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 nodeReference(parameterName) and setNodeReference(parameterName, node) or setCommonNodeReference(parameterName, node) methods of the parameter set node.

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
InputVolume noderef no none reference to volume node
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.