryData MET STRING Are the data associated with this object stored at Binary or ASCH Defined by derived objects ElementByteOrderMSB MET_ STRING BinaryDataByteOrderMSB MET_STRING Color MET FLOAT ARRAY 4 R G B alpha opacity 20 Position MET_FLOAT_ARRAY NDims X Y Z of real world coordinate of 0 0 0 index of image Orientation MET_FLOAT_MATRIX NDims NDims 0 0 0 1 0 2 speci
8. K specific wrapping examples and tests Certain examples such as the MetalmageViewer also require FLTK a cross platform user interface library available from http fitk org Install FLTK and then ITK to have every MetalO example built Numerous other ITK examples also rely on FLTK See the file Insight Examples MetalmageReadWrite for a working example on how to develop a program using Metalmage for IO Work is underway to add access to other MetaObjects e g tubes spheres etc via ITK s SpatialObjects in Insight Code SpatialObject Quick Start Data conversion via MetaHeaders This section assumes that you have some data that you wish to process using an application that reads Metalmages This section gives examples on how convert your data to the Metalmage format For uncompressed data i e data stored in a raw format as is often done for DICOM BMP and PNG formats conversion to Metalmage is actually just a matter of specifying a Metalmage Headerfile a MetaHeader that describes and points to the file s containing your data For compressed data i e data stored in JPEG or GIF formats you must first convert your data to a non compressed format Currently no data compression methods are supported by Metalmage but adding support for gz RLE and other compression formats is high on our To Do list One of the most robust image conversion software packages is ImageMagick http www imagemagick org Unix
9. MetalO Medical Image I O Made Simple Abstract Our goal was to create a simple flexible cross platform image file format that supported medical image application development This meant that the image file format and its associated image I O library had to support 1 Image acquisition information essential to the correct processing and alignment of medical images e g voxel element size and spacing and image position and orientation MSB Most significant bit Mac Sun and LSB Least significant bit PC byte ordering Arbitrary atomic pixel types char unsigned char short float etc N dimensional data Image data stored in one file or in one file per sub dimensional e g N 1 slice Text based headers that are easily read and edited Optionally storing data in a file s separate from the header to simplify conversion to from other formats Metal mage is the text based tagged file format for medical images that resulted We have now extended that file format to support a variety of objects that occur in medicine such a tubes for vessels needles etc blobs for arbitrary shaped objects cubes spheres etc The complete library is known at Metal O The central code of Metalmage MetalO is quite stable Metalmage has been in use for several years by a wide range of research at UNC Chapel Hill New features are occasionally added but backward compatibility will always be maintained Current info on MetaObjects is avail
10. O metaScene and metaGroup are also a useful objects that support multiple metaObjects All these objects are described in details next MetaObject Constructors Simple constructor MetaObject void Read a metafile and store the result in the current object MetaObject const char _ fileName Define the dimension of the object at construction time MetaObject unsigned int dim Member functions Specify the filename to read Optional void FileName const char fileName const char FileName void const Read a MetaFile bool Read const char _fileName NULL Write a MetaFile bool Write const char file Name NULL virtual bool Append const char _headName NULL Print the info about the metaObject virtual void PrintInfo void const Clear the information as well as the data of the metObject virtual void Clear void Field descriptions Name void Name const char _Name const char Name void const Color const float Color void const void Color float _r float _g float _b float a void Color const float color ID ID number of the current metaObject void ID int _id int ID void const Parent ID ID number of the parent metaObject void ParentID int _parentld int ParentID void const Binary Data Specify if the data is binary or not void BinaryData bool _binaryData bool BinaryData void const Binary Data Byte Order void BinaryDataByteOrderMSB bool _binaryDataByteO
11. Type Imag NDims 2 BinaryData True 15 BinaryDataByteOrderMSB Fals ElementSpacing 1 2 DimSize 8 8 ElementType MET CHAR ElementDataFile LOCAL Pixel Data MetaLandmark MetaLandmark is a simple list of landmarks The number of landmarks defining the object is set using the function NPoints int npnt How the position of the points is stored in the file By default the configuration is x y z red green blue alpha PointDim const char pointDim To access the internal list of points user should use the GetPoints function which returns the internal list by reference Note that the list is a list of pointers to point and is deleted automatically by the object itself so the user does not need to free the allocated memory Example Create a 3D Landmark MetaLandmark Landmark 3 Landmark ID 0 LandmarkPnt pnt Add some landmarks to the list of landmark points for unsigned int 1 0 1 lt 10 1 pnt new LandmarkPnt 3 pnt gt m_X 0 float 0 2 pnt gt m_X 1 1 pnt gt m_X 2 1 Landmark GetPoints push_back pnt MetaLine A metaLine is actually a polyline defined by a list of connected points A point on the line has a given position a normal and a color To set the position the local variable m_X should be filled in the point structure The variable m_V which is a double pointer to a float is used to assess the normal The normal has the dimension of the object minus one sin
12. able from http caddlab rad unc edu technologies metaObjects Table of Contents ADS aaa 1 Tableof o ei 2 Introduction and Installation ii ene ees 3 Obtaining Metal Os e NE 3 Installing The MetalO Packages o di 3 Metalmage as a stand alone package 0 cccccceccesceeeessecseecseeeneeeeeeeeeeseensecaecsaecnaecaaecaeeeaeeeaeeseeseeeeerentens 3 MetalO with the NLM s Insight toolkit ATK ccceccecscessseescesecesceseeeeceeeeesecaecaecseeeaeeeaeeneeeeeeeerenrens 4 Quick Start Data conversion via MetaHeaders c cccccccsssccssscesecceesseceeeeessecsseccessecesecesseceeeecsaeceeeeecsseeeeees 4 Reading a Brick f Byte Sinan a BS I ee cia 5 Reading DICOM and Other One Slice Per File Data Formats 0 ecececcsseecsssecseeeecneeeeceeeeeceeeaeeeeeaeeatenes 6 Metal Eabrary sce a nee eae E E ee ie 7 Mie ta by Cts e Mucha Hoek eee eee ee ee 8 Meri A e o eae ee 8 CONSTITUCIONES dE ainda cit 8 Member functions A adas cove di 8 Biel dC A eo seca ee 8 EX ii A A A a Rie esac aes asnos 10 MetaBlob A eG ane et Re ee Me dd ta O 12 EXAMPLE AR 12 MetaBllipse uc Aa 13 EXP A Re 13 Meta TOUS ara 13 Met A Ata 13 EONSTTUCIO a A is 13 Member functions HeaderSiZ ib 14 Field desert pttons A A A n 15 EXPLO A a sao 15 Me taland mark e e a t i Te 16 Example A A a 16 Met O e e lo deat 16 Ex e A AE 17 Meta odes tos ches ase bee e dnd eons 17 EXAMIple cer EE edo dae o o ee hls Gaol ae 17 Meta Tuba che hiv e O feet e e ti o e e
13. and PC versions available It has an application called convert that handles most of the popular 2D image formats IF YOU HAVE INSTALLED METAIO AS PART OF ITK USE THE PROGRAM Insight Examples Metalmagelmporter IT WILL ASK A SERIES OF QUESTIONS AND PRODUCE A METAIMAGE HEADER FOR YOU Reading a Brick of Bytes A brick of bytes is a volume of image data stored in a single file possibly with preceding and trailing non image data To correctly load these images the minimal information that you need to know is 1 Number of dimensions 2 Size of each dimension 3 Data type 4 Name of the data file For example let s say the data was 3 dimensional had 256 x 256 x 64 voxels used an unsigned short to represent the value at each voxel and was stored in the file image raw The resulting MetaHeader our naming convention would call this file image mhd file would read ObjectType Imag NDims 3 DimSize 256 256 64 ElementType MET USHORT ElementDataFile image raw this tag must be last in a MetalmageHeader That s it but this assumes quite a bit about the image data Specifically it assumes 1 There are not any non image data bytes header data at the beginning of the image data file image raw 2 The voxels are cubes the distance spanned by and between a voxel in each coordinate direction is unit e g 1x1x1mm voxel size and voxel spacing 3 The byte order of the data in
14. are in the stand alone MetalO package is as follows MetalO doc tests The top level contains the source files the header files and the CMakeLists txt file that is used by the CMake program to compile MetalO This document and the MetaObjects www pages are in the doc directory A sequence of simple tests is available in the tests directory The hierarchy of the software in the ITK distribution is as follows Insight Code Utilities MetalO doc tests Insight Code IO Insight Examples MetalmageReadWrite Metalmage Viewer MetalmageColorViewer Metalmagelmporter The files in Insight Code Utilities exactly match those in the stand alone MetalO package Routines to wrap metalmage so that it can be accessed via the itkImageIO Object Factory are in Insight Codc IO The details of the Examples are provided later in this documents Metalmage as a stand alone package If you downloaded MetalO separate from Insight you must also download and install CMake from www CMake org That www site provide details regarding installing CMake and using it to compile another program Follow those directions to create the MetalO library and tests A minimal description of the process is presented next 1 Install CMake 2 On Windows a Run CMake exe b Inthe source directory field browse to the top level of the MetalO directory c Inthe binary directory field enter the path and name of the source directory but add VC to the directory nam
15. ataFileNumStep enacts this ObjectType Imag NDims 3 DimSize 512 512 50 ElementType MET USHORT HeaderSize 1 ElementSize 11 3 ElementSpacing 1 1 2 ElementByteOrderMSB Fals ElementDataFile baseName 03d 1 100 2 The complete set of Metalmage Tags are given in the Reference section of this document The next section discusses how to use the Metalmage Library for image reading and writing in your own programs MetalO Library The base class of the MetalO library is the MetaObject class It defines a base set of tags that are common to all metaObjects such as Metalmages MetaTubes etc The tags are defined using the protected member functions SetupReadFields and SetupWriteFields These functions create a list of MetaFieldRecords to define the name type interdependence and necessity of each tag Helper functions for defining the fields are in MetaUtils cxx The types are defined via enums in MetaTypes h The derived classes add tags to the list via their own SetupReadFields and SetupWriteFields member functions The Metalmage subclass also re implements the Read and Write methods since non tag data i e the pixel values must also be read Compare the derived classes for MetaCube and Metalmage MetaObjects In this section we describe the metaObjects which have been implemented already If you want to implement other objects you can easily derive these classes metaObject is the base class for metal
16. ce a metaLine in a 3D space will have two normals a plane Note that the user does not need to allocate the memory for those variables this is done automatically in the constructor of the point To access the internal list of points user should use the GetPoints function which returns the internal list 16 by reference Note that the list is a list of pointers to point and is deleted automatically by the object itself so the user does not need to free the allocated memory Example Create a 3D MetaLine MetaLine Line 3 LinePnt pnt for unsigned int 1 0 1 lt 10 1 pnt new LinePnt 3 Define the position pnt gt m_X 0 float 0 2 pnt gt m_X 1 1 pnt gt m_X 2 1 Define the normals pnt gt m_V 0 0 float 0 3 pnt gt m_V 0 1 1 pnt gt m_V 0 2 1 pnt gt m_V 1 0 float 0 4 pnt gt m_V 1 1 1 1 pnt gt m_V 1 2 1 1 Line gt GetPoints push_back pnt Write the result Line BinaryData true Line Write myLine meta MetaSurface The definition of a metaSurface is quite similar to the metaLine s except for the normal which is only a NDim vector i e an array of floats where NDim is the dimension of the metaObject To access the internal list of points user should use the GetPoints function which returns the internal list by reference Note that the list is a list of pointers to point and is deleted automatically by the object itself so the user does
17. e this assumes that you are compiling using VC otherwise add an equally descriptive name for the directory to store the binaries in such as MetalO bcc for Borland d Press the configure button It will ask if you want to create the binary directory press yes Specify your compiler in the pull down menu field f Press the configure button a second time and then press okay to generate the Makefiles for your compiler e g MetalO dsw and related files for VC in the binary directory 3 On nix Cygwin machines a At an appropriate spot create a directory MetalO g or give it an equally descriptive name based on your compiler cd MetalO g c Run ccmake lt path to MetalO source directory gt d Press g to generate the makefiles for your compiler in the binary directory o To use MetalO in your stand alone programs 1 add the MetalO directory to your include paths 2 add include lt metalmage h gt to the top of the your file that performs your image IO 3 add the MetalO binary directory to your link paths and 4 link with the MetalO library See the files in MetalO tests for examples of how to read write Metalmages and other MetaObjects MetalO with the NLM s Insight toolkit ITK If you have downloaded and are installing MetalO as part of the Insight toolkit follow the standard installation procedure of Insight This will create the MetalO library and the IT
18. ee 18 Example tn ee ad ne e e el 18 RAS AA OO 18 Member functions es tee be cto de al anne wes 18 Example td eto da dead e eek ade dasa li e O E AE O 19 Annex Output File Example cira e a a e a a e a r aa a a TE 19 AMEX Spatial Objects iii A EA E Se 20 Reference Tags of Metalmage esseeessseesseeeessesresseserstesteresstetessesetstsstestsstetesttstestesttsteseetesststessesteseeseeeso 20 MetaQObj ect Tags dea 20 Tags Added by Metala gesn neen ni E E OAE A RE E E a 21 Introduction and Installation Obtaining MetalO MetalO is being distributed over the WWW by its developers in the CADDLab at UNC http caddlab rad unc edu technologies metaObjects MetalO is also being distributed with the National Library of Medicine s Insight Tookit ITK for medical image segmentation and registration http www itk org Installing The MetalO Package MetalO is a hierarchy of C classes and functions We have yet to find a modern C compiler that does not compile MetalO Know compatible compilers include G v2 95 and beyond and probably previous Microsoft Visual C 6 0 Sun s CC on Solaris 2 6 and beyond Intel compiler and compilers on other workstations including HPs SGIs and Alpha systems Please contact us Stephen R Aylward aylward unc edu Julien Jomier mailto jomier unc eduor via http caddlab rad unc edu if you encounter any incompatibilities between our code and your compiler The hierarchy of the softw
19. f each voxel ElementType MET_STRING One of enum type MET_UCHAR MET CHAR See MetalmageTypes h ElementDataFile MET_STRING One of the following Name of the file to be loaded A printf style string followed by the min max and step values to be used to pass an argument to the string to create list of file names to be loaded must be N 1 D blocks of data per file LIST X This specifies that starting on the next line is a list of files one filename per line in which the data is stored Each file by default contains an N 1 D block of data If a second argument is given its first character must be a number that specifies the 21 dimension of the data in each file For example ElementDataFile LIST 2D means that there will be a 2D block of data per file LOCAL Indicates that the data begins at the beginning of the next line 22
20. fy X Y Z direction in real world of X axis of image 111101 00001 00112 specify X Y Z direction in real world of Y axis of image etc AnatomicalOrientation MET_STRING Specify anatomic ordering of the axis Use only RIL A P S I per axis For example if the three letter code for column index row index slice index is ILP then the origin is at the superior right anterior corner of the volume and therefore the axes run from superior to inferior from right to left from anterior to posterior ElementSpacing MET FLOAT _ARRAY NDims The distance between voxel centers Tags Added by Metalmage In addition to the above tags Metalmage provides the following tags DimSize MET_INT_ARRAY NDims Number of elements per axis in data HeaderSize MET INT Number of Bytes to skip at the head of each data file Specify 1 to have Metalmage calculate the header size based on the assumption that the data occurs at the end of the file Modality MET_ STRING One of enum type MET MOD _CT MET MOD MR MET MOD US See MetalmageTypes h SequenceID MET_INT_ARRAY 4 Four values comprising a DICOM sequence Study Series Image numbers ElementMin MET FLOAT Minimum value in the data ElementMax MET FLOAT Maximum value in the data ElementNumberOfChannels MET_INT Number of values of type ElementType per voxel ElementSize MET FLOAT _ARRAY NDims Physical size o
21. mes should be separated by whitespace ObjectType Imag NDims 3 DimSize 512 512 100 ElementType MET USHORT HeaderSize 1 ElementSize 11 3 ElementSpacing 1 1 1 ElementByteOrderMSB Fals ElementDataFile LIST filenameOfSlicel filenameOfSlice2 filenameOfSlice3 filenameOfSlice4 one hundred filenames must be specified to specify the 100 slices in the volume The second way of specifying a series of files can be used if the filenames are numerically distinguished That is the files names should be able to be specified using a numeric substitution into a c style printf string for a range of values In pseudo code for i numBegin to numEnd step numStep sprintf sliceName baseName 03d i end The parameters of this system are numBegin numEnd numStep and the c style printf string e g baseName 03d The begin end and step parameters appear in order after the c style printf string ObjectType Imag NDims 3 DimSize 512 512 100 ElementType MET USHORT HeaderSize 1 ElementSize 1 1 3 ElementSpacing 1 1 1 ElementByteOrderMSB Fals ElementDataFile baseName 03d 1 100 1 This Metalmage will cause the files baseName 001 to baseName 100 to be read to create a 100 slice volume In this case because of the overlap of the slices it may be helpful to only consider every other slice in the volume Changing the slice spacing and the ElementD
22. numType _elementType int _elementNumberOfChannels 1 void elementData NULL Metalmage int x int _y int_z float elementSpacingX float elementSpacingY float _elementSpacingZ MET_ValueEnumType _elementType int_elementNumberOfChannels 1 void elementData NULL Member functions HeaderSize Return the size of the header int HeaderSize void const Quantity Total number of elements in the image int Quantity void const SubQuantity Number of elements in image spanning sub dimensions E g elements per line 2D sub image 3D sub volume const int SubQuantity void const int SubQuantity int _1 const ElementMin Max The default max returned is the largest allowed by ElemNBytes 12 bit uint16_t will give 4096 max This may not represent the true max Use _reCalc true to force a calcuation of the actual max element value bool ElementMinMaxValid void const void ElementMinMaxValid bool _elementMinMaxValid void ElementMinMaxRecalc void double ElementMin void const void ElementMin double _elementMin double ElementMax void const void ElementMax double _elementMax ElementByteOrderSwap These functions are available only after ReadlmageData or if _read_and_close TRUE when read void ElementByteOrderSwap void bool ElementByteOrderFix void ConverTo Converts to a new data type Rescales using Min and Max bool ConvertElementDataTo MET_ ValueEnumType _elementType MET_UCHAR double _
23. rderMSB bool BinaryDataByteOrderMSB void const Comments const char Comment void const void Comment const char comment Object Typename and optional subtype i e the type of the object const char ObjectTypeName void const void ObjectTypeName const char objectTypeName const char ObjectSubTypeName void const void ObjectSubTypeName const char objectSubTypeName Associated transformations Physical location in millimeters and with respect to machine coordinate system or the patient of the first element in the image Physical orientation of the object is defined as an NDims x NDims matrix Offset const float Offset void const float Offset int _1 const void Offset const float position void Offset int i float value Position const float Position void const float Position int _i const void Position const float _ position void Position int _i float value Origin const float Origin void const float Origin int _1 const void Origin const float position void Origin int _i float value Rotation const float Rotation void const float Rotation int 1 int _j const void Rotation const float orientation void Rotation int i int _j float value Orientation const float Orientation void const float Orientation int _1 int _j const void Orientation const float orientation void Orientation int i int _j float value Center of rotation of the object
24. rom metaObject MetaBlob A blob is defined by a list of points that describe the object The points can be inside the object if obtained by connected component for instance or only on the surface Note that a color RGBA can be associated which each point The required fields are The number of points defining the object NPoints int npnt How the position of the points is stored in the file By default the configuration is x y z red green blue alpha PointDim const char pointDim To access the internal list of points user should use the GetPoints function which returns the internal list by reference Note that the list is a list of pointers to point and is deleted automatically by the object itself so the user does not need to free the allocated memory Example Create a 3D blob MetaBlob blob 3 blob ID 0 define the ID of the blob Add 10 points to the blob BlobPnt pnt unsigned int i for 1 0 1 lt 10 1 gt pnt new BlobPnt 3 pnt gt m_X 0 float 0 2 pnt gt m_X 1 1 pnt gt m_X 2 1 blob GetPoints push_back pnt push the created point into the list of points Write the blob in binary format blob BinaryData true blob ElementT ype MET_ FLOAT blob Write myBlob meta Read the file blob Read myBlob meta blob PrintInfo Access the list of points std cout lt lt Accessing pointlist lt lt std endl MetaBlob PointListType plist
25. roperties 10 MetaObject tObj 3 Create a 3D metaObject tObj FileName testObject txt Define the name of the file tObj Comment TestObject Add some comments tObj ObjectTypeName Object Define the type of the object tObj ObjectSubTypeName MinorObject and the subtype as well We now define the position and the orientation as well as the spacing of the created object The position part tObj Position 0 1 tObj Position 1 2 tObj Position 2 3 The orientation part float orient 9 int i for 1 0 1 lt 9 i orient i 0 orient 0 1 orient 5 1 orient 7 1 tObj Orientation orient The element spacing part tObj ElementSpacing 0 1 tObj ElementSpacing 1 2 tObj ElementSpacing 2 1 Add user s defined fields tObj AddUserField MyName MET STRING strlen JulienAndStephen JulienAndStephen Write the object tObj Write Clear completely the object tObj Clear tObj ClearUserFields Specify that we want to read the field MyName tObj AddUserField MyName MET STRING Read the object tObj Read testObject txt Print the object t0bj PrintInfo Get the name in the file char name static_cast lt char gt tObj GetUserField MyName std cout lt lt name lt lt std endl delete the allocated pointer delete name 11 All of the following objects derive f
26. toMin 0 double _toMax 0 14 Field descriptions Modality Specify the modality of the image MET_ImageModalityEnumType Modality void const void Modality MET_ImageModalityEnumType _modality Dimension size Specify the size of the image in each dimension void DimSize const int _dimSize void DimSize int _i int value SequencelD DICOM designation of this image relative to other images acquired at the same time const float SequenceID void const float SequenceID int _1 const void SequencelD const float _sequenceID void SequenceID int _i float value ElementSize Optional Field Physical size in MM of each element in the image 0 xSize 1 ySize 2 zSize const float ElementSize void const float ElementSize int i const void ElementSize const float _pointSize void ElementSize int _i float value ElementType Pixel type MET ValueEnumType ElementType void const void ElementType MET ValueEnumType _elementType ElementNumberOfChannels Number of channels int ElementNumberOfChannels void const void ElementNumberOfChannels int _elementNumberOfChannels ElementData Returns a pointer to the data void ElementData void double ElementData int _1 const void ElementData void data bool ElementData int 1 double _v ElementDataFileName Set Get the filename const char ElementDataFileName void const void ElementDataFileName const char _dataFileName Example Object
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