CSOIsoGenerator

MLModule

genre	CSOModule
author	MeVis Medical Solutions AG
package	MeVisLab/Standard
dll	MLCSOModules
definition	MLCSOModules.def
see also	CSOManager
keywords	contour, isoline, isovalue, generate

Purpose

The module CSOIsoGenerator generates iso-contours for an entire image at a fixed iso value.

Usage

Attach a CSOList that is to be filled (attach a CSOManager or CSOListContainer to it) with the iso-CSOs and an image to this module.

Details

The module scans the input image in a slice-wise manner. The slice orientation is fixed and always the same as one would see in a standard 2D viewer (z-plane). If differently oriented slices should be used as a base for the generation of iso-contours, use an OrthoReformat3 module first.

Each slice is scanned by a marching squares algorithm that produces always closed CSOs. The border is treated as being always lower than the iso-value. The CSOs can be interpolated by a linear interpolation scheme and/or smoothed by applying a spline approximation (b-splines). A generated CSO yields approximately as many seed points as there are voxels on the isopath.

In addition to the smoothing by applying the spline approximation, a Laplacian smoothing can be applied after the spline approximation. This smoothing algorithm also applies a term that counters the shrinking effect typically caused by standard Laplacian smoothing.

A keeping mode lets the user adjust which CSOs on one slice should be kept; if the mode is set to All, all CSOs are kept (if they yield enough seed points if the according restricting is enabled). If it is set to Largest, only the largest CSO (measured in number of seed points) on a slice is kept of the proto-contours. The keeping modes Outmost and Inner apply an actual point-in-polygon test with using an arbitrary seed point as the point and all other CSOs as polygons. Testing one point is sufficient because iso-contours never cross. Note that all keeping modes apply to contours on the same slice only.

Windows

Default Panel

Input Fields

input0

name: input0, type: Image

The input image that should be scanned for iso-contours on its z-planes.

inCSOList

name: inCSOList, type: CSOList(MLBase)

The input CSOList that should be filled with scanned iso-contours.

For accessing this object via scripting, see the Scripting Reference: MLCSOListWrapper.

Parameter Fields

Field Index

Add To Group: Enum	Group Id: Integer	Send CSO events: Bool
Allow Undo: Bool	Group Label: String	Smoothing Factor: Float
Auto apply: Bool	Interpolate contours: Bool	Smoothing Mode: Enum
Auto Clear: Bool	Iso Value: Float	Smoothing Range: Integer
Auto Description: Enum	isProcessing: Bool	Start condition: Enum
Creation Mode: Enum	Keeping Mode: Enum	Start position: Vector3
Creator Id: Integer	Min. Num. Seeds: Integer	Time Point: Integer
done: Trigger	Mode: Enum	Update: Trigger
Empty group before generation: Bool	Num. Smoothing Passes: Integer	Use: Bool
Ensure clockwise orientation: Bool	progress: Float	Use Smooth: Bool
Generate For All Timepoints: Bool	Reduce CSOs to one seed point: Bool

Visible Fields

Mode

name: updateMode, type: Enum, default: AutoClear

Defines the update mode of this module.

Values:

Title	Name	Description
​Off	​Off	​The module does not compute anew if the input image changes.
​Auto Update	​AutoUpdate	​The module computes anew if the input image changes.
​Auto Clear	​AutoClear

Auto apply

name: autoApply, type: Bool, default: FALSE

If checked, the module computes anew if any field on the GUI is changed.

Update

name: apply, type: Trigger

When pressed, the module computes anew.

Empty group before generation

name: emptyGroupBeforeGeneration, type: Bool, default: FALSE

If checked, the module will empty the CSOGroup where it stores the generated iso-contours in. See Add To Group.

Add To Group

name: addCSOToGroupMode, type: Enum, default: AddToGroupByLabel

Defines how the module determines in which CSOGroup the generated iso-contours should be stored in.

Values:

Title	Name	Description
​None	​AddToGroupNone	​The generated iso-contours are not stored in any CSOGroup.
​By Label	​AddToGroupByLabel	​The generated iso-contours are stored in a CSOGroup that is given by a label in Group Label. If a CSOGroup with the given label does not already exist, it is created before being filled. The label “” is invalid; adding a CSO to the CSOGroup with label “” means adding the CSO to no CSOGroup.
​By Id	​AddToGroupById	​The generated iso-contours are stored in a CSOGroup that is given by an ID in Group Id. If a CSOGroup with the given ID does not already exist, it is created before being filled. The ID -1 is invalid; adding a CSO to the CSOGroup with ID -1 means adding the CSO to no CSOGroup.

Group Label

name: addCSOToGroupWithLabel, type: String

Sets the label of the CSOGroup newly generated iso-contours should be stored in.

If such a CSOGroup does not already exist, it is created.

If Empty group before generation is checked, the CSOGroup with this label is emptied before filled again.

Group Id

name: addCSOToGroupWithId, type: Integer, default: -1

Sets the ID of the CSOGroup newly generated iso-contours should be stored in.

If such a CSOGroup does not already exist, it is created.

If Empty group before generation is checked, the CSOGroup with this ID is emptied before filled again.

Creator Id

name: id, type: Integer, default: 0

Sets the creator ID to the generated iso-contours for a later identification.

This can be an arbitrary number.

Allow Undo

name: allowUndo, type: Bool, default: FALSE

If checked, the generation of CSOs can be undone, using the CSOList’s undo manager.

Send CSO events

name: sendCSOEvents, type: Bool, default: FALSE

If checked, the generation of individual CSOs triggers the sending of CSO application events.

Iso Value

name: isoValue, type: Float, default: 1200

Sets the iso-value for contour generation.

Interpolate contours

name: interpolate, type: Bool, default: TRUE

If checked, the generated CSOs are interpolated by a linear interpolation scheme regarding the voxel values and the iso-value.

Time Point

name: timePoint, type: Integer, default: 0

Sets the time point for which the CSOs are to be generated.

Generate For All Timepoints

name: generateForAllTimepoints, type: Bool, default: FALSE

If checked, all slices for all available timepoints are scanned.

Smoothing Mode

name: smoothingMode, type: Enum, default: SmoothingModeSplineApproximation

Defines the smoothing mode that is applied after the linear interpolation (Interpolate contours) and before the Laplacian smoothing (Use Smooth).

Values:

Title	Name
​None	​SmoothingModeNone
​Spline Approximation	​SmoothingModeSplineApproximation
​Spline Interpolation	​SmoothingModeSplineInterpolation

Use

name: useMinimumNumberSeeds, type: Bool, default: FALSE

If checked, the module only collects CSO on slices with an adjustable minimum number of seed points (Min. Num. Seeds) which are generated as much as voxels lie on the iso-path.

Min. Num. Seeds

name: minimumNumberSeedPoints, type: Integer, default: 50, minimum: 0

Sets the minimum number of seed points for a CSO to have in order to be collected. See Use.

Keeping Mode

name: keepingMode, type: Enum, default: KeepingModeAll

Defines the keeping mode to determine which of the CSO are to be kept on a slice.

Values:

Title	Name	Description
​All	​KeepingModeAll	​Keep all generated iso-contours.
​Largest	​KeepingModeLargest	​Keep only the largest CSO (with the most seed points).
​Outmost	​KeepingModeOutmost	​Keep only the outmost CSOs (or in other words, remove all inner CSOs).
​Inner	​KeepingModeInner	​Keep only the inner CSOs.

Auto Description

name: autoDescription, type: Enum, default: None

Defines the description set for each generated CSO.

Values:

Title	Name	Description
​None	​None	​No description is set.
​Slice	​Slice	​The slice index in which the CSO is located is set.
​Timepoint	​Timepoint	​Time point index where the CSO is located is set.
​Slice and Timepoint	​Slice and Timepoint	​Slice index and time point index where the CSO is located is set, separated by a space.

Ensure clockwise orientation

name: ensureClockwiseOrientation, type: Bool, default: FALSE

If checked, the module ensures that all generated iso-contours have a clockwise orientation.

Use Smooth

name: useSmooth, type: Bool, default: FALSE

If checked, a Laplacian smoothing is applied.

Num. Smoothing Passes

name: numSmoothPasses, type: Integer, default: 10, minimum: 0

Sets the number of passes of the Laplacian smoothing.

Smoothing Factor

name: smoothFactor, type: Float, default: 0.1, minimum: 0, maximum: 1

Sets the factor for Laplacian smoothing.

Smoothing Range

name: smoothRange, type: Integer, default: 1, minimum: 1

Sets the smoothing range for the neighborhood that is considered for smoothing.

A value of 1 means that the direct neighbors are taken into consideration, a value of 2 means that two points on the contour to each side of a point are considered for smoothing, and so on.

Reduce CSOs to one seed point

name: reduceCSOsToOnlyOneSeedPoint, type: Bool, default: TRUE

If checked, the resulting CSOs will have only one seed point and one path point list. All positions are then stored in that one path point list.

Otherwise, a seed point will be generated for each voxel.

Creation Mode

name: creationMode, type: Enum, default: All

Defines the creation mode.

Values:

Title	Name	Description
​All	​All	​Creates all iso-contours on all slices.
​Single	​Single	​Creates only the first found iso-contour on all slices.

Start condition

name: startCondition, type: Enum, default: Always

Defines a condition for starting to scan an iso-contour if Creation Mode is Single.

Values:

Title	Name
​Always	​Always
​Hit Lower Iso Value	​HitLowerIsoValue
​Hit Greater Iso Value	​HitGreaterIsoValue

Start position

name: startPosition, type: Vector3, default: 0 0 0

Sets a start position in world coordinates for scanning for iso-contours if Creation Mode is Single.

Hidden Fields

isProcessing

name: isProcessing, type: Bool, persistent: no

done

name: done, type: Trigger, persistent: no

Auto Clear

name: autoClear, type: Bool, default: FALSE

If checked, the module clears the input CSOList if no input image is attached and the fields Time Point or Generate For All Timepoints are changed.

progress

name: progress, type: Float, persistent: no