Segment editor

See examples of using Segment editor effects from Python scripts in the script repository.

Effect parameters

Setting/getting effect parameters:

• Numeric or string parameter values: Common parameters must be set using setCommonParameter(parameterName, parameterValue) method, while effect-specific parameters can be set using setParameter(parameterName, parameterValue) method of the effect. Both common and effect-specific parameters can be retrieved using parameter(parameterName) method (for string or enum type), integerParameter(parameterName) (for int type), doubleParameter(parameterName) (for float type).

• Node reference (noderef type) parameter: It holds a reference to a node object, therefore it must be get/set by calling GetNodeReference(referenceName) and SetNodeReferenceID(referenceName, nodeId) methods of the parameter set node. For common parameters (shared between multiple effects) referenceName equals to the parameter name. For effect-specific parameters referenceName is constructed as (effectName).(parameterName), for example Mask volume.InputVolume.

Fill between slices

Parameter	Type	Common	Default	Values
AutoUpdate	int	no	1	0 or 1

Grow from seeds

Parameter	Type	Common	Default	Values
SeedLocalityFactor	float	no	0.0	>=0.0
AutoUpdate	int	no	1	0 or 1

Hollow

Parameter	Type	Common	Default	Values
ApplyToAllVisibleSegments	int	no	0	0 or 1
ShellMode	enum	no	INSIDE_SURFACE	INSIDE_SURFACE, MEDIAL_SURFACE, OUTSIDE_SURFACE
ShellThicknessMm	float	no	3.0	>0.0

Islands

Parameter	Type	Common	Default	Values
Operation	enum	no	KEEP_LARGEST_ISLAND	KEEP_LARGEST_ISLAND, KEEP_SELECTED_ISLAND, REMOVE_SMALL_ISLANDS, REMOVE_SELECTED_ISLAND, ADD_SELECTED_ISLAND, SPLIT_ISLANDS_TO_SEGMENTS
MinimumSize	int	no	1000	>0

Logical operators

Parameter	Type	Common	Default	Values
Operation	enum	no	COPY	COPY, UNION, INTERSECT, SUBTRACT, INVERT, CLEAR, FILL
ModifierSegmentID	string	no		segment ID
BypassMasking	int	no	0	0 or 1

Margin

Parameter	Type	Common	Default	Values
ApplyToAllVisibleSegments	int	no	0	0 or 1
MarginSizeMm	float	no	3.0	<0.0 (shrink), >0.0 (grow)

Mask volume

Parameter	Type	Common	Default	Values
FillValue	float	no	0	any
BinaryMaskFillValueOutside	float	no	0	any
BinaryMaskFillValueInside	float	no	1	any
Operation	enum	no	FILL_OUTSIDE	FILL_INSIDE, FILL_OUTSIDE, FILL_INSIDE_AND_OUTSIDE
SoftEdgeMm	float	no	0.0	>=0.0
Mask volume.InputVolume	noderef	no	none	reference to volume node
Mask volume.OutputVolume	noderef	no	none	reference to volume node

Paint effect and Erase effect

Parameter	Type	Common	Default	Values
BrushMinimumAbsoluteDiameter	float	yes	0.01	>=0.0
BrushMaximumAbsoluteDiameter	float	yes	100.0	>0.0
BrushAbsoluteDiameter	float	yes	5.0	>=0.0
BrushRelativeDiameter	float	yes	3.0	>=0.0
BrushRelativeDiameter	int	yes	1	0 or 1
BrushSphere	int	yes	0	0 or 1
EditIn3DViews	int	yes	0	0 or 1
ColorSmudge	int	no	0	0 or 1
EraseAllSegments	int	no	0	0 or 1
BrushPixelMode	int	yes	0	0 or 1

Scissors

Parameter	Type	Common	Default	Values
ApplyToAllVisibleSegments	int	no	0	0 or 1
Operation	enum	no	EraseInside	EraseInside, EraseOutside, FillInside, FillOutside
Shape	enum	no	FreeForm	FreeForm, Circle, Rectangle
ShapeDrawCentered	int	no	0	0 (first click defines rectangle or circle boundary), 1 (click defines shape center)
SliceCutMode	enum	no	Unlimited	Unlimited, Positive, Negative, Symmetric
SliceCutDepthMm	float	no	0.0	>=0.0 (single slice = 0.0)

Smoothing

Parameter	Type	Common	Default	Values
ApplyToAllVisibleSegments	int	no	0	0 or 1
SmoothingMethod	enum	no	MEDIAN	MEDIAN, GAUSSIAN, MORPHOLOGICAL_OPENING, MORPHOLOGICAL_CLOSING, JOINT_TAUBIN
KernelSizeMm	float	no	3.0	>0.0
GaussianStandardDeviationMm	float	no	3.0	>0.0
JointTaubinSmoothingFactor	float	no	0.5	>0.0

Threshold

Parameter	Type	Common	Default	Values
AutoThresholdMethod	enum	no	OTSU	HUANG, INTERMODES, ISO_DATA, KITTLER_ILLINGWORTH, LI, MAXIMUM_ENTROPY, MOMENTS, OTSU, RENYI_ENTROPY, SHANBHAG, TRIANGLE, YEN
MinimumThreshold	float	no	25th percentile voxel value
MaximumThreshold	float	no	maximum voxel value
AutoThresholdMode	enum	no	SET_LOWER_MAX	SET_LOWER_MAX, SET_UPPER, SET_LOWER, SET_MIN_UPPER
BrushType	enum	no	CIRCLE	CIRCLE, BOX, DRAW, LINE
HistogramSetLower	enum	no	LOWER	MINIMUM, LOWER, AVERAGE
HistogramSetUpper	enum	no	UPPER	AVERAGE, UPPER, MAXIMUM

Examples

Examples for common operations on segmentations are provided in the script repository.