#include <mlDicomSEGSave.h>

Inheritance diagram for ml::DicomSEGSave:

Public Types
enum	{ NumSEGSaveDerivationModes = 4 }
	Modes in which way the exported file will be related to the other DICOM objects. More...

enum	SEGFSaveDerivationModes { Automatic = 0 , DerivationImageAndFrameOfReference , OnlyFrameOfReference , OnlyDerivationImage }
	Modes in which way the exported file will be related to the other DICOM objects. More...

Public Types inherited from ml::Module
enum	PERMITTED_TYPES { ONLY_SCALAR_TYPES , ONLY_DEFAULT_TYPES , ALL_REGISTERED_TYPES }
	See documentation of setVoxelDataTypeSupport. More...

enum	INPUT_STATE { DISCONNECTED = 0 , CONNECTED_BUT_INVALID = 1 , CONNECTED_AND_VALID = 2 , CONNECTED_BUT_NEEDS_UPDATE = 3 }
	See documentation of handleInput. More...

enum	INPUT_HANDLE { INVALIDATE = 0 , ALLOW_INVALID_INPUT = 2 }
	See documentation of handleInput. More...

Public Types inherited from ml::Base
enum	PersistenceInterface { PersistenceByString , PersistenceByTreeNode , PersistenceByStream }
	This enum describes the different persistence interfaces available. More...

Public Member Functions
	DicomSEGSave ()
	Constructor.

virtual	~DicomSEGSave ()
	Destructor.

const _FieldAddOnListType &	getFieldAddOnList () const
	Allow constant access to fieldAddOnList, especially for testing purposes.

Public Member Functions inherited from ml::DicomSaveBase
	DicomSaveBase (int numInputs=1, int numOutputs=0)
	Constructor, currently 0-3 input images are allowed to be set by derived modules.

const BoolField &	getCopyOtherInputTagsFld () const
	Access to internal fields fields, see corresponding member documentation for details.

BoolField &	getDumpPrivateTagValuesFld () const

const StringField &	getFileNameField () const

const NotifyField &	getInheritDICOMTagsFld () const

const BoolField &	getPostBadParamErrorsField () const

NotifyField &	getSaveField () const

StringField &	getStatusField () const

IntField &	getTagDumpSizeFld () const

StringField &	getTagDumpFld () const

Public Member Functions inherited from ml::Module
MLMetaProfilePtr &	getMetaProfile () const
	Returns the meta profile for the base operator.

const char *	getTypeNameFast () const
	Macro to declare methods for the ML runtime type system (see mlRuntimeSubClass.h).

	Module (int numInputImages, int numOutputImages)
	Constructor: Initializes `numInputImages` input images and `numOutputImages` output images of the module.

	~Module () override
	Destructor: Destroys this module.

InputConnectorField *	getInputImageField (MLint i) const
	Returns the field representing input image `i`. `i` must be a valid index.

OutputConnectorField *	getOutputImageField (MLint i=0) const
	Returns field representing output image `i`. `i` must be a valid index.

MLint	getNumInputImages () const
	Returns number of input images of this module.

MLint	getNumOutputImages () const
	Returns number of output images of this module.

PagedImage *	getOutputImage (MLint outputIndex=0) const
	Returns output image `outputIndex`. The index needs to be in the range [0, getNumOutputImages()-1].

InputConnectorField *	addInputImage (const char *name=nullptr)
	Adds a new input image with `name` to the module.

OutputConnectorField *	addOutputImage (const char *name=nullptr)
	Adds a new output image with `name` to the module.

PagedImage *	getInputImage (MLint inputIndex, bool getReal=false) const
	Returns the output image of the module connected to input `inputIndex`.

PagedImage *	getUpdatedInputImage (MLint inputIndex, bool getReal=false) const
	Convenience method for safe access to the input image at index `inputIndex`.

MLErrorCode	processAllPages (int outputIndex=-1, SubImageBox region=SubImageBox(), MLRequestProgressCB progressCallback=nullptr, void progressCallbackUserData=nullptr)
	Processes all pages of a module for easy implementation of page-based image processing of complete images.

MLErrorCode	processAllPages (ProcessAllPagesHandler &handler, SubImageBox region=SubImageBox(), MLRequestProgressCB progressCallback=nullptr, void progressCallbackUserData=nullptr)
	Process input images with a ProcessAllPagesHandler `handler` on a temporary output image (which allocates no data) For details, see processAllPages(-1) above.

MLErrorCode	processMissingPages (int outputIndex=0, SubImageBox region=SubImageBox(), MLRequestProgressCB progressCallback=nullptr, void progressCallbackUserData=nullptr)
	Processes all missing pages on the given output image.

void	clearOutputImage (MLint i=0)
	Clear cached output image pages of output image `i`.

MLint	getOutputImageInplace (MLint outputIndex=0) const
	Return optimization flag: Return index of input image whose input tile is used also as output page for output `outputIndex` in calculateOutputSubImage() (instead of allocating its own memory).

MLint	getBypass (MLint outputIndex=0) const
	Returns the currently bypass index or -1 if bypassing is disabled (default).

THREAD_SUPPORT	getThreadSupport () const
	Returns the multithreading mode supported by this module, default is NO_THREAD_SUPPORT.

bool	areRecursiveHandleNotificationsPermitted () const
	Returns if recursive entries in handleNotification are permitted.

MLint	getHandleNotificationEntryCounter () const
	A counter returning the current number of (recursive re)entries in handleNotification.

PERMITTED_TYPES	getVoxelDataTypeSupport () const
	Returns the current state of supported voxel data types.

bool	isSupportedVoxelDataType (MLDataType dt) const
	Check if a given data type is supported on the module as configured with setVoxelDataTypeSupport.

virtual INPUT_HANDLE	handleInput (int, INPUT_STATE) const
	This method may be reimplemented to enable support for invalid input images on the module.

INPUT_STATE	getInputState (MLint index)
	Returns the current state of the input connection.

INPUT_STATE	getUpdatedInputState (MLint index)
	Returns the updated state of the input image by calling updateImageProperties(index) and returning getInputState(index) afterwards.

bool	isInputImageField (Field *field) const
	Returns if the given field is an input image field. This can be used in handleNotification(), to check if one of the input images has changed.

void	touchOutputImageFields () const
	Touch all output image fields to indicate that the images have changed.

virtual void	beginSaveFields ()
	Called before all fields data contents of this modules are saved.

virtual void	endSaveFields ()
	Called after saving all field contents of this module.

Public Member Functions inherited from ml::FieldContainer
	FieldContainer ()
	Constructor.

	~FieldContainer () override
	Destructor: Deletes all added fields.

std::string	whoAmI (bool withInstanceName=true) const
	Returns type and instance name of format "ClassTypeName(instanceName)" if the instance name is not empty and `withInstanceName` is true.

Field *	addField (const char name, const char type, const char *value)
	Adds a new field with name `name`, type `type` and value `value` (coded as string) to the container.

Field *	addField (Field *field)
	Adds a `field`, the ownership of the field is passed to the FieldContainer.

BoolField *	addBool (const char *name)
	Creates a BoolField with `name` and adds it to the container. Default value is false.

BoolField *	addBool (const char *name, bool value)
	Creates a BoolField with `name` and adds it to the container.

IntField *	addInt (const char *name)
	Creates an IntField with `name` and adds it to the container. Default value is 0.

IntField *	addInt (const char *name, MLint value)
	Creates an IntField with `name` and adds it to the container.

EnumField *	addEnum (const char name, const char const *enumerationItemNames, MLint numEnumerationItems)
	Creates an EnumField field with `name` and adds it to the container.

EnumField *	addEnum (const char *name, const std::vector< std::string > &enumerationItemNames)
	Creates an EnumField field with `name` and adds it to the container.

template<typename EnumType >
TypedEnumField< EnumType > *	addEnum (const char *name, const EnumValues< EnumType > &values, EnumType initialValue)
	Creates a TypedEnumField field with `name` and adds it to the container.

FloatField *	addFloat (const char *name)
	Creates a FloatField with `name` and adds it to the container. Default value is 0.f.

FloatField *	addFloat (const char *name, float value)
	Creates a FloatField with `name` and adds it to the container.

ProgressField *	addProgress (const char *name)
	Creates a float ProgressField with `name` and adds it to the container. Default value is 0.f.

ProgressField *	addProgress (const char *name, float value)
	Creates a float ProgressField with `name` and adds it to the container.

DoubleField *	addDouble (const char *name)
	Creates a DoubleField with `name` and adds it to the container. Default value is 0.

DoubleField *	addDouble (const char *name, double value)
	Creates a DoubleField with `name` and adds it to the container.

StringField *	addString (const char *name)
	Creates a StringField with `name` and adds it to the container. Default value is empty string.

StringField *	addString (const char *name, const std::string &value)
	Creates a StringField with `name` and adds it to the container.

NotifyField *	addNotify (const char *name)
	Creates a NotifyField field with `name` and adds it to the container.

TriggerField *	addTrigger (const char *name)
	Creates a TriggerField field with `name` and adds it to the container.

BaseField *	addBase (const char *name)
	Creates a Base field with `name` and adds it to the container. Default value is NULL.

BaseField *	addBase (const char name, Base value)
	Creates a Base field with `name` and adds it to the container.

BaseField *	addBase (const char *name, const RefCountedBasePtr &value)
	Creates a Base field with `name` and adds it to the container. Sets the value from intrusive pointer.

template<typename T >
BaseField *	addBaseWithAllowedType (const char name, T value=nullptr)
	As above, but also sets the allowed type of the field.

template<typename T >
BaseField *	addBaseWithAllowedType (const char *name, const ::boost::intrusive_ptr< T > &value)
	As above, but also sets the allowed type of the field.

template<typename T >
TypedBaseField< T > *	addTypedBase (const char *name)
	Creates a TypedBaseField with `name` and adds it to the container. Default value is NULL.

template<typename T >
TypedBaseField< T > *	addTypedBase (const char name, T value)
	Creates a TypedBaseField with `name` and adds it to the container.

template<typename T >
TypedBaseField< T > *	addTypedBase (const char *name, const ::boost::intrusive_ptr< T > &value)
	Creates a TypedBaseField with `name` and adds it to the container. Sets the value from intrusive pointer.

SoNodeField *	addSoNode (const char *name)
	Creates a SoNodeField with `name` and adds it to the container. Default value is NULL.

SoNodeField *	addSoNode (const char name, SoNode value)
	Creates a SoNodeField with `name` and adds it to the container.

PointerField *	addPointer (const char *name)
	Creates a PointerField with `name` and adds it to the container.

Vector2Field *	addVector2 (const char *name)
	Creates a Vector2Field with `name` and adds it to the container.

Vector2Field *	addVector2 (const char *name, const Vector2 &value)
	Creates a Vector2Field with `name` and adds it to the container.

Vector2Field *	addVector2 (const char *name, double x, double y)
	Creates a Vector2Field with `name` and adds it to the container.

Vector3Field *	addVector3 (const char *name)
	Creates a Vector3Field with `name` and adds it to the container.

Vector3Field *	addVector3 (const char *name, const Vector3 &value)
	Creates a Vector3Field with `name` and adds it to the container.

Vector3Field *	addVector3 (const char *name, double x, double y, double z)
	Creates a Vector3Field with `name` and adds it to the container.

Vector4Field *	addVector4 (const char *name)
	Creates a Vector4Field with `name` and adds it to the container.

Vector4Field *	addVector4 (const char *name, const Vector4 &value)
	Creates a Vector4Field with `name` and adds it to the container.

Vector4Field *	addVector4 (const char *name, double x, double y, double z, double w)
	Creates a Vector4Field with `name` and adds it to the container.

Vector5Field *	addVector5 (const char *name)
	Creates a Vector5Field with `name` and adds it to the container.

Vector5Field *	addVector5 (const char *name, const Vector5 &value)
	Creates a Vector5Field with `name` and adds it to the container.

Vector6Field *	addVector6 (const char *name)
	Creates a Vector6Field with `name` and adds it to the container.

Vector6Field *	addVector6 (const char *name, const Vector6 &value)
	Creates a Vector6Field with `name` and adds it to the container.

Vector10Field *	addVector10 (const char *name)
	Creates a Vector10Field with `name` and adds it to the container.

Vector10Field *	addVector10 (const char *name, const Vector10 &value)
	Creates a Vector10Field with `name` and adds it to the container.

ImageVectorField *	addImageVector (const char *name)
	Creates a ImageVectorField with `name` and adds it to the container.

ImageVectorField *	addImageVector (const char *name, const ImageVector &value)
	Creates a ImageVectorField with `name` and adds it to the container.

ImageVectorField *	addImageVector (const char *name, MLint x, MLint y, MLint z, MLint c, MLint t, MLint u)
	Creates a ImageVectorField with `name` and adds it to the container.

SubImageBoxField *	addSubImageBox (const char *name)
	Creates a SubImageBoxField with `name` and adds it to the container.

SubImageBoxField *	addSubImageBox (const char *name, const SubImageBox &value)
	Creates a SubImageBoxField with `name` and adds it to the container.

SubImageBoxdField *	addSubImageBoxd (const char *name)
	Creates a SubImageBoxd field with `name` and adds it to the container.

SubImageBoxdField *	addSubImageBoxd (const char *name, const SubImageBoxd &value)
	Creates a SubImageBoxd field with `name` and adds it to the container.

ColorField *	addColor (const char *name)
	Creates a ColorField with `name` and adds it to the container.

ColorField *	addColor (const char *name, float r, float g, float b)
	Creates a ColorField with `name` and adds it to the container.

ColorField *	addColor (const char *name, const Vector3 &value)
	Creates a ColorField with `name` and adds it to the container.

PlaneField *	addPlane (const char *name)
	Creates a PlaneField with `name` and adds it to the container.

PlaneField *	addPlane (const char *name, double f0, double f1, double f2, double f3)
	Creates a PlaneField with `name` and adds it to the container.

PlaneField *	addPlane (const char *name, const Plane &value)
	Creates a PlaneField with `name` and adds it to the container.

RotationField *	addRotation (const char *name)
	Creates a RotationField with `name` and adds it to the container.

RotationField *	addRotation (const char *name, const Rotation &value)
	Creates a RotationField with `name` and adds it to the container.

Matrix2Field *	addMatrix2 (const char *name)
	Creates a Matrix2Field with `name` and adds it to the container.

Matrix2Field *	addMatrix2 (const char *name, const Matrix2 &value)
	Creates a Matrix2Field with `name` and adds it to the container.

Matrix3Field *	addMatrix3 (const char *name)
	Creates a Matrix3Field with `name` and adds it to the container.

Matrix3Field *	addMatrix3 (const char *name, const Matrix3 &value)
	Creates a Matrix3Field with `name` and adds it to the container.

Matrix4Field *	addMatrix4 (const char *name)
	Creates a Matrix4Field with `name` and adds it to the container.

Matrix4Field *	addMatrix4 (const char *name, const Matrix4 &value)
	Creates a Matrix4Field with `name` and adds it to the container.

Matrix5Field *	addMatrix5 (const char *name)
	Creates a Matrix5Field with `name` and adds it to the container.

Matrix5Field *	addMatrix5 (const char *name, const Matrix5 &value)
	Creates a Matrix5Field with `name` and adds it to the container.

Matrix6Field *	addMatrix6 (const char *name)
	Creates a Matrix6Field with `name` and adds it to the container.

Matrix6Field *	addMatrix6 (const char *name, const Matrix6 &value)
	Creates a Matrix6Field with `name` and adds it to the container.

MatrixField *	addMatrix (const char *name)
	Creates a MatrixField with `name` and adds it to the container.

MatrixField *	addMatrix (const char *name, const Matrix4 &value)
	Creates a MatrixField with `name` and adds it to the container.

MLDataTypeField *	addMLDataType (const char *name)
	Creates a MTDataTypeField with `name` and adds it to the container.

MLDataTypeField *	addMLDataType (const char *name, MLDataType value)
	Creates a MTDataTypeField with `name` and adds it to the container.

UniversalTypeField *	addUniversalType (const char *name)
	Creates an UniversalTypeField field with `name` and adds it to the container.

IntListField *	addIntList (const char *name)
	Creates an IntListField field with `name` and empty list value and adds it to the container.

IntListField *	addIntList (const char *name, const std::vector< MLint > &value)
	Creates an IntListField field with `name` and given list value and adds it to the container.

DoubleListField *	addDoubleList (const char *name)
	Creates an DoubleListField field with `name` and empty list value and adds it to the container.

DoubleListField *	addDoubleList (const char *name, const std::vector< double > &value)
	Creates an DoubleListField field with `name` and given list value and adds it to the container.

Vector2ListField *	addVector2List (const char *name)
	Creates an Vector2ListField field with `name` and empty list value and adds it to the container.

Vector2ListField *	addVector2List (const char *name, const std::vector< Vector2 > &value)
	Creates an Vector2ListField field with `name` and given list value and adds it to the container.

Vector3ListField *	addVector3List (const char *name)
	Creates an Vector3ListField field with `name` and empty list value and adds it to the container.

Vector3ListField *	addVector3List (const char *name, const std::vector< Vector3 > &value)
	Creates an Vector3ListField field with `name` and given list value and adds it to the container.

Vector4ListField *	addVector4List (const char *name)
	Creates an Vector4ListField field with `name` and empty list value and adds it to the container.

Vector4ListField *	addVector4List (const char *name, const std::vector< Vector4 > &value)
	Creates an Vector4ListField field with `name` and given list value and adds it to the container.

size_t	getNumFields () const
	Returns the number of added fields.

bool	hasField (const std::string &name) const
	Returns true if the field with name `name` exists; otherwise false is returned.

Field *	getField (const std::string &name) const
	Returns the pointer to the field with name `name`.

Field *	getField (MLint index) const
	Returns pointer of field at `index` if it exists. If not, -1 is returned.

MLint	getFieldIndex (Field *field) const
	Returns index of `field` if it exists. If not, -1 is returned.

void	setFieldStringValue (const std::string &name, const std::string &value)
	Sets the `value` of the field with `name` if it exists.

std::string	getFieldStringValue (const std::string &name) const
	Returns the string value of the field with `name` if it is found.

virtual void	deactivateAttachments ()
	Disables notification handling, i.e., all fields of this module will not send notifications to attached sensors and fields any more if their values are set or changed.

Public Member Functions inherited from ml::Base
	Base ()
	Constructor.

virtual	~Base ()
	Destructor.

virtual Base *	deepCopy () const
	Set addStateToTree version number that can be accessed via getAddStateVersion()

bool	isOfAllowedType (const std::vector< const RuntimeType * > &types) const
	Check if this object's type is equal to or derived from one of the types given in the argument.

virtual bool	isRefCountedBase () const
	Returns if the instance is derived from RefCountedBase.

virtual std::string	detailString () const
	Return a string describing this object.

virtual bool	implementsPersistence (PersistenceInterface) const
	Override this method to declare which persistence interfaces are implemented by your derived class.

virtual std::string	persistentState () const
	Returns a string describing the object's internal state.

virtual void	setPersistentState (const std::string &state)
	Restores the object's internal state from a string that had been previously generated using `persistentState()`.

virtual void	addStateToTree (TreeNode *) const
	Attaches the object state as children of the given parent node.

virtual void	readStateFromTree (TreeNode *)
	Reads the object state from the children of the given parent node.

virtual void	writeTo (AbstractPersistenceOutputStream *) const
	Write the objects state to the data stream object.

virtual void	readFrom (AbstractPersistenceInputStream *, int)
	Read the objects state from the data stream object.

Static Public Attributes
static const char *const	SEGSaveDerivationModeStrings [NumSEGSaveDerivationModes]
	String representations for the SEGSaveDerivationModes.

Protected Member Functions
void	handleNotification (Field *field) override
	Handles field changes of the field `field`.

void	activateAttachments () override
	Updates the internal module state after loading or cloning the module, and enables notification handling again.

ImageVector	_getExtentOfSegmentationBase () const
	Returns extent of the image which is used to determine the mask from, which means the extent of the BitImage in BINARY mode or extent of the input image otherwise; an 0-extent is always returned if input image is invalid or if required BitImage is not valid; further checks are not performed.

std::string	_checkConsistency () const override
	Checks for invalid parameters and return a textual description of the error if there is any, otherwise return an empty string.

void	_inheritFieldValuesFromDCMTree (DCMTree::Const_TreePtr dcmTree) override
	Overloads base class field inheritance and adds the additional tags needed by this class.

void	_updateInputState () override
	Overwrites base class and sets up additional stuff in commonInstanceReferenceModuleTags.

void	_addDerivationImageFunctionalGroupTagsIfEnabled (DCMTree::TreePtr dcmTree)
	Add Derivation Image Functional Group if enabled in _segSaveDerivationModeFld. May throw DCMTree::Exceptions.

std::string	_setSEGIODTags (DCMTree::TreePtr resultTree, PagedImage &inputPagedImage, const BitImage &inputBitImage)
	Creates and sets all tags for a valid Segmentation IOD dicom tree from inputPagedImage and inputBitimage into dcmTree; currently on bit masks can be written.

void	_setUpCompression (DCMTree::TreePtr resultTree)
	Add tags configuring the compression scheme.

std::string	_setUpTreeContent () override
	Sets the SEG DICOM tags in the tree; required that checkConsistency returns success.

	ML_MODULE_CLASS_HEADER (DicomSEGSave)
	Implements interface for the runtime type system of the ML.

Protected Member Functions inherited from ml::DicomSaveBase
DCMTree::Const_TreePtr	_getCurrentOriginalInputTree () const
	Returns content of the _currentOriginalInputTree after the recent call of _updateInputState().

DCMTree::TreePtr	_getCurrentModifiableTree () const
	Returns content of _currentModifiableTree after the recent call of _updateInputState().

PagedImage *	_getCurrentInImg () const
	Returns content of _currentInImg after the recent call of _updateInputState().

bool &	_getAllowNULLInputTree ()
	Provides access to _allowNULLInputTree.

virtual DCMTree::Const_TreePtr	_getInputDCMTree (DicomMessageCollector &dcmMsgCollector)
	Gets a DCMTree from the selected input or a nullptr tree if that is not available or empty.

virtual std::string	_getInputImageConfiguration (int inputImageConnector, DCMTree::Const_TreePtr &originalInputImageTree, DCMTree::TreePtr &resultDcmTree, PagedImage *&inImg)
	Returns some important parameters of the module's input image configuration:

virtual void	_updateTagDump (DCMTree::Const_TreePtr dcmTree)
	Updates the _dicomTagDumpFieldAddOn according to the content of dcmTree; called automatically by _save().

virtual void	_createInputModifierConnector ()
	If called then an input Base field for a DicomModifyList object is installed, typically called in constructor where fields are created.

virtual std::string	_applyInputModifiersIfAvailable (DCMTree::TreePtr dcmTree, const FieldContainer *treeInfos=nullptr)
	If an InputModifierConnector is available and modifiers are connected then apply them to dcmTree, otherwise the call is ignored.

virtual void	_save ()
	Saves the DICOM object in the file(s) defined by _fileNameFld.

Protected Member Functions inherited from ml::Module
void	handleNotificationInternal (Field *field, FieldSensor::Strength strength) override
	Called from FieldContainer whenever a field changes.

virtual void	provideCustomPage (int, const SubImageBox &, MLMemoryBlockHandle &)
	This method allows a Module to provide its own pages to the Host for the `outputIndex` output image.

void	handleNotificationOff ()
	Decreases lock counter for handleNotification calls.

void	handleNotificationOn ()
	Increases lock counter for handleNotification calls.

bool	isHandleNotificationOn ()
	Returns true if handleNotification calls are permitted, otherwise false.

void	setOutputImageInplace (MLint outputIndex=0, MLint inputIndex=0)
	Set optimization flag: If calculating a page in calculateOutputSubImage(), the output image page of output `outputIndex` shall use the same memory as the input page of input `inputIndex`.

void	unsetOutputImageInplace (MLint outputIndex=0)
	Clear optimization flag: output page of output at `outputIndex` and input tile shall use different memory buffers in calculateOutputSubImage().

void	setBypass (MLint outputIndex=0, MLint inputIndex=0)
	Sets the input image whose pages can also be used instead of output pages for the output image at `outputIndex` to avoid recalculations.

void	setClampPagesToImageExtent (bool flag=true)
	Enables/disables page clamping on all output images.

void	setThreadSupport (THREAD_SUPPORT supportMode)
	Pass any THREAD_SUPPORT `supportMode` to decide whether and what type of multithreading is supported by this module.

void	permitRecursiveHandleNotifications (bool enable)
	If this flag is set to `enable` =true, recursive entries in handleNotification are permitted.

void	setVoxelDataTypeSupport (PERMITTED_TYPES permTypes)
	Specifies which types this module supports.

virtual CalculateOutputImageHandler *	createCalculateOutputImageHandler (PagedImage *outputImage)
	Creates the CalculateOutputImageHandler for the given output image `outputImage`.

virtual void	calculateOutputImageProperties (int outputIndex, PagedImage *outputImage)
	Set properties of output image `outputImage` with output index `outputIndex`.

virtual SubImageBox	calculateInputSubImageBox (int, const SubImageBox &outputSubImageBox, int)
	Called by the Host to determine which input image region (tile) of input `inputIndex` is required to calculate a certain output image region (page) of output `outputIndex`.

virtual void	calculateOutputSubImage (SubImage outputSubImage, int outputIndex, SubImage inputSubImages)
	Calculate page `outputSubImage` of output image with index `outputIndex` given the input image tiles in array `inputSubImages`.

Static Protected Member Functions
static void	_addAndSetFractionalSEGPixelDataTag (DCMTree::TreePtr resultTree, PagedImage &inputPagedImage, bool determineImagePixelMax)
	In case of fractional segmentation this routine saves the image data which is expected with min/max range from [0,255], voxel type MLuint8Type and at most 4GB pixel data.

Protected Attributes
EnumField *	_segSaveDerivationModeFld
	Determines how the exported file is related to other DICOM objects.

BoolField *	_savePaddedPixelDataFld
	true writes padded frame data, false unpadded recommended).

BaseField *	_inputBitImageFld
	Input connector for a BitImage to be saved directly.

EnumField *	_compressionFld
	Selector for supported lossless compressions.

BoolField *	_populateSourceImageSequenceFld
	True fills Source image Sequence in Derivation Image Sequence with values, otherwise it's left empty.

_FieldAddOnListType	_fieldAddOnList
	Container which handles all internally used DicomModifyFieldAddOns.

EnhancedMFSEGObjectInfos	_inheritedSEGInfos
	Inherited information needed to fill SEG specific tags in result tree.

Protected Attributes inherited from ml::DicomSaveBase
TreeAndVolumeInputFieldAddOn	_dcmTreeInputFieldAddOn
	Field AddOn to manage selectors and input connectors for DCMTrees and MultiFileVolumes.

DicomTagDumpFieldAddOn	_dicomTagDumpFieldAddOn
	Field AddOns managing the DICOM tag dump as string field.

Additional Inherited Members
Static Public Member Functions inherited from ml::DicomSaveBase
static std::string	checkXYZValues (const ImageVector &ext)
	If Y and X are used as row and column, they can hold at most values of 65535, because these tags are of Vr US (unsigned short); NumberOfFrames tag is usually used for the z-slices and is an integer string and should not exceed is of type IS, which can hold up values up at most of 2^31-1; If any of these values exceed these ranges, a non empty error description is returned, otherwise an empty string.

static std::string	checkMaximumPixelDataSize (const PagedImage &inImg)
	Returns an empty string if the passed PagedImage describes an image whose pixel data would fit into a DICOM PixelData tag and also calls checkXYValues(); if any range is exceeded a non-empty error string is returned.

Static Public Member Functions inherited from ml::Module
static MLErrorCode	getTile (PagedImage image, SubImageBox loc, MLDataType datatype, void data, const ScaleShiftData &scaleShiftData=ScaleShiftData(), MLRequestProgressCB progressCallback=nullptr, void *progressCallbackUserData=nullptr)
	For documentation see Host::getTile() function with same signature.

static MLErrorCode	getTile (PagedImage image, SubImage &subimg, const ScaleShiftData &scaleShiftData=ScaleShiftData(), MLRequestProgressCB progressCallback=nullptr, void *progressCallbackUserData=nullptr)
	For documentation see Host::getTile() function with same signature and Module passed as reference.

static MLErrorCode	updateImageProperties (PagedImage *image)
	For documentation see Host::updateImageProperties() function with same signature.

static void	freeTile (void *data)
	For documentation see Host::freeTile().

static void	updateProgress (const char info1, const char info2)
	For documentation see Host::updateProgress().

static bool	shouldTerminate ()
	For documentation see Host::shouldTerminate().

static Field *	getPressedNotifyField ()
	For documentation see Host::getPressedNotifyField().

static void	adaptPageExtent (ImageVector &pageExtent, MLDataType imageType, const ImageVector &newImgExtent, const ImageVector &oldImgExtent, const ImageVector &pageUnit=ImageVector(0), const ImageVector &minPageExtent=ImageVector(0), const ImageVector &maxPageExtent=ImageVector(0))
	Adapt page size.

static std::string	getVoxelValueAsString (PagedImage image, const ImageVector &position, MLErrorCode errorCode=nullptr, const std::string &errorResult="")
	Returns the voxel value at position `position` of the image `image`.

static size_t	getNumModules ()
	Returns number of instantiated modules.

static Module *	getModule (size_t index)
	Returns pointer to instantiated module `index`.

static MLint	findModuleIndex (Module &module)
	Returns index of Module `module`. If not found -1 is returned.

static void	destroyModule ()
	Destroys static allocated tables to avoid memory leaks.

Protected Types inherited from ml::Module
enum	THREAD_SUPPORT { NO_THREAD_SUPPORT = PagedImage::NO_THREAD_SUPPORT , MULTITHREADED = PagedImage::MULTITHREADED , IO_THREAD = PagedImage::IO_THREAD }
	Enumerator deciding whether and which type of multithreading is supported by this module. More...

Detailed Description

Definition at line 50 of file mlDicomSEGSave.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Modes in which way the exported file will be related to the other DICOM objects.

Enumerator
NumSEGSaveDerivationModes

Definition at line 61 of file mlDicomSEGSave.h.

◆ SEGFSaveDerivationModes

enum ml::DicomSEGSave::SEGFSaveDerivationModes

Modes in which way the exported file will be related to the other DICOM objects.

Enumerator
Automatic	Automatically selects one the the other SegSaveDerivationModes.
DerivationImageAndFrameOfReference	The exported files are created with the Derivation Image Functional Group and the Frame of Reference information.
OnlyFrameOfReference	The exported files are created with the Frame of Reference information.
OnlyDerivationImage	The exported files are created with the Derivation Image Functional Group.

Definition at line 64 of file mlDicomSEGSave.h.

Constructor & Destructor Documentation

◆ DicomSEGSave()

ml::DicomSEGSave::DicomSEGSave ( )

Constructor.

◆ ~DicomSEGSave()

virtual ml::DicomSEGSave::~DicomSEGSave ( )

virtual

Destructor.

Member Function Documentation

◆ _addAndSetFractionalSEGPixelDataTag()

static void ml::DicomSEGSave::_addAndSetFractionalSEGPixelDataTag	(	DCMTree::TreePtr	resultTree,
		PagedImage &	inputPagedImage,
		bool	determineImagePixelMax )

staticprotected

In case of fractional segmentation this routine saves the image data which is expected with min/max range from [0,255], voxel type MLuint8Type and at most 4GB pixel data.

Parameters

resultTree	The DCMTree in which the pixel data tag is inserted.
inputPagedImage	The valid image from which the MLuint8 pixel data with min/max range from inside [0,255] can be retrieved with getTile.
determineImagePixelMax	If true the the maximum value from image pixel data is calculated and as for LargestImagePixelVale tag, otherwise 255 is used as default.

◆ _addDerivationImageFunctionalGroupTagsIfEnabled()

void ml::DicomSEGSave::_addDerivationImageFunctionalGroupTagsIfEnabled ( DCMTree::TreePtr dcmTree )

protected

Add Derivation Image Functional Group if enabled in _segSaveDerivationModeFld. May throw DCMTree::Exceptions.

◆ _checkConsistency()

std::string ml::DicomSEGSave::_checkConsistency ( ) const

overrideprotectedvirtual

Checks for invalid parameters and return a textual description of the error if there is any, otherwise return an empty string.

Implements ml::DicomSaveBase.

◆ _getExtentOfSegmentationBase()

ImageVector ml::DicomSEGSave::_getExtentOfSegmentationBase ( ) const

protected

Returns extent of the image which is used to determine the mask from, which means the extent of the BitImage in BINARY mode or extent of the input image otherwise; an 0-extent is always returned if input image is invalid or if required BitImage is not valid; further checks are not performed.

◆ _inheritFieldValuesFromDCMTree()

void ml::DicomSEGSave::_inheritFieldValuesFromDCMTree ( DCMTree::Const_TreePtr dcmTree )

overrideprotectedvirtual

Overloads base class field inheritance and adds the additional tags needed by this class.

Implements ml::DicomSaveBase.

◆ _setSEGIODTags()

std::string ml::DicomSEGSave::_setSEGIODTags	(	DCMTree::TreePtr	resultTree,
		PagedImage &	inputPagedImage,
		const BitImage &	inputBitImage )

protected

Creates and sets all tags for a valid Segmentation IOD dicom tree from inputPagedImage and inputBitimage into dcmTree; currently on bit masks can be written.

Parameters

resultTree	Must be the valid tree pointer into which all tags shall be inserted.
inputPagedImage	The ML PagedImage providing all image properties and perhaps DICOM inheritance information.
inputBitImage	The bitImage providing the SEG mask content.

Returns: An empty string on success, otherwise a descriptive string describing the problem.

◆ _setUpCompression()

void ml::DicomSEGSave::_setUpCompression ( DCMTree::TreePtr resultTree )

protected

Add tags configuring the compression scheme.

◆ _setUpTreeContent()

std::string ml::DicomSEGSave::_setUpTreeContent ( )

overrideprotectedvirtual

Sets the SEG DICOM tags in the tree; required that checkConsistency returns success.

Returns: An empty string on success, otherwise a textual description of the error.

Implements ml::DicomSaveBase.

◆ _updateInputState()

void ml::DicomSEGSave::_updateInputState ( )

overrideprotectedvirtual

Overwrites base class and sets up additional stuff in commonInstanceReferenceModuleTags.

Reimplemented from ml::DicomSaveBase.

◆ activateAttachments()

void ml::DicomSEGSave::activateAttachments ( )

overrideprotectedvirtual

Updates the internal module state after loading or cloning the module, and enables notification handling again.

Reimplemented from ml::DicomSaveBase.

◆ getFieldAddOnList()

const _FieldAddOnListType & ml::DicomSEGSave::getFieldAddOnList ( ) const

inline

Allow constant access to fieldAddOnList, especially for testing purposes.

Definition at line 76 of file mlDicomSEGSave.h.

◆ handleNotification()

void ml::DicomSEGSave::handleNotification ( Field * field )

overrideprotectedvirtual

Handles field changes of the field field.

Reimplemented from ml::DicomSaveBase.

◆ ML_MODULE_CLASS_HEADER()

ml::DicomSEGSave::ML_MODULE_CLASS_HEADER ( DicomSEGSave )

protected

Implements interface for the runtime type system of the ML.

Member Data Documentation

◆ _compressionFld

EnumField* ml::DicomSEGSave::_compressionFld

protected

Selector for supported lossless compressions.

Definition at line 144 of file mlDicomSEGSave.h.

◆ _fieldAddOnList

_FieldAddOnListType ml::DicomSEGSave::_fieldAddOnList

protected

Container which handles all internally used DicomModifyFieldAddOns.

Definition at line 150 of file mlDicomSEGSave.h.

◆ _inheritedSEGInfos

EnhancedMFSEGObjectInfos ml::DicomSEGSave::_inheritedSEGInfos

protected

Inherited information needed to fill SEG specific tags in result tree.

Definition at line 153 of file mlDicomSEGSave.h.

◆ _inputBitImageFld

BaseField* ml::DicomSEGSave::_inputBitImageFld

protected

Input connector for a BitImage to be saved directly.

Definition at line 141 of file mlDicomSEGSave.h.

◆ _populateSourceImageSequenceFld

BoolField* ml::DicomSEGSave::_populateSourceImageSequenceFld

protected

True fills Source image Sequence in Derivation Image Sequence with values, otherwise it's left empty.

Definition at line 147 of file mlDicomSEGSave.h.

◆ _savePaddedPixelDataFld

BoolField* ml::DicomSEGSave::_savePaddedPixelDataFld

protected

true writes padded frame data, false unpadded recommended).

Definition at line 138 of file mlDicomSEGSave.h.

◆ _segSaveDerivationModeFld

EnumField* ml::DicomSEGSave::_segSaveDerivationModeFld

protected

Determines how the exported file is related to other DICOM objects.

Definition at line 135 of file mlDicomSEGSave.h.

◆ SEGSaveDerivationModeStrings

const char* const ml::DicomSEGSave::SEGSaveDerivationModeStrings[NumSEGSaveDerivationModes]

static

String representations for the SEGSaveDerivationModes.

Definition at line 73 of file mlDicomSEGSave.h.

The documentation for this class was generated from the following file:

FMEstable/ReleaseMeVis/Projects/DICOM/MLDicomOutputs/Sources/mlDicomSEGSave.h

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

◆ SEGFSaveDerivationModes

Constructor & Destructor Documentation

◆ DicomSEGSave()

◆ ~DicomSEGSave()

Member Function Documentation

◆ _addAndSetFractionalSEGPixelDataTag()

◆ _addDerivationImageFunctionalGroupTagsIfEnabled()

◆ _checkConsistency()

◆ _getExtentOfSegmentationBase()

◆ _inheritFieldValuesFromDCMTree()

◆ _setSEGIODTags()

◆ _setUpCompression()

◆ _setUpTreeContent()

◆ _updateInputState()

◆ activateAttachments()

◆ getFieldAddOnList()

◆ handleNotification()

◆ ML_MODULE_CLASS_HEADER()

Member Data Documentation

◆ _compressionFld

◆ _fieldAddOnList

◆ _inheritedSEGInfos

◆ _inputBitImageFld

◆ _populateSourceImageSequenceFld

◆ _savePaddedPixelDataFld

◆ _segSaveDerivationModeFld

◆ SEGSaveDerivationModeStrings