CSOConvertToImage

MLModule

genre	CSOModule
authors	Olaf Konrad, Frank Heckel
package	MeVisLab/Standard
dll	MLCSOModules
definition	MLCSOModules.def
see also	CSOConvertTo3DMask, CSOInterpolate
keywords	contour, fill, voxelize, rasterize

Purpose

The module CSOConvertToImage converts all CSOs of the input CSOList to a ML image. It rasterizes or voxelizes the CSOs with the according Voxelize flag set to 'true' into the output image. If a CSO is in-plane, it also can be filled.

Usage

Attach a CSOList and an ML image to the module's inputs, adjust the parameters and press Update.

Details

The contour itself is converted into a 6-connected line of voxels. This is computed by following a contour's segments through the voxels by applying a derivate of a marching cubes scheme. In this scheme, the cells are checked for which cell's side the contour segments are crossing.

A filling of the voxelized contours is computed by applying a marching cube algorithm where the CSO's plane equation is evaluated (it can be evaluated to 'is above-', 'is below-' and 'is on plane', resulting in a scalar). Additionally, all cells' middle points in the vicinity of the voxelized CSO are projected onto the CSO's plane and are checked for being inside the CSO. If a certain amount of cells are determined in this fashion, a sufficiently 'thick' security margin is computed, so that all the remaining cells can be computed by applying a recursive marching cube algorithm that test only against the plane equation.

The set voxels of the rasterized CSO itself and the set of voxels of the according filling are disjunctive.

If CSOs are crossing each other or are embracing each other, they will generate voxels at same positions. In such cases, the resulting ML image value can be determined by using a certain logic mode. This can be an adding of those voxel values, a replacing with the greater or lower voxel value, or an applying of an XOR operation. The result of the latter depends on the order of computing and may lead to different results if the CSOs' voxel write mode involves either their ids or different constants. If the voxel write mode of all CSOs is set to Module (the default), however, the XOR operation can safely be used for generating holes in contours by using other contours. If the voxel write mode is different and different voxel write values are used, such holes are produced as well, but if there are an odd number of CSOs (more than 1), the resulting voxel value cannot predicted for sure.

Note that the border voxels can be generated with anti-aliased values, but the border voxels of those holes will not be anti-aliased.

The module can either convert all incoming CSOs at once on each notification, or just those which cross any demanded image page. Note that the voxel count, the generation of markers and the voxel bounding box fields are only valid if the generation mode is set to Complete.

The OnDemand mode is intended to be used in interactive systems.

Additionally, the module can output all target voxels as markers and as CSOVoxelSet. In both representations, the Boolean logic is not applied and thus, crossing or overlapping CSOs result in doubly existing markers or CSOVoxels.

Windows

Default Panel

Input Fields

input0

name: input0, type: Image

The reference input image. Values of the input image can also be copied to the module's output.

inCSOList

name: inCSOList, type: MLBase

The input CSOList.

Output Fields

output0

name: output0, type: Image

The output image.

outputXMarkerList

name: outputXMarkerList, type: MLBase

Output marker list. The creation of markers is optional, see Create marker list.

outputVoxelSet

name: outputVoxelSet, type: MLBase

Output CSOVoxelSet. The creation of markers is optional, see Create CSO voxel set.

Parameter Fields

Field Index

Auto apply: Bool	Ignore time points: Bool	String: String
Background: Float	isProcessing: Bool	Subsample: Integer
Clear: Trigger	Logic for Overlapping CSOs: Enum	Update: Trigger
Copy input image: Bool	Margin: Integer	Use Always Foreground Value Of Module: Bool
Create CSO voxel set: Bool	Marker Generation Mode: Enum	Use global subsample: Bool
Create marker list: Bool	Mode: Enum	Use image values: Bool
done: Trigger	Num. Threads: Integer	useAntiAliasing: Bool
Draw to all time points: Bool	progress: Float	Volume Threshold: Double
End (endVoxelBoundingBox): Vector3	Remove Outside Voxels Mode: String	Voxel: Integer
End (endWorldBoundingBox): Vector3	removeBorderVoxelsByVolume: Bool	Voxelize Border: Bool
Fill: Bool	removeOutsideVoxels: Bool	X: Integer
Finishing: Bool	Repaint: Bool	Y: Integer
Foreground: Float	Start (startVoxelBoundingBox): Vector3	Z: Integer
Generation Mode: Enum	Start (startWorldBoundingBox): Vector3

Visible Fields

Mode

name: updateMode, type: Enum, default: Off

Defines how the module react on input changes. This includes touching, connecting and disconnecting of inputs as well as notifications of the CSOList (if enabled).

Values:

Title	Name	Description
Off	Off	The module does not react on input changes.
Auto Update	AutoUpdate	The module computes anew if any input changes or a valid notification is triggered.

Auto apply

name: autoApply, type: Bool, default: FALSE

If checked, the module computes anew on any change of a field on the GUI.

Update

name: apply, type: Trigger

If pressed, the module computes anew.

Foreground

name: foregroundValue, type: Float, default: 4095

Sets the object voxel value if the CSO's voxel write mode is set to Module (which is the default), and if the module is not using image values for the object voxels (Use image values).

Background

name: backgroundValue, type: Float, default: 0

Sets the background voxel value if the module is not copying the input image's values (Use image values).

Use image values

name: useImageValues, type: Bool, default: FALSE

If checked, the input image's voxel values are used as object voxel values.

Fill

name: fillSurface, type: Bool, default: TRUE

If checked, the CSOs which are in-plane are filled.

Copy input image

name: copyInputImage, type: Bool, default: FALSE

If checked, the background of the output image is filled with the voxel values of the input image.

Repaint

name: listenInteractionNotifications, type: Bool, default: FALSE

If checked, and the module's Mode is set to Auto Update, each repaint notification of the CSOList leads to a new computation of the output.

Finishing

name: listenInteractionFinished, type: Bool, default: TRUE

If checked, and the module's Mode is set to Auto Update, each interaction finished notification of the CSOList leads to a new computation of the output.

Margin

name: boundingBoxMargin, type: Integer, default: 0, minimum: 0

Sets an augmentation value for the voxel bounding box.

Start (startVoxelBoundingBox)

name: startVoxelBoundingBox, type: Vector3, persistent: no

Shows the upper front left corner position of the voxel bounding box.

End (endVoxelBoundingBox)

name: endVoxelBoundingBox, type: Vector3, persistent: no

Shows the lower rear right corner position of the voxel bounding box.

Start (startWorldBoundingBox)

name: startWorldBoundingBox, type: Vector3, persistent: no

Shows the upper front left corner of the bounding box in world coordinates.

End (endWorldBoundingBox)

name: endWorldBoundingBox, type: Vector3, persistent: no

Shows the lower rear right corner of the bounding box in world coordinates.

String

name: voxelBoundingBoxString, type: String, persistent: no

Shows the voxel bounding boxes start and end position as a string consisting of six 3D coordinates separated by a space.

Use Always Foreground Value Of Module

name: useAlwaysForegroundValueOfModule, type: Bool, default: FALSE

If checked, the voxel write mode of the CSO or CSOGroup are ignored and the foreground value of the module is used in any case.

Clear

name: clear, type: Trigger

If pressed, the output image of the module is cleared and invalidated.

Voxelize Border

name: voxelizeCSO, type: Bool, default: FALSE

If checked, the path points of the CSOs themselves are voxelized into the output image.

Use global subsample

name: useGlobalSubsample, type: Bool, default: TRUE

If checked, the module uses the Subsample value for subsampling in order to determine border voxel values for useAntiAliasing or for removeBorderVoxelsByVolume.

Otherwise, the module uses the explicit subsample values for x, y and z directions (X, Y and Z).

Subsample

name: antiAliasSubSample, type: Integer, default: 4, minimum: 1, maximum: 6

Sets a global subsample value that is used if Use global subsample is checked.

X

name: antiAliasSubSampleX, type: Integer, default: 4, minimum: 1, maximum: 6

Sets the explicit subsample value in x-direction. Is used if Use global subsample is unchecked.

Y

name: antiAliasSubSampleY, type: Integer, default: 4, minimum: 1, maximum: 6

Sets the explicit subsample value in y-direction. Is used if Use global subsample is unchecked.

Z

name: antiAliasSubSampleZ, type: Integer, default: 4, minimum: 1, maximum: 6

Sets the explicit subsample value in z-direction. Is used if Use global subsample is unchecked.

Volume Threshold

name: removeBorderVoxelVolumeThreshold, type: Double, default: 0.6, minimum: 0, maximum: 1

Sets a threshold value for the border handling. If the border voxel is covered by a less percentage by the CSO, if can be removed from the resulting voxel set.

Ignore time points

name: ignoreTimePoints, type: Bool, default: FALSE

If checked, the timepoint indices of the input CSOs are ignored and the CSOs of all timepoint indices are voxelized into the first t-dimension of the output image.

Draw to all time points

name: drawToAllTimePoints, type: Bool, default: FALSE

If checked, all CSOs are voxelized into all t-dimensions of the output image.

Create marker list

name: createMarkerList, type: Bool, default: FALSE

If checked, a marker list output is filled with a marker per converted voxel of a CSO.

The value of a marker is the id of the originating CSO.

Marker Generation Mode

name: markerGenerationMode, type: Enum, default: CSOMarkerGenerationModeFromVoxels

Defines whether the markers are being generated before or after applying the Boolean logic to the resulting voxels.

Values:

Title	Name	Description
Voxels	CSOMarkerGenerationModeFromVoxels	Markers are being generated after the Boolean logic has been applied.
CSOs	CSOMarkerGenerationModeFromCSOs	Markers are being generated before the Boolean logic has been applied. That means that some markers may have the same position.

Voxel

name: voxelCount, type: Integer, persistent: no

Shows the amount of resulting voxels in the output image.

Create CSO voxel set

name: createCSOVoxelSet, type: Bool, default: FALSE, deprecated name: createCSOVoxelFormat

If checked, a CSOVoxelSet is created. This is a sparse representation of the resulting mask image.

Logic for Overlapping CSOs

name: voxelSetMode, type: Enum, default: VoxelSetModeReplaceMax

Defines how voxels of overlapping CSOs are handled.

Values:

Title	Name	Description
Add	VoxelSetModeAdd	Values of voxels at the same position are added.
Replace Max	VoxelSetModeReplaceMax	The maximum value of voxels at the same position is set.
Replace Min	VoxelSetModeReplaceMin	The minimum value of voxels at the same position is set.
XOR	VoxelSetModeXOR	And XOR operation is applied to the voxel position. That means that the voxel is set if the number of resulting voxels for a position is uneven, and the voxel is unset (background) if the number is even. By using this option, holes in contours can be modelled.

Generation Mode

name: generationMode, type: Enum, default: GenerationModeComplete

Defines the generation mode.

Values:

Title	Name	Description
Complete	GenerationModeComplete	On computing the result, all CSOs are being converted to voxels and the result is held in an internal structure for being copied to the output page if demanded.
On Demand	GenerationModeOnDemand	Only the CSOs are voxelized that are being cut by a requested output page and the result is written into an internal storage.

Num. Threads

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

Sets the number of threads for parallel computation.

Remove Outside Voxels Mode

name: removeOutsideVoxelsMode, type: String, default: Disabled

Defines the border mode. Only available if Voxelize Border is checked.

Possible values are:

Value	Meaning
Disabled	No border handling, all border voxels are written into the output image
Midpoint	If the midpoint of a voxel lies within a CSO, it is written into the output image, otherwise it is skipped
Volume	If the volume (projected area) of the portion of the voxel that lies within the CSO is greater than Volume Threshold, it is written into the output image, otherwise it is skipped
AntiAliasing	The value of the output voxel is proportional to the projected area that lies within the CSO

Hidden Fields

isProcessing

name: isProcessing, type: Bool, default: FALSE

done

name: done, type: Trigger

removeOutsideVoxels

name: removeOutsideVoxels, type: Bool, default: FALSE

Hidden field, is set by scripting. Do not change!

useAntiAliasing

name: useAntiAliasing, type: Bool, default: FALSE

Hidden field, is set by scripting. Do not change!

removeBorderVoxelsByVolume

name: removeBorderVoxelsByVolume, type: Bool, default: FALSE

progress

name: progress, type: Float, persistent: no