DICOM file reader. More...
#include <VolumeViz/readers/SoVRDicomFileReader.h>
Public Member Functions | |
virtual SoType | getTypeId () const |
Returns the type identifier for this specific instance. | |
SoVRDicomFileReader () | |
Constructor. | |
virtual int | setFilename (const SbString &filename) |
Specify the name of a DICOM file or a file containing a list of DICOM files to load. | |
int | setFilenamePattern (const SbString &pattern) |
Specify a pattern of DICOM files to load. | |
int | setFilenameList (const SbStringList &filenameList) |
Specify a list of DICOM files to load. | |
SbBool | setFilenameList (const SbString &format, const int startIndex=0, const int endIndex=INT_MAX, const int indexStep=1) |
Specify a list of DICOM files to load, using a sprintf-like format. | |
bool | setFilenameListFromSeries (const SbString &base) |
Specify a DICOM file and load all image files in the same directory that are part of the same "series" based on the series UID (0x0020,0x000E). | |
void | loadInMemory () |
Load the DICOM data into contiguous memory if possible. | |
SbBool | setDirectory (const SbString &folder) |
Specify a directory containing DICOM files to load. | |
virtual ReadError | getDataChar (SbBox3f &size, SoDataSet::DataType &type, SbVec3i32 &dim) override |
Gets the characteristics (file header) of the data volume. | |
virtual SbBool | setOutputDataType (SbBool doChange, SoDataSet::DataType type) |
Requests that the input be converted (if necessary) to the specified data type. | |
virtual void | getSubSlice (const SbBox2i32 &subSlice, int sliceNumber, void *data) |
Must copy the rectangular part defined by subSlice of the XY slice sliceNumber to the memory referenced by data. | |
int | getNumSignificantBits () |
This method is optional. | |
virtual SoVolumeReader::ReaderType | getReaderType () |
Returns the reader type. | |
const SoVRDicomData & | getDicomData () const |
Returns an instance of SoVRDicomData for the first image of this volume. | |
const SiDicomDataSet * | getDicomDataSet (const size_t sliceIdx) const |
Returns a DICOM data object for the specified slice containing all the DICOM attributes. | |
void | loadSliceDicomData (int slice, SoVRDicomData &dicomData) const |
Loads the Dicom data of the given slice. | |
virtual SbBool | isThreadSafe () const |
SoVRDicomFileReader is thread safe. | |
virtual void | closeAllHandles () |
Close all file handles currently opened by the reader. | |
virtual void | restoreAllHandles () |
Restore all file handles closed by closeAllHandles method. | |
Public Member Functions inherited from SoVolumeReader | |
SoVolumeReader () | |
Constructor. | |
virtual SbBool | setInputDataRange (SbBool doChange, double min, double max) |
Requests that the input be converted from the specified range to the range depending on the output data type. | |
virtual void | getSubSlice (const SbBox2i32 &subSlice, int sliceNumber, SoBufferObject *dataBuffer) |
Same as getSubSlice( const SbBox2i32& subSlice, int sliceNumber, void * data ) but using an SoBufferObject as the target of the data. | |
SbVec3i32 | getNumVoxels (const SbVec3i32 &realSize, const SbVec3i32 &subsamplingLevel) |
Utility function provided by SoVolumeReader for subclass readers to call. | |
SbVec3i32 | getSizeToAllocate (const SbVec3i32 &realSize, const SbVec3i32 &subsamplingLevel) |
Utility function provided by SoVolumeReader for subclass readers to call. | |
SbString | getFilename () const |
Returns the path of the file. | |
virtual SbBool | isDataConverted () const |
Returns TRUE if the data is already organized in tiles for the LDM module. | |
virtual void | reloadTileMinMax () |
virtual SbBool | getTileSize (SbVec3i32 &size) |
Returns tile dimensions in voxels when using data stored in tiles. | |
virtual SoBufferObject * | readTile (int index, const SbBox3i32 &tilePosition) |
Given an index, reads a tile if the data is organized in tiles (for LDM). | |
virtual SbBool | readXTraceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const SbVec2i32 &tracePosition) |
Read directly from the data source, a trace inside a tile. | |
virtual SbBool | readYSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition) |
Read directly from the data source, an orthoslice on the Y axis (Zaxis == 1) inside a tile. | |
virtual SbBool | readZSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition) |
Read directly from the data source, an orthoslice on the Z axis (Zaxis == 2) inside a tile. | |
virtual SbBool | readXSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition) |
Read directly from the data source, an orthoslice on the X axis (Zaxis == 0) inside a tile. | |
virtual SbBool | isIgnoredFile () const |
Should return TRUE if at least one file has been ignored during reading. | |
virtual SbString | getOriginalFilename () const |
Returns original file name from which the data has been converted to LDM format if stored in file. | |
virtual SbBool | getMinMax (int64_t &min, int64_t &max) |
Returns min and max for integer data type, if available. | |
virtual SbBool | getMinMax (double &min, double &max) |
Returns min max for float data type, if available. | |
virtual SbBool | getHistogram (std::vector< int64_t > &numVox) |
Returns histogram if available. | |
virtual SbBool | setDirectCoordSysAutoDetection (SbBool autoValue) |
Sets whether or not the reader should automatically try to detect if the coordinate system used is direct or not. | |
virtual SbBool | getDirectCoordSysAutoDetection () |
Return automatic detection value. | |
virtual SbBool | setDirectCoorSys (SbBool directCoord) |
Specify if the coordinate system used is direct or not. | |
virtual SbBool | getDirectCoordSys () |
Return whether the coordinate system used is direct or not. | |
virtual SbVec2d | getTileMinMax (int index) const |
Returns the minimum and maximum data values for the given tile. | |
virtual SoVolumeWriter * | getConfiguredWriter () |
Returns a volume writer that corresponds to this reader (same format, parameters, etc). | |
CoordinateType | getCoordinateType () |
Returns coordinate type used by the data set. | |
const float * | getRectilinearCoordinates (Axis axis) const |
Returns the coordinates for the specified axis. | |
void | setRectilinearCoordinates (const float *x, const float *y, const float *z) |
Sets rectilinear coordinates for the data set. | |
virtual SbBool | isRGBA () const |
Returns TRUE if the data set contains RGBA color values. | |
void | setRGBA (const SbBool flag) |
Specifies if data must be considered as RGBA. | |
virtual SoDEPRECATED SbBool | readTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition) |
Given an index, reads a tile if the data is organized in tiles (for LDM). | |
virtual SoDEPRECATED SbBool | readTile (int index, SoBufferObject *buffer, const SbBox3i32 &tilePosition) |
Same as readTile(int index, unsigned char*& buffer, const SbBox3i32& tilePosition) but using an SoBufferObject (allocated by LDM) as the target of the data. | |
virtual SoDEPRECATED int | getBorderFlag () |
Returns border (overlap) value if stored in file. | |
virtual SoDEPRECATED SbBool | getMinMax (int &min, int &max) |
Returns min max if stored in file. | |
Public Member Functions inherited from SoFieldContainer | |
void | setToDefaults () |
Sets all fields in this object to their default values. | |
SbBool | hasDefaultValues () const |
Returns TRUE if all of the object's fields have their default values. | |
SbBool | fieldsAreEqual (const SoFieldContainer *fc) const |
Returns TRUE if this object's fields are exactly equal to fc's fields. | |
void | copyFieldValues (const SoFieldContainer *fc, SbBool copyConnections=FALSE) |
Copies the contents of fc's fields into this object's fields. | |
SoNONUNICODE SbBool | set (const char *fieldDataString) |
Sets one or more fields in this object to the values specified in the given string, which should be a string in the Open Inventor file format. | |
SbBool | set (const SbString &fieldDataString) |
Sets one or more fields in this object to the values specified in the given string, which should be a string in the Open Inventor file format. | |
void | get (SbString &fieldDataString) |
Returns the values of the fields of this object in the Open Inventor ASCII file format in the given string. | |
virtual int | getFields (SoFieldList &list) const |
Appends references to all of this object's fields to resultList, and returns the number of fields appended. | |
virtual int | getAllFields (SoFieldList &list) const |
Returns a list of fields, including the eventIn's and eventOut's. | |
virtual SoField * | getField (const SbName &fieldName) const |
Returns a the field of this object whose name is fieldName. | |
virtual SoField * | getEventIn (const SbName &fieldName) const |
Returns a the eventIn with the given name. | |
virtual SoField * | getEventOut (const SbName &fieldName) const |
Returns the eventOut with the given name. | |
SbBool | getFieldName (const SoField *field, SbName &fieldName) const |
Returns the name of the given field in the fieldName argument. | |
SbBool | enableNotify (SbBool flag) |
Notification at this Field Container is enabled (if flag == TRUE) or disabled (if flag == FALSE). | |
SbBool | isNotifyEnabled () const |
Notification is the process of telling interested objects that this object has changed. | |
virtual void | setUserData (void *data) |
Sets application data. | |
void * | getUserData (void) const |
Gets user application data. | |
Public Member Functions inherited from SoBase | |
virtual void | touch () |
Marks an instance as modified, simulating a change to it. | |
virtual SbName | getName () const |
Returns the name of an instance. | |
virtual void | setName (const SbName &name) |
Sets the name of an instance. | |
void | setSynchronizable (const bool b) |
Sets this to be a ScaleViz synchronizable object. | |
bool | isSynchronizable () const |
Gets the ScaleViz synchronizable state of this object. | |
Public Member Functions inherited from SoRefCounter | |
void | ref () const |
Adds a reference to an instance. | |
void | unref () const |
Removes a reference from an instance. | |
void | unrefNoDelete () const |
unrefNoDelete() should be called when it is desired to decrement the reference count, but not delete the instance if this brings the reference count to zero. | |
int | getRefCount () const |
Returns current reference count. | |
void | lock () const |
lock this instance. | |
void | unlock () const |
unlock this instance. | |
Public Member Functions inherited from SoTypedObject | |
SbBool | isOfType (const SoType &type) const |
Returns TRUE if this object is of the type specified in type or is derived from that type. | |
template<typename TypedObjectClass > | |
SbBool | isOfType () const |
Returns TRUE if this object is of the type of class TypedObjectClass or is derived from that class. | |
Static Public Member Functions | |
static SoType | getClassTypeId () |
Returns the type identifier for this class. | |
Static Public Member Functions inherited from SoVolumeReader | |
static SoType | getClassTypeId () |
Returns the type identifier for this class. | |
static SoVolumeReader * | getAppropriateReader (const SbString &filename) |
Returns a preconfigured SoVolumeReader instance that can be used to load the given file (based on the filename extension). | |
Static Public Member Functions inherited from SoFieldContainer | |
static SoType | getClassTypeId () |
Returns the type of this class. | |
Static Public Member Functions inherited from SoBase | |
static SoType | getClassTypeId () |
Returns type identifier for this class. | |
Static Public Member Functions inherited from SoTypedObject | |
static SoType | getClassTypeId () |
Returns the type identifier for this class. | |
Additional Inherited Members | |
Public Types inherited from SoVolumeReader | |
enum | ReadError { RD_NO_ERROR , RD_FILE_NOT_FOUND_ERROR , RD_INVALID_DATA_ERROR , RD_UNSUPPORTED_DATA_TYPE_ERROR , RD_FILE_FORMAT_NOT_VALID_ERROR , RD_UNKNOWN_ERROR } |
Read error. More... | |
enum | Axis { X , Y , Z } |
Which axis to handle. More... | |
enum | ReaderType { NO_READER , AM , AVS , DICOM , GENERIC , LDM , MEMORY , RASTERSTACK , SEGY , VOL , VOX , TIFF , MRC } |
Available reader type. More... | |
enum | CoordinateType { COORDINATES_UNIFORM = 0 , COORDINATES_RECTILINEAR } |
Coordinate type used by this data set. More... | |
Protected Member Functions inherited from SoVolumeReader | |
virtual | ~SoVolumeReader () |
Destructor. | |
void * | getBuffer (int64_t offset, unsigned int size) |
Returns a pointer to a buffer of size bytes corresponding to a part of the file at offset bytes from the beginning of the file. | |
int64_t | fileSize () |
Returns the size of the file when file I/O is handled by this class. | |
Static Protected Member Functions inherited from SoVolumeReader | |
static bool | registerVolumeReaderExtension (const SbString &fileExtension, const SoType &readerType) |
Register an SoVolumeReader class to handle a file extension. | |
static bool | unregisterVolumeReaderExtensions (const SoType &readerType) |
Unregister all filename extensions associated with the specified SoVolumeReader class. | |
static int | bytesToInt (const unsigned char *ptr, int sizeBytes) |
Utility method that returns an integer from sizeBytes bytes starting at address ptr. | |
static void | swapBytes (int *intPtr, int sizeBytes) |
Utility method to convert an integer into the correct architecture (little/big endian). | |
static void | swapBytesN (void *buffer, int numElements, int numBytesPerElement) |
Utility method to swap bytes of each element of an array of numElements elements. | |
static SbBool | isValidFloat (const float val) |
Utility method to check if value is a valid IEEE 754 floating point number. | |
static SbBox3f | adjustFlatExtent (const SbString &fileName, const SbBox3f &extent, const SbVec3i32 &dim) |
VolumeViz doesn't handles empty extent (for ex. | |
Protected Attributes inherited from SoVolumeReader | |
SoDEPRECATED SbBool | m_dataConverted |
Volume reader for the DICOM file format. VolumeViz automatically selects this reader if a filename is given and the file extension is ".dc3", ".dic", ".dcm", or ".dicom".
DICOM is a widely used format for storing medical image data (CT, MRI, etc), defined by the National Electrical Manufacturers Association (NEMA) (http://medical.nema.org).
SoVRDicomFileReader can load a volume from a single DICOM file or from a list of DICOM files (stack of images). Loading a volume from a single DICOM file is the same as loading any other format supported by VolumeViz (see setFilename(const SbString& filename)). Loading a volume from a list of DICOM files can be done by:
Unlike a raster stack, the position of each slice in a DICOM volume is determined by the location value in its file header and not by the order of the file name in the list. Also unlike a raster stack consisting of (for example) JPEG or PNG images, a DICOM file in the list may contain more than one slice of the volume. The reader handles this automatically. The first file in the list is considered the "reference" for the volume and all slices must be compatible with this one. Specifically this means that subsequent files must have the same width, height, data type and so on.
Note when using a list file: If the file extension is not ".dc3", ".dic" or ".dicom" VolumeViz will not automatically select the DICOM volume reader. You can either give the list file one of the DICOM file extensions or force VolumeViz to use the DICOM reader by explicitly creating an instance of SoVRDicomFileReader and calling the SoVolumeData method setReader().
The volume reader will automatically get the volume dimensions, data type, extent (voxel size/spacing) and number of significant bits from the DICOM file header. The reader will also apply the data adjustment (if any) specified by the RescaleSlope and RescaleIntercept tags in the DICOM file header, i.e.: actualValue = slope * storedValue + intercept. As part of this process the reader will automatically convert unsigned data to the corresponding signed data type if necessary (in other words if the rescale calculation produces negative values). The application can also explicitly specify the volume data type. This allows, for example, converting float data values to more compact integer values.
Note: The DICOM reader only uses the rescale slope and intercept values from the first file in the list. It does not currently handle the (less common) case where each file contains different rescale values.
Photometric Interpretation:
Volume extent:
The volume reader will compute the volume's width in X and height in Y from the volume dimensions and the voxel size. For example, if the volume dimension in X is 512 (voxels) and the voxel size in X is 0.408 mm, then the volume width is (approximately) 209 mm. The reader will compute the volume's depth in Z from the min and max slice locations specified in the file header(s). Note that for a DICOM data set, the volume 'position' is considered to be the center of the first voxel, however VolumeViz considers the volume extent (SoVolumeData::extent) to include all of the first and last voxels. Therefore the extent 'min' is alwaya the outside corner of the first voxel.
Data Range:
Use an SoDataRange node to specify the actual (or desired) range of data values to be mapped. For example, a typical initial data range for DICOM data calibrated in Hounsfield units might be -1000 to 3000.
Coordinate Systems:
In a medical imaging application there are at least three related coordinate systems.
Anatomical coordinates: The three standard viewing planes are Axial, Coronal and Sagittal. The Axial plane divides the body into Superior (head) and Inferior (foot) sections. The Coronal plane is a vertical plane dividing the body into Anterior (front) and Posterior (back) sections. The Sagittal plane divides the body longitudinally into Right and Left sections. The orientation of the patient in a medical data set is often specified using three letters to identify the primary axes, where each letter is one of the section names.
DICOM volumes typically have LPS (Left, Posterior, Superior) orientation. In this case VolumeViz considers that the direction:
In other words, the default camera view is looking at the top of the head with the body "face down".
When viewing a slice, also remember that the volume is always a 3D object to Open Inventor and you must also set the 'axis' field on the SoOrthoSlice node. See the dicomImageViewer example in the examples/source/Medical/Input directory.
DICOM Attributes
All DICOM attributes, including hierarchical data like Structured Reports, can be traversed and queried using SiDicomDataSet (see getDicomDataSet()). See the DicomSimpleViewer example in the examples/source/VolumeViz/examples directory.
Definition at line 198 of file SoVRDicomFileReader.h.
SoVRDicomFileReader::SoVRDicomFileReader | ( | ) |
Constructor.
|
virtual |
Close all file handles currently opened by the reader.
Reimplemented from SoVolumeReader.
|
static |
Returns the type identifier for this class.
|
overridevirtual |
Gets the characteristics (file header) of the data volume.
See SoDataSet::setVolumeData().
You can use the convenience method setFilename() to specify the file location, in which case you will not have to open the file yourself. Then you can use the convenience method getBuffer() to read the header in order to get the requested information.
NOTE: We strongly recommend that readers implement this version of getDataChar, introduced in VolumeViz 5.1, because it uses SbVec3i32 for the volume dimension.
Implements SoVolumeReader.
const SoVRDicomData & SoVRDicomFileReader::getDicomData | ( | ) | const |
Returns an instance of SoVRDicomData for the first image of this volume.
Note that the first image of the volume does not necessarily correspond to first file of file list. Images are automatically sorted using the Image Postion Patient attribute.
This object can be queried for DICOM specific info, using for example the SoVRDicomData::getDicomInfo() method.
To conveniently access the DICOM attributes, see getDicomDataSet() method.
const SiDicomDataSet * SoVRDicomFileReader::getDicomDataSet | ( | const size_t | sliceIdx | ) | const |
Returns a DICOM data object for the specified slice containing all the DICOM attributes.
sliceIdx | The index of the slice to extract the dataset from. |
|
virtual |
This method is optional.
It returns the number of significant bits of the volume data.
If it is not implemented, the default return value is 0, meaning the number of bits depends on the data type. See the last parameter of SoVolumeData::setVolumeData(). This method is called immediately after getDataChar().
Reimplemented from SoVolumeReader.
|
inlinevirtual |
Returns the reader type.
Reimplemented from SoVolumeReader.
Definition at line 348 of file SoVRDicomFileReader.h.
|
virtual |
Must copy the rectangular part defined by subSlice of the XY slice sliceNumber to the memory referenced by data.
Slices will not always be read sequentially.
subSlice | 2D region of the slice to return. |
sliceNumber | Slice number on the volume Z axis (first slice is 0). |
data | Copy the data into this buffer. |
You can use the convenience method getBuffer() to read data from file. Note: setFilename() must have been called previously.
Reimplemented from SoVolumeReader.
|
virtual |
Returns the type identifier for this specific instance.
Reimplemented from SoVolumeReader.
|
virtual |
SoVRDicomFileReader is thread safe.
Reimplemented from SoVolumeReader.
void SoVRDicomFileReader::loadInMemory | ( | ) |
Load the DICOM data into contiguous memory if possible.
Once the data is loaded, no additional file I/O is necessary and data access calls to the reader, e.g. getSubSlice(), will be fast.
Example:
Notes:
Since Open Inventor 10.3
void SoVRDicomFileReader::loadSliceDicomData | ( | int | slice, |
SoVRDicomData & | dicomData | ||
) | const |
Loads the Dicom data of the given slice.
To conveniently access the DICOM attributes, see getDicomDataSet method.
|
virtual |
Restore all file handles closed by closeAllHandles method.
Reimplemented from SoVolumeReader.
Specify a directory containing DICOM files to load.
Each file in this folder that has a supported extension (currently ".dc3", ".dic", ".dcm", or ".dicom") will be loaded. If the DICOM files have an unsupported extension, use the setFilenameList function instead.
All the DICOM files in the specified directory should be part of the same volume data set. If not, the results are undefined.
folder | The folder from which to load files. |
Since Open Inventor 9.4.1
|
virtual |
Specify the name of a DICOM file or a file containing a list of DICOM files to load.
Using a list file is the same as loading a stack of images using the SoVRRasterStackReader except the list file should not contain any header. Each line in the list file may be a full path containing directory names or a simple file name. Simple file names are assumed to be in the same directory as the list file. The application can also specify a list of file paths using the setFilenameList() method. This is useful, for example, if the application user is allowed to select a list of files in a file selection dialog. All the specified files should be part of the same volume data set.
Returns 0 if successful.
Reimplemented from SoVolumeReader.
SbBool SoVRDicomFileReader::setFilenameList | ( | const SbString & | format, |
const int | startIndex = 0 , |
||
const int | endIndex = INT_MAX , |
||
const int | indexStep = 1 |
||
) |
Specify a list of DICOM files to load, using a sprintf-like format.
This will iterate from startIndex to endIndex (included) with increment of indexStep. For each step, this will add a file of name f, where f is format sprintf-ed with the current iteration index. All the specified files should be part of the same volume data set.
format | The format of the file name, which must be an absolute file path. e.g. "c:/testData/Brain.%04d.dcm", where "%04d" will be replaced by the current index, producing "c:/testData/Brain.0000.dcm" and so on. |
startIndex | The index of the first file to add |
endIndex | The index of the last file to add |
indexStep | the stride to use (e.g. 2 will skip one out of two files, by generating indices 0, 2, 4, ...) |
Since Open Inventor 9.4.1
int SoVRDicomFileReader::setFilenameList | ( | const SbStringList & | filenameList | ) |
Specify a list of DICOM files to load.
All the specified files should be part of the same volume data set. Returns 0 if successful.
Note: SbStringList is a list of pointers, not a list of objects, so the destructor for this class does not free the memory associated with the SbString objects. The application is responsible for deleting each object in the list.
bool SoVRDicomFileReader::setFilenameListFromSeries | ( | const SbString & | base | ) |
Specify a DICOM file and load all image files in the same directory that are part of the same "series" based on the series UID (0x0020,0x000E).
base | The path to a DICOM image file. |
int SoVRDicomFileReader::setFilenamePattern | ( | const SbString & | pattern | ) |
Specify a pattern of DICOM files to load.
pattern | e.g. "data_directory/image_file*.dcm" |
|
virtual |
Requests that the input be converted (if necessary) to the specified data type.
This allows, for instance, conversion of float data to unsigned byte. By default no conversion is done. If doChange is FALSE no type conversion is done. Always returns TRUE.
Reimplemented from SoVolumeReader.