MPRPath

MLModule

genre	Resample
author	MeVis Medical Solutions AG
package	MeVisLab/Standard
dll	MLResample1
definition	MLResample1.def
see also	MPR, PathToKeyFrame, SoView2DMarkerEditor
inherits from	MPRLight
keywords	multi, planar, reformat, slice, keyframes

Purpose

The module MPRPath extracts a curved multi-planar reformatted image defined by a path of keyframes.

It generates the MPR image at a given keyframe, the complete image stack along the path, and a cross-section along the path at a given angle (0-360°).

It is derived from the MPR module, and hence shares most parameters.

Usage

The module requires a KeyFrameList at its input.

This is typically generated by the PathToKeyFrame module, e.g., from a list of markers generated with a SoView2DMarkerEditor (see the example network) or by a skeletonization algorithm.

Any ML module can generate an ml.KeyFrameList or ml.XMarkerList itself and export it as an ml.Base field.

The coordinate system used in the input lists is the world coordinate system.

Details

Each keyframe in the KeyFrameList provided at the input of this module specifies the position of a single output MPR slice in world coordinates and its orientation.

The orientation is defined by a path tangent vector t orthogonal to the MPR slice and an up vector u describing the “vertical” direction. The world coordinate vectors wx, wy, wz of an output MPR slice are given by:

(wx, wy, wz) = (u x t, u, t),

where u x t denotes the cross-product.

Optionally, it is also possible to align the MPR slice along the path. The MPR slice is then centered at the position of the current keyframe, aligned along the orientation of the path at the current keyframe and rotated by Path Angle. Thus the world coordinate vectors defining the orientation are then defined by:

(wx, wy, wz) = (t, u, t x u)

and a rotation around t by Path Angle.

The curved MPR (CPR) output image at output2 is a 2D image in which each voxel column corresponds to a keyframe of the input KeyFrameList. If Path Angle is 0, the voxels in each column are resampled along a line in the negative x direction of the corresponding MPR slice.

Hence, the column vector c is computed from the keyframe’s tangent and up vector by:

c = - u x t.

If Path Angle is > 0, the column vector is rotated counterclockwise by this angle (viewing in the path direction).

The world coordinates of the CPR in output2 cannot be described via a matrix anymore; therefore, it is possible to transform an inputMarkerList into an outputMarkerList, taking into account the individual world coordinate systems of each CPR image column. To do so, every marker is associated with the keyframe whose CPR column is closest to the marker, maximizing the likelihood that it is visualized. (Currently, every marker is output exactly once, even if multiple CPR columns intersect with its world position.)

Images

Definition of Path with Markers:

Curved Cross-Section along Path:

3D Open Inventor Scene Output:

Reorientation of MPR by Aligning to Path:

Windows

Default Panel

Input Fields

input0

name: input0, type: Image

Input image

see also MPRLight.input0

frames

name: frames, type: KeyFrameList(MLBase)

KeyFrameList, usually directly connected from PathToKeyFrame

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

inputMarkerList

name: inputMarkerList, type: XMarkerList(MLBase)

XMarkerList to be transformed into the rectilinear CPR coordinate system

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

Output Fields

output0

name: output0, type: Image

The output MPR slice at the position specified by the Current Key Frame parameter.

see also MPRLight.output0

output1

name: output1, type: Image

The complete stack of output MPR slices for all keyframes.

output2

name: output2, type: Image

The curved MPR image with columns resampled orthogonal to the input path.

outputSlice

name: outputSlice, type: SoNode

An Open Inventor scene representing the path and the current MPR slice in 3D.

outputMarkerList

name: outputMarkerList, type: XMarkerList(MLBase)

Transformed version of inputMarkerList that can be overlaid on output2 (see Details).

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

Parameter Fields

Field Index

Activate clip plane: Bool	Enable rendering of MPR slice: Bool	outputSizeX: Integer
Align output slice along path: Bool	enableCurrentSlice: Bool	outputSizeY: Integer
Alpha: Float	enablePlaneEdit: Bool	pageSizeX: Integer
Aspect Ratio: Double	Field Of View: Double	pageSizeY: Integer
autoCenter: Bool	fieldOfViewX: Double	Path Angle: Double
axial: Trigger	fieldOfViewY: Double	Plane (plane): Plane
axialOnInput: Trigger	Fill Value: Double	Plane (curvedMprPlane): Plane
Blend Mode: Enum	Flip Clip Plane: Bool	representInputSlice: Trigger
Border Color: Color	Image Color: Color	Rotation: Rotation
Border Handling: Enum	inputSliceNo: Integer	sagittal: Trigger
centeredTranslation: Vector3	Interactive manipulator: Bool	sagittalOnInput: Trigger
Clip Plane Offset: Float	Interpolation: Enum	Size (slabSize): Double
coronal: Trigger	Markers correspond to frames: Bool	Size (curvedMprSlabSize): Double
coronalOnInput: Trigger	maxKeyFrame: Integer	snapCurrentSliceToIntegerIfOrthogonal: Bool
Current Key Frame: Integer	Memory Access: Enum	Time Projection: Enum
currentSlice: Double	Mode (slabMode): Enum	Time Span: Integer
currentSliceMax: Integer	Mode (curvedMprSlabMode): Enum	Time Start: Integer
currentSliceMin: Integer	numberOfSlices: Integer	Translation: Vector3
currentSliceRounded: Integer	On (showUpVectors): Bool	Up-Vector Color: Color
Depth Projection: Enum	On (borderOn): Bool	upVector: Vector3
disableDirectVoxelCopy: Bool	On (drawImageOn): Bool	Use Key Frame Distance For Slice Thickness: Bool
Draw axes: Bool	Output Size: Integer	Use Z buffer: Bool
Enable: Bool	outputSizeMode: Enum	useUpVector: Bool

Visible Fields

Rotation

name: rotation, type: Rotation, default: 0 0 1 0

Shows the rotation at the current keyframe.

Translation

name: translation, type: Vector3, default: 0 0 0

Shows the translation at the current keyframe.

Plane (plane)

name: plane, type: Plane, default: 0 0 1 0

Shows the plane at the current keyframe.

Fill Value

name: fillValue, type: Double, default: 0, deprecated name: fillvalue

Sets a value used for regions outside of the input image.

Field Of View

name: fieldOfView, type: Double, default: 100

Sets the extent of the MPR slice in the world coordinate system (in mm).

Output Size

name: outputSize, type: Integer, default: 256, minimum: 1

Sets the size of the output MPR slice in (X,Y) pixels. This value is also used as the height of the curved MPR image (output2) in pixels.

Aspect Ratio

name: aspectRatio, type: Double, default: 1

Sets the aspect ratio of the output0 and output1.

Mode (slabMode)

name: slabMode, type: Enum, default: SizeInSlicesForward

Defines how the slab size is calculated.

Values:

Title	Name
Mm	SizeInMm
Mm Forward	SizeInMmForward
Slices	SizeInSlices
Slices Forward	SizeInSlicesForward
Slices Negative First	SizeInSlicesNegativeFirst

Size (slabSize)

name: slabSize, type: Double, default: 1, minimum: 0.01, deprecated name: outputDepth

Interpolation

name: interpolation, type: Enum, default: Trilinear, deprecated name: Mode

Defines the interpolation scheme.

Values:

Title	Name	Deprecated Name	Description
Nearest Neighbor	NearestNeighbor	Nearest Neigbour	No interpolation, picks the nearest input image voxel.
Trilinear	Trilinear	Trilinear(skip border),TrilinearSkipBorder	Trilinear filtering. The 8-voxel-neighborhood is used for linear interpolation.

Border Handling

name: borderHandling, type: Enum, default: UseFillValue

See MPR for details.

Memory Access

name: memoryAccess, type: Enum, default: Global, deprecated name: pagedInputImage

Defines the type of memory access.

Falls back to VirtualVolume if no sufficient memory space is available.

Values:

Title	Name	Deprecated Name	Description
Global	Global	FALSE,Paged,TRUE	Slower than Global, except for small MPR’s in large input images. The output MPR is split into tiles that are processed individually. For each tile, the module requests the corresponding 3D region of the input image. If not enough memory is available, the module falls back to VirtualVolume access.
Virtual Volume	VirtualVolume		Slowest, but works on huge datasets. All pages of the input image are requested via the virtual volume mechanism, thus only small portions of the input image are needed at the same time.

Enable

name: enableSlabProjection, type: Bool, default: FALSE

If checked, the projection of the slab to a single slice is enabled.

This applies to the output0 and to the curved MPR output2.

Depth Projection

name: depthSlabRenderMode, type: Enum, default: Maximum

Defines the projection mode for the slab depth.

Values:

Title	Name
Minimum	Minimum
Maximum	Maximum
Average	Average
Keep Dimension	KeepDimension

Time Projection

name: timeSlabRenderMode, type: Enum, default: Maximum

Defines the temporal projection mode.

Values:

Title	Name
Minimum	Minimum
Maximum	Maximum
Average	Average
Keep Dimension	KeepDimension

Time Start

name: timeSlabStart, type: Integer, default: 0

Sets the temporal start position.

Time Span

name: timeSlabSize, type: Integer, default: 1

Sets the number of time points that are projected.

Current Key Frame

name: currentKeyFrame, type: Integer, default: 0, minimum: 0, maximum: :field:`maxKeyFrame`

Sets the index of the current keyframe.

Path Angle

name: pathAngle, type: Double, default: 0, minimum: 0, maximum: 360

Sets the angle (in degrees) about wich the column vectors of the curved MPR image (output2) are rotated.

If Align output slice along path is activated, the MPR slice at output0 and the Open Inventor scene output are also rotated.

Plane (curvedMprPlane)

name: curvedMprPlane, type: Plane, persistent: no

Shows the plane spanned by the current keyframe’s tangent and the corresponding column vector of the curved MPR image.

The section of this plane and the current MPR slice yields the line along which the voxel column in the curved MPR image are resampled.

Align output slice along path

name: alignAlongPath, type: Bool, default: FALSE

If checked, the MPR slice at output0 as well as the Open Inventor scene output are rotated to lie in the defined path of keyframes.

Size (curvedMprSlabSize)

name: curvedMprSlabSize, type: Double, default: 1, minimum: 0.01, deprecated name: thicknessOfCurvedMPR

Sets the number of slices of the curved MPR.

If the value is greater than one, the module provides a stack of curved MPR slices at output2 instead of a single curved MPR slice.

Markers correspond to frames

name: markersOnFrames, type: Bool, default: TRUE

If checked, a faster transformation algorithm is used.

This algorithm only works if there is a 1:1 correspondence between the inputMarkerList and the frames, which is a common use case; for example, if connecting the resampled path from PathToKeyFrame.

Mode (curvedMprSlabMode)

name: curvedMprSlabMode, type: Enum, default: SizeInSlices

Defines how the slab size of the curved MPR is defined.

Values:

Title	Name
Mm	SizeInMm
Mm Forward	SizeInMmForward
Slices	SizeInSlices
Slices Forward	SizeInSlicesForward
Slices Negative First	SizeInSlicesNegativeFirst

Use Key Frame Distance For Slice Thickness

name: useKeyFrameDistanceForSliceThickness, type: Bool, default: TRUE

If checked, the slice thickness (z voxel size) of output0 is calculated from the distance between the current keyframe and next/previous frames. Otherwise, the voxel size is calculated as in the MPR module.

On (showUpVectors)

name: showUpVectors, type: Bool, default: FALSE

If checked, up vectors are rendered for each MPR.

Enable rendering of MPR slice

name: showFrame, type: Bool, default: TRUE

If checked, the MPR slice data is rendered.

Up-Vector Color

name: upVectorColor, type: Color, default: 1 1 1

Sets the color of the up vector.

Image Color

name: imageColor, type: Color, default: 1 1 1, deprecated name: baseColor

Sets the color of the MPR slices.

Border Color

name: borderColor, type: Color, default: 1 1 1

Sets the color of the border.

On (borderOn)

name: borderOn, type: Bool, default: TRUE

If checked, a border around the MPR slice is rendered.

On (drawImageOn)

name: drawImageOn, type: Bool, default: TRUE

If checked, the rendering of the MPR image in Open Inventor is enabled.

Interactive manipulator

name: manipulatorOn, type: Bool, default: TRUE

If checked, an interactive manipulator is available.

If allows for translating, scaling, and rotating the MPR slice in the Open Inventor scene.

Activate clip plane

name: clipPlaneOn, type: Bool, default: FALSE

If checked, the clip plane at the MPR is activated.

Flip Clip Plane

name: flipClipPlane, type: Bool, default: FALSE

If checked, the clip plane at the MPR clips the other half-plane.

Clip Plane Offset

name: clipPlaneOffset, type: Float, default: 0

Sets an offset for the clip plane (distance to the MPR).

Draw axes

name: axesOn, type: Bool, default: FALSE, deprecated name: drawVectors

If checked, axes are rendered at the MPR.

Alpha

name: alphaFactor, type: Float, default: 1, minimum: 0, maximum: 1

Sets the alpha factor of the MPR slice in Open Inventor.

Use Z buffer

name: zBuffer, type: Bool, default: TRUE

If checked, the z-buffer test is active.

Blend Mode

name: blendMode, type: Enum, default: BLEND_REPLACE

Defines the used blend mode.

Values:

Title	Name
Replace	BLEND_REPLACE
Screen	BLEND_SCREEN
Add	BLEND_ADD
Minimum	BLEND_MINIMUM
Maximum	BLEND_MAXIMUM
Reverse Subtract	BLEND_REVERSE_SUBTRACT
Subtract	BLEND_SUBTRACT
Blend	BLEND_BLEND
Premultiplied Blend	BLEND_PREMULTIPLIED_BLEND

Hidden Fields

enablePlaneEdit

name: enablePlaneEdit, type: Bool, default: FALSE

autoCenter

name: autoCenter, type: Bool, default: FALSE

centeredTranslation

name: centeredTranslation, type: Vector3, persistent: no

outputSizeMode

name: outputSizeMode, type: Enum, default: AspectRatio

Values:

Title	Name
Aspect Ratio	AspectRatio
Independent	Independent
Automatic	Automatic

fieldOfViewX

name: fieldOfViewX, type: Double, default: 100

fieldOfViewY

name: fieldOfViewY, type: Double, default: 100

outputSizeX

name: outputSizeX, type: Integer, default: 256

outputSizeY

name: outputSizeY, type: Integer, default: 256

pageSizeX

name: pageSizeX, type: Integer, default: 128

pageSizeY

name: pageSizeY, type: Integer, default: 128

useUpVector

name: useUpVector, type: Bool, default: FALSE, deprecated name: forceUpright

If checked, the MPR slice’s y-axis are forced to be close to the world y-axis (or z-axis if the MPR slice normal is parallel to the y-axis).

upVector

name: upVector, type: Vector3, default: 0 1 0

disableDirectVoxelCopy

name: disableDirectVoxelCopy, type: Bool, default: FALSE

inputSliceNo

name: inputSliceNo, type: Integer, default: 0

representInputSlice

name: representInputSlice, type: Trigger

axial

name: axial, type: Trigger

sagittal

name: sagittal, type: Trigger

coronal

name: coronal, type: Trigger

axialOnInput

name: axialOnInput, type: Trigger

sagittalOnInput

name: sagittalOnInput, type: Trigger

coronalOnInput

name: coronalOnInput, type: Trigger

enableCurrentSlice

name: enableCurrentSlice, type: Bool, default: FALSE

currentSlice

name: currentSlice, type: Double, default: 0, minimum: :field:`currentSliceMin`, maximum: :field:`currentSliceMax`

currentSliceRounded

name: currentSliceRounded, type: Integer, default: 0

numberOfSlices

name: numberOfSlices, type: Integer, default: 0

currentSliceMin

name: currentSliceMin, type: Integer, default: 0

currentSliceMax

name: currentSliceMax, type: Integer, default: 0

snapCurrentSliceToIntegerIfOrthogonal

name: snapCurrentSliceToIntegerIfOrthogonal, type: Bool, default: TRUE

maxKeyFrame

name: maxKeyFrame, type: Integer, default: 0